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<li class="toctree-l2"><a class="reference internal" href="dump.html">dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-vtk-command"><span class="xref std std-doc">dump vtk</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><span class="xref std std-doc">dump h5md</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-netcdf-command"><span class="xref std std-doc">dump netcdf</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_adios.html">dump atom/adios command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_adios.html#dump-custom-adios-command">dump custom/adios command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-modify-options-for-dump-image-movie">dump_modify options for dump image/movie</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_modify.html#dump-modify-command-for-image-movie-options"><span class="xref std std-doc">dump_modify</span> command for image/movie options</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_netcdf.html#dump-netcdf-mpiio-command">dump netcdf/mpiio command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">dump vtk command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="dump-vtk-command">
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<span id="index-0"></span><h1>dump vtk command<a class="headerlink" href="#dump-vtk-command" title="Link to this heading"></a></h1>
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">dump </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">vtk</span><span class="w"> </span><span class="n">N</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">args</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li><p>ID = user-assigned name for the dump</p></li>
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<li><p>group-ID = ID of the group of atoms to be dumped</p></li>
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<li><p>vtk = style of dump command (other styles such as <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"><span class="doc">dump</span></a> doc page)</p></li>
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<li><p>N = dump every this many timesteps</p></li>
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<li><p>file = name of file to write dump info to</p></li>
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<li><p>args = same as arguments for <a class="reference internal" href="dump.html"><span class="doc">dump_style custom</span></a></p></li>
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</ul>
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</section>
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<section id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">dump </span><span class="nv nv-Identifier">dmpvtk</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">vtk</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump</span><span class="o">*</span><span class="n">.myforce.vtk</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">vx</span><span class="w"> </span><span class="n">fx</span>
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<span class="k">dump </span><span class="nv nv-Identifier">dmpvtp</span><span class="w"> </span><span class="nv nv-Identifier">flow</span><span class="w"> </span><span class="n">vtk</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump</span><span class="o">*</span><span class="n">.</span><span class="o">%</span><span class="n">.displace.vtp</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">c_myD[1]</span><span class="w"> </span><span class="n">c_myD[2]</span><span class="w"> </span><span class="n">c_myD[3]</span><span class="w"> </span><span class="n">v_ke</span>
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</pre></div>
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</div>
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</section>
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<section id="description">
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<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
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<p>Dump a snapshot of atom quantities to one or more files every <span class="math notranslate nohighlight">\(N\)</span>
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timesteps in a format readable by the <a class="reference external" href="https://www.vtk.org">VTK visualization toolkit</a> or other visualization tools that use it, such
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as <a class="reference external" href="https://www.paraview.org">ParaView</a>. The time steps on which dump
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output is written can also be controlled by a variable; see the
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<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command for details.</p>
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<p>This dump style is similar to <a class="reference internal" href="dump.html"><span class="doc">dump_style custom</span></a> but uses
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the VTK library to write data to VTK simple legacy or XML format,
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depending on the filename extension specified for the dump file. This
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can be either <em>*.vtk</em> for the legacy format or <em>*.vtp</em> and <em>*.vtu</em>,
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respectively, for XML format; see the <a class="reference external" href="https://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
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description of these formats. Since this naming convention conflicts
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with the way binary output is usually specified (see below), the
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<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify binary</span></a> command allows setting of a
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binary option for this dump style explicitly.</p>
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<p>Only information for atoms in the specified group is dumped. The
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<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify thresh and region</span></a> commands can also
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alter what atoms are included; see details below.</p>
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<p>As described below, special characters (”*”, “%”) in the filename
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determine the kind of output.</p>
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<div class="admonition warning">
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<p class="admonition-title">Warning</p>
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<p>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.</p>
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</div>
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<div class="admonition warning">
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<p class="admonition-title">Warning</p>
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<p>Unless the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify sort</span></a> option is invoked,
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the lines of atom information written to dump files will be in an
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indeterminate order for each snapshot. This is even true when
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running on a single processor, if the <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify sort</span></a> option is on, which it is by default. In this case
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atoms are re-ordered periodically during a simulation, due to spatial
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sorting. It is also true when running in parallel, because data for
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a single snapshot is collected from multiple processors, each of
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which owns a subset of the atoms.</p>
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</div>
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<p>For the <em>vtk</em> style, sorting is off by default. See the
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<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> page for details.</p>
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<hr class="docutils" />
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<p>The dimensions of the simulation box are written to a separate file
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for each snapshot (either in legacy VTK or XML format depending on the
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format of the main dump file) with the suffix <em>_boundingBox</em> appended
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to the given dump filename.</p>
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<p>For an orthogonal simulation box this information is saved as a
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rectilinear grid (legacy .vtk or .vtr XML format).</p>
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<p>Triclinic simulation boxes (non-orthogonal) are saved as
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hexahedrons in either legacy .vtk or .vtu XML format.</p>
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<p>Style <em>vtk</em> allows you to specify a list of atom attributes to be
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written to the dump file for each atom. The list of possible attributes
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is the same as for the <a class="reference internal" href="dump.html"><span class="doc">dump_style custom</span></a> command; see its
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documentation page for a listing and an explanation of each attribute.</p>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>Since position data is required to write VTK files the atom
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attributes “x y z” do not have to be specified explicitly; they will
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be included in the dump file regardless. Also, in contrast to the
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<em>custom</em> style, the specified <em>vtk</em> attributes are rearranged to
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ensure correct ordering of vector components (except for computes and
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fixes - these have to be given in the right order) and duplicate
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entries are removed.</p>
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</div>
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<p>The VTK format uses a single snapshot of the system per file, thus
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a wildcard “*” must be included in the filename, as discussed below.
