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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>compute temp/asphere command</li>
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<div class="section" id="compute-temp-asphere-command">
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<span id="index-0"></span><h1>compute temp/asphere command<a class="headerlink" href="#compute-temp-asphere-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 temp/asphere keyword value ...
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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>temp/asphere = style name of this compute command</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>bias</em> or <em>dof</em></li>
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</ul>
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<pre class="literal-block">
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<em>bias</em> value = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias
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<em>dof</em> value = <em>all</em> or <em>rotate</em>
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all = compute temperature of translational and rotational degrees of freedom
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rotate = compute temperature of just rotational degrees of freedom
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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<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 temp/asphere
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compute myTemp mobile temp/asphere bias tempCOM
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compute myTemp mobile temp/asphere dof rotate
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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 temperature of a group of
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aspherical particles, including a contribution from both their
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translational and rotational kinetic energy. This differs from the
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usual <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> command, which assumes point
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particles with only translational kinetic energy.</p>
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<p>Only finite-size particles (aspherical or spherical) can be included
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in the group. For 3d finite-size particles, each has 6 degrees of
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freedom (3 translational, 3 rotational). For 2d finite-size
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particles, each has 3 degrees of freedom (2 translational, 1
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rotational).</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">This choice for degrees of freedom (dof) assumes that all
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finite-size aspherical or spherical particles in your model will
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freely rotate, sampling all their rotational dof. It is possible to
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use a combination of interaction potentials and fixes that induce no
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torque or otherwise constrain some of all of your particles so that
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this is not the case. Then there are less dof and you should use the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify extra</em></a> command to adjust the dof
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accordingly.</p>
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</div>
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<p>For example, an aspherical particle with all three of its shape
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parameters the same is a sphere. If it does not rotate, then it
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should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
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uniaxial aspherical particle has two of its three shape parameters the
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same. If it does not rotate around the axis perpendicular to its
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circular cross section, then it should have 5 dof instead of 6 in 3d.
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The latter is the case for uniaxial ellipsoids in a <a class="reference internal" href="pair_gayberne.html"><em>GayBerne model</em></a> since there is no induced torque around the
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optical axis. It will also be the case for biaxial ellipsoids when
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exactly two of the semiaxes have the same length and the corresponding
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relative well depths are equal.</p>
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<p>The translational kinetic energy is computed the same as is described
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by the <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> command. The rotational
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kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
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for the aspherical particle and w is its angular velocity, which is
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computed from its angular momentum.</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">For <a class="reference internal" href="dimension.html"><em>2d models</em></a>, particles are treated as
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ellipsoids, not ellipses, meaning their moments of inertia will be the
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same as in 3d.</p>
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</div>
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<p>A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute. The formula for the components of the
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tensor is the same as the above formula, except that v^2 and w^2 are
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replaced by vx*vy and wx*wy for the xy component, and the appropriate
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elements of the inertia tensor are used. The 6 components of the
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vector are ordered xx, yy, zz, xy, xz, yz.</p>
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<p>The number of atoms contributing to the temperature is assumed to be
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constant for the duration of the run; use the <em>dynamic</em> option of the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command if this is not the case.</p>
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<p>This compute subtracts out translational degrees-of-freedom due to
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fixes that constrain molecular motion, such as <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> and <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>. This means the
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temperature of groups of atoms that include these constraints will be
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computed correctly. If needed, the subtracted degrees-of-freedom can
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be altered using the <em>extra</em> option of the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command.</p>
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<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span>this howto section</span></a> of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting.</p>
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<hr class="docutils" />
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<p>The keyword/value option pairs are used in the following ways.</p>
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<p>For the <em>bias</em> keyword, <em>bias-ID</em> refers to the ID of a temperature
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compute that removes a “bias” velocity from each atom. This allows
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compute temp/sphere to compute its thermal temperature after the
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translational kinetic energy components have been altered in a
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prescribed way, e.g. to remove a flow velocity profile. Thermostats
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that use this compute will work with this bias term. See the doc
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pages for individual computes that calculate a temperature and the doc
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pages for fixes that perform thermostatting for more details.</p>
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<p>For the <em>dof</em> keyword, a setting of <em>all</em> calculates a temperature
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that includes both translational and rotational degrees of freedom. A
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setting of <em>rotate</em> calculates a temperature that includes only
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rotational degrees of freedom.</p>
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<hr class="docutils" />
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
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options.</p>
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<p>The scalar value calculated by this compute is “intensive”. The
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vector values are “extensive”.</p>
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<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><em>units</em></a>. The
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vector values will be in energy <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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<p>This compute is part of the ASPHERE package. It is only enabled if
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LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
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<p>This compute requires that atoms store angular momementum and a
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quaternion as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a>
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command.</p>
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<p>All particles in the group must be finite-size. They cannot be point
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particles, but they can be aspherical or spherical as defined by their
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shape attribute.</p>
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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_temp.html"><em>compute temp</em></a></p>
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<p><strong>Default:</strong> none</p>
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