This has been developed with the central purpose of developing semi-empirical models from quantum simulations and x-ray diffraction data. They should be generally useful for anyone running VASP or LAMMPS simulations, as well those studying x-ray diffraction patterns. Use it as you please, feel free to modify, chop-up or ruin this code as much as you like. Programs will tell you how to run them if run without any arguements, in general the name of the code should be self explanatory. Feel free to contact me with requests.
- python-numpy (generic math and numerics toolkit)
- python-scipy (generic science toolkit)
- python-matplotlib (2-D plotting)
- python-mayavi2 (3-d plotting)
- qhull & qvoronoi (voronoi and neighbor analysis)
- python-gtk2
- LAMMPS compiled with a python wrapper, with lammps.py in the PYTHONPATH
- analysis - Generic tools for manipulating data and generating analyses with many applications e.g.: FFTs, band pass, multidimensional curve fitting, etc.
- diffraction - Tools for x-ray pattern analysis and some curve fitting.
- gmice - A couple of tools for running codes remotely on our HPC server.
- moldyn - Scripts for reading LAMMPS molecular dynamics output data, some analysis and plotting.
- vasp - Scripts that plot and post-process VASP output data.
- potfitting - Tools for potential fitting and analyzing potentials.
- plotremote - tools for running these scripts from a remote server, makes working remotely easier when coupled with a file transfer system like dropbox.
Edit your .bashrc (or equivalent) and add:
matcalcdir="/path/to/matcalc/repo"
matcalcsubdirs=${matcalcdir}:$(find ${matcalcdir} -maxdepth 1 -type d | tr '\n' ':' | sed 's/:$//')
export PYTHONPATH=$PYTHONPATH:${matcalcsubdirs}
export PATH=$PATH:${matcalcsubdirs}- Plot your POSCAR with a handy 3-D visualizer:
poscarPlot.py POSCAR- Plot the energy vs time of your OUTCAR:
outcarPlotETime.py OUTCAR- Generate a gorgeous equation of state plot from a collection of OUTCARs, can even compare against an empirical potential
outcarsPlotEOS.py dir/to/eos/files Cu_lammps.eam