forked from lijiext/lammps
124 lines
4.4 KiB
Plaintext
124 lines
4.4 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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dump h5md command :h3
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[Syntax:]
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dump ID group-ID h5md N file.h5 args :pre
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ID = user-assigned name for the dump :ulb,l
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group-ID = ID of the group of atoms to be imaged :l
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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
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N = dump every this many timesteps :l
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file.h5 = name of file to write to :l
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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. :l
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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 = {yes} or {no}
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create_group value = {yes} or {no}
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author value = quoted string :pre
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For the elements {position}, {velocity}, {force} and {species}, 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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every N_element :pre
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that follows directly the element declaration.
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:ule
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[Examples:]
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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" :pre
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[Description:]
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Dump a snapshot of atom coordinates every N timesteps in the
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"HDF5"_HDF5_ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
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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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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 {file_from}) to an already open dump ID and that concerns
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another particle group must specify {create_group yes}.
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:link(h5md,http://nongnu.org/h5md/)
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Each data element is written every N*N_element steps. For {image}, no
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subinterval is needed as it must be present at the same interval as
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{position}. {image} must be given after {position} 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 {position} element, if present. Else it is stored
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every N steps.
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NOTE: Because periodic boundary conditions are enforced only on
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timesteps when neighbor lists are rebuilt, the coordinates of an atom
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written to a dump file may be slightly outside the simulation box.
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[Use from write_dump:]
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It is possible to use this dump style with the
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"write_dump"_write_dump.html 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 {file_from} keyword.
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Typically, the {species} 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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dump h5md1 all h5md 100 dump.h5 position image
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write_dump all h5md dump.h5 file_from h5md1 species :pre
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:line
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[Restrictions:]
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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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The {h5md} 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 "Making
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LAMMPS"_Section_start.html#start_3 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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"Making LAMMPS"_Section_start.html#start_3 section for more info.) and
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(ii) having the "HDF5"_HDF5_ws 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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:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
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:line
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[Related commands:]
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"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
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:line
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:link(h5md_cpc)
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[(de Buyl)] 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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"\[arXiv:1308.6382\]"_http://arxiv.org/abs/1308.6382/.
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