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<title>compute hexorder/atom command &mdash; LAMMPS 17 Dec 2015 documentation</title>
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<div class="section" id="compute-hexorder-atom-command">
<span id="index-0"></span><h1>compute hexorder/atom command<a class="headerlink" href="#compute-hexorder-atom-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID hexorder/atom keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>hexorder/atom = style name of this compute command</li>
<li>one or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>degree</em> or <em>nnn</em> or <em>cutoff</em>
<em>cutoff</em> value = distance cutoff
<em>nnn</em> value = number of nearest neighbors
<em>degree</em> value = degree <em>n</em> of order parameter
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all hexorder/atom
compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates <em>qn</em> the bond-orientational
order parameter for each atom in a group. The hexatic (<em>n</em> = 6) order
parameter was introduced by <a class="reference internal" href="#nelson"><span>Nelson and Halperin</span></a> as a way to detect
hexagonal symmetry in two-dimensional systems. For each atom, <em>qn</em>
is a complex number (stored as two real numbers) defined as follows:</p>
<img alt="_images/hexorder.jpg" class="align-center" src="_images/hexorder.jpg" />
<p>where the sum is over the <em>nnn</em> nearest neighbors
of the central atom. The angle theta
is formed by the bond vector rij and the <em>x</em> axis. theta is calculated
only using the <em>x</em> and <em>y</em> components, whereas the distance from the
central atom is calculated using all three
<em>x</em>, <em>y</em>, and <em>z</em> components of the bond vector.
Neighbor atoms not in the group
are included in the order parameter of atoms in the group.</p>
<p>The optional keyword <em>cutoff</em> defines the distance cutoff
used when searching for neighbors. The default value, also
the maximum allowable value, is the cutoff specified
by the pair style.</p>
<p>The optional keyword <em>nnn</em> defines the number of nearest
neighbors used to calculate <em>qn</em>. The default value is 6.
If the value is NULL, then all neighbors up to the
distance cutoff are used.</p>
<p>The optional keyword <em>degree</em> sets the degree <em>n</em> of the order parameter.
The default value is 6. For a perfect hexagonal lattice with
<em>nnn</em> = 6,
<em>q*6 = exp(6 i phi) for all atoms, where the constant 0 &lt; phi &lt; pi/3
depends only on the orientation of the lattice relative to the *x</em> axis.
In an isotropic liquid, local neighborhoods may still exhibit
weak hexagonal symmetry, but because the orientational correlation
decays quickly with distance, the value of phi will be different for
different atoms, and so when <a href="#id1"><span class="problematic" id="id2">*</span></a>q*6 is averaged over all the atoms
in the system, <a href="#id3"><span class="problematic" id="id4">|&lt;*q*6&gt;|</span></a> &lt;&lt; 1.</p>
<p>The value of <em>qn</em> is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
<em>nnn</em> neighbors within the distance cutoff.</p>
<p>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This
difficulty can be circumvented by writing a dump file, and using the
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the order parameter for
snapshots in the dump file. The rerun script can use a
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all pairs in
the neighbor list.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts <em>qn</em>, a complex number restricted to the
unit disk of the complex plane i.e. Re(<em>qn</em>)^2 + Im(<em>qn</em>)^2 &lt;= 1 .</p>
<p>These values can be accessed by any command that uses
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
options.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_orientorder_atom.html"><em>compute orientorder/atom</em></a>, <a class="reference internal" href="compute_coord_atom.html"><em>compute coord/atom</em></a>, <a class="reference internal" href="compute_centro_atom.html"><em>compute centro/atom</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are <em>cutoff</em> = pair style cutoff, <em>nnn</em> = 6, <em>degree</em> = 6</p>
<hr class="docutils" />
<p id="nelson"><strong>(Nelson)</strong> Nelson, Halperin, Phys Rev B, 19, 2457 (1979).</p>
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