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206 lines
8.2 KiB
HTML
206 lines
8.2 KiB
HTML
<HTML>
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<HEAD>
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<TITLE>Pizza.py Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="Pizza.py Toolkit">
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<META NAME="author" CONTENT="http://www.sandia.gov/~sjplimp/pizza.html - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2005) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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<BODY>
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<CENTER><A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> - <A HREF = "Manual.html">Pizza.py Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A>
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</CENTER>
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<HR>
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<H1></H1>
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<CENTER><H3>Pizza.py Documentation
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</H3></CENTER>
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<H4>Version info:
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</H4>
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<P>The Pizza.py "version" is the date when it was released, such as 1 May
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2010. Pizza.py is updated continuously. Whenever we fix a bug or add a
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feature, we release it immediately, and post a notice on <A HREF = "http://www.cs.sandia.gov/pizza/bug.html">this page of
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the WWW site</A>. Each dated copy of Pizza.py contains all the
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features and bug-fixes up to and including that version date. The
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version date is printed to the screen and logfile every time you run
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Pizza.py. It is also in the file src/version.h and in the Pizza.py
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directory name created when you unpack a tarball.
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</P>
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<UL><LI>If you browse the HTML or PDF doc pages on the Pizza.py WWW site, they
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always describe the most current version of Pizza.py.
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<LI>If you browse the HTML or PDF doc pages included in your tarball, they
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describe the version you have.
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</UL>
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<P>Pizza.py is a loosely integrated collection of tools written in
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Python, many of which provide pre- and post-processing capability for
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the <A HREF = "http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS</A> molecular dynamics and <A HREF = "cccell">ChemCell</A> cell
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simulator packages. There are tools to create input files, convert
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between file formats, process log and dump files, create plots, and
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visualize and animate simulation snapshots.
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</P>
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<P>The name Pizza.py is meant to evoke the aroma of a collection of
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"toppings" that the user can combine in different ways on a "crust" of
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basic functionality, with Python as the "cheese" that glues everything
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together.
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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
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Plimpton</A> at <A HREF = "http://www.sandia.gov">Sandia National
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Laboratories</A>, a US Department of Energy (<A HREF = "http://www.doe.gov">DOE</A>)
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laboratory. Many of the tools were written by Matt Jones, a BYU
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student who spent a summer at Sandia. The <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> at
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www.cs.sandia.gov/~sjplimp/pizza.html has more information about
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Pizza.py and its uses.
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</P>
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<HR>
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<P>The Pizza.py documentation is organized into the following sections.
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If you find errors or omissions in this manual or have suggestions for
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useful information to add, please send an email to sjplimp@sandia.gov
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so we can improve the Pizza.py documentation.
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</P>
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<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
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<A HREF = "http://www.easysw.com/htmldoc">htmldoc</A>
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</P>
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<OL><LI><A HREF = "Section_intro.html">Introduction</A>
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<UL> 1.1 <A HREF = "Section_intro.html#1_1">What is Pizza.py</A>
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<BR>
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1.2 <A HREF = "Section_intro.html#1_2">Open source distribution</A>
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<BR>
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1.3 <A HREF = "Section_intro.html#1_3">Acknowledgements</A>
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<BR></UL>
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<LI><A HREF = "Section_install.html">Installing Pizza.py</A>
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<UL> 2.1 <A HREF = "Section_install.html#2_1">Installing Python</A>
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<BR>
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2.2 <A HREF = "Section_install.html#2_2">Running Pizza.py</A>
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<BR>
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2.3 <A HREF = "Section_install.html#2_3">Setting up the DEFAULTS.py file</A>
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<BR>
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2.4 <A HREF = "Section_install.html#2_4">Installing additional Python packages</A>
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<BR>
