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https://asciireactor.com/otho/lammps-graphene.git
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153 lines
3.5 KiB
Bash
Executable File
153 lines
3.5 KiB
Bash
Executable File
#!/bin/bash
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# A script to create a LAMMPS input data file from an atomic data dump
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# by LAMMPS.
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#
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# Usage: ./lammps_dump_to_input.sh <input file> <output file>
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# Currently, this program assumes all atoms are carbon ("1").
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# It also assumes the LAMMPS dump file correctly reported the
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# number of atoms.
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input_file=$1
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output_file=$2
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default_output_file="fromdump.input"
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# Test validity of input and output files and step number.
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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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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 $output_file; then
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echo Output file looks good.
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else
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Cannot write to output file. Exiting.
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exit 4
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fi
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# Read info from the LAMMPS dump.
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num_atoms=0
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line_num=0
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while read -r line; do
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if [[ -z "$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 [[ $(echo "$line"|cut -d' ' -f1,2,3) == "ITEM: BOX BOUNDS" ]]; then
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read -r xlo xhi other
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read -r ylo yhi other
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read -r zlo zhi other
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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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exit 5
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fi
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fi
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# Collect atomic data.
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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 "$words" ]]; do
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column=$(echo $line|cut -d' ' -f$i)
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case $column in
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"id") id_pos=$((i-2)) ;;
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"x") x_pos=$((i-2)) ;;
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"y") y_pos=$((i-2)) ;;
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"z") z_pos=$((i-2)) ;;
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esac
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(( i++ ))
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done
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for index in $(seq 1 $num_atoms); do
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read -r atomic_data
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atom_id[$index]=$(echo "$atomic_data"|cut --fields=$id_pos -d' ')
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coords[$index]=$(echo "$atomic_data"|
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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 [ $num_atoms -eq 0 ]; then
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echo No atoms found. Exiting.
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exit 6
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fi
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# Bubble sort atoms by atom_id.
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echo Sorting atoms.
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size=$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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if [[ ${atom_id[$index]} < ${atom_id[$index-1]} ]]; then
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temp_id=${atom_id[$((index-1))]}
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temp_coords=${coords[$((index-1))]}
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atom_id[$((index-1))]=${atom_id[$index]}
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coords[$((index-1))]=${coords[$index]}
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atom_id[$index]=$temp_id
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coords[$index]=$temp_coords
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made_swap="true"
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fi
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done
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done
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# Write new LAMMPS input data.
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echo Writing LAMMPS input data to $output_file.
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echo -n "LAMMPS input data file created using " > $output_file
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echo "OAU LAMMPS dump->LAMMPS input script." >> $output_file
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echo "" >> $output_file
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echo "$num_atoms atoms" >> $output_file
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echo "" >> $output_file
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echo "" >> $output_file
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echo "1 atom types" >> $output_file
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echo "" >> $output_file
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echo "$xlo $xhi xlo xhi" >> $output_file
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echo "$ylo $yhi ylo yhi" >> $output_file
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echo "$zlo $zhi zlo zhi" >> $output_file
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echo "" >> $output_file
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echo "Masses" >> $output_file
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echo "" >> $output_file
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echo "1 12.01" >> $output_file
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echo "" >> $output_file
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echo "Atoms" >> $output_file
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echo "" >> $output_file
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for index in $(seq 1 $num_atoms); do
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echo "$index 1 ${coords[$index]}" >> $output_file
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done
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# Finished.
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echo Done.
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exit 0 |