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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>compute gyration/chunk command</li>
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<div class="section" id="compute-gyration-chunk-command">
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<span id="index-0"></span><h1>compute gyration/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">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">chunkID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</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>gyration/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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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>tensor</em></li>
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</ul>
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<pre class="literal-block">
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<em>tensor</em> value = none
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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</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="n">molecule</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span>
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<span class="n">compute</span> <span class="mi">2</span> <span class="n">molecule</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span> <span class="n">tensor</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 radius of gyration Rg for
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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>This compute calculates the radius of gyration Rg for each chunk,
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which includes all effects due to atoms passing thru periodic
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boundaries.</p>
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<p>Rg is a measure of the size of a chunk, and is computed by this
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formula</p>
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<img alt="_images/compute_gyration.jpg" class="align-center" src="_images/compute_gyration.jpg" />
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<p>where M is the total mass of the chunk, Rcm is the center-of-mass
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position of the chunk, and the sum is over all atoms in the
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chunk.</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>If the <em>tensor</em> keyword is specified, then the scalar Rg value is not
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calculated, but an Rg tensor is instead calculated for each chunk.
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The formula for the components of the tensor is the same as the above
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formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
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Rcmy) for the xy component, etc. The 6 components of the tensor are
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ordered xx, yy, zz, xy, xz, yz.</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 coordinates of an atom contribute to Rg in “unwrapped” form,
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by using the image flags associated with each atom. See the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></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"><span class="doc">read_data</span></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"><span class="doc">set image</span></a> command.</p>
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</div>
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<p>The simplest way to output the results of the compute gyration/chunk
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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">gyration</span><span class="o">/</span><span class="n">chunk</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 vector if the <em>tensor</em> keyword is not
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specified and a global array if it is. The length of the vector or
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number of rows in the array = the number of chunks <em>Nchunk</em> as
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calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. If the <em>tensor</em> keyword
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is specified, the global array has 6 columns. The vector or array can
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be accessed by any command that uses global values from a compute as
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input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview
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of LAMMPS output options.</p>
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<p>All the vector or array values calculated by this compute are
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“intensive”. The vector or array values will be in distance
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<a class="reference internal" href="units.html"><span class="doc">units</span></a>, since they are the square root of values
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represented by the formula above.</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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<p><strong>Related commands:</strong> none</p>
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<p><a class="reference internal" href="compute_gyration.html"><span class="doc">compute gyration</span></a></p>
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<p><strong>Default:</strong> none</p>
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