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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li>compute cluster/atom command</li>
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<div class="section" id="compute-cluster-atom-command">
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<span id="index-0"></span><h1>compute cluster/atom command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">cluster</span><span class="o">/</span><span class="n">atom</span> <span class="n">cutoff</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
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<li>cluster/atom = style name of this compute command</li>
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<li>cutoff = distance within which to label atoms as part of same cluster (distance units)</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">cluster</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.0</span>
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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</h2>
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<p>Define a computation that assigns each atom a cluster ID.</p>
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<p>A cluster is defined as a set of atoms, each of which is within the
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cutoff distance from one or more other atoms in the cluster. If an
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atom has no neighbors within the cutoff distance, then it is a 1-atom
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cluster. The ID of every atom in the cluster will be the smallest
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atom ID of any atom in the cluster.</p>
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<p>Only atoms in the compute group are clustered and assigned cluster
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IDs. Atoms not in the compute group are assigned a cluster ID = 0.</p>
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<p>The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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too frequently or to have multiple compute/dump commands, each of a
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<em>clsuter/atom</em> style.</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">If you have a bonded system, then the settings of
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<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included when computing the clusters. This
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does not apply when using long-range coulomb (<em>coul/long</em>, <em>coul/msm</em>,
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<em>coul/wolf</em> or similar. One way to get around this would be to set
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special_bond scaling factors to very tiny numbers that are not exactly
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zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
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use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to compute the clusters for
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snapshots in the dump file. The rerun script can use a
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<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command that includes all pairs in
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the neighbor list.</p>
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</div>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a per-atom vector, which can be accessed by
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any command that uses per-atom values from a compute as input. See
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<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
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LAMMPS output options.</p>
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<p>The per-atom vector values will be an ID > 0, as explained above.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="compute_coord_atom.html"><span class="doc">compute coord/atom</span></a></p>
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<p><strong>Default:</strong> none</p>
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