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<li>dump h5md command</li>
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<div class="section" id="dump-h5md-command">
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<span id="index-0"></span><h1>dump h5md command<a class="headerlink" href="#dump-h5md-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>dump ID group-ID h5md N file.h5 args
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID = user-assigned name for the dump</li>
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<li>group-ID = ID of the group of atoms to be imaged</li>
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<li>h5md = style of dump command (other styles <em>atom</em> or <em>cfg</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>local</em> or <em>custom</em> are discussed on the <a class="reference internal" href="dump.html"><em>dump</em></a> doc page)</li>
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<li>N = dump every this many timesteps</li>
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<li>file.h5 = name of file to write to</li>
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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.</li>
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</ul>
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<pre class="literal-block">
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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 = <em>yes</em> or <em>no</em>
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create_group value = <em>yes</em> or <em>no</em>
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author value = quoted string
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</pre>
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<p>For the elements <em>position</em>, <em>velocity</em>, <em>force</em> and <em>species</em>, 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</p>
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<div class="highlight-python"><div class="highlight"><pre>every N_element
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</pre></div>
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</div>
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<p>that follows directly the element declaration.</p>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><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></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Dump a snapshot of atom coordinates every N timesteps in the
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<a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> based <a class="reference external" href="http://nongnu.org/h5md/">H5MD</a> file format <a class="reference internal" href="#h5md-cpc"><span>(de Buyl)</span></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.</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 <em>file_from</em>) to an already open dump ID and that concerns
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another particle group must specify <em>create_group yes</em>.</p>
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<p>Each data element is written every N*N_element steps. For <em>image</em>, no
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subinterval is needed as it must be present at the same interval as
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<em>position</em>. <em>image</em> must be given after <em>position</em> 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 <em>position</em> element, if present. Else it is stored
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every N steps.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">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.</p>
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</div>
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<p><strong>Use from write_dump:</strong></p>
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<p>It is possible to use this dump style with the
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<a class="reference internal" href="write_dump.html"><em>write_dump</em></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 <em>file_from</em> keyword.</p>
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<p>Typically, the <em>species</em> 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.</p>
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<div class="highlight-python"><div class="highlight"><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></div>
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</div>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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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.</p>
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<p>The <em>h5md</em> 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 class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></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 class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.) and
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(ii) having the <a class="reference external" 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.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="undump.html"><em>undump</em></a></p>
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<hr class="docutils" />
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<p id="h5md-cpc"><strong>(de Buyl)</strong> 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 class="reference external" href="http://arxiv.org/abs/1308.6382/">[arXiv:1308.6382]</a>.</p>
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