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 www.cs.sandia.gov/~sjplimp/pizza.html 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 sjplimp@sandia.gov so we can improve the Pizza.py documentation.

PDF file of the entire manual, generated by htmldoc

1. Introduction
   1.1 What is Pizza.py
   1.2 Open source distribution
   1.3 Acknowledgements
   
2. Installing Pizza.py
   2.1 Installing Python
   2.2 Running Pizza.py
   2.3 Setting up the DEFAULTS.py file
   2.4 Installing additional Python packages
   2.5 Installing other software
   
3. Basics of using Pizza.py
   3.1 Python syntax
   3.2 Pizza.py command line arguments
   3.3 Pizza.py extensions to the Python interpreter
   3.4 Using Pizza.py tools
   3.5 Runnning Pizza.py and Python scripts
   3.6 Error messages
   
4. Tools within Pizza.py
5. Example scripts
6. Extending Pizza.py

List of tools in Pizza.py: