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102 lines
5.6 KiB
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<CENTER><A HREF = "Section_basics.html">Previous Section</A> - <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> -
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<A HREF = "Manual.html">Pizza.py Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A> - <A HREF = "Section_examples.html">Next
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Section</A>
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</CENTER>
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<HR>
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<H3>4. Tools within Pizza.py
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</H3>
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<P><A HREF = "Section_basics.html#3_4">Th previous section</A> describes how Pizza.py
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tools are used in Pizza.py.
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</P>
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<P>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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</P>
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<P>These are the different categories of Pizza.py tools:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >LAMMPS in/out files</TD><TD > chain, data, dump, log, patch, bdump, ldump, tdump</TD></TR>
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<TR><TD >ChemCell in/out files</TD><TD > cdata, clog, dump</TD></TR>
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<TR><TD >Visualization</TD><TD > gl, rasmol, raster, svg, vmd</TD></TR>
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<TR><TD >File conversion</TD><TD > cfg, ensight, pdbfile, vtk, xyz</TD></TR>
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<TR><TD >GUI wrappers</TD><TD > animate, image, plotview, vcr</TD></TR>
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<TR><TD >Plotting</TD><TD > gnu, matlab</TD></TR>
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<TR><TD >Miscellaneous</TD><TD > histo, mdump, pair, vec
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</TD></TR></TABLE></DIV>
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<P>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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</P>
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<P>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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</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 = "data.html">cdata.py</A></TD><TD > Read, write, manipulate <A HREF = "http://www.cs.sandia.gov/~sjplimp/cell.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/cell.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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<P>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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</P>
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<CENTER><IMG SRC = "tools.jpg">
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</CENTER>
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</HTML>
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