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dump_h5md.txt
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.. index:: dump h5md
dump h5md command
=================
Syntax
""""""
.. parsed-literal::
dump ID group-ID h5md N file.h5 args
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be imaged
* h5md = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* N = dump every this many timesteps
* file.h5 = name of file to write to
* 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.
.. parsed-literal::
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 = *yes* or *no*
create_group value = *yes* or *no*
author value = quoted string
For the elements *position*, *velocity*, *force* and *species*, 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
.. parsed-literal::
every N_element
that follows directly the element declaration.
Examples
""""""""
.. parsed-literal::
dump h5md1 all h5md 100 dump_h5md.h5 position image
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
Description
"""""""""""
Dump a snapshot of atom coordinates every N timesteps in the
`HDF5 <HDF5_ws_>`_ based `H5MD <h5md_>`_ file format :ref:`(de Buyl) <h5md_cpc>`.
HDF5 files are binary, portable and self-describing. This dump style
will write only one file, on the root node.
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 *file_from*) to an already open dump ID and that concerns
another particle group must specify *create_group yes*.
.. _h5md: http://nongnu.org/h5md/
Each data element is written every N*N_element steps. For *image*, no
subinterval is needed as it must be present at the same interval as
*position*. *image* must be given after *position* in any case. The
box information (edges in each dimension) is stored at the same
interval than the *position* element, if present. Else it is stored
every N steps.
.. 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.
**Use from write_dump:**
It is possible to use this dump style with the
:doc:`write_dump <write_dump>` command. In this case, the subintervals
must not be set at all. The write_dump command can be used either to
create a new file or to add current data to an existing dump file by
using the *file_from* keyword.
Typically, the *species* 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.
.. parsed-literal::
dump h5md1 all h5md 100 dump.h5 position image
write_dump all h5md dump.h5 file_from h5md1 species
----------
Restrictions
""""""""""""
The number of atoms per snapshot cannot change with the h5md style.
The position data is stored wrapped (box boundaries not enforced, see
note above). Only orthogonal domains are currently supported. This is
a limitation of the present dump h5md command and not of H5MD itself.
The *h5md* dump style is part of the USER-H5MD package. It is only
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info. It also
requires (i) building the ch5md library provided with LAMMPS (See the
:ref:`Making LAMMPS <start_3>` section for more info.) and
(ii) having the `HDF5 <HDF5_ws_>`_ library installed (C bindings are
sufficient) on your system. The library ch5md is compiled with the
h5cc wrapper provided by the HDF5 library.
.. _HDF5_ws: http://www.hdfgroup.org/HDF5/
----------
Related commands
""""""""""""""""
:doc:`dump <dump>`, :doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`
----------
.. _h5md_cpc:
**(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured,
efficient, and portable file format for molecular data,
Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
`[arXiv:1308.6382] <http://arxiv.org/abs/1308.6382/>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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