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<li><a class="reference internal" href="#">compute gyration command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
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<div class="section" id="compute-gyration-command">
<span id="index-0"></span><h1>compute gyration command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<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>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>gyration = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<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>
</pre></div>
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</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
periodic boundaries.</p>
<p>Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula</p>
<img alt="_images/compute_gyration.jpg" class="align-center" src="_images/compute_gyration.jpg" />
<p>where M is the total mass of the group, Rcm is the center-of-mass
position of the group, and the sum is over all atoms in the group.</p>
<p>A Rg^2 tensor, stored as a 6-element vector, is also calculated by
this compute. The formula for the components of the tensor is the
same as the above formula, except that (Ri - Rcm)^2 is replaced by
(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
components of the vector are ordered xx, yy, zz, xy, xz, yz. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a &#8220;squared&#8221; value, since the cross-terms may be negative
and taking a sqrt() would be invalid.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to Rg in &#8220;unwrapped&#8221; form,
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 &#8220;unwrapped&#8221; coordinates.
See the Atoms section of the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (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>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar and vector values calculated by this compute are
&#8220;intensive&#8221;. The scalar and vector values will be in distance and
distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a> respectively.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_gyration_chunk.html"><span class="doc">compute gyration/chunk</span></a></p>
<p><strong>Default:</strong> none</p>
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