lammps-graphene/README.md

Library Created for the Materials Simulations Laboratory, University of South Florida

Otho Ulrich, coder


Structure:

msl/scripts -- contains BASH scripts that comprise the functionality of the library
msl/bin -- contains binary files to be called by scripts
msl/code -- ontains source code for some binaries
msl/materials -- contains structure inputs from other students
msl/potentials -- contains potential files used by LAMMPS
msl/notes -- notes taken throughout the project

Maintaining these directories as provided is important for most of the scripts 
to work properly.





# Available Scripts
The usage of each script and an in-depth explanation is available at the
beginning of each file. To see the usage of a script, type

head <name of script>

Or open the file in a text editor, where you can view the in-depth explanation.


# Programs
Two primary programs exist

[1]
msl/scripts/populate_units_from_bicrystal_samples.sh

	This program takes structures such as those generated by Kien, applies
periodic boundary conditions and relaxes the samples and boxes, thus creating
unit cells for the defective graphene lattice. Read the script file itself for
more info. The scripts used by this program are

msl/scripts/bicrystal/stage1.sh
msl/scripts/bicrystal/stage2.sh
msl/scripts/bicrystal/stage3.sh

These scripts in turn use some scripts from

msl/analysis/

and maybe a few others.


[2]
msl/scripts/conduct_biaxial_stress_test_on_unit_bicrystals.sh

This script is meant to take the bicrystal units from the previous script,
then conduct the hydrostatic biaxial strain on those samples, and produce
the stress-strain curves using a number of scripts under the directories

msl/strain
msl/analysis

However, the coordinate transformations -- both those written by me and those
developed by Dr. Oleynik -- have yet to work properly. In other words, this
program is still under development. Fix it if you can!



# Submission Scripts
There are submissions scripts in msl/scripts/circe and msl/scripts/cluster.
These are mainly for internal use by other scripts, specifically scripts
that make submissions to these systems.

msl/scripts/run contain scripts that are closely related to cluster submissions.
These scripts either make submissions or are called within submissions, depending
on the needs of the program.



# LAMMPS scripts
There are a number of LAMMPS input script templates in msl/scripts/lammps.
These are often called "<something>.in" by other students in the MSL. I used
the extension .lmp for clarity, instead. These templates are used by other
scripts that submit LAMMPS runs.

msl/scripts/manip contains scripts for manipulating LAMMPS atomic data input
files.




# Other Scripts
Several scripts exist to convert file types, under msl/scripts/conv

I believe these are pretty self-explanatory.


There are BASH function libraries under /msl/scripts/func. These exist to
perform operations on different types of files, mostly parsing information.
They are well-commented and will hopefully be of use to anyone writing
programs to manipulate the files in question.

There is a JMOL script under msl/scripts/jmol for creating an animation in JMOL.

msl/scripts/util contains utility scripts, such as updating the script library on
the cluster, or cleaning directories of temporary files.

msl/scripts/xmgrace contains batch scripts that can be used by xmgrace to produce
pre-defined graphs.