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<CENTER><A HREF = "Manual.html">Previous Section</A> - <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> - <A HREF = "Manual.html">Pizza.py
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Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A> - <A HREF = "Section_install.html">Next
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Section</A>
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</CENTER>
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<HR>
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<H3>1. Introduction
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</H3>
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<P>These sections describe what Pizza.py is, what it means to be
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open-source software, and acknowledge the funding and people who have
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contributed to Pizza.py.
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</P>
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1.1 <A HREF = "#1_1">What is Pizza.Py</A><BR>
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1.2 <A HREF = "#1_2">Open source distribution</A><BR>
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1.3 <A HREF = "#1_3">Acknowledgements</A> <BR>
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<HR>
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<A NAME = "1_1"></A><H4>1.1 What is Pizza.py
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</H4>
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<P>Pizza.py is a loosely integrated collection of tools, many of which
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provide pre- and post-processing capabilities for the <A HREF = "http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS</A>
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molecular dynamics and <A HREF = "http://www.cs.sandia.gov/~sjplimp/chemcell.html">ChemCell</A> cell simulator packages.
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</P>
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<P>There are tools to create input files, convert between file formats to
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connect to other codes, process log and dump files, plot output, and
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visualize and animate simulation snapshots.
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</P>
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<P>Python is used in Pizza.py in 3 ways:
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</P>
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<UL><LI>to provide an interactive and scripting interface to the tools
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<LI>as a language for writing tools
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<LI>to wrap existing stand-alone codes
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</UL>
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<P>Python makes it easy for users of Pizza.py to:
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</P>
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<UL><LI>experiment with tools interactively
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<LI>automate tasks as script files of commands
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<LI>extend tools or create new ones
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</UL>
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<P>The topmost level of Pizza.py adds a modest bit of functionality to
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the Python interpreter to make it easier to invoke tools and pass data
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between them. As such, Python is an ideal "framework" or "glue"
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language that enables various tools to be hooked together, while also
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providing a rich programming environment of its own.
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</P>
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<HR>
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<A NAME = "1_2"></A><H4>1.2 Open source distribution
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</H4>
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<P>Pizza.py comes with no warranty of any kind. As each source file
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states in its header, it is distributed free-of-charge, under the
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terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A> (GPL). This is often referred
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to as open-source distribution - see <A HREF = "http://www.gnu.org">www.gnu.org</A> or
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<A HREF = "http://www.opensource.org">www.opensource.org</A> for more details. The legal text of
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the GPL is in the LICENSE file that is included in the Pizza.py
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distribution.
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</P>
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<P>Here is a summary of what the GPL means for Pizza.py users:
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</P>
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<P>(1) Anyone is free to use, modify, or extend Pizza.py in any way they
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choose, including for commercial purposes.
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</P>
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<P>(2) If you distribute a modified version of Pizza.py, it must remain
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open-source, meaning you distribute it under the terms of the GPL.
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You should clearly annotate such a code as a derivative version of
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Pizza.py.
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</P>
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<P>(3) If you release any code that includes Pizza.py source code, then
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it must also be open-sourced, meaning you distribute it under the
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terms of the GPL.
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</P>
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<P>(4) If you give Pizza.py to someone else, the GPL LICENSE file and
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source file headers (including the GPL notices) should remain part of
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the code.
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</P>
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<P>In the spirit of an open-source code, these are various ways you can
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contribute to making Pizza.py better. You can send email to
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sjplimp@sandia.gov on any of these items.
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</P>
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<UL><LI>If you write a Pizza.py script that is generally useful or illustrates
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how to do something cool with Pizza.py, it can be added to the
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Pizza.py distribution. Ditto for a picture or movie that can be added
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to the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW site</A>.
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<LI>If you add a new method to one of the tools or create a new tool that
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is useful for Pizza.py or LAMMPS or ChemCell users, it can be added to
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the Pizza.py distribution. See the ToDo list at the beginning of the
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src/*.py files for features that haven't yet been implemented.
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<LI>If you find a bug, report it.
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<LI>Report if you find an error or omission in the <A HREF = "Manual.html">Pizza.py
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documentation</A> or on the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A>, or have a
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suggestion for something to clarify or include.
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<LI>Point prospective users to the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> or link to it
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from your WWW site.
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</UL>
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<HR>
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<H4><A NAME = "1_3"></A>1.3 Acknowledgements
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</H4>
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<P>Pizza.py has been developed at <A HREF = "http://www.sandia.gov">Sandia National Laboratories</A>
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which is a multiprogram laboratory operated by Sandia Corporation, a
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Lockheed Martin Company, for the United States Department of Energy's
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National Nuclear Security Administration under contract
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DE-AC04-94AL85000.
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</P>
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<P>Funding for Pizza.py development has come from the US Department of
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Energy (<A HREF = "http://www.doe.gov">DOE</A>), through its LDRD and Genomes-to-Life programs.
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The latter effort has been funded by DOE's <A HREF = "http://www.sc.doe.gov/ascr/home.html">OASCR</A> and
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<A HREF = "http://www.er.doe.gov/production/ober/ober_top.html">OBER</A> offices as part of the US Department of Energy's
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Genomics:GTL program (<A HREF = "http://www.doegenomestolife.org">www.doegenomestolife.org</A>) under the
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<A HREF = "http://www.genomes2life.org">project</A>, "Carbon Sequestration in Synechococcus Sp.: From
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Molecular Machines to Hierarchical Modeling".
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</P>
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<P>The maintainer of Pizza.py is <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>.
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</P>
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<P>Matt Jones, a BYU student who was a summer intern at Sandia, wrote
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several of the coolest tools in Pizza.py and about half the code in
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the initial version.
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</P>
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<P>Others who have written tools or scripts that are part of the Pizza.py
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distribution are listed on the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza/thanks.html">Pizza.py WWW site</A>.
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</P>
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