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pizza.py Toolkit
www.cs.sandia.gov
Pizza.py is a loosely integrated collection of tools, many of which provide pre- and post-processing capability for the LAMMPS molecular dynamics package. There are tools to create input files, convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots. Software packages that are wrapped by Pizza.py, so they can be invoked from Python, include GnuPlot, MatLab, Raster3d, and RasMol.
 
Lammps
www.cs.sandia.gov
This is the home page for the classical molecular dynamics code LAMMPS, which stands for Large-scale Atomic/Molecular Massively Parallel Simulator.

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