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https://asciireactor.com/otho/lammps-graphene.git
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88 lines
2.0 KiB
Bash
Executable File
88 lines
2.0 KiB
Bash
Executable File
#!/bin/bash
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# Usage: ./graph_energy_afo_x_displacement.sh <LAMMPS dump file> <output file>
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# This program creates xmgrace-readable output from a LAMMPS dump file.
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# Independent variable: x displacement of each atom
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# Dependent variable: energy of correlated atom
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script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*/scripts\).*@\1@')
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source $script_dir/func/dump_parsing.src
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source $script_dir/func/utility.src
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# Test validity of input and output files, and create list of input files.
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dump_file=$1
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xmgrace_file=$2
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default_output_file=script_output.xm
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if [ -z $dump_file ]; then
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echo No input file specified. Exiting.
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exit 1
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fi
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echo Using input file $dump_file.
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if [ -w $dump_file -a -r $dump_file ]; then
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echo $dump_file looks good.
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else
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echo Cannot access $dump_file. Exiting.
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exit 1
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fi
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if [ -z $xmgrace_file ]; then
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xmgrace_file=${default_output_file}
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echo No output file specified. Using $xmgrace_file.
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fi
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if `! touch $xmgrace_file`; then
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echo Cannot access $xmgrace_file. Exiting.
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exit 2
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fi
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echo Output to $xmgrace_file.
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> $xmgrace_file
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> equilibrium_energy.tmp
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num_atoms=$(parse_num_atoms_from_dump $dump_file)
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echo Found $num_atoms atoms.
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# Index entries by atom ID
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for atom_id in $(seq 1 $num_atoms); do
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Z[$atom_id]=$(parse_coord x $dump_file $atom_id)
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U[$atom_id]=$(parse_atomic_pressure $dump_file $atom_id)
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done
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# Bubble sort by x value. -- Not finished and not necessary
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# size=$num_atoms
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# count=0
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# until [[ $made_swap == "false" ]]; do
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# made_swap="false"
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# for index in $(seq 2 $size); do
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# diff1=$(sed -n 5p ${info_array[$((index-1))]})
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# diff2=$(sed -n 5p ${info_array[$index]})
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# if [[ $(echo "$diff1 > $diff2"|bc) == "1" ]]; then
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# temp_info=${info_array[$((index-1))]}
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# info_array[$((index-1))]=${info_array[$index]}
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# info_array[$index]=$temp_info
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# made_swap="true"
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# fi
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# done
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#
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# done
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# Write array to xmgrace-readable file.
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echo Writing $num_atoms entries to table.
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for index in $(seq 1 $num_atoms ); do
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echo ${Z[$index]} ${U[$index]} >> $xmgrace_file
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done
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clean
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echo Done.
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exit 0
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