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429 lines
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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_commands.html">3. Commands</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_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li>compute command</li>
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<div class="section" id="compute-command">
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<span id="index-0"></span><h1>compute command<a class="headerlink" href="#compute-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 style args
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID = user-assigned name for the computation</li>
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<li>group-ID = ID of the group of atoms to perform the computation on</li>
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<li>style = one of a list of possible style names (see below)</li>
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<li>args = arguments used by a particular style</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 1 all temp
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compute newtemp flow temp/partial 1 1 0
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compute 3 all ke/atom
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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 will be performed on a group of atoms.
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Quantities calculated by a compute are instantaneous values, meaning
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they are calculated from information about atoms on the current
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timestep or iteration, though a compute may internally store some
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information about a previous state of the system. Defining a compute
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does not perform a computation. Instead computes are invoked by other
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LAMMPS commands as needed, e.g. to calculate a temperature needed for
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a thermostat fix or to generate thermodynamic or dump file output.
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See this <a class="reference internal" href="Section_howto.html#howto-15"><span>howto section</span></a> for a summary of
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various LAMMPS output options, many of which involve computes.</p>
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<p>The ID of a compute can only contain alphanumeric characters and
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underscores.</p>
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<hr class="docutils" />
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<p>Computes calculate one of three styles of quantities: global,
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per-atom, or local. A global quantity is one or more system-wide
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values, e.g. the temperature of the system. A per-atom quantity is
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one or more values per atom, e.g. the kinetic energy of each atom.
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Per-atom values are set to 0.0 for atoms not in the specified compute
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group. Local quantities are calculated by each processor based on the
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atoms it owns, but there may be zero or more per atom, e.g. a list of
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bond distances. Computes that produce per-atom quantities have the
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word “atom” in their style, e.g. <em>ke/atom</em>. Computes that produce
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local quantities have the word “local” in their style,
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e.g. <em>bond/local</em>. Styles with neither “atom” or “local” in their
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style produce global quantities.</p>
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<p>Note that a single compute produces either global or per-atom or local
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quantities, but never more than one of these.</p>
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<p>Global, per-atom, and local quantities each come in three kinds: a
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single scalar value, a vector of values, or a 2d array of values. The
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doc page for each compute describes the style and kind of values it
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produces, e.g. a per-atom vector. Some computes produce more than one
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kind of a single style, e.g. a global scalar and a global vector.</p>
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<p>When a compute quantity is accessed, as in many of the output commands
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discussed below, it can be referenced via the following bracket
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notation, where ID is the ID of the compute:</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="21%" />
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<col width="79%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>c_ID</td>
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<td>entire scalar, vector, or array</td>
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</tr>
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<tr class="row-even"><td>c_ID[I]</td>
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<td>one element of vector, one column of array</td>
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</tr>
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<tr class="row-odd"><td>c_ID[I][J]</td>
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<td>one element of array</td>
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</tr>
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</tbody>
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</table>
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<p>In other words, using one bracket reduces the dimension of the
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quantity once (vector -> scalar, array -> vector). Using two brackets
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reduces the dimension twice (array -> scalar). Thus a command that
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uses scalar compute values as input can also process elements of a
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vector or array.</p>
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<p>Note that commands and <a class="reference internal" href="variable.html"><em>variables</em></a> which use compute
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quantities typically do not allow for all kinds, e.g. a command may
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require a vector of values, not a scalar. This means there is no
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ambiguity about referring to a compute quantity as c_ID even if it
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produces, for example, both a scalar and vector. The doc pages for
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various commands explain the details.</p>
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<hr class="docutils" />
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<p>In LAMMPS, the values generated by a compute can be used in several
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ways:</p>
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<ul class="simple">
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<li>The results of computes that calculate a global temperature or
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pressure can be used by fixes that do thermostatting or barostatting
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or when atom velocities are created.</li>
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<li>Global values can be output via the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> or <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command.
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Or the values can be referenced in a <a class="reference internal" href="variable.html"><em>variable equal</em></a> or
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<a class="reference internal" href="variable.html"><em>variable atom</em></a> command.</li>
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<li>Per-atom values can be output via the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
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or the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> command. Or they can be
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time-averaged via the <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a> command or
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reduced by the <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> command. Or the
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per-atom values can be referenced in an <a class="reference internal" href="variable.html"><em>atom-style variable</em></a>.</li>
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<li>Local values can be reduced by the <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> command, or histogrammed by the <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a> command, or output by the <a class="reference internal" href="dump.html"><em>dump local</em></a> command.</li>
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</ul>
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<p>The results of computes that calculate global quantities can be either
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“intensive” or “extensive” values. Intensive means the value is
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independent of the number of atoms in the simulation,
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e.g. temperature. Extensive means the value scales with the number of
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atoms in the simulation, e.g. total rotational kinetic energy.
