mirror of
https://asciireactor.com/otho/lammps-graphene.git
synced 2024-11-22 03:25:05 +00:00
88 lines
2.7 KiB
Bash
88 lines
2.7 KiB
Bash
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#!/bin/bash
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script_dir=`echo $0|sed 's/\(.*\)\/[^/]*/\1/'`
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# Used to determine angle for displacement calculations.
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reference_atom=37
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# Usage: loc_x <LAMMPS input file> <atom #>
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function loc_x { cat $1|grep "^$2\s*[0-9]"|sed "s/^$2\s*1\s*\([-0-9.]*\)\s*[-0-9.]*\s*[-0-9.]*\s*/\1/"; }
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function loc_y { cat $1|grep "^$2\s*[0-9]"|sed "s/^$2\s*1\s*[-0-9.]*\s*\([-0-9.]*\)\s*[-0-9.]*\s*/\1/"; }
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# Usage: pullout <LAMMPS input file> <atom #> <x displacement> <y disp>
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#
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# Return LAMMPS input file text after adding displacement*sin(theta) to
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# y coord, and displacement*cos(theta) to the x coord, of indicated atom #.
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function pullout {
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newloc_x=$(bc <<< "$(loc_x $1 $2) + $3")
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newloc_y=$(bc <<< "$(loc_y $1 $2) + $4")
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# echo $1 $2 $3 $4 > /dev/stderr
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cat $1|sed "s/^\($2\s*1\s*\)\([-0-9.]*\)\(\s*\)\([-0-9.]*\)\(\s*\)\([-0-9.]*\)\(\s*$\)/\1${newloc_x}\3${newloc_y}\5\6\7/"
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}
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function clean.func {
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if [ -z $1 ]; then
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dir="."
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else
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dir="$1"
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fi
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echo -n "Cleaning temporary files in \"$dir\"... "
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rm ${dir}/*tmp* 2> /dev/null
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echo Done.
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exit 0
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}
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if [[ -z $* ]]; then
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echo No list given. Exiting.
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exit 1
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fi
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list=" $* "
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for runtype in $list; do
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mkdir $runtype
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rm $runtype/*
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pulled_atom=$(grep 'group' $runtype.in|grep 'pulled'|sed 's/^.*id *\([0-9]*\).*$/\1/')
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echo "Creating coordinate tables and input scripts."
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for increment in $(seq 0 5 900); do
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displacement=$(bc <<< "scale=2; $increment / 100"|sed 's/^\([0-9]\)*$/\1\.00/'|sed 's/\.\([0-9]\)\s*$/\.\10/'|sed 's/^\./0\./')
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delta_x=$( bc <<< "scale=6; $(loc_x $runtype.input ${pulled_atom}) - $(loc_x $runtype.input ${reference_atom})" )
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delta_y=$( bc <<< "scale=6; $(loc_y $runtype.input ${pulled_atom}) - $(loc_y $runtype.input ${reference_atom})" )
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slope=$( bc <<< "scale=5; ${delta_y} / ${delta_x}" )
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theta=$( bc -l <<< "a(${slope})" )
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disp_x=$(bc -l <<< "$displacement * c($theta)")
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disp_y=$(bc -l <<< "$displacement * s($theta)")
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# echo $displacement $theta $delta_y $delta_x
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# echo "$(loc_x $runtype.input ${pulled_atom}) $(loc_y $runtype.input ${pulled_atom}) "
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input_filename="$runtype.$displacement.input.tmp"
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in_filename="$runtype.$displacement.in.tmp"
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pullout $runtype.input $pulled_atom $disp_x $disp_y > $input_filename
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cat $runtype.in|sed "s/^\(read_data\s*\)\([-_a-zA-Z0-9]*\)\.input\s*/\1${input_filename}/"|sed "s/DISPLACEMENT/$displacement/g" > $runtype.$displacement.in.tmp
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echo -n "$displacement "
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done
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echo
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echo "Processing LAMMPS inputs."
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for LAMMPS_input in $(find . -regextype sed -regex ".*/$runtype\.[0-9.]*\.in\.tmp"|sort -n); do
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displacement=$(echo $LAMMPS_input|sed "s/.*\/$runtype\.\([0-9.]\+\)*\.in\.tmp/\1/")
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../../bin/lmp_serial.icc < $LAMMPS_input > $runtype/log.$displacement
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echo -n "$displacement "
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done
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done
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echo
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echo Done.
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clean.func
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