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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
<H3>dump h5md command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dump ID group-ID h5md N file.h5 args
</PRE>
<UL><LI>ID = user-assigned name for the dump
<LI>group-ID = ID of the group of atoms to be imaged
<LI>h5md = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
<LI>N = dump every this many timesteps
<LI>file.h5 = name of file to write to
<LI>args = list of data elements to dump, with their dump "subintervals".
At least one element must be given and image may only be present if
position is specified first.
<PRE> position options
image
velocity options
force options
species options
file_from ID: do not open a new file, re-use the already opened file from dump ID
box value = <I>yes</I> or <I>no</I>
create_group value = <I>yes</I> or <I>no</I>
author value = quoted string
</PRE>
<P>For the elements <I>position</I>, <I>velocity</I>, <I>force</I> and <I>species</I>, one may specify
a sub-interval to write the data only every N_element iterations of the dump
(i.e. every N*N_element time steps). This is specified by the option
</P>
<PRE> every N_element
</PRE>
<P>that follows directly the element declaration.
</P>
</UL>
<P><B>Examples:</B>
</P>
<PRE>dump h5md1 all h5md 100 dump_h5md.h5 position image
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
</PRE>
<PRE>dump h5md1 all h5md 100 dump_h5md.h5 velocity author "L. Ammps"
</PRE>
<P><B>Description:</B>
</P>
<P>Dump a snapshot of atom coordinates every N timesteps in the <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A>
based <A HREF = "http://nongnu.org/h5md/">H5MD</A> file format <A HREF = "#h5md_cpc">(de Buyl et al.)</A>.
HDF5 files are binary, portable and self-describing.
This dump style will write only one file, on the root node.
</P>
<P>Several dumps may write to the same file, by using file_from and referring to a
previously defined dump.
Several groups may also be stored within the same file by defining several dumps.
A dump that refers (via <I>file_from</I>) to an already open dump ID and that
concerns another particle group must specify <I>create_group yes</I>.
</P>
<P>Each data element is written every N*N_element steps. For <I>image</I>, no
subinterval is needed as it must be present at the same interval as <I>position</I>.
<I>image</I> must be given after <I>position</I> in any case.
The box information (edges in each dimension) is stored at the same interval
than the <I>position</I> element, if present. Else it is stored every N steps.
</P>
<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.
</P>
<P><B>Use from write_dump:</B>
</P>
<P>It is possible to use this dump style with the <A HREF = "write_dump.html">write_dump</A> command.
In this case, the subintervals must not be set at all.
<I>write_dump</I> can be used either alone or in conjunction with <I>file_from</I> so that
fixed-in-time data can be stored in the same file as time-dependent data.
</P>
<P>Typically, the <I>species</I> data is fixed. The following two commands store the
position data every 100 timesteps, with the image data, and store once the
species data in the same file.
</P>
<PRE>dump h5md1 all h5md 100 dump.h5 position image
write_dump all h5md dump.h5 file_from h5md1 species
</PRE>
<HR>
<P><B>Restrictions:</B>
</P>
<UL>
<LI>The number of atoms per snapshot cannot change with the h5md style.
<LI>The position data is stored wrapped (box boundaries not enforced, see note above).
<LI>Only orthogonal domains are currently supported. This is a limitation of the
present package and not of H5MD itself.
</UL>
<P>The <I>h5md</I> dump style is part of the USER-H5MD package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info. It also requires
(i) building the ch5md library provided with LAMMPS (See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.) and
(ii) having the <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A> library installed (C bindings are sufficient).
The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library.
</P>
<HR>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "undump.html">undump</A>
</P>
<HR>
<A NAME = "h5md_cpc"></A>
<P><B>(de Buyl et al.)</B> de Buyl, Colberg and Hofling, H5MD: A structured, efficient,
and portable file format for molecular data, Comp. Phys. Comm. 185(6),
1546-1553 (2014) - <A HREF = "http://arxiv.org/abs/1308.6382/">[arXiv:1308.6382]</A>.
</P>
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