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https://asciireactor.com/otho/lammps-graphene.git
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100 lines
2.9 KiB
Plaintext
100 lines
2.9 KiB
Plaintext
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#!/bin/bash
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# Usage: loc_x <LAMMPS input file> <atom #>
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loc_x() { cat $1|grep "^$2\s*[0-9]"|
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sed "s/^$2\s*1\s*\([-0-9.]*\)\s*[-0-9.]*\s*[-0-9.]*\s*/\1/"; }
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loc_y() { cat $1|grep "^$2\s*[0-9]"|
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sed "s/^$2\s*1\s*[-0-9.]*\s*\([-0-9.]*\)\s*[-0-9.]*\s*/\1/"; }
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# Usage:
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# pullout <LAMMPS input file> "<atom #> <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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pullout() {
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if [[ $3 == 0 && $4 == 0 ]]; then exit 0; fi
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count=0
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echo $2: $3, $4 > outputsomething
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for atom in $2; do
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((count++))
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newloc_x=$(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/" > cmd.pullout.tmp.$count
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done
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echo cmd.pullout.tmp.$count
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rm -f cmd.pullout.tmp.* >> /dev/null 2> /dev/null
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}
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# Usage: get_pulled_atoms <LAMMPS input file>
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#
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# Return a list of atoms from LAMMPS group "pulled" from LAMMPS input file.
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get_pulled_atoms() {
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# grep 'group' $1|grep 'pulled'|sed 's/^.*id[\s]*\([0-9\s]*\)[\s]*$/\1/'
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grep 'group' $1|grep 'pulled'|sed 's/[^0-9\s]?/'
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}
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# Usage: convert_to_pull_displacement <value> <order>
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#
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# Converts int to a decimal number in angstroms where int is 1/order angstroms.
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convert_to_pull_displacement() {
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echo $(bc <<< "scale=2; $1 / $2"|
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sed 's/^\([0-9]\)*$/\1\.00/'|
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sed 's/\.\([0-9]\)\s*$/\.\10/'|
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sed 's/^\./0\./')
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}
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# Print the three-dimensional extremes of the atom coordinates in a LAMMPS
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# input file.
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# Usage: print_extremes <LAMMPS input file>
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# Output: <x_min> <x_max> <y_min> <y_max> <z_min> <z_max>
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print_extremes() {
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input_file=$1
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found_atoms="false"
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while read -r line; do
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if [[ $found_atoms == "false" ]]; then
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if [[ $line == "Atoms" ]]; then found_atoms="true"; fi
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continue
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fi
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atom_num=$(echo $line|sed 's/^\s*\([0-9]*\).*/\1/')
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x_cur=$(echo $line|sed 's/^\s*[0-9]\+\s\+[0-9]\+\s\+\([0-9.-]\+\).*$/\1/')
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y_cur=$(echo $line|sed 's/^\s*[0-9]\+\s\+[0-9]\+\s\+[0-9.-]\+\s*\([0-9.-]\+\).*$/\1/')
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z_cur=$(echo $line|sed 's/^\s*[0-9]\+\s\+[0-9]\+\s\+[0-9.-]\+\s*[0-9.-]\+\s*\([0-9.-]\+\)\s*$/\1/')
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if [[ ! $atom_num -ge 1 ]]; then continue; fi
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if [[ $atom_num == "1" ]]; then
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x_max=$x_cur; x_min=$x_cur
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y_max=$y_cur; y_min=$y_cur
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z_max=$z_cur; z_min=$z_cur
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fi
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if [[ $(bc <<< "$x_cur > $x_max") == "1" ]]; then
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x_max=$x_cur
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fi
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if [[ $(bc <<< "$x_cur < $x_min") == "1" ]]; then
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x_min=$x_cur
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fi
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if [[ $(bc <<< "$y_cur > $y_max") == "1" ]]; then
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y_max=$y_cur
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fi
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if [[ $(bc <<< "$y_cur < $y_min") == "1" ]]; then
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y_min=$y_cur
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fi
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if [[ $(bc <<< "$z_cur > $z_max") == "1" ]]; then
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z_max=$z_cur
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fi
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if [[ $(bc <<< "$z_cur < $z_min") == "1" ]]; then
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z_min=$z_cur
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fi
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done < $input_file
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echo "$x_min $x_max $y_min $y_max $z_min $z_max"
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}
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