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<title>compute temp/cs command — LAMMPS 15 May 2015 version documentation</title>
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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_start.html">2. Getting Started</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 class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li>compute temp/cs command</li>
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<div class="section" id="compute-temp-cs-command">
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<span id="index-0"></span><h1>compute temp/cs command<a class="headerlink" href="#compute-temp-cs-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/cs group1 group2
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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/cs = style name of this compute command</li>
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<li>group1 = group-ID of either cores or shells</li>
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<li>group2 = group-ID of either shells or cores</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 oxygen_c-s all temp/cs O_core O_shell
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compute core_shells all temp/cs cores shells
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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 system based
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on the center-of-mass velocity of atom pairs that are bonded to each
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other. This compute is designed to be used with the adiabatic
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core/shell model of <a class="reference internal" href="#mitchellfinchham"><span>(Mitchell and Finchham)</span></a>. See
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<a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 25</span></a> of the manual for an
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overview of the model as implemented in LAMMPS. Specifically, this
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compute enables correct temperature calculation and thermostatting of
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core/shell pairs where it is desirable for the internal degrees of
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freedom of the core/shell pairs to not be influenced by a thermostat.
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A compute of this style can be used by any command that computes a
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temperature via <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> e.g. <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, etc.</p>
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<p>Note that this compute does not require all ions to be polarized,
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hence defined as core/shell pairs. One can mix core/shell pairs and
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ions without a satellite particle if desired. The compute will
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consider the non-polarized ions according to the physical system.</p>
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<p>For this compute, core and shell particles are specified by two
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respective group IDs, which can be defined using the
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<a class="reference internal" href="group.html"><em>group</em></a> command. The number of atoms in the two groups
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must be the same and there should be one bond defined between a pair
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of atoms in the two groups. Non-polarized ions which might also be
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included in the treated system should not be included into either of
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these groups, they are taken into account by the <em>group-ID</em> (2nd
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argument) of the compute.</p>
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<p>The temperature is calculated by the formula KE = dim/2 N k T, where
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KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
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dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
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in the group, k = Boltzmann constant, and T = temperature. Note that
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the velocity of each core or shell atom used in the KE calculation is
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the velocity of the center-of-mass (COM) of the core/shell pair the
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atom is part of.</p>
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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 for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz. Again, the velocity of each core or shell atom is its
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COM velocity.</p>
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<p>The change this fix makes to core/shell atom velocities is essentially
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computing the temperature after a “bias” has been removed from the
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velocity of the atoms. This “bias” is the velocity of the atom
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relative to the COM velocity of the core/shell pair. If this compute
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is used with a fix command that performs thermostatting then this bias
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will be subtracted from each atom, thermostatting of the remaining COM
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velocity will be performed, and the bias will be added back in. This
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means the thermostating will effectively be performed on the
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core/shell pairs, instead of on the individual core and shell atoms.
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Thermostatting fixes that work in this way include <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>fix temp/berendsen</em></a>, and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>.</p>
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<p>The internal energy of core/shell pairs can be calculated by the
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<a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a> command, if chunks are
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defined as core/shell pairs. See <a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 25</span></a> for more discussion on how to do this.</p>
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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.</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>The number of core/shell pairs contributing to the temperature is
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assumed to be constant for the duration of the run. No fixes should
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be used which generate new molecules or atoms during a simulation.</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>, <a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="mitchellfinchham"><strong>(Mitchell and Finchham)</strong> Mitchell, Finchham, J Phys Condensed Matter,
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5, 1031-1038 (1993).</p>
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