mirror of
https://asciireactor.com/otho/lammps-graphene.git
synced 2024-11-21 21:25:06 +00:00
108 lines
2.9 KiB
Bash
Executable File
108 lines
2.9 KiB
Bash
Executable File
#!/bin/bash
|
|
|
|
# Usage: ./apply_strain.sh <sample directory>
|
|
|
|
# Expects "initial.input" to be an equilibrium state at 0 strain.
|
|
|
|
script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
|
|
bin_dir="$script_dir/../bin"
|
|
potential_dir="$script_dir/../potentials/"
|
|
|
|
source $script_dir/func/input_parsing.src
|
|
|
|
#lammps_executable="srun $bin_dir/lmp_msl-mkl"
|
|
lammps_executable="$bin_dir/lmp_serial"
|
|
|
|
sample_dir=$1
|
|
|
|
# Check initial input.
|
|
initial_input="$sample_dir/initial.input"
|
|
|
|
if [[ ! -r $initial_input ]]; then
|
|
echo -n "Data file not found or " >> /dev/stderr
|
|
echo "cannot be read for ${initial_input}." >> /dev/stderr
|
|
exit 1
|
|
fi
|
|
|
|
# Setup strain sequence.
|
|
strain_sequence=$(seq 5 5 500|
|
|
sed 's/^\([0-9]\)$/00\1/'|
|
|
sed 's/^\([0-9]\)\([0-9]\)$/0\1\2/')
|
|
strain[0]="000"
|
|
index=1;
|
|
for strain in $strain_sequence; do
|
|
strain[$((index++))]=$strain
|
|
done
|
|
num_strains=$((index -1))
|
|
|
|
# Move to sample directory for strain sequence.
|
|
origin_dir=$(pwd)
|
|
cd $sample_dir
|
|
|
|
# Setup work space.
|
|
mkdir -p strain_runs
|
|
#mkdir -p strain_inputs
|
|
|
|
# Use initial.input as 1.0000.input
|
|
#cp initial.input strain_inputs/1.000.input
|
|
|
|
# Load parameters for biaxial strain program.
|
|
# echo "$equilibrium_Lx $equilibrium_Ly $equilibrium_Lz 0.005 0.005 0.0" > strain_runs/strain_params
|
|
|
|
# Run strain sequence.
|
|
cd strain_runs
|
|
prev_strain_id="000"
|
|
|
|
# First minimize initial state.
|
|
mkdir -p min.000
|
|
cd min.000
|
|
cp ../../initial.input equilibrium.input
|
|
|
|
cat $script_dir/lammps/strain.lmp|
|
|
sed "s@_DATA_FILE@equilibrium.input@"|
|
|
sed "s@_OUTPUT_DIR@.@"|
|
|
sed "s@_BOND_LENGTH_HISTOGRAM_FILE@bond_length_histogram@"|
|
|
sed "s@_POTENTIAL_FILE@${potential_dir}/ch.sedrebo@" > strain.lmp
|
|
$lammps_executable < strain.lmp > log.lmp
|
|
|
|
cd ..
|
|
echo 'Initial structure "ready." Stretching...'
|
|
|
|
# Conduct the stretch sequence.
|
|
for index in $(seq 1 $num_strains); do
|
|
strain_id=${strain[$index]}
|
|
|
|
# Prepare next minimization.
|
|
mkdir -p min.$strain_id
|
|
cd min.$strain_id
|
|
|
|
# Create stretched input.
|
|
grep "STRAIN=$strain_id" ../../strain_lengths.tmp > box_lengths
|
|
read strain new_Lx new_Ly other < box_lengths
|
|
echo "$prev_strain_id"
|
|
pwd
|
|
|
|
final_prev_cooorddump_file=$(find ../min.$prev_strain_id -name '*.coorddump'|sort -r|sed -n 1p)
|
|
echo $final_prev_cooorddump_file
|
|
$bin_dir/lammps_dump_input $final_prev_cooorddump_file stretched.input.tmp $new_Lx $new_Ly
|
|
#sed -e "s@# LAMMPS data file@LAMMPS data file edited\n@" stretched.input.tmp|sed -e "s@\s*atoms@ atoms\n@"|sed 's/ / /' > stretched.input
|
|
sed -e "s@[0-9.-]\+\s\+[0-9.-]\+\s\+zlo zhi@0.0 3.350 zlo zhi@" stretched.input.tmp > stretched.input
|
|
rm stretched.input.tmp
|
|
|
|
# Run minimization.
|
|
cat $script_dir/lammps/strain.lmp|
|
|
sed "s@_DATA_FILE@stretched.input@"|
|
|
sed "s@_OUTPUT_DIR@.@"|
|
|
sed "s@_BOND_LENGTH_HISTOGRAM_FILE@bond_length_histogram@"|
|
|
sed "s@_POTENTIAL_FILE@${potential_dir}/ch.sedrebo@" > strain.lmp
|
|
$lammps_executable < strain.lmp > log.lmp
|
|
|
|
# Prepare for next strain.
|
|
cd ..
|
|
echo -n "$strain_id "
|
|
prev_strain_id=$strain_id
|
|
done
|
|
|
|
echo -ne "\n"
|
|
cd $origin_dir
|