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<a class="reference internal" href="thermo_style.html"><em>Thermodynamic output</em></a> will normalize extensive
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values by the number of atoms in the system, depending on the
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“thermo_modify norm” setting. It will not normalize intensive values.
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If a compute value is accessed in another way, e.g. by a
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<a class="reference internal" href="variable.html"><em>variable</em></a>, you may want to know whether it is an
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intensive or extensive value. See the doc page for individual
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computes for further info.</p>
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<hr class="docutils" />
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<p>LAMMPS creates its own computes internally for thermodynamic output.
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Three computes are always created, named “thermo_temp”,
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“thermo_press”, and “thermo_pe”, as if these commands had been invoked
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in the input script:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute thermo_temp all temp
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compute thermo_press all pressure thermo_temp
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compute thermo_pe all pe
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</pre></div>
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</div>
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<p>Additional computes for other quantities are created if the thermo
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style requires it. See the documentation for the
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<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command.</p>
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<p>Fixes that calculate temperature or pressure, i.e. for thermostatting
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or barostatting, may also create computes. These are discussed in the
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documentation for specific <a class="reference internal" href="fix.html"><em>fix</em></a> commands.</p>
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<p>In all these cases, the default computes LAMMPS creates can be
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replaced by computes defined by the user in the input script, as
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described by the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> and <a class="reference internal" href="fix_modify.html"><em>fix modify</em></a> commands.</p>
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<p>Properties of either a default or user-defined compute can be modified
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via the <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command.</p>
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<p>Computes can be deleted with the <a class="reference internal" href="uncompute.html"><em>uncompute</em></a> command.</p>
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<p>Code for new computes can be added to LAMMPS (see <a class="reference internal" href="Section_modify.html"><em>this section</em></a> of the manual) and the results of their
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calculations accessed in the various ways described above.</p>
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<hr class="docutils" />
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<p>Each compute style has its own doc page which describes its arguments
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and what it does. Here is an alphabetic list of compute styles
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available in LAMMPS. They are also given in more compact form in the
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Compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
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<p>There are also additional compute styles (not listed here) submitted
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by users which are included in the LAMMPS distribution. The list of
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these with links to the individual styles are given in the compute
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section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
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<ul class="simple">
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<li><a class="reference internal" href="compute_bond_local.html"><em>angle/local</em></a> - theta and energy of each angle</li>
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<li><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a> - angular momentum for each chunk</li>
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<li><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a> - attributes of body sub-particles</li>
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<li><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a> - distance and energy of each bond</li>
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<li><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a> - centro-symmetry parameter for each atom</li>
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<li><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a> - assign chunk IDs to each atom</li>
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<li><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a> - cluster ID for each atom</li>
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<li><a class="reference internal" href="compute_cna_atom.html"><em>cna/atom</em></a> - common neighbor analysis (CNA) for each atom</li>
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<li><a class="reference internal" href="compute_com.html"><em>com</em></a> - center-of-mass of group of atoms</li>
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<li><a class="reference internal" href="compute_com_chunk.html"><em>com/chunk</em></a> - center-of-mass for each chunk</li>
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<li><a class="reference internal" href="compute_contact_atom.html"><em>contact/atom</em></a> - contact count for each spherical particle</li>
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<li><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a> - coordination number for each atom</li>
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<li><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a> - Peridynamic damage for each atom</li>
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<li><a class="reference internal" href="compute_dihedral_local.html"><em>dihedral/local</em></a> - angle of each dihedral</li>
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<li><a class="reference internal" href="compute_dilatation_atom.html"><em>dilatation/atom</em></a> - Peridynamic dilatation for each atom</li>
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<li><a class="reference internal" href="compute_displace_atom.html"><em>displace/atom</em></a> - displacement of each atom</li>
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<li><a class="reference internal" href="compute_erotate_asphere.html"><em>erotate/asphere</em></a> - rotational energy of aspherical particles</li>
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<li><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a> - rotational energy of rigid bodies</li>
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<li><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a> - rotational energy of spherical particles</li>
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<li><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere/atom</em></a> - rotational energy for each spherical particle</li>
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<li><a class="reference internal" href="compute_event_displace.html"><em>event/displace</em></a> - detect event on atom displacement</li>
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<li><a class="reference internal" href="compute_group_group.html"><em>group/group</em></a> - energy/force between two groups of atoms</li>
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<li><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a> - radius of gyration of group of atoms</li>
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<li><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a> - radius of gyration for each chunk</li>