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Otherwise the dump files will get overwritten with the new snapshot
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each time.</p>
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<hr class="docutils" />
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<p>Dumps are performed on timesteps that are a multiple of N (including
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timestep 0) and on the last timestep of a minimization if the
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minimization converges. Note that this means a dump will not be
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performed on the initial timestep after the dump command is invoked,
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if the current timestep is not a multiple of N. This behavior can be
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changed via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command, which
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can also be useful if the dump command is invoked after a minimization
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ended on an arbitrary timestep. N can be changed between runs by
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using the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command.
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The <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command
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also allows a variable to be used to determine the sequence of
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timesteps on which dump files are written. In this mode a dump on the
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first timestep of a run will also not be written unless the
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<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command is used.</p>
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<p>Dump filenames can contain two wildcard characters. If a “*”
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character appears in the filename, then one file per snapshot is
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written and the “*” character is replaced with the timestep value.
|
|
For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
|
|
tmp.dump20000.vtk, etc. Note that the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify pad</span></a>
|
|
command can be used to ensure all timestep numbers are the same length
|
|
(e.g. 00010), which can make it easier to read a series of dump files
|
|
in order with some post-processing tools.</p>
|
|
<p>If a “%” character appears in the filename, then each of P processors
|
|
writes a portion of the dump file, and the “%” character is replaced
|
|
with the processor ID from 0 to P-1 preceded by an underscore character.
|
|
For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, …
|
|
tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast
|
|
mode of output on parallel machines that support parallel I/O for output.</p>
|
|
<p>By default, P = the number of processors meaning one file per
|
|
processor, but P can be set to a smaller value via the <em>nfile</em> or
|
|
<em>fileper</em> keywords of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.
|
|
These options can be the most efficient way of writing out dump files
|
|
when running on large numbers of processors.</p>
|
|
<p>For the legacy VTK format “%” is ignored and P = 1, i.e., only
|
|
processor 0 does write files.</p>
|
|
<p>Note that using the “*” and “%” characters together can produce a
|
|
large number of small dump files!</p>
|
|
<p>If <em>dump_modify binary</em> is used, the dump file (or files, if “*” or
|
|
“%” is also used) is written in binary format. A binary dump file
|
|
will be about the same size as a text version, but will typically
|
|
write out much faster.</p>
|
|
</section>
|
|
<hr class="docutils" />
|
|
<section id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
|
<p>The <em>vtk</em> style does not support writing of gzipped dump files.</p>
|
|
<p>The <em>vtk</em> dump style is part of the VTK package. It is only
|
|
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
|
<p>To use this dump style, you also must link to the VTK library. See
|
|
the info in lib/vtk/README and ensure the Makefile.lammps file in that
|
|
directory is appropriate for your machine.</p>
|
|
<p>The <em>vtk</em> dump style supports neither buffering or custom format
|
|
strings.</p>
|
|
</section>
|
|
<section id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
|
<p><a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>,
|
|
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a>, <a class="reference internal" href="undump.html"><span class="doc">undump</span></a></p>
|
|
</section>
|
|
<section id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
|
<p>By default, files are written in ASCII format. If the file extension
|
|
is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.</p>
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</section>
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