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<title>compute cluster/atom command — LAMMPS 15 May 2015 version documentation</title>
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<div class="local-toc"><ul>
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<li><a class="reference internal" href="#">compute cluster/atom command</a><ul>
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<li><a class="reference internal" href="#syntax">Syntax</a></li>
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<li><a class="reference internal" href="#examples">Examples</a></li>
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<li><a class="reference internal" href="#description">Description</a></li>
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<li><a class="reference internal" href="#restrictions">Restrictions</a></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<a class="headerlink" href="#compute-cluster-atom-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>compute ID group-ID cluster/atom cutoff
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</pre></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"><em>compute</em></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 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>compute 1 all cluster/atom 1.0
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</pre></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>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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<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>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 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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<blockquote>
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<div>none</div></blockquote>
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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="compute_coord_atom.html"><em>compute coord/atom</em></a></p>
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<p><strong>Default:</strong> none</p>
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