# Materials-Studio-script

**Repository Path**: baoshanboy/Materials-Studio-script

## Basic Information

- **Project Name**: Materials-Studio-script
- **Description**: perl script of Materials Studio
- **Primary Language**: Perl
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 6
- **Created**: 2021-12-23
- **Last Updated**: 2022-05-24

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Materials-Studio-script
All scripts can be run in Materials Studio, a software modeling Monte Carlo, Molecular Dynamics.
All scripts can be executed on server, in order to free your PC

## All.pl
Including all the script of this repository.

## AtomsXYZ.pl
Print trajectory of every atom you need to the AtomsXYZ.txt from \*.trj and \*.xtd file

## Center\_update.pl
Print trajectory of geometry center of every molecules, including zeolite

## Config.pl
Alkane diffuses in the channel of zeolite, recorded in the **MOR-C12.xsd**, now we need execute the *dlpoly*, a molecular dynamics package, rather than the *Materilas studio*. The input file of *dlpoly*, named as CONFIG, can be transferred via the **MOR-C12.xsd** by this perl script. It is worthing noting that the force field of this task is taken from the [ref 1](https://pubs.acs.org/doi/10.1021/ct900315r) and [ref 2](https://pubs.acs.org/doi/10.1021/ja0476056).

## CreateMoleAndGeomOpt.pl
Create a methanol molecule and geometry optimization is done by compass force field

## Deformation.pl
Calculate the Length, Width, Height and angle, which can demonstrate the deformation of alkane when it diffuses in the channel of zeolite.

## DipoleAndBond.pl
Print dipole moment and trajectory of every atoms in bonds to DipoleMoment.txt

## Energy.pl
Calculate the energy of MOR\_CH4.xsd using compass force field

## EnergyExtract.pl
Extract the all kinds of energy data from *std* file.

## Forcite.pl
Do molecular dynamics, such as NPT, NVT, N$\mu$T Simulation

## GeomOpt.pl
Do geometry optimization in \*.xsd file using compass force field

## MS.sh
Commit computational job to qsub. In MS.sh, you can rewrite cores of CPU, name of jobs, etc. There is one thing to be noted that you must change location of  *RunMatScript.sh*

## MSD.pl
Calculate Mean Square Displacement, which often is applied in the computation of diffusion coefficient

## Molecule.pl
Print trajectory of center of every molecule according to number of atoms in this molecule

## PEC.pl
Calculate the potential energy component.

## rdf.pl
Calculating radial distribution function and structure factor between set A and B


## SavePDB.pl
Import \*.xtd file and save as \*.pdb file

## SaveUnFix.pl
Import \*.xtd file and unfix the coordination of every atoms, and then save as \*.xsd file, which is the appropriate step to consider the flexibility of zeolite framework in doing molecular dynamics by compass force field

## SorptionAdsorptionIsotherm.pl
Calculate Isotherm

## SorptionFixedLoading.pl and SorptionFixedPressure.pl
Calculate structure, adsorption energy and dendity using GCMC simulation

## STCF.pl
Calculate SpaceTimeCorrelationFunction

## Torsion.pl
Calculate the torsion or dihedral of C-C chain in the C12H26 from the trajectory file 

## Transfer.pl
Transfer a cif file to be xyz and pdb or a new cif file and then output the lattice information.


## Xtd2UnFix.sh
Import \*xtd file, to carry out *SaveUnFix.pl* and then copy the output, \*.xsd to destination directory


## xsd\_qsub.sh
Carry out the command, *qsub MS.sh*

## castep\_geomopt\_CsPbBr3.pl
Carry out geometry optimization task of CsPbBr3.

Something to be noticed:
* OptimizeCell must be "Yes"
* It can not calculate the Mulliken analysis, so Mulliken should be deleted.

## castep\_geomopt\_graphene.pl
Carry out the geometry optimization task of Graphene