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119 lines
3.4 KiB
Markdown
Executable File
119 lines
3.4 KiB
Markdown
Executable File
Library Created for the Materials Simulations Laboratory, University of South Florida
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Otho Ulrich, coder
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Structure:
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msl/scripts -- contains BASH scripts that comprise the functionality of the library
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msl/bin -- contains binary files to be called by scripts
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msl/code -- ontains source code for some binaries
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msl/materials -- contains structure inputs from other students
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msl/potentials -- contains potential files used by LAMMPS
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msl/notes -- notes taken throughout the project
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Maintaining these directories as provided is important for most of the scripts
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to work properly.
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# Available Scripts
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The usage of each script and an in-depth explanation is available at the
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beginning of each file. To see the usage of a script, type
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head <name of script>
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Or open the file in a text editor, where you can view the in-depth explanation.
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# Programs
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Two primary programs exist
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[1]
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msl/scripts/populate_units_from_bicrystal_samples.sh
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This program takes structures such as those generated by Kien, applies
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periodic boundary conditions and relaxes the samples and boxes, thus creating
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unit cells for the defective graphene lattice. Read the script file itself for
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more info. The scripts used by this program are
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msl/scripts/bicrystal/stage1.sh
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msl/scripts/bicrystal/stage2.sh
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msl/scripts/bicrystal/stage3.sh
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These scripts in turn use some scripts from
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msl/analysis/
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and maybe a few others.
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[2]
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msl/scripts/conduct_biaxial_stress_test_on_unit_bicrystals.sh
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This script is meant to take the bicrystal units from the previous script,
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then conduct the hydrostatic biaxial strain on those samples, and produce
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the stress-strain curves using a number of scripts under the directories
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msl/strain
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msl/analysis
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However, the coordinate transformations -- both those written by me and those
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developed by Dr. Oleynik -- have yet to work properly. In other words, this
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program is still under development. Fix it if you can!
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# Submission Scripts
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There are submissions scripts in msl/scripts/circe and msl/scripts/cluster.
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These are mainly for internal use by other scripts, specifically scripts
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that make submissions to these systems.
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msl/scripts/run contain scripts that are closely related to cluster submissions.
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These scripts either make submissions or are called within submissions, depending
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on the needs of the program.
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# LAMMPS scripts
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There are a number of LAMMPS input script templates in msl/scripts/lammps.
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These are often called "<something>.in" by other students in the MSL. I used
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the extension .lmp for clarity, instead. These templates are used by other
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scripts that submit LAMMPS runs.
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msl/scripts/manip contains scripts for manipulating LAMMPS atomic data input
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files.
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# Other Scripts
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Several scripts exist to convert file types, under msl/scripts/conv
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I believe these are pretty self-explanatory.
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There are BASH function libraries under /msl/scripts/func. These exist to
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perform operations on different types of files, mostly parsing information.
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They are well-commented and will hopefully be of use to anyone writing
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programs to manipulate the files in question.
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There is a JMOL script under msl/scripts/jmol for creating an animation in JMOL.
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msl/scripts/util contains utility scripts, such as updating the script library on
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the cluster, or cleaning directories of temporary files.
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msl/scripts/xmgrace contains batch scripts that can be used by xmgrace to produce
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pre-defined graphs.
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