mirror of
https://asciireactor.com/otho/lammps-graphene.git
synced 2024-11-25 01:15:07 +00:00
88 lines
2.7 KiB
Bash
88 lines
2.7 KiB
Bash
|
#!/bin/bash
|
||
|
|
|
||
|
|
|
||
|
|
script_dir=`echo $0|sed 's/\(.*\)\/[^/]*/\1/'`
|
||
|
|
|
||
|
|
# Used to determine angle for displacement calculations.
|
||
|
|
reference_atom=37
|
||
|
|
|
||
|
|
|
||
|
|
# Usage: loc_x <LAMMPS input file> <atom #>
|
||
|
|
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/"; }
|
||
|
|
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/"; }
|
||
|
|
|
||
|
|
# Usage: pullout <LAMMPS input file> <atom #> <x displacement> <y disp>
|
||
|
|
#
|
||
|
|
# Return LAMMPS input file text after adding displacement*sin(theta) to
|
||
|
|
# y coord, and displacement*cos(theta) to the x coord, of indicated atom #.
|
||
|
|
function pullout {
|
||
|
|
newloc_x=$(bc <<< "$(loc_x $1 $2) + $3")
|
||
|
|
newloc_y=$(bc <<< "$(loc_y $1 $2) + $4")
|
||
|
|
# echo $1 $2 $3 $4 > /dev/stderr
|
||
|
|
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/"
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
function clean.func {
|
||
|
|
if [ -z $1 ]; then
|
||
|
|
dir="."
|
||
|
|
else
|
||
|
|
dir="$1"
|
||
|
|
fi
|
||
|
|
|
||
|
|
echo -n "Cleaning temporary files in \"$dir\"... "
|
||
|
|
|
||
|
|
rm ${dir}/*tmp* 2> /dev/null
|
||
|
|
|
||
|
|
echo Done.
|
||
|
|
exit 0
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
if [[ -z $* ]]; then
|
||
|
|
echo No list given. Exiting.
|
||
|
|
exit 1
|
||
|
|
fi
|
||
|
|
|
||
|
|
list=" $* "
|
||
|
|
for runtype in $list; do
|
||
|
|
mkdir $runtype
|
||
|
|
rm $runtype/*
|
||
|
|
pulled_atom=$(grep 'group' $runtype.in|grep 'pulled'|sed 's/^.*id *\([0-9]*\).*$/\1/')
|
||
|
|
|
||
|
|
echo "Creating coordinate tables and input scripts."
|
||
|
|
|
||
|
|
for increment in $(seq 0 5 900); do
|
||
|
|
displacement=$(bc <<< "scale=2; $increment / 100"|sed 's/^\([0-9]\)*$/\1\.00/'|sed 's/\.\([0-9]\)\s*$/\.\10/'|sed 's/^\./0\./')
|
||
|
|
delta_x=$( bc <<< "scale=6; $(loc_x $runtype.input ${pulled_atom}) - $(loc_x $runtype.input ${reference_atom})" )
|
||
|
|
delta_y=$( bc <<< "scale=6; $(loc_y $runtype.input ${pulled_atom}) - $(loc_y $runtype.input ${reference_atom})" )
|
||
|
|
slope=$( bc <<< "scale=5; ${delta_y} / ${delta_x}" )
|
||
|
|
theta=$( bc -l <<< "a(${slope})" )
|
||
|
|
disp_x=$(bc -l <<< "$displacement * c($theta)")
|
||
|
|
disp_y=$(bc -l <<< "$displacement * s($theta)")
|
||
|
|
# echo $displacement $theta $delta_y $delta_x
|
||
|
|
# echo "$(loc_x $runtype.input ${pulled_atom}) $(loc_y $runtype.input ${pulled_atom}) "
|
||
|
|
input_filename="$runtype.$displacement.input.tmp"
|
||
|
|
in_filename="$runtype.$displacement.in.tmp"
|
||
|
|
pullout $runtype.input $pulled_atom $disp_x $disp_y > $input_filename
|
||
|
|
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
|
||
|
|
|
||
|
|
echo -n "$displacement "
|
||
|
|
done
|
||
|
|
echo
|
||
|
|
|
||
|
|
echo "Processing LAMMPS inputs."
|
||
|
|
|
||
|
|
for LAMMPS_input in $(find . -regextype sed -regex ".*/$runtype\.[0-9.]*\.in\.tmp"|sort -n); do
|
||
|
|
displacement=$(echo $LAMMPS_input|sed "s/.*\/$runtype\.\([0-9.]\+\)*\.in\.tmp/\1/")
|
||
|
|
../../bin/lmp_serial.icc < $LAMMPS_input > $runtype/log.$displacement
|
||
|
|
echo -n "$displacement "
|
||
|
|
done
|
||
|
|
done
|
||
|
|
|
||
|
|
echo
|
||
|
|
echo Done.
|
||
|
|
|
||
|
|
clean.func
|
||
|
|
|