add doc pages

various tools.  Here's the list of tools in Pizza.py:

</P>

<DIV ALIGN=center><TABLE  BORDER=1 >

<TR><TD ><A HREF = "animate.html">animate.py</A></TD><TD > Animate a series of image files</TD></TR>

<TR><TD ><A HREF = "bdump.html">bdump.py</A></TD><TD > Read LAMMPS dump local files with bond info</TD></TR>

<TR><TD ><A HREF = "cdata.html">cdata.py</A></TD><TD > Read, write, manipulate <A HREF = "http://chemcell.sandia.gov">Chemcell</A> data files</TD></TR>

<TR><TD ><A HREF = "chain.html">chain.py</A></TD><TD > Create bead-spring chains for LAMMPS input</TD></TR>

<TR><TD ><A HREF = "clog.html">clog.py</A></TD><TD > Read <A HREF = "http://chemcell.sandia.gov">ChemCell</A> log files and extract species data</TD></TR>

<TR><TD ><A HREF = "data.html">data.py</A></TD><TD > Read, write, manipulate LAMMPS data files</TD></TR>

<TR><TD ><A HREF = "dump.html">dump.py</A></TD><TD > Read, write, manipulate LAMMPS dump files and atom attributes</TD></TR>

<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>

<TR><TD ><A HREF = "gl.html">gl.py</A></TD><TD > 3d interactive visualization via OpenGL</TD></TR>

<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>

<TR><TD ><A HREF = "histo.html">histo.py</A></TD><TD > Particle density histogram from a dump</TD></TR>

<TR><TD ><A HREF = "image.html">image.py</A></TD><TD > View and manipulate images</TD></TR>

<TR><TD ><A HREF = "ldump.html">ldump.py</A></TD><TD > Read LAMMPS dump files with line info</TD></TR>

<TR><TD ><A HREF = "log.html">log.py</A></TD><TD > Read LAMMPS log files and extract thermodynamic data</TD></TR>

<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>

<TR><TD ><A HREF = "ldump.html">mdump.py</A></TD><TD > Read, write, manipulate mesh dump files</TD></TR>

<TR><TD ><A HREF = "pair.html">pair.py</A></TD><TD > Compute LAMMPS pairwise energies</TD></TR>

<TR><TD ><A HREF = "patch.html">patch.py</A></TD><TD > Create patchy Lennard-Jones particles for LAMMPS input</TD></TR>

<TR><TD ><A HREF = "pdbfile.html">pdbfile.py</A></TD><TD > Read, write PDB files in combination with LAMMPS snapshots</TD></TR>

<TR><TD ><A HREF = "plotview.html">plotview.py</A></TD><TD > Plot multiple vectors from a data set</TD></TR>

<TR><TD ><A HREF = "rasmol.html">rasmol.py</A></TD><TD > 3d visualization via <A HREF = "http://openrasmol.org">RasMol</A> program</TD></TR>

<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>

<TR><TD ><A HREF = "sdata.html">sdata.py</A></TD><TD > Read, write, manipulate <A HREF = "http://sparta.sandia.gov">SPARTA</A> surface files</TD></TR>

<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>

<TR><TD ><A HREF = "tdump.html">tdump.py</A></TD><TD > Read LAMMPS dump files with triangle info</TD></TR>

<TR><TD ><A HREF = "vcr.html">vcr.py</A></TD><TD > VCR-style GUI for 3d interactive OpenGL visualization</TD></TR>

<TR><TD ><A HREF = "vec.html">vec.py</A></TD><TD > Create numeric vectors from columns in file or list of vecs</TD></TR>

<TR><TD ><A HREF = "vtk.html">vtk.py</A></TD><TD > Convert LAMMPS snapshots to VTK format</TD></TR>

<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>

<TR><TD ><A HREF = "xyz.html">xyz.py</A></TD><TD > Convert LAMMPS snapshots to XYZ format 

<TR><TD ><A HREF = "doc/animate.html">animate.py</A></TD><TD > Animate a series of image files</TD></TR>

