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86 lines
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86 lines
4.0 KiB
Plaintext
"Previous Section"_Section_basics.html - "Pizza.py WWW Site"_pws -
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"Pizza.py Documentation"_pd - "Pizza.py Tools"_pt - "Next
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Section"_Section_examples.html :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(pt,Section_tools.html)
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:line
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4. Tools within Pizza.py :h3
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"Th previous section"_Section_basics.html#3_4 describes how Pizza.py
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tools are used in Pizza.py.
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Help on the syntax for invoking a tool and using its methods and
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settings can be accessed interactively within Pizza.py itself by
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typing "? tool" or "?? tool". Typing "??" gives a one-line
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description of each tool.
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These are the different categories of Pizza.py tools:
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LAMMPS in/out files: chain, data, dump, log, patch, bdump, ldump, tdump
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ChemCell in/out files: cdata, clog, dump
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Visualization: gl, rasmol, raster, svg, vmd
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File conversion: cfg, ensight, pdbfile, vtk, xyz
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GUI wrappers: animate, image, plotview, vcr
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Plotting: gnu, matlab
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Miscellaneous: histo, mdump, pair, vec :tb(s=:)
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Within the plotting and viz categories, individual tools share many
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common methods, so the tools can often be used interchangeably. For
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example, the same script can produce an animation using either
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Raster3d or SVG to generate the movie frames, by simply changing the
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line that creates the visualizer object, or by passing the object into
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the script as an argument.
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This is the complete list of tools in Pizza.py; the link is to each
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tool's documentation page.
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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"_data.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(ccell,http://www.cs.sandia.gov/~sjplimp/cell.html)
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:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
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This diagram represents the different ways tools can be interconnected
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by Pizza.py. Tools within the same red box are tools that are
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(roughly) interchangeable.
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:c,image(tools.jpg)
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