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<li><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a> - heat flux through a group of atoms</li>
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<li><a class="reference internal" href="compute_hexorder_atom.html"><em>hexorder/atom</em></a> - bond orientational order parameter q6</li>
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<li><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a> - angle of each improper</li>
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<li><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a> - inertia tensor for each chunk</li>
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<li><a class="reference internal" href="compute_ke.html"><em>ke</em></a> - translational kinetic energy</li>
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<li><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a> - kinetic energy for each atom</li>
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<li><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a> - translational kinetic energy of rigid bodies</li>
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<li><a class="reference internal" href="compute_msd.html"><em>msd</em></a> - mean-squared displacement of group of atoms</li>
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<li><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a> - mean-squared displacement for each chunk</li>
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<li><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a> - MSD and non-Gaussian parameter of group of atoms</li>
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<li><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a> - angular velocity for each chunk</li>
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<li><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</em></a> - Steinhardt bond orientational order parameters Ql</li>
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<li><a class="reference internal" href="compute_pair.html"><em>pair</em></a> - values computed by a pair style</li>
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<li><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a> - distance/energy/force of each pairwise interaction</li>
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<li><a class="reference internal" href="compute_pe.html"><em>pe</em></a> - potential energy</li>
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<li><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a> - potential energy for each atom</li>
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<li><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a> - Peridynamic plasticity for each atom</li>
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<li><a class="reference internal" href="compute_pressure.html"><em>pressure</em></a> - total pressure and pressure tensor</li>
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<li><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a> - convert atom attributes to per-atom vectors/arrays</li>
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<li><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a> - convert local attributes to localvectors/arrays</li>
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<li><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a> - extract various per-chunk attributes</li>
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<li><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a> - radial distribution function g(r) histogram of group of atoms</li>
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<li><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a> - combine per-atom quantities into a single global value</li>
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<li><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a> - same as compute reduce, within a region</li>
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<li><a class="reference internal" href="compute_slice.html"><em>slice</em></a> - extract values from global vector or array</li>
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<li><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a> - calculate bispectrum coefficients for each atom</li>
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<li><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a> - derivative of bispectrum coefficients for each atom</li>
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<li><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a> - virial contribution from bispectrum coefficients for each atom</li>
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<li><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a> - stress tensor for each atom</li>
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<li><a class="reference internal" href="compute_temp.html"><em>temp</em></a> - temperature of group of atoms</li>
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<li><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a> - temperature of aspherical particles</li>
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<li><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a> - temperature of each chunk</li>
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<li><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a> - temperature after subtracting center-of-mass velocity</li>
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<li><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a> - temperature excluding box deformation velocity</li>
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<li><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial</em></a> - temperature excluding one or more dimensions of velocity</li>
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<li><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a> - temperature excluding a binned velocity profile</li>
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<li><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a> - temperature excluding ramped velocity component</li>
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<li><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a> - temperature of a region of atoms</li>
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<li><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a> - temperature of spherical particles</li>
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<li><a class="reference internal" href="compute_ti.html"><em>ti</em></a> - thermodyanmic integration free energy values</li>
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<li><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a> - torque applied on each chunk</li>
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<li><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a> - velocity-autocorrelation function of group of atoms</li>
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<li><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a> - velocity of center-of-mass for each chunk</li>
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<li><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a> - Voronoi volume and neighbors for each atom</li>
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</ul>
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<p>There are also additional compute styles submitted by users which are
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included in the LAMMPS distribution. The list of these with links to
|
|
the individual styles are given in the compute section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
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<p>There are also additional accelerated compute styles included in the
|
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LAMMPS distribution for faster performance on CPUs and GPUs. The list
|
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of these with links to the individual styles are given in the pair
|
|
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></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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<blockquote>
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<div>none</div></blockquote>
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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="uncompute.html"><em>uncompute</em></a>, <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a>, <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>,
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<a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a></p>
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<p><strong>Default:</strong> none</p>
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