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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13911 f3b2605a-c512-4ea7-a41b-209d697bcdaa
137 lines
4.9 KiB
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137 lines
4.9 KiB
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<HTML>
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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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</CENTER>
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<HR>
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<H3>dump h5md command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>dump ID group-ID h5md N file.h5 args
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</PRE>
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<UL><LI>ID = user-assigned name for the dump
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<LI>group-ID = ID of the group of atoms to be imaged
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<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)
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<LI>N = dump every this many timesteps
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<LI>file.h5 = name of file to write to
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<LI>args = list of data elements to dump, with their dump "subintervals".
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At least one element must be given and image may only be present if
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position is specified first.
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<PRE> position options
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image
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velocity options
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force options
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species options
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file_from ID: do not open a new file, re-use the already opened file from dump ID
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box value = <I>yes</I> or <I>no</I>
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create_group value = <I>yes</I> or <I>no</I>
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author value = quoted string
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</PRE>
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<P>For the elements <I>position</I>, <I>velocity</I>, <I>force</I> and <I>species</I>, one
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may specify a sub-interval to write the data only every N_element
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iterations of the dump (i.e. every N*N_element time steps). This is
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specified by the option
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</P>
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<PRE> every N_element
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</PRE>
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<P>that follows directly the element declaration.
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</P>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>dump h5md1 all h5md 100 dump_h5md.h5 position image
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dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
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dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Dump a snapshot of atom coordinates every N timesteps in the
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<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)</A>.
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HDF5 files are binary, portable and self-describing. This dump style
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will write only one file, on the root node.
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</P>
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<P>Several dumps may write to the same file, by using file_from and
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referring to a previously defined dump. Several groups may also be
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stored within the same file by defining several dumps. A dump that
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refers (via <I>file_from</I>) to an already open dump ID and that concerns
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another particle group must specify <I>create_group yes</I>.
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</P>
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<P>Each data element is written every N*N_element steps. For <I>image</I>, no
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subinterval is needed as it must be present at the same interval as
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<I>position</I>. <I>image</I> must be given after <I>position</I> in any case. The
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box information (edges in each dimension) is stored at the same
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interval than the <I>position</I> element, if present. Else it is stored
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every N steps.
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</P>
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<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
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on timesteps when neighbor lists are rebuilt, the coordinates of an
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atom written to a dump file may be slightly outside the simulation
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box.
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</P>
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<P><B>Use from write_dump:</B>
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</P>
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<P>It is possible to use this dump style with the
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<A HREF = "write_dump.html">write_dump</A> command. In this case, the subintervals
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must not be set at all. The write_dump command can be used either to
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create a new file or to add current data to an existing dump file by
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using the <I>file_from</I> keyword.
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</P>
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<P>Typically, the <I>species</I> data is fixed. The following two commands
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store the position data every 100 timesteps, with the image data, and
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store once the species data in the same file.
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</P>
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<PRE>dump h5md1 all h5md 100 dump.h5 position image
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write_dump all h5md dump.h5 file_from h5md1 species
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</PRE>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>The number of atoms per snapshot cannot change with the h5md style.
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The position data is stored wrapped (box boundaries not enforced, see
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note above). Only orthogonal domains are currently supported. This is
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a limitation of the present dump h5md command and not of H5MD itself.
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</P>
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<P>The <I>h5md</I> dump style is part of the USER-H5MD package. It is only
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enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info. It also
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requires (i) building the ch5md library provided with LAMMPS (See the
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<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.) and
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(ii) having the <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A> library installed (C bindings are
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sufficient) on your system. The library ch5md is compiled with the
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h5cc wrapper provided by the HDF5 library.
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</P>
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<HR>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "undump.html">undump</A>
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</P>
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<HR>
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<A NAME = "h5md_cpc"></A>
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<P><B>(de Buyl)</B> de Buyl, Colberg and Hofling, H5MD: A structured,
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efficient, and portable file format for molecular data,
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Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
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<A HREF = "http://arxiv.org/abs/1308.6382/">[arXiv:1308.6382]</A>.
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</P>
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</HTML>
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