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structure_generators
README
VMD-input.py
bohr2ang.py
cfg2lammps.py
h2.out
h2.vmd
h2.xyz
lmp2data.py
lmp2radii.c
lmp2radii.py
lmp2radii.pyx
lmp2radii_col.py
lmp2xyz.py
radii.vmd
restart2data-pEFF.cpp
setup.py

README

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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