1The directory structure_generators includes several scripts for
2generating LAMMPS structure files:
3
4- Be-solid.pl: beryllium solid box
5- h2.pl: rectangular lattice of hydrogen atoms
6- Diamond.pl: diamond A4 box
7- Li-hydride: Lithium hydride solid box
8- Li-solid: Lithium solid box (Li-solid-angstromg produces data file in Angstroms)
9- Uniform-electron-gas.pl: uniform electron gas on an NaCl lattice
10
11- bohr2ang.py: converts an eFF structure file described in bohr to
12  its corresponding version in Angstroms
13
14And other useful scripts for processing pEFF related information are
15included, such as:
16
17- cfg2lammps.py: Python script for converting an eff cfg file into a
18  LAMMPS data/script file pair
19
20- lmp2radii.py/pyx: Python/Cython scripts for post-processing a lammps
21  trajectory to extract electron radii/frame.
22
23Note: the corresponding .c, and .so files are the c source and binary
24library (loadable Python module) created by Cython automatically when
25compiling lmp2radii.pyx in place with Cython (python setup.py
26build_ext --inplace).
27
28- radii.vmd: a TCL script for adding radial changes per trajectory
29  frame to an xyz LAMMPS trajectory of an pEFF run.
30
31- lmp2any.py: Python scipt for extracting quantities from a custom
32  lammps dump
33
34- lmp2radii-col.py: Same as lmp2radii.py, but takes a column
35  descriptor for the radius
36
37- VMD-input.py: Automatically calls the necessary scripts to produce a
38  VMD ready script that loads variable radii into VMD
39
40NOTE: you must set the graphical representation in VMD to represent
41electrons using transparency (this requires selecting and applying the
42corresponding atom types).
43
44For further details see the descriptors in each file, or contact:
45Andres Jaramillo-Botero: ajaramil@wag.caltech.edu
46
47Acknowledgments: Thanks to Axel Kohlmeyer (Temple Univ) for his help
48with VMD.
49