Tutorials

This repository is created to provided neat implementation of some common computations in LAMMPS, QUANTUM ESPRESSO and VASP. Other modules such as Material Studio and SIESTA may also be added in the future.

Code to automate various caluculation along with some common mistakes and error is included. Content is frequently revised to update the most optimum solution.

Building the conda environment

All dependencies are included in environment.yml file. We can either have environment setup in our own project directory or in the envs directory of the miniconda folder. The advantage of installing in miniconda folder is that we can use same env for different packages and it saves bandwidth and storage. The first method on the other hand is more robust. Prcedure is as follows

First of all if mamba do not exists then install it via

conda activate base
conda install mamba -n base -c conda-forge

To setup env in project dir

mamba env create --prefix ./env --file environment.yml --force

or to setup in miniconda envs dir

mamba env create --name basic --file environment.yml --force

Update the conda env

If you add (remove) dependencies to (from) the environment.yml file or the requirements.txt file after the environment has already been created, then you can re-create the environment with the following command.

To update env in project ./env dir

conda activate base
mamba env update --prefix ./env --file environment.yml  --prune

To update in Miniconda envs dir

conda activate base
mamba env update --name basic --file environment.yml  --prune

Remove the conda env

If you are low on storage and want to completely remove the conda env. You can do it by

conda deactivate
conda env remove --prefix ./env
# or to remove from conda env dirs
conda env remove --name basic

Quick Tips

Monkhorst-Pack Scheme

1. Quantum Espresso => The generated grid is always gamma centered.
2. VASP => The odd grid is gamma centered while even grid is not.

Commonly used conversion factors

For extended list click here

Pressure:
1 eV/Angstrom3 = 160.21766208 GPa
1 Ha/Bohr3 = 29421.02648438959 GPa
1 atm = 1.01325 bar = 0.000101325 GPa
1 GPa = 10 kbar

Force:
1 Ry/Bohr = 25.71104309541616 eV/Angstrom
1 Ha/Bohr = 51.42208619083232 eV/Angstrom

Energy:
1 Hartree = 2 Ryd = 27.211396 eV (nist - 27.21138386)
1 kJ/mol = 0.0103642688 eV/atom
1 Joule = 6.24150965x10^(18) eV (CODATA)
1 eV = 1.6021766208*10^(-19) Joules

Length:
1 Bohr = 0.529177208 Angstrom

Temperature:
kb=(3.166815*10^(-6)) Ha/K = (8.617343*10^(-5)) eV/K
1 eV = kb*T = 11604.505008 K (~10^4 K)

Some useful bash script

loop over array

grids=("4 4 1" "8 8 1" "16 16 1" "24 24 1" "16 16 2" "8 8 2")

# By Index
for ((i=0; i < ${#grids[@]}; i++)); do
    grid=${grids[$i]}
    echo $grid
done

# By Item 
for grid in "${grids[@]}"; do
    echo $grid
done

Declaring dictionary in bash

declare -A animals=( ["moo"]="cow" ["woof"]="dog")

# How to use
echo ${animals["moo"]}
# output: cow

Ignoring case while matching pattern in awk

calculate the line number containg CELL_PARA in INCAR-scf.pw file while ignoring case

line_no=$(awk -v IGNORECASE=1 "/CELL_PARA/ {print NR}" INCAR-scf.pw)

Formatting XDATCAR to render inside OVITO

When doing relaxation with isif=4 in vasp, the trajectory file 'XDATCAR' can not be viewed directly in ovito visualtion software. You have to delete some initial lines for it to work. you can achieve it by

awk 'NR>7{print}' XDATCAR > XDATCAR_REV

Extracting Detailed Node info

Sometimes the performance across the amd nodes is not consistent. To dive into what is causing the issue you can see detailed infromation about node using

# To display complete info about every node
scontrol show node

# To display info about specific node
#    scontrol show node <nodeName>
scontrol show node cn513-05-l

# To see active features you can pipe it into grep 
scontrol show node cn513-05-l | grep  "ActiveFeatures" 

Small script to print info about every node used in the calculation. It will read the nodelist from std.out

#!/bin/bash
nodeList=$(grep "NodeList" std.out | awk '{print $2}')
nodeList=$(echo ${nodeList//,/ })
echo "Node List: $nodeList"
for node in $nodeList; do
    activeFeatures=$(scontrol show node $node| grep "ActiveFeatures")
    echo "$node => $activeFeatures"
done

Worth visiting

• https://chengcheng-xiao.github.io
• https://www.educative.io/answers/what-is-the-difference-between-openmp-and-openmpi
• http://gebi.df.uba.ar/support/
• http://staff.ustc.edu.cn/~zqj/posts/Transforming-between-supercell-and-primitive-cell/