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The directory structure_generators includes several scripts for
generating LAMMPS structure files:
- Be-solid.pl: beryllium solid box
- h2.pl: rectangular lattice of hydrogen atoms
- Diamond.pl: diamond A4 box
- Li-hydride: Lithium hydride solid box
- Li-solid: Lithium solid box (Li-solid-angstromg produces data file in Angstroms)
- Uniform-electron-gas.pl: uniform electron gas on an NaCl lattice
- bohr2ang.py: converts an eFF structure file described in bohr to
its corresponding version in Angstroms
And other useful scripts for processing pEFF related information are
included, such as:
- cfg2lammps.py: Python script for converting an eff cfg file into a
LAMMPS data/script file pair
- lmp2radii.py/pyx: Python/Cython scripts for post-processing a lammps
trajectory to extract electron radii/frame.
Note: the corresponding .c, and .so files are the c source and binary
library (loadable Python module) created by Cython automatically when
compiling lmp2radii.pyx in place with Cython (python setup.py
build_ext --inplace).
- radii.vmd: a TCL script for adding radial changes per trajectory
frame to an xyz LAMMPS trajectory of an pEFF run.
- lmp2any.py: Python scipt for extracting quantities from a custom
lammps dump
- lmp2radii-col.py: Same as lmp2radii.py, but takes a column
descriptor for the radius
- VMD-input.py: Automatically calls the necessary scripts to produce a
VMD ready script that loads variable radii into VMD
NOTE: you must set the graphical representation in VMD to represent
electrons using transparency (this requires selecting and applying the
corresponding atom types).
For further details see the descriptors in each file, or contact:
Andres Jaramillo-Botero: ajaramil@wag.caltech.edu
Acknowledgments: Thanks to Axel Kohlmeyer (Temple Univ) for his help
with VMD.
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