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1. Introduction

These sections describe what is, what it means to be open-source software, and acknowledge the funding and people who have contributed to

1.1 What is Pizza.Py
1.2 Open source distribution
1.3 Acknowledgements

1.1 What is is a loosely integrated collection of tools, many of which provide pre- and post-processing capabilities for the LAMMPS molecular dynamics and ChemCell cell simulator packages.

There are tools to create input files, convert between file formats to connect to other codes, process log and dump files, plot output, and visualize and animate simulation snapshots.

Python is used in in 3 ways:

Python makes it easy for users of to:

The topmost level of adds a modest bit of functionality to the Python interpreter to make it easier to invoke tools and pass data between them. As such, Python is an ideal "framework" or "glue" language that enables various tools to be hooked together, while also providing a rich programming environment of its own.

1.2 Open source distribution comes with no warranty of any kind. As each source file states in its header, it is distributed free-of-charge, under the terms of the GNU Public License (GPL). This is often referred to as open-source distribution - see or for more details. The legal text of the GPL is in the LICENSE file that is included in the distribution.

Here is a summary of what the GPL means for users:

(1) Anyone is free to use, modify, or extend in any way they choose, including for commercial purposes.

(2) If you distribute a modified version of, it must remain open-source, meaning you distribute it under the terms of the GPL. You should clearly annotate such a code as a derivative version of

(3) If you release any code that includes source code, then it must also be open-sourced, meaning you distribute it under the terms of the GPL.

(4) If you give to someone else, the GPL LICENSE file and source file headers (including the GPL notices) should remain part of the code.

In the spirit of an open-source code, these are various ways you can contribute to making better. You can send email to on any of these items.

1.3 Acknowledgements has been developed at Sandia National Laboratories which is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Funding for development has come from the US Department of Energy (DOE), through its LDRD and Genomes-to-Life programs. The latter effort has been funded by DOE's OASCR and OBER offices as part of the US Department of Energy's Genomics:GTL program ( under the project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling".

The maintainer of is Steve Plimpton.

Matt Jones, a BYU student who was a summer intern at Sandia, wrote several of the coolest tools in and about half the code in the initial version.

Others who have written tools or scripts that are part of the distribution are listed on the WWW site.