<TR><TD ><A HREF = "doc/bdump.html">bdump.py</A></TD><TD > Read LAMMPS dump local files with bond info</TD></TR>

<TR><TD ><A HREF = "doc/cdata.html">cdata.py</A></TD><TD > Read, write, manipulate <A HREF = "http://chemcell.sandia.gov">Chemcell</A> data files</TD></TR>

<TR><TD ><A HREF = "doc/chain.html">chain.py</A></TD><TD > Create bead-spring chains for LAMMPS input</TD></TR>

<TR><TD ><A HREF = "doc/clog.html">clog.py</A></TD><TD > Read <A HREF = "http://chemcell.sandia.gov">ChemCell</A> log files and extract species data</TD></TR>

<TR><TD ><A HREF = "doc/data.html">data.py</A></TD><TD > Read, write, manipulate LAMMPS data files</TD></TR>

<TR><TD ><A HREF = "doc/dump.html">dump.py</A></TD><TD > Read, write, manipulate LAMMPS dump files and atom attributes</TD></TR>

<TR><TD ><A HREF = "doc/ensight.html">ensight.py</A></TD><TD > Convert LAMMPS snapshots to <A HREF = "http://www.ensight.com">Ensight</A> format</TD></TR>

<TR><TD ><A HREF = "doc/gl.html">gl.py</A></TD><TD > 3d interactive visualization via OpenGL</TD></TR>

<TR><TD ><A HREF = "doc/gnu.html">gnu.py</A></TD><TD > Create plots via <A HREF = "http://www.gnuplot.info">GnuPlot</A> plotting program</TD></TR>

<TR><TD ><A HREF = "doc/histo.html">histo.py</A></TD><TD > Particle density histogram from a dump</TD></TR>

<TR><TD ><A HREF = "doc/image.html">image.py</A></TD><TD > View and manipulate images</TD></TR>

<TR><TD ><A HREF = "doc/ldump.html">ldump.py</A></TD><TD > Read LAMMPS dump files with line info</TD></TR>

<TR><TD ><A HREF = "doc/log.html">log.py</A></TD><TD > Read LAMMPS log files and extract thermodynamic data</TD></TR>

<TR><TD ><A HREF = "doc/matlab.html">matlab.py</A></TD><TD > Create plots via <A HREF = "http://www.mathworks.com">MatLab</A> numerical analysis program</TD></TR>

<TR><TD ><A HREF = "doc/ldump.html">mdump.py</A></TD><TD > Read, write, manipulate mesh dump files</TD></TR>

<TR><TD ><A HREF = "doc/pair.html">pair.py</A></TD><TD > Compute LAMMPS pairwise energies</TD></TR>

<TR><TD ><A HREF = "doc/patch.html">patch.py</A></TD><TD > Create patchy Lennard-Jones particles for LAMMPS input</TD></TR>

<TR><TD ><A HREF = "doc/pdbfile.html">pdbfile.py</A></TD><TD > Read, write PDB files in combination with LAMMPS snapshots</TD></TR>

<TR><TD ><A HREF = "doc/plotview.html">plotview.py</A></TD><TD > Plot multiple vectors from a data set</TD></TR>

<TR><TD ><A HREF = "doc/rasmol.html">rasmol.py</A></TD><TD > 3d visualization via <A HREF = "http://openrasmol.org">RasMol</A> program</TD></TR>

<TR><TD ><A HREF = "doc/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>

<TR><TD ><A HREF = "doc/sdata.html">sdata.py</A></TD><TD > Read, write, manipulate <A HREF = "http://sparta.sandia.gov">SPARTA</A> surface files</TD></TR>

<TR><TD ><A HREF = "doc/svg.html">svg.py</A></TD><TD > 3d visualization via <A HREF = "http://www.w3.org/Graphics/SVG">SVG</A> files</TD></TR>

<TR><TD ><A HREF = "doc/tdump.html">tdump.py</A></TD><TD > Read LAMMPS dump files with triangle info</TD></TR>

