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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_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</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_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</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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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li>compute msd/chunk command</li>
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<div class="section" id="compute-msd-chunk-command">
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<span id="index-0"></span><h1>compute msd/chunk command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<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">chunk</span> <span class="n">chunkID</span>
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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"><span class="doc">compute</span></a> command</li>
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<li>msd/chunk = style name of this compute command</li>
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<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<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">chunk</span> <span class="n">molchunk</span>
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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</h2>
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<p>Define a computation that calculates the mean-squared displacement
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(MSD) for multiple chunks of atoms.</p>
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<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section_howto 23</span></a> for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.</p>
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<p>Four quantites are calculated by this compute for each chunk. The
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first 3 quantities are the squared dx,dy,dz displacements of the
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center-of-mass. The 4th component is the total squared displacement,
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i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
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calculations include all effects due to atoms passing thru periodic
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boundaries.</p>
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<p>Note that only atoms in the specified group contribute to the
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calculation. The <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command
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defines its own group; atoms will have a chunk ID = 0 if they are not
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in that group, signifying they are not assigned to a chunk, and will
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thus also not contribute to this calculation. You can specify the
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“all” group for this command if you simply want to include atoms with
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non-zero chunk IDs.</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 chunks.</p>
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<p>The displacement of the center-of-mass of the chunk is from its
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original center-of-mass position, calculated on the timestep this
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compute command was first invoked.</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">The number of chunks <em>Nchunk</em> calculated by the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command must remain constant each
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time this compute is invoked, so that the displacement for each chunk
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from its original position can be computed consistently. If <em>Nchunk</em>
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does not remain constant, an error will be generated. If needed, you
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can enforce a constant <em>Nchunk</em> by using the <em>nchunk once</em> or <em>ids
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once</em> options when specifying the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></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">This compute stores the original position (of the
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center-of-mass) of each chunk. When a displacement is calculated on a
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later timestep, it is assumed that the same atoms are assigned to the
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same chunk ID. However LAMMPS has no simple way to insure this is the
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case, though you can use the <em>ids once</em> option when specifying the
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<a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. Note that if
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this is not the case, the MSD calculation does not have a sensible
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meaning.</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">The initial coordinates of the atoms in each chunk are stored in
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“unwrapped” form, by using the image flags associated with each atom.
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See the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command for a discussion of
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“unwrapped” coordinates. See the Atoms section of the
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<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for a discussion of image flags and
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how they are set for each atom. You can reset the image flags
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(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><span class="doc">set image</span></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"><span class="doc">restart file</span></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-chunk
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quantities will also have the same ID, and thus be initialized
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correctly with chunk reference positions from the restart file.</p>
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</div>
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<p>The simplest way to output the results of the compute com/msd
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calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
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command, for example:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
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<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">msd</span> <span class="n">cc1</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
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</pre></div>
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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 array where the number of rows = the
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number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of columns =
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4 for dx,dy,dz and the total displacement. These values can be
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accessed by any command that uses global array values from a compute
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as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an
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overview of LAMMPS output options.</p>
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<p>The array values are “intensive”. The array values will be in
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distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</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</h2>
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<p><a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a></p>
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<p><strong>Default:</strong> none</p>
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