<p>The deformation fix changes the box size and/or shape over time, so
each atom in the simulation box can be thought of as having a
“streaming” velocity. For example, if the box is being sheared in x,
relative to y, then atoms at the bottom of the box (low y) have a
small x velocity, while atoms at the top of the box (hi y) have a
large x velocity. This position-dependent streaming velocity is
subtracted from each atom’s actual velocity to yield a thermal
velocity which is used to compute the temperature.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last"><aclass="reference internal"href="fix_deform.html"><spanclass="doc">Fix deform</span></a> has an option for remapping either
atom coordinates or velocities to the changing simulation box. When
using this compute in conjunction with a deforming box, fix deform
should NOT remap atom positions, but rather should let atoms respond
to the changing box by adjusting their own velocities (or let <aclass="reference internal"href="fix_deform.html"><spanclass="doc">fix deform</span></a> remap the atom velocities, see it’s remap
option). If fix deform does remap atom positions, then they appear to
move with the box but their velocity is not changed, and thus they do
NOT have the streaming velocity assumed by this compute. LAMMPS will
warn you if fix deform is defined and its remap setting is not
consistent with this compute.</p>
</div>
<p>After the streaming velocity has been subtracted from each atom, the
temperature is calculated by the formula KE = dim/2 N k T, where KE =
total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
or 3 = dimensionality of the simulation, N = number of atoms in the
group, k = Boltzmann constant, and T = temperature. Note that v in
the kinetic energy formula is the atom’s thermal velocity.</p>
<p>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.</p>
<p>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <em>dynamic</em> option of the
<aclass="reference internal"href="compute_modify.html"><spanclass="doc">compute_modify</span></a> command if this is not the case.</p>
<p>The removal of the box deformation velocity component by this fix is
essentially computing the temperature after a “bias” has been removed
from the velocity of the atoms. If this compute is used with a fix
command that performs thermostatting then this bias will be subtracted
from each atom, thermostatting of the remaining thermal velocity will
be performed, and the bias will be added back in. Thermostatting
fixes that work in this way include <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nvt</span></a>, <aclass="reference internal"href="fix_temp_rescale.html"><spanclass="doc">fix temp/rescale</span></a>, <aclass="reference internal"href="fix_temp_berendsen.html"><spanclass="doc">fix temp/berendsen</span></a>, and <aclass="reference internal"href="fix_langevin.html"><spanclass="doc">fix langevin</span></a>.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">The temperature calculated by this compute is only accurate if
the atoms are indeed moving with a stream velocity profile that
matches the box deformation. If not, then the compute will subtract
off an incorrect stream velocity, yielding a bogus thermal
temperature. You should NOT assume that your atoms are streaming at
the same rate the box is deforming. Rather, you should monitor their
velocity profile, e.g. via the <aclass="reference internal"href="fix_ave_chunk.html"><spanclass="doc">fix ave/chunk</span></a>
command. And you can compare the results of this compute to <aclass="reference internal"href="compute_temp_profile.html"><spanclass="doc">compute temp/profile</span></a>, which actually calculates the
stream profile before subtracting it. If the two computes do not give
roughly the same temperature, then your atoms are not streaming
consistent with the box deformation. See the <aclass="reference internal"href="fix_deform.html"><spanclass="doc">fix deform</span></a> command for more details on ways to get atoms
to stream consistently with the box deformation.</p>
</div>
<p>This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as <aclass="reference internal"href="fix_shake.html"><spanclass="doc">fix shake</span></a> and
<aclass="reference internal"href="fix_rigid.html"><spanclass="doc">fix rigid</span></a>. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<em>extra</em> option of the <aclass="reference internal"href="compute_modify.html"><spanclass="doc">compute_modify</span></a> command.</p>
<p>See <aclass="reference internal"href="Section_howto.html#howto-16"><spanclass="std std-ref">this howto section</span></a> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <aclass="reference internal"href="Section_howto.html#howto-15"><spanclass="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar value calculated by this compute is “intensive”. The
vector values are “extensive”.</p>
<p>The scalar value will be in temperature <aclass="reference internal"href="units.html"><spanclass="doc">units</span></a>. The
vector values will be in energy <aclass="reference internal"href="units.html"><spanclass="doc">units</span></a>.</p>
Built with <ahref="http://sphinx-doc.org/">Sphinx</a> using a <ahref="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <ahref="https://readthedocs.org">Read the Docs</a>.