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<title>compute msd/chunk command — LAMMPS 15 May 2015 version documentation</title>
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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>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<a class="headerlink" href="#compute-msd-chunk-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/chunk chunkID
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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/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"><em>compute chunk/atom</em></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<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/chunk molchunk
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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) 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"><em>compute chunk/atom</em></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"><em>compute chunk/atom</em></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span>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"><em>compute chunk/atom</em></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 warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">The number of chunks <em>Nchunk</em> calculated by the
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<a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command must remain
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constant each time this compute is invoked, so that the displacement
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for each chunk from its original position can be computed
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consistently. If <em>Nchunk</em> does not remain constant, an error will be
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generated. If needed, you can enforce a constant <em>Nchunk</em> by using
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the <em>nchunk once</em> or <em>ids once</em> options when specifying the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</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"><em>compute chunk/atom</em></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 warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">The initial coordinates of the atoms in each chunk are
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stored in “unwrapped” form, by using the image flags associated with
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each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion
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of “unwrapped” coordinates. See the Atoms section of the
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<a class="reference internal" href="read_data.html"><em>read_data</em></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"><em>set image</em></a> command.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Unlike the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command,
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this compute does not store the initial center-of-mass coorindates of
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its molecules in a restart file. Thus you cannot continue the MSD per
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chunk calculation of this compute when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>.</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"><em>fix ave/time</em></a>
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command, for example:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
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compute myChunk all com/msd cc1
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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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"><em>compute chunk/atom</em></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>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"><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.html"><em>compute msd</em></a></p>
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<p><strong>Default:</strong> none</p>
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