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89 lines
2.9 KiB
Bash
Executable File
89 lines
2.9 KiB
Bash
Executable File
# This program will create graphene bicrystal unit cells that can constitute
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# an infinite lattice when periodic boundary conditions are applied (in 2d).
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# Usage: ./populate_bicrystals.sh <root dir> [source dir]
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# The program will create a unit cell from any POSCAR files found under
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# [source dir] (or pwd if [source dir] is not specified]. It will create a
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# new directory structure under <root dir>, maintaining naming and directory
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# conventions. The program uses LAMMPS sample minimization and simulation box
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# relaxation to create the lowest possible energy state from the given lattice.
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# The program is meant to be used to minimize samples created by Kien in the MSL. The program should minimize all samples and output
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# unit cells that can then be used in future LAMMPS PBC simulations.
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# The program is organized into three stages: preparation, minimization, and
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# analysis
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# In stage 1, the program will find all files ending in .POSCAR in any
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# subdirectories of user's current pwd, convert them to jmol cartesian
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# snapshots, then populate a new directory tree under <root dir> with
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# these snapshots. The program will then convert each jmol snapshot to a
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# LAMMPS input file and shrink the initial box around the sample. The
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# program will also populate an info file for each sample, and store at
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# this time the grain boundary mismatch angle in that file. The current info
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# file format as of 2014 July 19 is:
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# All angles in degrees
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# All energies in eV (presuming metal units in LAMMPS)
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# <sample dir>/<sample name>
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# ==============
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# <misorientation angle>
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# <num atoms> atoms
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# <formation energy> - <formation energy of pristine graphene>
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# <initial box dimensions>
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# <final box dimensions>
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# Coordinations
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# -------------
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# 4: # atoms
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# 3: # atoms
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# 2: # atoms
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# 1: # atoms
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# In stage 2, the program will run relax_sample_and_box.sh on each sample
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# from stage 1, thus creating a unit cell for PBC from each sample.
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# In stage 3, the program will then check bond lengths for each sample and
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# report any outliers in that sample's info file. Next, a JMOL snapshot will
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# be generated. Finally, the system's change in energy over the minimzation
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# will be calculated and stored in the info file. A report is then produced
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# in <root dir> containing a print of all info files.
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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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root_dir=$1
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if [[ -z $2 ]]; then source_dir=$(pwd); else source_dir=$2; fi
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source $script_dir/func/utility.src
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# (Stage 1) -- Preparation
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$script_dir/bicrystal/stage1.sh $root_dir $source_dir
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echo -e "\nStage 1 complete. \n"
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# (Stage 2) -- Minimization
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$script_dir/bicrystal/stage2.sh $root_dir
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echo -e "Stage 2 complete.\n"
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# (Stage 3) -- Analysis
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echo "Please run stage 3 manually: scripts/bicrystal/stage3.sh $root_dir"
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# $script_dir/bicrystal/stage3.sh $root_dir
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# echo -e "Stage 3 complete.\n"
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echo Program complete.
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