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