Pizza.py Users Manual
Author: http://pizza.sandia.gov - Sandia National Laboratories

"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c :link(pws,http://pizza.sandia.gov) :link(pd,Manual.html) :link(pc,Section_tools.html) :line

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Pizza.py Documentation :c,h3 Version info: :h4 The Pizza.py "version" is the date when it was released, such as 1 May 2010. Pizza.py is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on "this page of the WWW site"_bug. Each dated copy of Pizza.py contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run Pizza.py. It is also in the file src/version.h and in the Pizza.py directory name created when you unpack a tarball. If you browse the HTML or PDF doc pages on the Pizza.py WWW site, they always describe the most current version of Pizza.py. :ulb,l If you browse the HTML or PDF doc pages included in your tarball, they describe the version you have. :ule,l Pizza.py is a loosely integrated collection of tools written in Python, many of which provide pre- and post-processing capability for the "LAMMPS"_lammps molecular dynamics and "ChemCell"_cccell cell simulator packages. There are tools to create input files, convert between file formats, process log and dump files, create plots, and visualize and animate simulation snapshots. The name Pizza.py is meant to evoke the aroma of a collection of "toppings" that the user can combine in different ways on a "crust" of basic functionality, with Python as the "cheese" that glues everything together. The maintainer of Pizza.py is "Steve Plimpton"_http://www.sandia.gov/~sjplimp at "Sandia National Laboratories"_sandia, a US Department of Energy ("DOE"_doe) laboratory. Many of the tools were written by Matt Jones, a BYU student who spent a summer at Sandia. The "Pizza.py WWW Site"_pws at http://pizza.sandia.gov has more information about Pizza.py and its uses. :link(sandia,http://www.sandia.gov) :link(bug,http://www.cs.sandia.gov/pizza/bug.html) :link(sjp,http://www.cs.sandia.gov/~sjplimp) :link(doe,http://www.doe.gov) :link(lammps,http://www.cs.sandia.gov/~sjplimp/lammps.html) :link(ccell,http://www.cs.sandia.gov/~sjplimp/chemcell.html) :line The Pizza.py documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to sjplimp@sandia.gov so we can improve the Pizza.py documentation. "PDF file"_Manual.pdf of the entire manual, generated by "htmldoc"_http://www.easysw.com/htmldoc "Introduction"_Section_intro.html :olb,l 1.1 "What is Pizza.py"_1_1 :ulb,b 1.2 "Open source distribution"_1_2 :b 1.3 "Acknowledgements"_1_3 :ule,b "Installing Pizza.py"_Section_install.html :l 2.1 "Installing Python"_2_1 :ulb,b 2.2 "Running Pizza.py"_2_2 :b 2.3 "Setting up the DEFAULTS.py file"_2_3 :b 2.4 "Installing additional Python packages"_2_4 :b 2.5 "Installing other software"_2_5 :ule,b "Basics of using Pizza.py"_Section_basics.html :l 3.1 "Python syntax"_3_1 :ulb,b 3.2 "Pizza.py command line arguments"_3_2 :b 3.3 "Pizza.py extensions to the Python interpreter"_3_3 :b 3.4 "Using Pizza.py tools"_3_4 :b 3.5 "Runnning Pizza.py and Python scripts"_3_5 :b 3.6 "Error messages"_3_6 :ule,b "Tools within Pizza.py"_Section_tools.html :l "Example scripts"_Section_examples.html :l "Extending Pizza.py"_Section_extend.html :l :ole :line List of tools in Pizza.py: "animate.py"_animate.html; Animate a series of image files "bdump.py"_bdump.html; Read LAMMPS dump local files with bond info "cdata.py"_cdata.html; Read, write, manipulate "ChemCell"_ccell data files "chain.py"_chain.html; Create bead-spring chains for LAMMPS input "cfg.py"_cfg.html; Convert LAMMPS snapshots to CFG format "clog.py"_clog.html; Read "ChemCell"_ccell log files and extract species data "data.py"_data.html; Read, write, manipulate LAMMPS data files "dump.py"_dump.html; Read, write, manipulate dump files and particle attributes "ensight.py"_ensight.html; Convert LAMMPS snapshots to "Ensight"_ensight format "gl.py"_gl.html; 3d interactive visualization via OpenGL "gnu.py"_gnu.html; Create plots via "GnuPlot"_gnuplot plotting program "histo.py"_histo.html; Particle density histogram from a dump "image.py"_image.html; View and manipulate images "ldump.py"_ldump.html; Read LAMMPS dump files with line info "log.py"_log.html; Read LAMMPS log files and extract thermodynamic data "matlab.py"_matlab.html; Create plots via "MatLab"_matlab numerical analysis program "mdump.py"_mdump.html; Read, write, manipulate mesh dump files "pair.py"_pair.html; Compute LAMMPS pairwise energies "patch.py"_patch.html; Create patchy Lennard-Jones particles for LAMMPS input "pdbfile.py"_pdbfile.html; Read, write PDB files in combo with LAMMPS snapshots "plotview.py"_plotview.html; Plot multiple vectors from a data set "rasmol.py"_rasmol.html; 3d visualization via "RasMol"_rasmol program "raster.py"_raster.html; 3d visualization via "Raster3d"_raster3d program "svg.py"_svg.html; 3d visualization via "SVG"_svg files "tdump.py"_tdump.html; Read LAMMPS dump files with triangle info "vcr.py"_vcr.html; VCR-style GUI for 3d interactive OpenGL visualization "vec.py"_vec.html; Create numeric vectors from columns in file or list of vecs "vtk.py"_vtk.html; Convert LAMMPS snapshots to VTK format "vmd.py"_vmd.html; Wrapper on "VMD visualization package"_vmd "xyz.py"_xyz.html; Convert LAMMPS snapshots to XYZ format :tb(s=;) :link(gnuplot,http://www.gnuplot.info) :link(matlab,http://www.mathworks.com) :link(rasmol,http://www.openrasmol.org) :link(raster3d,http://www.bmsc.washington.edu/raster3d/raster3d.html) :link(svg,http://www.w3.org/Graphics/SVG) :link(ensight,http://www.ensight.com) :link(vmd,http://www.ks.uiuc.edu/Research/vmd) :link(1_1,Section_intro.html#1_1) :link(1_2,Section_intro.html#1_2) :link(1_3,Section_intro.html#1_3) :link(2_1,Section_install.html#2_1) :link(2_2,Section_install.html#2_2) :link(2_3,Section_install.html#2_3) :link(2_4,Section_install.html#2_4) :link(2_5,Section_install.html#2_5) :link(3_1,Section_basics.html#3_1) :link(3_2,Section_basics.html#3_2) :link(3_3,Section_basics.html#3_3) :link(3_4,Section_basics.html#3_4) :link(3_5,Section_basics.html#3_5) :link(3_6,Section_basics.html#3_6)