The Pizza.py "version" is the date when it was released, such as 1 May 2010. Pizza.py is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of Pizza.py contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run Pizza.py. It is also in the file src/version.h and in the Pizza.py directory name created when you unpack a tarball.
Pizza.py is a loosely integrated collection of tools written in Python, many of which provide pre- and post-processing capability for the LAMMPS molecular dynamics and ChemCell cell simulator packages. There are tools to create input files, convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots.
The name Pizza.py is meant to evoke the aroma of a collection of "toppings" that the user can combine in different ways on a "crust" of basic functionality, with Python as the "cheese" that glues everything together.
The maintainer of Pizza.py is Steve Plimpton at Sandia National Laboratories, a US Department of Energy (DOE) laboratory. Many of the tools were written by Matt Jones, a BYU student who spent a summer at Sandia. The Pizza.py WWW Site at http://pizza.sandia.gov has more information about Pizza.py and its uses.
The Pizza.py documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to email@example.com so we can improve the Pizza.py documentation.
PDF file of the entire manual, generated by htmldoc
List of tools in Pizza.py:
|animate.py||Animate a series of image files|
|bdump.py||Read LAMMPS dump local files with bond info|
|cdata.py||Read, write, manipulate ChemCell data files|
|chain.py||Create bead-spring chains for LAMMPS input|
|cfg.py||Convert LAMMPS snapshots to CFG format|
|clog.py||Read ChemCell log files and extract species data|
|data.py||Read, write, manipulate LAMMPS data files|
|dump.py||Read, write, manipulate dump files and particle attributes|
|ensight.py||Convert LAMMPS snapshots to Ensight format|
|gl.py||3d interactive visualization via OpenGL|
|gnu.py||Create plots via GnuPlot plotting program|
|histo.py||Particle density histogram from a dump|
|image.py||View and manipulate images|
|ldump.py||Read LAMMPS dump files with line info|
|log.py||Read LAMMPS log files and extract thermodynamic data|
|matlab.py||Create plots via MatLab numerical analysis program|
|mdump.py||Read, write, manipulate mesh dump files|
|pair.py||Compute LAMMPS pairwise energies|
|patch.py||Create patchy Lennard-Jones particles for LAMMPS input|
|pdbfile.py||Read, write PDB files in combo with LAMMPS snapshots|
|plotview.py||Plot multiple vectors from a data set|
|rasmol.py||3d visualization via RasMol program|
|raster.py||3d visualization via Raster3d program|
|svg.py||3d visualization via SVG files|
|tdump.py||Read LAMMPS dump files with triangle info|
|vcr.py||VCR-style GUI for 3d interactive OpenGL visualization|
|vec.py||Create numeric vectors from columns in file or list of vecs|
|vtk.py||Convert LAMMPS snapshots to VTK format|
|vmd.py||Wrapper on VMD visualization package|
|xyz.py||Convert LAMMPS snapshots to XYZ format|