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2.5 <A HREF = "Section_install.html#2_5">Installing other software</A>
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<BR></UL>
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<LI><A HREF = "Section_basics.html">Basics of using Pizza.py</A>
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<UL> 3.1 <A HREF = "Section_basics.html#3_1">Python syntax</A>
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<BR>
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3.2 <A HREF = "Section_basics.html#3_2">Pizza.py command line arguments</A>
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<BR>
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3.3 <A HREF = "Section_basics.html#3_3">Pizza.py extensions to the Python interpreter</A>
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<BR>
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3.4 <A HREF = "Section_basics.html#3_4">Using Pizza.py tools</A>
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<BR>
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3.5 <A HREF = "Section_basics.html#3_5">Runnning Pizza.py and Python scripts</A>
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<BR>
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3.6 <A HREF = "Section_basics.html#3_6">Error messages</A>
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<BR></UL>
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<LI><A HREF = "Section_tools.html">Tools within Pizza.py</A>
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<LI><A HREF = "Section_examples.html">Example scripts</A>
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<LI><A HREF = "Section_extend.html">Extending Pizza.py</A>
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</OL>
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<HR>
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<P>List of tools in Pizza.py:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD ><A HREF = "animate.html">animate.py</A></TD><TD > Animate a series of image files</TD></TR>
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<TR><TD ><A HREF = "bdump.html">bdump.py</A></TD><TD > Read LAMMPS dump local files with bond info</TD></TR>
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<TR><TD ><A HREF = "cdata.html">cdata.py</A></TD><TD > Read, write, manipulate <A HREF = "http://www.cs.sandia.gov/~sjplimp/chemcell.html">ChemCell</A> data files</TD></TR>
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<TR><TD ><A HREF = "chain.html">chain.py</A></TD><TD > Create bead-spring chains for LAMMPS input</TD></TR>
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<TR><TD ><A HREF = "cfg.html">cfg.py</A></TD><TD > Convert LAMMPS snapshots to CFG format</TD></TR>
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<TR><TD ><A HREF = "clog.html">clog.py</A></TD><TD > Read <A HREF = "http://www.cs.sandia.gov/~sjplimp/chemcell.html">ChemCell</A> log files and extract species data</TD></TR>
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<TR><TD ><A HREF = "data.html">data.py</A></TD><TD > Read, write, manipulate LAMMPS data files</TD></TR>
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<TR><TD ><A HREF = "dump.html">dump.py</A></TD><TD > Read, write, manipulate dump files and particle attributes</TD></TR>
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<TR><TD ><A HREF = "ensight.html">ensight.py</A></TD><TD > Convert LAMMPS snapshots to <A HREF = "http://www.ensight.com">Ensight</A> format</TD></TR>
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<TR><TD ><A HREF = "gl.html">gl.py</A></TD><TD > 3d interactive visualization via OpenGL</TD></TR>
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<TR><TD ><A HREF = "gnu.html">gnu.py</A></TD><TD > Create plots via <A HREF = "http://www.gnuplot.info">GnuPlot</A> plotting program</TD></TR>
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<TR><TD ><A HREF = "histo.html">histo.py</A></TD><TD > Particle density histogram from a dump</TD></TR>
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<TR><TD ><A HREF = "image.html">image.py</A></TD><TD > View and manipulate images</TD></TR>
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<TR><TD ><A HREF = "ldump.html">ldump.py</A></TD><TD > Read LAMMPS dump files with line info</TD></TR>
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<TR><TD ><A HREF = "log.html">log.py</A></TD><TD > Read LAMMPS log files and extract thermodynamic data</TD></TR>
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<TR><TD ><A HREF = "matlab.html">matlab.py</A></TD><TD > Create plots via <A HREF = "http://www.mathworks.com">MatLab</A> numerical analysis program</TD></TR>
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<TR><TD ><A HREF = "mdump.html">mdump.py</A></TD><TD > Read, write, manipulate mesh dump files</TD></TR>
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<TR><TD ><A HREF = "pair.html">pair.py</A></TD><TD > Compute LAMMPS pairwise energies</TD></TR>
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<TR><TD ><A HREF = "patch.html">patch.py</A></TD><TD > Create patchy Lennard-Jones particles for LAMMPS input</TD></TR>
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<TR><TD ><A HREF = "pdbfile.html">pdbfile.py</A></TD><TD > Read, write PDB files in combo with LAMMPS snapshots</TD></TR>
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<TR><TD ><A HREF = "plotview.html">plotview.py</A></TD><TD > Plot multiple vectors from a data set</TD></TR>
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<TR><TD ><A HREF = "rasmol.html">rasmol.py</A></TD><TD > 3d visualization via <A HREF = "http://www.openrasmol.org">RasMol</A> program</TD></TR>
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<TR><TD ><A HREF = "raster.html">raster.py</A></TD><TD > 3d visualization via <A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A> program</TD></TR>
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<TR><TD ><A HREF = "svg.html">svg.py</A></TD><TD > 3d visualization via <A HREF = "http://www.w3.org/Graphics/SVG">SVG</A> files</TD></TR>
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<TR><TD ><A HREF = "tdump.html">tdump.py</A></TD><TD > Read LAMMPS dump files with triangle info</TD></TR>
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<TR><TD ><A HREF = "vcr.html">vcr.py</A></TD><TD > VCR-style GUI for 3d interactive OpenGL visualization</TD></TR>
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<TR><TD ><A HREF = "vec.html">vec.py</A></TD><TD > Create numeric vectors from columns in file or list of vecs</TD></TR>
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<TR><TD ><A HREF = "vtk.html">vtk.py</A></TD><TD > Convert LAMMPS snapshots to VTK format</TD></TR>
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<TR><TD ><A HREF = "vmd.html">vmd.py</A></TD><TD > Wrapper on <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD visualization package</A></TD></TR>
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<TR><TD ><A HREF = "xyz.html">xyz.py</A></TD><TD > Convert LAMMPS snapshots to XYZ format
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</TD></TR></TABLE></DIV>
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</HTML>
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