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45 lines
1.3 KiB
Bash
Executable File
45 lines
1.3 KiB
Bash
Executable File
#!/bin/bash
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# Creates a LAMMPS output file from a jmol snapshot, provided the jmol
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# is in xyz format. Box size is arbitrary, as currently written. LAMMPS
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# file is written to stdout.
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# Only works with carbon.
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# Usage: ./xyz_to_lammps_input.sh <jmol file>
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script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
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source $script_dir/func/utility.src
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xyz_file=$1
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cat $xyz_file|sed 's/C/1/' > $xyz_file.tmp
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num_atoms=$(( $(cat $xyz_file.tmp|wc -l) - 2))
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new_filename=`echo $xyz_file.tmp|sed 's/xyz/input/'`
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echo "LAMMPS Input file created using OAU xyz->input script." # > $new_filename
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echo "" # >> $new_filename
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echo "${num_atoms} atoms" # >> $new_filename
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echo "" # >> $new_filename
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echo "1 atom types" # >> $new_filename
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echo "" # >> $new_filename
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echo "-30 30 xlo xhi" # >> $new_filename
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echo "-30 30 ylo yhi" # >> $new_filename
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echo "-30 30 zlo zhi" # >> $new_filename
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echo "" # >> $new_filename
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echo "Masses" # >> $new_filename
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echo "" # >> $new_filename
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echo "1 12.01" # >> $new_filename
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echo "" # >> $new_filename
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echo "Atoms" # >> $new_filename
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echo "" # >> $new_filename
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for atom_id in $(seq 1 $num_atoms); do
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line_num=$((atom_id + 2))
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echo -n "$atom_id "
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sed -n ${line_num}p $xyz_file.tmp|sed 's/C/1/'
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done
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# cat $1.tmp.2 # >> $new_filename
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