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<div class="section" id="compute-msd-nongauss-command">
<span id="index-0"></span><h1>compute msd/nongauss command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">msd</span><span class="o">/</span><span class="n">nongauss</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>msd/nongauss = style name of this compute command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
</ul>
<pre class="literal-block">
<em>com</em> value = <em>yes</em> or <em>no</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">msd</span><span class="o">/</span><span class="n">nongauss</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="n">upper</span> <span class="n">msd</span><span class="o">/</span><span class="n">nongauss</span> <span class="n">com</span> <span class="n">yes</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.</p>
<p>A vector of three quantites is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx*dx + dy*dy +
dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion paramter NGP =
3*drfourth/(5*drsquared*drsquared), i.e.</p>
<img alt="_images/compute_msd_nongauss.jpg" class="align-center" src="_images/compute_msd_nongauss.jpg" />
<p>The NGP is a commonly used quantity in studies of dynamical
heterogeneity. Its minimum theoretical value (-0.4) occurs when all
atoms have the same displacement magnitude. NGP=0 for Brownian
diffusion, while NGP &gt; 0 when some mobile atoms move faster than
others.</p>
<p>If the <em>com</em> option is set to <em>yes</em> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated.</p>
<p>See the <a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a> doc page for further important
NOTEs, which also apply to this compute.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The vector values are &#8220;intensive&#8221;. The first vector value will be in
distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>, the second is in distance^4 units, and
the 3rd is dimensionless.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The option default is com = no.</p>
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