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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_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</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 coord/atom command</li>
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<div class="section" id="compute-coord-atom-command">
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<span id="index-0"></span><h1>compute coord/atom command<a class="headerlink" href="#compute-coord-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 coord/atom cutoff type1 type2 ...
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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"><em>compute</em></a> command</li>
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<li>coord/atom = style name of this compute command</li>
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<li>cutoff = distance within which to count coordination neighbors (distance units)</li>
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<li>typeN = atom type for Nth coordination count (see asterisk form below)</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<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 coord/atom 2.0
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compute 1 all coord/atom 6.0 1 2
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compute 1 all coord/atom 6.0 2*4 5*8 *
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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>Define a computation that calculates one or more coordination numbers
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for each atom in a group.</p>
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<p>A coordination number is defined as the number of neighbor atoms with
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specified atom type(s) that are within the specified cutoff distance
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from the central atom. Atoms not in the group are included in a
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coordination number of atoms in the group.</p>
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<p>The <em>typeN</em> keywords allow you to specify which atom types contribute
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to each coordination number. One coordination number is computed for
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each of the <em>typeN</em> keywords listed. If no <em>typeN</em> keywords are
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listed, a single coordination number is calculated, which includes
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atoms of all types (same as the “*” format, see below).</p>
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<p>The <em>typeN</em> keywords can be specified in one of two ways. An explicit
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numeric value can be used, as in the 2nd example above. Or a
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wild-card asterisk can be used to specify a range of atom types. This
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takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the number of
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atom types, then an asterisk with no numeric values means all types
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from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).</p>
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<p>The value of all coordination numbers will be 0.0 for atoms not in the
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specified compute group.</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.</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"><em>special_bonds</em></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"><em>special_bonds</em></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 in the coordination count. One way
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to get around this, is to write a dump file, and use the
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<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the coordination for snapshots
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in the dump file. The rerun script can use a
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></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>If single <em>type1</em> keyword is specified (or if none are specified),
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this compute calculates a per-atom vector. If multiple <em>typeN</em>
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keywords are specified, this compute calculates a per-atom array, with
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N columns. These values can be accessed by any command that uses
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per-atom values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
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options.</p>
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<p>The per-atom vector or array values will be a number >= 0.0, as
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explained above.</p>
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</div>
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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>
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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_cluster_atom.html"><em>compute cluster/atom</em></a></p>
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<p><strong>Default:</strong> none</p>
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