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<div class="section" id="compute-property-atom-command">
<span id="index-0"></span><h1>compute property/atom 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="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">input1</span> <span class="n">input2</span> <span class="o">...</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>property/atom = style name of this compute command</li>
<li>input = one or more atom attributes</li>
</ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">proc</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
<span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
<span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
<span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
<span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span>
<span class="n">shapex</span><span class="p">,</span><span class="n">shapey</span><span class="p">,</span> <span class="n">shapez</span><span class="p">,</span>
<span class="n">quatw</span><span class="p">,</span> <span class="n">quati</span><span class="p">,</span> <span class="n">quatj</span><span class="p">,</span> <span class="n">quatk</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
<span class="n">end1x</span><span class="p">,</span> <span class="n">end1y</span><span class="p">,</span> <span class="n">end1z</span><span class="p">,</span> <span class="n">end2x</span><span class="p">,</span> <span class="n">end2y</span><span class="p">,</span> <span class="n">end2z</span><span class="p">,</span>
<span class="n">corner1x</span><span class="p">,</span> <span class="n">corner1y</span><span class="p">,</span> <span class="n">corner1z</span><span class="p">,</span>
<span class="n">corner2x</span><span class="p">,</span> <span class="n">corner2y</span><span class="p">,</span> <span class="n">corner2z</span><span class="p">,</span>
<span class="n">corner3x</span><span class="p">,</span> <span class="n">corner3y</span><span class="p">,</span> <span class="n">corner3z</span><span class="p">,</span>
<span class="n">nbonds</span><span class="p">,</span>
<span class="n">vfrac</span><span class="p">,</span> <span class="n">s0</span><span class="p">,</span>
<span class="n">spin</span><span class="p">,</span> <span class="n">eradius</span><span class="p">,</span> <span class="n">ervel</span><span class="p">,</span> <span class="n">erforce</span><span class="p">,</span>
<span class="n">rho</span><span class="p">,</span> <span class="n">drho</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">de</span><span class="p">,</span> <span class="n">cv</span><span class="p">,</span>
<span class="n">i_name</span><span class="p">,</span> <span class="n">d_name</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
<span class="n">proc</span> <span class="o">=</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">processor</span> <span class="n">that</span> <span class="n">owns</span> <span class="n">atom</span>
<span class="nb">type</span> <span class="o">=</span> <span class="n">atom</span> <span class="nb">type</span>
<span class="n">mass</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">mass</span>
<span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span> <span class="o">=</span> <span class="n">unscaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">,</span><span class="n">zs</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xu</span><span class="p">,</span><span class="n">yu</span><span class="p">,</span><span class="n">zu</span> <span class="o">=</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">ix</span><span class="p">,</span><span class="n">iy</span><span class="p">,</span><span class="n">iz</span> <span class="o">=</span> <span class="n">box</span> <span class="n">image</span> <span class="n">that</span> <span class="n">the</span> <span class="n">atom</span> <span class="ow">is</span> <span class="ow">in</span>
<span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">velocities</span>
<span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">forces</span> <span class="n">on</span> <span class="n">atoms</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">charge</span>
<span class="n">mux</span><span class="p">,</span><span class="n">muy</span><span class="p">,</span><span class="n">muz</span> <span class="o">=</span> <span class="n">orientation</span> <span class="n">of</span> <span class="n">dipole</span> <span class="n">moment</span> <span class="n">of</span> <span class="n">atom</span>
<span class="n">mu</span> <span class="o">=</span> <span class="n">magnitude</span> <span class="n">of</span> <span class="n">dipole</span> <span class="n">moment</span> <span class="n">of</span> <span class="n">atom</span>
<span class="n">radius</span><span class="p">,</span><span class="n">diameter</span> <span class="o">=</span> <span class="n">radius</span><span class="p">,</span><span class="n">diameter</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
<span class="n">omegax</span><span class="p">,</span><span class="n">omegay</span><span class="p">,</span><span class="n">omegaz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">velocity</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
<span class="n">angmomx</span><span class="p">,</span><span class="n">angmomy</span><span class="p">,</span><span class="n">angmomz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">momentum</span> <span class="n">of</span> <span class="n">aspherical</span> <span class="n">particle</span>
<span class="n">shapex</span><span class="p">,</span><span class="n">shapey</span><span class="p">,</span><span class="n">shapez</span> <span class="o">=</span> <span class="mi">3</span> <span class="n">diameters</span> <span class="n">of</span> <span class="n">aspherical</span> <span class="n">particle</span>
<span class="n">quatw</span><span class="p">,</span><span class="n">quati</span><span class="p">,</span><span class="n">quatj</span><span class="p">,</span><span class="n">quatk</span> <span class="o">=</span> <span class="n">quaternion</span> <span class="n">components</span> <span class="k">for</span> <span class="n">aspherical</span> <span class="ow">or</span> <span class="n">body</span> <span class="n">particles</span>
<span class="n">tqx</span><span class="p">,</span><span class="n">tqy</span><span class="p">,</span><span class="n">tqz</span> <span class="o">=</span> <span class="n">torque</span> <span class="n">on</span> <span class="n">finite</span><span class="o">-</span><span class="n">size</span> <span class="n">particles</span>
<span class="n">end12x</span><span class="p">,</span> <span class="n">end12y</span><span class="p">,</span> <span class="n">end12z</span> <span class="o">=</span> <span class="n">end</span> <span class="n">points</span> <span class="n">of</span> <span class="n">line</span> <span class="n">segment</span>
<span class="n">corner123x</span><span class="p">,</span> <span class="n">corner123y</span><span class="p">,</span> <span class="n">corner123z</span> <span class="o">=</span> <span class="n">corner</span> <span class="n">points</span> <span class="n">of</span> <span class="n">triangle</span>
<span class="n">nbonds</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">bonds</span> <span class="n">assigned</span> <span class="n">to</span> <span class="n">an</span> <span class="n">atom</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>PERI package per-atom properties:
vfrac = ???
