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