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Command Commands

The document provides a series of commands and instructions for using various computational tools including VMD, DeepMD-Kit, Packmol, LAMMPS, and Quantum Espresso in a WSL environment. It covers file conversions, environment activation, and running simulations, along with basic Linux commands and Excel data handling. Additionally, it emphasizes the importance of using WSL for conversions to avoid errors.

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22 views4 pages

Command Commands

The document provides a series of commands and instructions for using various computational tools including VMD, DeepMD-Kit, Packmol, LAMMPS, and Quantum Espresso in a WSL environment. It covers file conversions, environment activation, and running simulations, along with basic Linux commands and Excel data handling. Additionally, it emphasizes the importance of using WSL for conversions to avoid errors.

Uploaded by

ijazulhaq856
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOCX, PDF, TXT or read online on Scribd
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Vmd

 Topo writelammpsdata filename.data molecule # for converting a file from vmd to lammps
input data file … for other atom_style format change the molecule
 topo clearbonds
 animate write pdb file.pdb
 set cen [measure center $sel]
 set sel [atomselect all]
 $sel moveby {25.0 25.0 -5.0)
 Mergemols {mol_id1 mol_id2}
 Animate write psd file.psf

DeepMD-Kit:

conda activate deepmd : for activating deepmd enviroment in wsl

Packmol

Tolerance 2.0 # minimum distance between any two atoms

Output test.pdb # output file from packmol other formats: pdb, tinker, xyz,moldy

Filetype pdb # input output file type

Structure water.pdb # start of the first type of molecule e.g water

Number 20000 # number of repetition

Inside cube 0. 0. 0. 40.

End structure

Structure # second molecule


.

End strucuture

Packmol < inputfile # packmol read in command

Lammps

Run command: mpirun -np 5 lmp_mpi -in pvdf.in -e screen

mpiexec -np 5 lmp_mpi -in msd.in -e screen

mpiexec -np 6 lmp_mpi -in msd.in

linux

mkdir : making new directory

clear : clear the window

exit: for exiting the window.

wsl:

\\wsl$ , for accessing wsl in windows

htop , for checking how many processors are working or not.

nproc, no. of processors the pc.

conda create -n deepmd deepmd-kit lammps horovod -c conda-forge

conda activate deepmd : for activating deepmd enviroment in wsl


dpkg --get-selections

apt list –installed , to get the list of all installed packages

excel:

dpdata: to covert output of DFT for deepmd

import dpdata

# Create a LabeledSystem object from the OUTCAR file

dsys = dpdata.LabeledSystem("OUTCAR")

# Convert the data to the DeePMD-kit format (npy) and save it in the 'deepmd_data' directory

dsys.to("deepmd/npy", "deepmd_data", set_size=dsys.get_nframes())

QE:
for setting the commands to path

export PATH=$PATH:/mnt/c/Users/USER/Downloads/Quantum_espresso/qe-7.3.1/bin

mpirun --oversubscribe -np 64 pw.x -in scf.in | tee scf.out

used pw.x < inputfile> outputfile

First copy the install directory of qe to the path and then run with pw.x

Use ./run_example/ in wsl for running the qe examples.

ALWAYS USE WSL FOR CONVERSION ( cmd usually gives error): for refrence : C:\Users\USER\
Downloads\Quantum_espresso\qe-7.3.1\PW\examples\water
window:

alt+p : for showin whats inside the file without opening it.

Alt+tab: shows all the tabs like apple

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