forked from lijiext/lammps
113 lines
4.5 KiB
Plaintext
113 lines
4.5 KiB
Plaintext
.. index:: compute temp/region
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compute temp/region command
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===========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID temp/region region-ID
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp/region = style name of this compute command
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* region-ID = ID of region to use for choosing atoms
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Examples
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""""""""
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.. parsed-literal::
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compute mine flow temp/region boundary
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Description
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"""""""""""
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Define a computation that calculates the temperature of a group of
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atoms in a geometric region. This can be useful for thermostatting
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one portion of the simulation box. E.g. a McDLT simulation where one
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side is cooled, and the other side is heated. A compute of this style
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can be used by any command that computes a temperature,
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e.g. :doc:`thermo_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, etc.
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Note that a *region*\ -style temperature can be used to thermostat with
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:doc:`fix temp/rescale <fix_temp_rescale>` or :doc:`fix langevin <fix_langevin>`, but should probably not be used with
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Nose/Hoover style fixes (:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, or :doc:`fix nph <fix_nh>`), if the
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degrees-of-freedom included in the computed T varies with time.
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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 both the group and region, k = Boltzmann constant, and T =
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temperature.
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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.
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The number of atoms contributing to the temperature is calculated each
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time the temperature is evaluated since it is assumed atoms can
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enter/leave the region. Thus there is no need to use the *dynamic*
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option of the :doc:`compute_modify <compute_modify>` command for this
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compute style.
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The removal of atoms outside the region by this fix is essentially
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computing the temperature after a "bias" has been removed, which in
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this case is the velocity of any atoms outside the region. If this
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compute is used with a fix command that performs thermostatting then
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this bias will be subtracted from each atom, thermostatting of the
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remaining thermal velocity will be performed, and the bias will be
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added back in. Thermostatting fixes that work in this way include
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:doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`. This means that when this compute
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is used to calculate the temperature for any of the thermostatting
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fixes via the :doc:`fix modify temp <fix_modify>` command, the thermostat
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will operate only on atoms that are currently in the geometric
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region.
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Unlike other compute styles that calculate temperature, this compute
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does not subtract out degrees-of-freedom due to fixes that constrain
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motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`. This is because those degrees of freedom
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(e.g. a constrained bond) could apply to sets of atoms that straddle
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the region boundary, and hence the concept is somewhat ill-defined.
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If needed the number of subtracted degrees-of-freedom can be set
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explicitly using the *extra* option of the
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:doc:`compute_modify <compute_modify>` command.
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See :ref:`this howto section <howto_16>` of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting.
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**Output info:**
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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. See :ref:`this section <howto_15>` for an overview of LAMMPS output
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options.
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The scalar value calculated by this compute is "intensive". The
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vector values are "extensive".
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The scalar value will be in temperature :doc:`units <units>`. The
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vector values will be in energy :doc:`units <units>`.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`compute temp <compute_temp>`, :doc:`compute pressure <compute_pressure>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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