mirror of
https://asciireactor.com/otho/lammps-graphene.git
synced 2024-11-24 09:05:06 +00:00
70 lines
1.5 KiB
Bash
70 lines
1.5 KiB
Bash
|
#!/bin/bash
|
||
|
|
|
||
|
|
# Usage: ./stretch_box.sh <LAMMPS input file> <strain> [<current strain>]
|
||
|
|
|
||
|
|
# Program to biaxially strain a simulation box and the atoms contained within.
|
||
|
|
|
||
|
|
|
||
|
|
# Setup.
|
||
|
|
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*/scripts\).*@\1@')
|
||
|
|
|
||
|
|
source $script_dir/func/input_parsing.src
|
||
|
|
source $script_dir/func/utility.src
|
||
|
|
|
||
|
|
|
||
|
|
input_file=$1
|
||
|
|
|
||
|
|
current_strain=".0000"
|
||
|
|
if [[ -z $2 ]]; then
|
||
|
|
;
|
||
|
|
fi
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
# Gather information.
|
||
|
|
simulation_box_lengths $input_file > tmp.boxlengths
|
||
|
|
read Lx Ly Lz < tmp.boxlengths
|
||
|
|
rm tmp.boxlengths
|
||
|
|
|
||
|
|
found_atoms="false"
|
||
|
|
while read line; do
|
||
|
|
if [[ $found_atoms == "false" && $(echo $line|cut -d' ' -f1) == Atoms ]];
|
||
|
|
then read toss; found_atoms="true"; continue; fi
|
||
|
|
if [[ found_atoms == "true"]]; then
|
||
|
|
echo $line > $input_buf
|
||
|
|
read atom_id atom_type pos_x pos_y pos_z < $input_buf
|
||
|
|
pos_x[$atom_id]=$pos_x
|
||
|
|
pos_y[$atom_id]=$pos_y
|
||
|
|
pos_z[$atom_id]=$pos_z
|
||
|
|
fi
|
||
|
|
done < $input_file
|
||
|
|
|
||
|
|
# Organize arguments.
|
||
|
|
strain=$2
|
||
|
|
NewLx=$(bc <<< "scale=10; Lx * (1 + $strain) / (1 + $current_strain)")
|
||
|
|
NewLx=$(bc <<< "scale=10; Lx * (1 + $strain) / (1 + $current_strain)")
|
||
|
|
NewLx=$(bc <<< "scale=10; Lx * (1 + $strain) / (1 + $current_strain)")
|
||
|
|
#x
|
||
|
|
#y
|
||
|
|
#z
|
||
|
|
|
||
|
|
|
||
|
|
# Print new LAMMPS input to stdout.
|
||
|
|
while read -r line; do
|
||
|
|
dimension=$(echo $line|sed 's/^\s*[0-9.-]\+\s\+[0-9.-]\+\s\+\([xyz]\)lo.*$/\1/')
|
||
|
|
if [[ $dimension == "x" ]]; then
|
||
|
|
echo "$xlo $xhi xlo xhi"
|
||
|
|
continue;
|
||
|
|
fi
|
||
|
|
if [[ $dimension == "y" ]]; then
|
||
|
|
echo "$ylo $yhi ylo yhi"
|
||
|
|
continue;
|
||
|
|
fi
|
||
|
|
if [[ $dimension == "z" ]]; then
|
||
|
|
echo "$zlo $zhi zlo zhi"
|
||
|
|
continue;
|
||
|
|
fi
|
||
|
|
echo $line
|
||
|
|
done < $input_file
|