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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13916 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/doc2/Section_packages.html

@@ -48,6 +48,7 @@ packages, more details are provided.
 <TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >COMPRESS</TD><TD > I/O compression</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump.html">dump */gz</A></TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >CORESHELL</TD><TD > adiabatic core/shell model</TD><TD > Hendrik Heenen (Technical U of Munich)</TD><TD > <A HREF = "Section_howto.html#howto_25">Section_howto 6.25</A></TD><TD > coreshell</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
@@ -130,6 +131,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
 <TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-H5MD</TD><TD > dump output via HDF5</TD><TD > Pierre de Buyl (KU Leuven)</TD><TD > <A HREF = "dump_h5md.html">dump h5md</A></TD><TD > -</TD><TD > -</TD><TD > h5md</TD></TR>
 <TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
@@ -443,6 +445,25 @@ Contact him directly if you have questions.
 </P>
 <HR>
 
+<H4>USER-H5MD package 
+</H4>
+<P>This package contains a <A HREF = "dump_h5md.html">dump h5md</A> command for
+performing a dump of atom properties in HDF5 format.  <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5
+files</A> are binary, portable and self-describing and can be
+examined and used by a variety of auxiliary tools.  The output HDF5
+files are structured in a format called H5MD, which was designed to
+store molecular data, and can be used and produced by various MD and
+MD-related codes.  The <A HREF = "doc/dump_h5md.html">dump h5md</A> command gives a
+citation to a paper describing the format.
+</P>
+
+
+<P>The person who created this package and the underlying H5MD format is
+Pierre de Buyl at KU Leuven (see http://pdebuyl.be).  Contact him
+directly if you have questions.
+</P>
+<HR>
+
 <H4>USER-INTEL package 
 </H4>
 <P>This package provides options for performing neighbor list and

doc/doc2/genindex.html

@@ -807,12 +807,12 @@
   <dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
   </dt>
@@ -846,6 +846,10 @@
   </dt>
 
       
+  <dt><a href="dump_h5md.html#index-0">dump h5md</a>
+  </dt>
+
+      
   <dt><a href="dump_image.html#index-0">dump image</a>
   </dt>