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add doc for dump_h5md

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Pierre de Buyl
2014-08-14 14:02:29 +02:00
committed by Pierre de Buyl
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commit f2a34ec70e
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<HTML>
<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>
</CENTER>
<HR>
<H3>dump h5md command
</H3>
<P><B>Syntax:</B>
</P>
<P>dump ID group-ID h5md N file.h5
</P>
<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
</UL>
<P><B>Examples:</B>
</P>
<P>dump h5md1 all h5md 100 dump_h5md.h5
</P>
<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.
</P>
<P>This dump style will write only one file, on the root node.
</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>
<HR>
<P><B>Restrictions:</B>
</P>
<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>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dump h5md command :h3
[Syntax:]
dump ID group-ID h5md N file.h5
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file.h5 = name of file to write to :l
:ule
[Examples:]
dump h5md1 all h5md 100 dump_h5md.h5
[Description:]
Dump a snapshot of atom coordinates every N timesteps in the "HDF5"_HDF5_ws
based "H5MD"_h5md file format.
:link(h5md,http://nongnu.org/h5md/)
This dump style will write only one file, on the root node.
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.
:line
[Restrictions:]
The {h5md} dump style is part of the USER-H5MD package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. It also requires
(i) building the ch5md library provided with LAMMPS (See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.) and
(ii) having the "HDF5"_HDF5_ws library installed (C bindings are sufficient).
The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library.
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
:line
[Related commands:]
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html