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https://asciireactor.com/otho/lammps-graphene.git
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134 lines
2.6 KiB
Bash
Executable File
134 lines
2.6 KiB
Bash
Executable File
#!/bin/bash
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# A script to create an xyz file from an atomic data dump
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# by LAMMPS.
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#
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# Usage: ./create_xyz.sh <input file> <output file> <step number>
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# Currently, this program assumes all atoms are carbon ("C").
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# It also assumes the LAMMPS output file correctly reported the
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# number of atoms. Step number can be used if the output file is
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# intended as part of a jmol animation.
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# Test validity of input and output files and step number.
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input_file=$1
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if [ -z $input_file ]; then
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echo No input file given. Exiting.
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exit 2
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fi
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if [ -r $input_file ]
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then
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echo Using input file $input_file.
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else
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echo Cannot read $input_file. Exiting.
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exit 3
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fi
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default_output_file="script_output.xyz"
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output_file=$2
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if [ -z $output_file ]; then
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echo No output file given. Using $default_output_file.
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output_file=$default_output_file
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else
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echo Output to $output_file.
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fi
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if touch $output_file; then
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echo Output file looks good.
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else
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Cannot write to output file. Exiting.
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exit 4
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fi
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step_line=""
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if [ -z $3 ]; then
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echo No step number specified. Creating singular output.
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else
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if [ $3 -ge 0 ]; then
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step_line="STEP $3"
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echo Output intended for animation step $3.
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else
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echo Invalid step number. Exiting.
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exit 5
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fi
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fi
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# Read atom list from the input file.
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#
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# Assuming LAMMPS output atom table format:
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# id element x y z f[x] f[y] f[z].
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num_atoms=0
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line_num=0
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while read -r line; do
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if [ -z "$line" ]; then continue; fi
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if [ $(( ++line_num )) -eq 1 ]; then
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if [ "$line" != "ITEM: TIMESTEP" ]; then
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echo Are you sure $input_file is a LAMMPS xyz output file?
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fi
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fi
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if [ "$line" == "ITEM: NUMBER OF ATOMS" ]; then
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read -r num_atoms
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if [ $num_atoms -gt 0 ]; then
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echo Number of atoms found: $num_atoms
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continue
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else
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echo Number of atoms not found.
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fi
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fi
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if [[ $(echo $line|cut -f1,2 -d' ') == "ITEM: ATOMS" ]]; then
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echo Compiling coordinate list.
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i=3; words=$(echo $line|wc -w);
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while [[ "$i" -le "$words" ]]; do
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if [[ $(echo $line|cut -d' ' -f$i) == "x" ]]; then x_pos=$((i-2)); fi
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if [[ $(echo $line|cut -d' ' -f$i) == "y" ]]; then y_pos=$((i-2)); fi
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if [[ $(echo $line|cut -d' ' -f$i) == "z" ]]; then z_pos=$((i-2)); fi
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(( i++ ))
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done
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for index in $(seq 1 $num_atoms); do
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read -r coord_data
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coords[$index]=$(echo "$coord_data"|cut --fields=$x_pos,$y_pos,$z_pos -d' ')
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done
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fi
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done < $input_file
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if [ $num_atoms -eq 0 ]; then
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echo No atoms found. Exiting.
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exit 6
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fi
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# Write atom list to output file.
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echo Writing xyz format to $output_file.
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echo $num_atoms > $output_file
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echo $step_line >> $output_file
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for index in $(seq 1 $num_atoms); do
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echo C ${coords[$index]} >> $output_file
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done
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echo Done.
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exit 0 |