# DisbaTomo
**Repository Path**: ucaslilong/DisbaTomo
## Basic Information
- **Project Name**: DisbaTomo
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No
## Statistics
- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-02-11
- **Last Updated**: 2022-02-11
## Categories & Tags
**Categories**: Uncategorized
**Tags**: None
## README
# DisbaTomo
Inversion of multimode dispersion curves of surface wave
The forwarding program is from [disba](https://github.com/keurfonluu/disba),
which is a computationally efficient Python library for the modeling of
surface wave dispersion that implements a subset of codes from Computer
Programs in Seismology (CPS) in Python compiled just-in-time with numba.
The optimization part is based on python pacakge `scipy.optimize`,
where the gradient is implemented in C++[[1]](#1), and converted into the library
that can be imported by python with the help of pybind11.
## Installation
There are two circumstances: with sudo permission and without sudo permission.
The prior is typically for PC, and the latter is usually for clusters.
### With sudo permission
1. Install git, [eigen3](https://eigen.tuxfamily.org/index.php?title=Main_Page) and
[cmake](https://cmake.org/) through the package manager according to the
system, e.g. apt-get, homebrew, pacman.
2. Make sure your c++ compiler support c++14
3. Install python packages
1. Install miniconda
```bash
> wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh
> bash ./Miniconda3-py38_4.9.2-Linux-x86_64.sh
> source .bashrc
```
2. Create environment
```bash
> conda create -n disba python=3.8
> conda activate disba
> conda install numpy scipy matplotlib pyyaml mpi4py pandas
> pip install disba mpi_master_slave
```
### Without sudo permission
We use [spack](https://spack.io/) to install required softwares and libraries, which
is a package manager for supercomputers, Linux, and macOS.
1. Install spack
```bash
> git clone https://github.com/spack/spack.git
> echo ". spack/share/spack/setup-env.sh" >> .bashrc
> source ~/.bashrc
```
2. Install gcc of higher version
```bash
> spack info gcc
> spack install ${A_VERSION_OF_GCC}
> spack location -i gcc
# spack compiler find ${LOCATION_OF_GCC_NEW_VERSION}
> spack compiler find $(spack location -i gcc)
```
${A_VERSION_OF_GCC} is a version of gcc which you can choose from the list
that "spack info gcc" shows, e.g. `gcc@9.3.0`.
${LOCATION_OF_GCC_NEW_VERSION} is seen from "spack location -i gcc",
e.g. `/home/test/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-9.3.0-swta24mlro2t4z7rfka55y3aum2ckm32`
3. Install eigen3, git and cmake
```bash
> spack install eigen
> spack install cmake
> spack install git
```
4. Manage and load package using `lmod`
```bash
> spack install lmod
> echo ". $(spack location -i lmod)/lmod/lmod/init/bash" >> .bashrc
> source .bashrc
> module avail
```
5. Load package and software
```bash
> module load ${MODULE_NAME}
```
${MODULE_NAME} can be found from "module avail", and we need to load
gcc, cmake, git and eigen3. when I installed, the command was below:
```bash
> module load gcc-9.3.0-gcc-4.8.5-swta24m
> module load cmake-3.18.4-gcc-9.3.0-nesdphq
> module load git-2.29.0-gcc-9.3.0-y4b63yo
> module load eigen-3.3.8-gcc-9.3.0-txefvoy
```
You can add these module load command to your .bashrc.
6. Install python package (the same procedure as above)
7. Install problems
1. tar (child): lbzip2: cannot exec: no such file or directory
Solution:
```bash
> spack install bzip2
> export PATH=$(spack location -i bzip2):$PATH
```
2. Error: COmmandNotFoundError: spack requires 'patch'
Solutiin:
```bash
> spack install patch
> export PATH=$(spack location -i patch):$PATH
```
### Compilation
After installing requirements, the program is installed in the following.
```bash
> git clone https://github.com/pan3rock/DisbaTomo.git
> cd DisbaTomo
> git submodule init
> git submodule update
> mkdir build
> cd build
> cmake ..
> make -j4
```
## Usage
### Determine L-curve
```bash
> cd .. # in {DisbaTomo/}
> mkdir examples
> cp -r demo/* examples/
> cd examples/regular-large
> mpirun -np 4 ../../python/determine_lcurve.py
> ../../python/plot_lcurve.py 0
```
### Inversion
```bash
> mpirun -np 4 ../../python/inversion.py --num_init 20
> ../../python/plot_inversion.py --data 0 --plot_model --plot_init
> ../../python/plot_inversion.py --data 0 --plot_model
> ../../python/plot_inversion.py --data 0 --plot_disp
```
### Plot sensitivity kernel
The sensitivity is defined in [[1]](#1).
```bash
> ../../python/forward.py --data data/0.txt
> ../../python/plot_disp.py disp.txt
> ../../python/plot_kernel.py model_output.txt --disp disp.txt --fmin 0.01 --fmax 0.4 --cmin 2.8 --cmax 4.5 --plot_dispersion --vmax 0.35 --mode 0 --out k0.png
> ../../python/plot_kernel.py model_output.txt --disp disp.txt --fmin 0.01 --fmax 0.4 --cmin 2.8 --cmax 4.5 --plot_dispersion --vmax 0.35 --mode 1 --out k1.png
> ../../python/plot_kernel.py model_output.txt --disp disp.txt --fmin 0.01 --fmax 0.4 --cmin 2.8 --cmax 4.5 --plot_dispersion --vmax 0.35 --mode 2 --out k2.png
> ../../python/plot_kernel.py model_output.txt --disp disp.txt --fmin 0.01 --fmax 0.4 --cmin 2.8 --cmax 4.5 --plot_dispersion --vmax 0.35 --mode 3 --out k3.png
```
### Compute and display dispersion curves
```bash
> ../../python/forward.py -c config_forward2.yml --mode 3
> ../../python/plot_model.py model_data.txt --out model_data.png
> ../../python/plot_disp.py disp.txt --out disp_data.png
```
### Configure file
TODO: translate into English
Brocher and Gardner empirical relation have been provided, and you can add other
formula in `python/empirical_relation.py`.
## References
[1]
Pan, L., Chen, X., Wang, J., Yang, Z., & Zhang, D. (2019). Sensitivity analysis of dispersion curves of Rayleigh waves with fundamental and higher modes. Geophysical Journal International, 216(2), 1276–1303. https://doi.org/10.1093/gji/ggy479