s0 = ???
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">USER</span><span class="o">-</span><span class="n">EFF</span> <span class="ow">and</span> <span class="n">USER</span><span class="o">-</span><span class="n">AWPMD</span> <span class="n">package</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">properties</span><span class="p">:</span>
<span class="n">spin</span> <span class="o">=</span> <span class="n">electron</span> <span class="n">spin</span>
<span class="n">eradius</span> <span class="o">=</span> <span class="n">electron</span> <span class="n">radius</span>
<span class="n">ervel</span> <span class="o">=</span> <span class="n">electron</span> <span class="n">radial</span> <span class="n">velocity</span>
<span class="n">erforce</span> <span class="o">=</span> <span class="n">electron</span> <span class="n">radial</span> <span class="n">force</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>USER-SPH package per-atom properties:
rho = ???
drho = ???
e = ???
de = ???
cv = ???
</pre></div>
</div>
<pre class="literal-block">
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> per-atom properties:
i_name = custom integer vector with name
d_name = custom integer vector with name
</pre>
</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="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">xs</span> <span class="n">vx</span> <span class="n">fx</span> <span class="n">mux</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="nb">type</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">ix</span> <span class="n">iy</span> <span class="n">iz</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that simply stores atom attributes for each atom
in the group. This is useful so that the values can be used by other
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a> that take computes as
inputs. See for example, the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a>,
<a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_histo.html"><span class="doc">fix ave/histo</span></a>,
<a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>, and <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a> commands.</p>
<p>The list of possible attributes is the same as that used by the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, which describes their meaning, with some
additional quantities that are only defined for certain <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a>. Basically, this augmented list gives an
input script access to any per-atom quantity stored by LAMMPS.</p>
<p>The values are stored in a per-atom vector or array as discussed
below. Zeroes are stored for atoms not in the specified group or for
quantities that are not defined for a particular particle in the group
(e.g. <em>shapex</em> if the particle is not an ellipsoid).</p>
<p>The additional quantities only accessible via this command, and not
directly via the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, are as follows.</p>
<p><em>Shapex</em>, <em>shapey</em>, and <em>shapez</em> are defined for ellipsoidal particles
and define the 3d shape of each particle.</p>
<p><em>Quatw</em>, <em>quati</em>, <em>quatj</em>, and <em>quatk</em> are defined for ellipsoidal
particles and body particles and store the 4-vector quaternion
representing the orientation of each particle. See the <a class="reference internal" href="set.html"><span class="doc">set</span></a>
command for an explanation of the quaternion vector.</p>
<p><em>End1x</em>, <em>end1y</em>, <em>end1z</em>, <em>end2x</em>, <em>end2y</em>, <em>end2z</em>, are defined for
line segment particles and define the end points of each line segment.</p>
<p><em>Corner1x</em>, <em>corner1y</em>, <em>corner1z</em>, <em>corner2x</em>, <em>corner2y</em>,
<em>corner2z</em>, <em>corner3x</em>, <em>corner3y</em>, <em>corner3z</em>, are defined for
triangular particles and define the corner points of each triangle.</p>
<p><em>Nbonds</em> is available for all molecular atom styles and refers to the
number of explicit bonds assigned to an atom. Note that if the
<a class="reference internal" href="newton.html"><span class="doc">newton bond</span></a> command is set to <em>on</em>, which is the
default, then every bond in the system is assigned to only one of the
two atoms in the bond. Thus a bond between atoms I,J may be tallied
for either atom I or atom J. If <a class="reference internal" href="newton.html"><span class="doc">newton bond off</span></a> is set,
it will be tallied with both atom I and atom J.</p>
<p>The <em>i_name</em> and <em>d_name</em> attributes refer to custom integer and
floating-point properties that have been added to each atom via the
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command. When that command
is used specific names are given to each attribute which are what is
specified as the &#8220;name&#8221; portion of <em>i_name</em> or <em>d_name</em>.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom vector or per-atom array depending
on the number of input values. If a single input is specified, a
per-atom vector is produced. If two or more inputs are specified, a
per-atom array is produced where the number of columns = the number of
inputs. The vector or array can be accessed by any command that uses
per-atom values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The vector or array values will be in whatever <a class="reference internal" href="units.html"><span class="doc">units</span></a> the
corresponding attribute is in, e.g. velocity units for vx, charge
units for q, etc.</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="dump.html"><span class="doc">dump custom</span></a>, <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a>, <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a>, <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>,
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
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