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sjplimp
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<div class="section" id="dump-command">
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<span id="index-0"></span><h1>dump command<a class="headerlink" href="#dump-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-h5md-command">
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<h1><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command<a class="headerlink" href="#dump-h5md-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-image-command">
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<h1><a class="reference internal" href="dump_image.html"><em>dump image</em></a> command<a class="headerlink" href="#dump-image-command" title="Permalink to this headline">¶</a></h1>
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</div>
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@ -143,24 +146,32 @@
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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 dumped</li>
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<li>style = <em>atom</em> or <em>atom/mpiio</em> or <em>cfg</em> or <em>cfg/mpiio</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>xyz/mpiio</em> or <em>image</em> or <em>movie</em> or <em>molfile</em> or <em>local</em> or <em>custom</em> or <em>custom/mpiio</em></li>
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<li>style = <em>atom</em> or <em>atom/gz</em> or <em>atom/mpiio</em> or <em>cfg</em> or <em>cfg/gz</em> or <em>cfg/mpiio</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>xyz/gz</em> or <em>xyz/mpiio</em> or <em>h5md</em> or <em>image</em> or <em>movie</em> or <em>molfile</em> or <em>local</em> or <em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em></li>
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<li>N = dump every this many timesteps</li>
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<li>file = name of file to write dump info to</li>
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<li>args = list of arguments for a particular style</li>
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</ul>
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<pre class="literal-block">
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<em>atom</em> args = none
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<em>atom/gz</em> args = none
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<em>atom/mpiio</em> args = none
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<em>cfg</em> args = same as <em>custom</em> args, see below
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<em>cfg/gz</em> args = same as <em>custom</em> args, see below
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<em>cfg/mpiio</em> args = same as <em>custom</em> args, see below
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<em>dcd</em> args = none
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<em>xtc</em> args = none
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<em>xyz</em> args = none
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</pre>
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<pre class="literal-block">
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<em>xyz/gz</em> args = none
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</pre>
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<pre class="literal-block">
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<em>xyz/mpiio</em> args = none
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</pre>
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<pre class="literal-block">
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<em>h5md</em> args = discussed on <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> doc page
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</pre>
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<pre class="literal-block">
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<em>image</em> args = discussed on <a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page
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</pre>
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<pre class="literal-block">
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@ -179,7 +190,7 @@
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f_ID[N] = Nth column of local array calculated by a fix with ID
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</pre>
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<pre class="literal-block">
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<em>custom</em> or <em>custom/mpiio</em> args = list of atom attributes
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<em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em> args = list of atom attributes
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possible attributes = id, mol, proc, procp1, type, element, mass,
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x, y, z, xs, ys, zs, xu, yu, zu,
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xsu, ysu, zsu, ix, iy, iz,
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@ -224,6 +235,7 @@ i_name = per-atom integer vector with name, managed by fix property/atom
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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 myDump all atom 100 dump.atom
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dump myDump all atom/mpiio 100 dump.atom.mpiio
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dump myDump all atom/gz 100 dump.atom.gz
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dump 2 subgroup atom 50 dump.run.bin
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dump 2 subgroup atom 50 dump.run.mpiio.bin
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dump 4a all custom 100 dump.myforce.* id type x y vx fx
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@ -274,6 +286,16 @@ multiple processors, each of which owns a subset of the atoms.</p>
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default. For the <em>dcd</em>, <em>xtc</em>, <em>xyz</em>, and <em>molfile</em> styles, sorting by
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atom ID is on by default. See the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> doc
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page for details.</p>
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<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are identical
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in command syntax to the corresponding styles without “gz”, however,
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they generate compressed files using the zlib library. Thus the filename
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suffix ”.gz” is mandatory. This is an alternative approach to writing
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compressed files via a pipe, as done by the regular dump styles, which
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may be required on clusters where the interface to the high-speed network
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disallows using the fork() library call (which is needed for a pipe).
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For the remainder of this doc page, you should thus consider the <em>atom</em>
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and <em>atom/gz</em> styles (etc) to be inter-changeable, with the exception
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of the required filename suffix.</p>
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<p>As explained below, the <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and
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<em>xyz/mpiio</em> styles are identical in command syntax and in the format
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of the dump files they create, to the corresponding styles without
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@ -645,8 +667,13 @@ per-atom quantities which could then be output into dump files.</p>
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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>To write gzipped dump files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option - see the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of the documentation.</p>
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<p>To write gzipped dump files, you must either compile LAMMPS with the
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-DLAMMPS_GZIP option or use the styles from the COMPRESS package
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- see the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of
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the documentation.</p>
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<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are part
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of the COMPRESS package. They are only enabled if LAMMPS was built
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with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
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<p>The <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and <em>xyz/mpiio</em> styles
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are part of the MPIIO package. They are only enabled if LAMMPS was
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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.</p>
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@ -668,7 +695,8 @@ machines.</p>
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</div>
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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_image.html"><em>dump image</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>,
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<p><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>,
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<a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>,
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<a class="reference internal" href="undump.html"><em>undump</em></a></p>
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</div>
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<div class="section" id="default">
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