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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>compute cna/atom command</li>
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<div class="section" id="compute-cna-atom-command">
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<span id="index-0"></span><h1>compute cna/atom command<a class="headerlink" href="#compute-cna-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 cna/atom cutoff
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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>cna/atom = style name of this compute command</li>
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<li>cutoff = cutoff distance for nearest neighbors (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<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 cna/atom 3.08
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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 the CNA (Common Neighbor
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Analysis) pattern for each atom in the group. In solid-state systems
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the CNA pattern is a useful measure of the local crystal structure
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around an atom. The CNA methodology is described in <a class="reference internal" href="#faken"><span>(Faken)</span></a>
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and <a class="reference internal" href="#tsuzuki"><span>(Tsuzuki)</span></a>.</p>
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<p>Currently, there are five kinds of CNA patterns LAMMPS recognizes:</p>
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<ul class="simple">
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<li>fcc = 1</li>
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<li>hcp = 2</li>
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<li>bcc = 3</li>
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<li>icosohedral = 4</li>
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<li>unknown = 5</li>
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</ul>
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<p>The value of the CNA pattern will be 0 for atoms not in the specified
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compute group. Note that normally a CNA calculation should only be
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performed on mono-component systems.</p>
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<p>The CNA calculation can be sensitive to the specified cutoff value.
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You should insure the appropriate nearest neighbors of an atom are
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found within the cutoff distance for the presumed crystal strucure.
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E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
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neighbors for perfect BCC crystals. These formulas can be used to
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obtain a good cutoff distance:</p>
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<img alt="_images/cna_cutoff1.jpg" class="align-center" src="_images/cna_cutoff1.jpg" />
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<p>where a is the lattice constant for the crystal structure concerned
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and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
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for HCP crystals.</p>
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<p>Also note that since the CNA calculation in LAMMPS uses the neighbors
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of an owned atom to find the nearest neighbors of a ghost atom, the
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following relation should also be satisfied:</p>
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<img alt="_images/cna_cutoff2.jpg" class="align-center" src="_images/cna_cutoff2.jpg" />
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<p>where Rc is the cutoff distance of the potential, Rs is the skin
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distance as specified by the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> command, and
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cutoff is the argument used with the compute cna/atom command. LAMMPS
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will issue a warning if this is not the case.</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 (e.g. 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 with a
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<em>cna/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 a number from 0 to 5, as explained
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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_centro_atom.html"><em>compute centro/atom</em></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="faken"><strong>(Faken)</strong> Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).</p>
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<p id="tsuzuki"><strong>(Tsuzuki)</strong> Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).</p>
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