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157 lines
6.6 KiB
Plaintext
157 lines
6.6 KiB
Plaintext
<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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"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c
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:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html)
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:link(pd,Manual.html)
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:link(pc,Section_tools.html)
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:line
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<H1></H1>
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Pizza.py Documentation :c,h3
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Version info: :h4
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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 "this page of
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the WWW site"_bug. 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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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. :ulb,l
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If you browse the HTML or PDF doc pages included in your tarball, they
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describe the version you have. :ule,l
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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 "LAMMPS"_lammps molecular dynamics and "ChemCell"_cccell 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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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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The maintainer of Pizza.py is "Steve
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Plimpton"_http://www.cs.sandia.gov/~sjplimp at "Sandia National
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Laboratories"_sandia, a US Department of Energy ("DOE"_doe)
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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 "Pizza.py WWW Site"_pws 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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:link(sandia,http://www.sandia.gov)
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:link(bug,http://www.cs.sandia.gov/pizza/bug.html)
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:link(sjp,http://www.cs.sandia.gov/~sjplimp)
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:link(doe,http://www.doe.gov)
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:link(lammps,http://www.cs.sandia.gov/~sjplimp/lammps.html)
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:link(ccell,http://www.cs.sandia.gov/~sjplimp/chemcell.html)
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:line
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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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"PDF file"_Manual.pdf of the entire manual, generated by
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"htmldoc"_http://www.easysw.com/htmldoc
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"Introduction"_Section_intro.html :olb,l
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1.1 "What is Pizza.py"_1_1 :ulb,b
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1.2 "Open source distribution"_1_2 :b
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1.3 "Acknowledgements"_1_3 :ule,b
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"Installing Pizza.py"_Section_install.html :l
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2.1 "Installing Python"_2_1 :ulb,b
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2.2 "Running Pizza.py"_2_2 :b
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2.3 "Setting up the DEFAULTS.py file"_2_3 :b
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2.4 "Installing additional Python packages"_2_4 :b
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2.5 "Installing other software"_2_5 :ule,b
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"Basics of using Pizza.py"_Section_basics.html :l
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3.1 "Python syntax"_3_1 :ulb,b
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3.2 "Pizza.py command line arguments"_3_2 :b
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3.3 "Pizza.py extensions to the Python interpreter"_3_3 :b
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3.4 "Using Pizza.py tools"_3_4 :b
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3.5 "Runnning Pizza.py and Python scripts"_3_5 :b
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3.6 "Error messages"_3_6 :ule,b
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"Tools within Pizza.py"_Section_tools.html :l
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"Example scripts"_Section_examples.html :l
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"Extending Pizza.py"_Section_extend.html :l
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:ole
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:line
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List of tools in Pizza.py:
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"animate.py"_animate.html; Animate a series of image files
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"bdump.py"_bdump.html; Read LAMMPS dump local files with bond info
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"cdata.py"_cdata.html; Read, write, manipulate "ChemCell"_ccell data files
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"chain.py"_chain.html; Create bead-spring chains for LAMMPS input
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"cfg.py"_cfg.html; Convert LAMMPS snapshots to CFG format
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"clog.py"_clog.html; Read "ChemCell"_ccell log files and extract species data
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"data.py"_data.html; Read, write, manipulate LAMMPS data files
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"dump.py"_dump.html; Read, write, manipulate dump files and particle attributes
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"ensight.py"_ensight.html; Convert LAMMPS snapshots to "Ensight"_ensight format
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"gl.py"_gl.html; 3d interactive visualization via OpenGL
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"gnu.py"_gnu.html; Create plots via "GnuPlot"_gnuplot plotting program
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"histo.py"_histo.html; Particle density histogram from a dump
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"image.py"_image.html; View and manipulate images
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"ldump.py"_ldump.html; Read LAMMPS dump files with line info
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"log.py"_log.html; Read LAMMPS log files and extract thermodynamic data
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"matlab.py"_matlab.html; Create plots via "MatLab"_matlab numerical analysis program
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"mdump.py"_mdump.html; Read, write, manipulate mesh dump files
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"pair.py"_pair.html; Compute LAMMPS pairwise energies
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"patch.py"_patch.html; Create patchy Lennard-Jones particles for LAMMPS input
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"pdbfile.py"_pdbfile.html; Read, write PDB files in combo with LAMMPS snapshots
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"plotview.py"_plotview.html; Plot multiple vectors from a data set
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"rasmol.py"_rasmol.html; 3d visualization via "RasMol"_rasmol program
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"raster.py"_raster.html; 3d visualization via "Raster3d"_raster3d program
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"svg.py"_svg.html; 3d visualization via "SVG"_svg files
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"tdump.py"_tdump.html; Read LAMMPS dump files with triangle info
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"vcr.py"_vcr.html; VCR-style GUI for 3d interactive OpenGL visualization
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"vec.py"_vec.html; Create numeric vectors from columns in file or list of vecs
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"vtk.py"_vtk.html; Convert LAMMPS snapshots to VTK format
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"vmd.py"_vmd.html; Wrapper on "VMD visualization package"_vmd
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"xyz.py"_xyz.html; Convert LAMMPS snapshots to XYZ format :tb(s=;)
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:link(gnuplot,http://www.gnuplot.info)
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:link(matlab,http://www.mathworks.com)
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:link(rasmol,http://www.openrasmol.org)
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:link(raster3d,http://www.bmsc.washington.edu/raster3d/raster3d.html)
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:link(svg,http://www.w3.org/Graphics/SVG)
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:link(ensight,http://www.ensight.com)
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:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
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:link(1_1,Section_intro.html#1_1)
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:link(1_2,Section_intro.html#1_2)
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:link(1_3,Section_intro.html#1_3)
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:link(2_1,Section_install.html#2_1)
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:link(2_2,Section_install.html#2_2)
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:link(2_3,Section_install.html#2_3)
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:link(2_4,Section_install.html#2_4)
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:link(2_5,Section_install.html#2_5)
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:link(3_1,Section_basics.html#3_1)
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:link(3_2,Section_basics.html#3_2)
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:link(3_3,Section_basics.html#3_3)
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:link(3_4,Section_basics.html#3_4)
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:link(3_5,Section_basics.html#3_5)
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:link(3_6,Section_basics.html#3_6)
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