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lammps/doc/compute_temp_deform.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/deform command :h3
[Syntax:]
compute ID group-ID temp/deform :pre
ID, group-ID are documented in "compute"_compute.html command
temp/deform = style name of this compute command :ul
[Examples:]
compute myTemp all temp/deform :pre
[Description:]
Define a computation that calculates the temperature of a group of
atoms, after subtracting out a streaming velocity induced by the
simulation box changing size and/or shape, for example in a
non-equilibrium MD (NEMD) simulation. The size/shape change is
induced by use of the "fix deform"_fix_deform.html command. A compute
of this style is created by the "fix nvt/sllod"_fix_nvt_sllod.html
command to compute the thermal temperature of atoms for thermostatting
purposes. A compute of this style can also be used by any command
that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
The deformation fix changes the box size and/or shape over time, so
each point 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 points at the bottom of the box (low y) have a
small x velocity, while points 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.
IMPORTANT NOTE: "Fix deform"_fix_deform.html has an option for
remapping either atom coordinates or velocities to the changing
simulation box. To use this compute, fix deform should NOT remap atom
positions, but rather should let atoms respond to the changing box by
adjusting their own velocities (or let fix deform remap the atom
velocities). If fix deform does remap atom positions, their velocity
is not changed, and thus they do not have the streaming velocity
assumed by this compute. LAMMPS will warn you if the fix deform
setting is not consistent with this compute.
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.
A 6-component kinetic energy tensor 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 number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
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 "fix nvt"_fix_nvt.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. 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
{extra} option of the "compute_modify"_compute_modify.html command.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation. The vector
values are "extensive", meaning they scale with the number of atoms in
the simulation.
[Restrictions:] none
[Related commands:]
"compute temp/ramp"_compute_temp_ramp.html, "fix
deform"_fix_deform.html, "fix nvt/sllod"_fix_nvt_sllod.html
[Default:] none
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