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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 class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<div class="section" id="compute-msd-command">
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<span id="index-0"></span><h1>compute msd command<a class="headerlink" href="#compute-msd-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 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 = 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> or <em>average</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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<em>average</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
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compute 1 upper msd com yes average 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) of the group of atoms, including all effects due to atoms
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passing thru periodic boundaries. For computation of the non-Gaussian
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parameter of mean-squared displacement, see the <a class="reference internal" href="compute_msd_nongauss.html"><em>compute msd/nongauss</em></a> command.</p>
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<p>A vector of four quantites is calculated by this compute. The first 3
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elements of the vector are the squared dx,dy,dz displacements, summed
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and averaged over atoms in the group. The 4th element is the total
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squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
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averaged over atoms in the group.</p>
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<p>The slope of the mean-squared displacement (MSD) versus time is
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proportional to the diffusion coefficient of the diffusing atoms.</p>
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<p>The displacement of an atom is from its reference position. This is
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normally the original position at the time
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the compute command was issued, unless the <em>average</em> keyword is set to <em>yes</em>.
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The value of the displacement will be
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0.0 for atoms not in the specified compute group.</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 calculated.</p>
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<p>If the <em>average</em> option is set to <em>yes</em> then the reference position of
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an atom is based on the average position of that atom, corrected for
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center-of-mass motion if requested. The average position is a running
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average over all previous calls to the compute, including the current
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call. So on the first call it is current position, on the second call
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it is the arithmetic average of the current position and the position
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on the first call, and so on. Note that when using this option, the
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precise value of the mean square displacement will depend on the
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number of times the compute is called. So, for example, changing the
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frequency of thermo output may change the computed displacement. Also,
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the precise values will be changed if a single simulation is broken up
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into two parts, using either multiple run commands or a restart
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file. It only makes sense to use this option if the atoms are not
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diffusing, so that their average positions relative to the center of
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mass of the system are stationary. The most common case is crystalline
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solids undergoing thermal motion.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Initial coordinates are stored in “unwrapped” form, by using the
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image flags associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion of “unwrapped” coordinates.
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See the Atoms section of the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a
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discussion of image flags and how they are set for each atom. You can
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reset the image flags (e.g. to 0) before invoking this compute by
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using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">If you want the quantities calculated by this compute to be
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continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>, then
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you should use the same ID for this compute, as in the original run.
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This is so that the fix this compute creates to store per-atom
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quantities will also have the same ID, and thus be initialized
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correctly with atom reference positions from the restart file. When
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<em>average</em> is set to yes, then the atom reference positions are
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restored correctly, but not the number of samples used obtain them. As
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a result, the reference positions from the restart file are combined
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with subsequent positions as if they were from a single sample,
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instead of many, which will change the values of msd somewhat.</p>
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</div>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global vector of length 4, which can be
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accessed by indices 1-4 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 vector values will be in
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distance^2 <a class="reference internal" href="units.html"><em>units</em></a>.</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_msd_nongauss.html"><em>compute msd/nongauss</em></a>, <a class="reference internal" href="compute_displace_atom.html"><em>compute displace_atom</em></a>, <a class="reference internal" href="fix_store_state.html"><em>fix store/state</em></a>, <a class="reference internal" href="compute_msd_chunk.html"><em>compute msd/chunk</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 are com = no, average = no.</p>
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