<TR><TD ><A HREF = "doc/vcr.html">vcr.py</A></TD><TD > VCR-style GUI for 3d interactive OpenGL visualization</TD></TR>

<TR><TD ><A HREF = "doc/vec.html">vec.py</A></TD><TD > Create numeric vectors from columns in file or list of vecs</TD></TR>

<TR><TD ><A HREF = "doc/vtk.html">vtk.py</A></TD><TD > Convert LAMMPS snapshots to VTK format</TD></TR>

<TR><TD ><A HREF = "doc/vmd.html">vmd.py</A></TD><TD > Wrapper on <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD visualization package</A></TD></TR>

<TR><TD ><A HREF = "doc/xyz.html">xyz.py</A></TD><TD > Convert LAMMPS snapshots to XYZ format 

</TD></TR></TABLE></DIV>

The "FAQ"_FAQ.html lists typical tasks that can be performed with

various tools.  Here's the 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

"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 LAMMPS dump files and atom 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"_ldump.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 combination 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

"sdata.py"_sdata.html; Read, write, manipulate "SPARTA"_sparta surface files

"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=;)

"animate.py"_doc/animate.html; Animate a series of image files

"bdump.py"_doc/bdump.html; Read LAMMPS dump local files with bond info

"cdata.py"_doc/cdata.html; Read, write, manipulate "Chemcell"_ccell data files

"chain.py"_doc/chain.html; Create bead-spring chains for LAMMPS input

"clog.py"_doc/clog.html; Read "ChemCell"_ccell log files and extract species data

"data.py"_doc/data.html; Read, write, manipulate LAMMPS data files

"dump.py"_doc/dump.html; Read, write, manipulate LAMMPS dump files and atom attributes

"ensight.py"_doc/ensight.html; Convert LAMMPS snapshots to "Ensight"_ensight format

"gl.py"_doc/gl.html; 3d interactive visualization via OpenGL

"gnu.py"_doc/gnu.html; Create plots via "GnuPlot"_gnuplot plotting program

"histo.py"_doc/histo.html; Particle density histogram from a dump

"image.py"_doc/image.html; View and manipulate images

"ldump.py"_doc/ldump.html; Read LAMMPS dump files with line info

"log.py"_doc/log.html; Read LAMMPS log files and extract thermodynamic data

"matlab.py"_doc/matlab.html; Create plots via "MatLab"_matlab numerical analysis program

"mdump.py"_doc/ldump.html; Read, write, manipulate mesh dump files

"pair.py"_doc/pair.html; Compute LAMMPS pairwise energies

"patch.py"_doc/patch.html; Create patchy Lennard-Jones particles for LAMMPS input

"pdbfile.py"_doc/pdbfile.html; Read, write PDB files in combination with LAMMPS snapshots

"plotview.py"_doc/plotview.html; Plot multiple vectors from a data set

"rasmol.py"_doc/rasmol.html; 3d visualization via "RasMol"_rasmol program

"raster.py"_doc/raster.html; 3d visualization via "Raster3d"_raster3d program

"sdata.py"_doc/sdata.html; Read, write, manipulate "SPARTA"_sparta surface files

"svg.py"_doc/svg.html; 3d visualization via "SVG"_svg files

"tdump.py"_doc/tdump.html; Read LAMMPS dump files with triangle info

"vcr.py"_doc/vcr.html; VCR-style GUI for 3d interactive OpenGL visualization

"vec.py"_doc/vec.html; Create numeric vectors from columns in file or list of vecs

"vtk.py"_doc/vtk.html; Convert LAMMPS snapshots to VTK format

"vmd.py"_doc/vmd.html; Wrapper on "VMD visualization package"_vmd

"xyz.py"_doc/xyz.html; Convert LAMMPS snapshots to XYZ format :tb(s=;)

:link(gnuplot,http://www.gnuplot.info)

:link(matlab,http://www.mathworks.com)