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