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
• Uniform-electron-gas.pl: uniform electron gas on an NaCl lattice

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

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.