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76 lines
2.2 KiB
Bash
76 lines
2.2 KiB
Bash
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#!/bin/bash
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# This program will statically apply biaxial strain on a sample or samples
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# by some delta-strain.
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# Usage: ./biaxial_stress_test.sh <root dir> [source dir]
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# For any samples found under [source dir] (or current directory if
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# [source dir] is not supplied), this program will search for LAMMPS input
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# called "minimized.input." This program assumes the structure to be a cell
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# intended for periodic boundary conditions.
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# For each of these inputs, the program will call "stretch.x," a c++
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# program that will created a new LAMMPS input file with a box size larger
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# by delta-strain in the x and y dimensions, and transform the atomic
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# coordinates so that each atom's position relative to the simulation box
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# remains unchanged.
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# The program will then run a minimization and repeat this process until
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# a maximum strain is reached.
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script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
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bin_dir="$script_dir/../bin"
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root_dir=$1
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if [[ -z $2 ]]; then source_dir=$(pwd); else source_dir=$2; fi
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source $script_dir/func/utility.src
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source $script_dir/func/input_parsing.src
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input_files=$(find $source_dir -name 'minimized.input')
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num_files=$(echo $input_files|wc -l)
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echo Found $num_files input files. Creating initial states.
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origin_dir=$(pwd)
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count="0"
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for input_file in $input_files; do
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# create new directory and set initial.input.
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file_name=$(basename $input_file)
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sample_dir=$(dirname $input_file)
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new_dir=$(echo $sample_dir|sed "s@^$source_dir@$root_dir/@"|sed 's@/*$@@')
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mkdir -p $new_dir
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cp $input_file $new_dir/initial.input
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cd $new_dir
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simulation_box_lengths initial.input > box_lengths.tmp
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read Lx Ly Lz < box_lengths.tmp
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# Setup strain lengths because cluster doesn't have bc.
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strain_sequence=$(seq 5 5 500|
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sed 's/^\([0-9]\)$/00\1/'|
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sed 's/^\([0-9]\)\([0-9]\)$/0\1\2/')
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> strain_lengths.tmp
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pwd
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for strain in $strain_sequence; do
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new_Lx=$(bc <<< "scale=10; $Lx * (1.$strain)")
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new_Ly=$(bc <<< "scale=10; $Ly * (1.$strain)")
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echo "STRAIN=$strain $new_Lx $new_Ly" >> strain_lengths.tmp
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done
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#sbatch $script_dir/cluster/strain_loop.sub .
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$script_dir/run/apply_strain.sh .
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(( count++ ))
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cd $origin_dir
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done
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echo $count threads submitted.
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