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