These sections describe what Pizza.py is, what it means to be open-source software, and acknowledge the funding and people who have contributed to Pizza.py.
1.1 What is Pizza.PyPizza.py 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 Pizza.py in 3 ways:
Python makes it easy for users of Pizza.py to:
The topmost level of Pizza.py 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.
Pizza.py 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 www.gnu.org or www.opensource.org for more details. The legal text of the GPL is in the LICENSE file that is included in the Pizza.py distribution.
Here is a summary of what the GPL means for Pizza.py users:
(1) Anyone is free to use, modify, or extend Pizza.py in any way they choose, including for commercial purposes.
(2) If you distribute a modified version of Pizza.py, 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 Pizza.py.
(3) If you release any code that includes Pizza.py source code, then it must also be open-sourced, meaning you distribute it under the terms of the GPL.
(4) If you give Pizza.py 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 Pizza.py better. You can send email to sjplimp@sandia.gov on any of these items.
Pizza.py 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 Pizza.py 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 (www.doegenomestolife.org) under the project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling".
The maintainer of Pizza.py is Steve Plimpton.
Matt Jones, a BYU student who was a summer intern at Sandia, wrote several of the coolest tools in Pizza.py and about half the code in the initial version.
Others who have written tools or scripts that are part of the Pizza.py distribution are listed on the Pizza.py WWW site.