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https://asciireactor.com/otho/lammps-graphene.git
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97 lines
2.8 KiB
Bash
97 lines
2.8 KiB
Bash
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#!/bin/bash
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# Stage 1 of the bicrystal unit population program.
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#
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# This program will find all files ending in .POSCAR in any subdirectories
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# of [source dir] (or pwd if [source dir] is not specified), convert them
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# to jmol cartesian snapshots, then populate a new directory tree under
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# <root dir> with these snapshots.
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# The program will then convert each jmol snapshot to a LAMMPS input file
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# and shrink the simulation box around the sample. The program will also
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# populate an info file for each sample, and store at this time the grain
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# boundary mismatch angle in that file.
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# Usage: ./stage1.sh <root dir> [source dir]
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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=$2; fi
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source_dir=$(echo "$source_dir"|sed 's@\([a-zA-Z0-9_-.]\)/*$@\1@')
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root_dir=$(echo "$root_dir"|sed 's@\([a-zA-Z0-9_-.]\)/*$@\1@')
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source $script_dir/func/utility.src
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# Locate all *.POSCAR under $1
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POSCAR_files=$(find $source_dir -name '*.POSCAR')
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#echo $POSCAR_files
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num_files=$(echo $POSCAR_files|wc -w)
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echo $num_files POSCAR files found.
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echo Processing files. Output to $root_dir.
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count=0
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echo -n "0% complete."
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for POSCAR_file in $POSCAR_files; do
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# gather info
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file_name=$(basename $POSCAR_file)
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sample_name=$(echo $file_name|sed 's/.POSCAR//')
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sample_dir=$(dirname $POSCAR_file)
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# create new directory
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new_dir=$(echo $sample_dir|sed "s@^$source_dir@$root_dir/@"|sed 's/.POSCAR//'|sed 's@/$@@')
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mkdir -p $new_dir
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# ylconv VASP:xyz, move to new dir
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xyz_initial="${new_dir}/${sample_name}_initial.xyz"
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$bin_dir/ylconv -svasp:xyz $POSCAR_file > $xyz_initial 2> /dev/null
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# echo $file_name
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# echo $sample_name
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# echo $sample_dir
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# echo $new_dir
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# echo $xyz_initial
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# convert to LAMMPS input
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#echo $new_dir
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#echo $sample_name
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LAMMPS_input="${new_dir}/${sample_name}.input"
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#echo $LAMMPS_input
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#echo "$script_dir/conv/xyz_to_lammps_input.sh $xyz_initial > $LAMMPS_input.tmp"
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$script_dir/conv/xyz_to_lammps_input.sh $xyz_initial > $LAMMPS_input.tmp
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# shrink box
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$script_dir/manip/shrink_box.sh $LAMMPS_input.tmp > $LAMMPS_input
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# create info file, write basic information
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info_file=${new_dir}/info
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echo "$sample_dir/$sample_name" > $info_file
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for iteration in $(seq $(echo "$sample_dir/$sample_name"|wc -c)); do echo -n "="; done >> $info_file
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echo -ne "\n" >> $info_file
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# parse grain mismatch angle and save to info file
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#mismatch_angle=$(head -n1 $POSCAR_file|sed 's/^.*angle\=\s*\([0-9.]\)\s*$//')
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mismatch_angle=$(head -n1 $POSCAR_file|sed 's/^.*\=\s*\([0-9]\)[^0-9]*/\1/')
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echo "$mismatch_angle" >> $info_file
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clean $new_dir > /dev/null
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(( count++ ))
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ratio=$(echo "
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scale=2
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count = $count
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num = $num_files
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ratio = count / num
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ratio
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" | bc)
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percent=$(echo $ratio|sed 's/\.//')
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echo -ne "\r${percent}% complete."
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done
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