<spanid="index-0"></span><h1>compute hexorder/atom command<aclass="headerlink"href="#compute-hexorder-atom-command"title="Permalink to this headline">¶</a></h1>
<divclass="section"id="syntax">
<h2>Syntax<aclass="headerlink"href="#syntax"title="Permalink to this headline">¶</a></h2>
<divclass="highlight-python"><divclass="highlight"><pre>compute ID group-ID hexorder/atom keyword values ...
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<ulclass="simple">
<li>ID, group-ID are documented in <aclass="reference internal"href="compute.html"><em>compute</em></a> command</li>
<li>hexorder/atom = style name of this compute command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>degree</em></li>
</ul>
<preclass="literal-block">
<em>n</em> value = degree of order parameter
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</div>
<divclass="section"id="examples">
<h2>Examples<aclass="headerlink"href="#examples"title="Permalink to this headline">¶</a></h2>
<divclass="highlight-python"><divclass="highlight"><pre>compute 1 all hexorder/atom
compute 1 all hexorder/atom n 4
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<divclass="section"id="description">
<h2>Description<aclass="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 <aclass="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>
<p>where the sum is over the <em>n</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>n</em> sets the degree of the order parameter.
The default value is 6. For a perfect hexagonal lattice,
<ahref="#id1"><spanclass="problematic"id="id2">*</span></a>q*6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
depends only on the orientation of the lattice relative to the x 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 <ahref="#id3"><spanclass="problematic"id="id4">|<*q*6>|</span></a><< 1.</p>
<p>The value of <em>qn</em> will be zero for atoms not in the
specified compute group. If the atom has less than <em>n</em> neighbors (within
the potential cutoff), then <em>qn</em> is set to zero.</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>
<divclass="admonition warning">
<pclass="first admonition-title">Warning</p>
<pclass="last">If you have a bonded system, then the settings of
<aclass="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 <aclass="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. One way
to get around this, is to write a dump file, and use the
<aclass="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
<aclass="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 of <em>qn</em>, respectively.</p>
<p>These values can be accessed by any command that uses
per-atom values from a compute as input. See <aclass="reference internal"href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The per-atom array contain pairs of numbers representing the
real and imaginary parts of <em>qn</em>, a complex number subject to the
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