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https://asciireactor.com/otho/lammps-graphene.git
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47 lines
1.7 KiB
Bash
47 lines
1.7 KiB
Bash
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#!/bin/bash
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# Usage: ./relax_sample_and_box.sh <data file>
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# This program will minimize the energy state of a graphene sample while
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# simultaneously relaxing the simulation box around the sample such that
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# the cuboid is a near approximation of the mechanical structure of the
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# sample. The simulation relaxes the box only in the x and y dimensions.
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# The program will populate a LAMMPS script in <data file>'s directory
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# based on scripts/lammps/relax_sample_and_box.lmp, then run it, creating
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# output in the same directory. log.lmp is created, along with #.dump for
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# the initial and final states.
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script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
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bin_dir="$script_dir/../bin"
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potential_dir="$script_dir/../potentials/"
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if [[ -z $1 ]]; then
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echo No data file given. Exiting.
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exit 1
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fi
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data_file=$1
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sample_name=$(echo $data_file|sed 's@.*/\(a-zA-Z0-9_-\).input@\1@')
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sample_dir=$(dirname $data_file)
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if [[ ! -r $data_file ]]; then
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echo "Data file not found or cannot be read for ${data_file}." >> /dev/stderr
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exit 1
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fi
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cat $script_dir/lammps/relax_sample_and_box.lmp|
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sed "s@_DATA_FILE@${data_file}@"|
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sed "s@_OUTPUT_DIR@${sample_dir}@"|
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sed "s@_BOND_LENGTH_HISTOGRAM_FILE@${sample_dir}/bond_length_histogram@"|
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sed "s@_POTENTIAL_FILE@${potential_dir}/ch.sedrebo@" > $sample_dir/relax_sample_and_box.lmp
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# To run on single machine
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$bin_dir/lmp_serial < $sample_dir/relax_sample_and_box.lmp > $sample_dir/log.lmp
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# To run on circe
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# $script_dir/circe/lammps_exec.sh $sample_dir/relax_sample_and_box.lmp $sample_dir/log.lmp
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# To run on msl cluster
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# sbatch $script_dir/cluster/LAMMPS_1core.sub $sample_dir/relax_sample_and_box.lmp $sample_dir/log.lmp >> /dev/null
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