69 lines
2.0 KiB
HTML
69 lines
2.0 KiB
HTML
<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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<P>dump ID group-ID h5md N file.h5
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</P>
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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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</UL>
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<P><B>Examples:</B>
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</P>
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<P>dump h5md1 all h5md 100 dump_h5md.h5
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</P>
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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 <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5</A>
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based <A HREF = "http://nongnu.org/h5md/">H5MD</A> file format.
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</P>
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<P>This dump style will write only one file, on the root node.
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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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<HR>
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<P><B>Restrictions:</B>
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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 enabled if
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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 requires
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(i) building the ch5md library provided with LAMMPS (See the <A HREF = "Section_start.html#start_3">Making
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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 sufficient).
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The library ch5md is compiled with the 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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</HTML>
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