127 lines
4.8 KiB
ReStructuredText
127 lines
4.8 KiB
ReStructuredText
.. 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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.. code-block:: LAMMPS
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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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.. code-block:: LAMMPS
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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 atoms in a
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geometric region. This can be useful for thermostatting one portion of the
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simulation box. For example, a McDLT simulation where one side is cooled, and
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the other side is heated. A compute of this style can be used by any command
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that computes a temperature (e.g., :doc:`thermo_modify <thermo_modify>`,
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:doc:`fix temp/rescale <fix_temp_rescale>`).
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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
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: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>`,
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or :doc:`fix nph <fix_nh>`) if the degrees of freedom included in the computed
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temperature vary with time.
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The temperature is calculated by the formula
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.. math::
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\text{KE} = \frac{\text{dim}}{2} N k_B T,
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where KE = is the total kinetic energy of the group of atoms (sum of
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:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
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:math:`N` is the number of atoms in both the group and region, :math:`k_B` is
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the Boltzmann constant, and :math:`T` temperature.
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A symmetric tensor, stored as a six-element vector, is also calculated
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by this compute for use in the computation of a pressure tensor by the
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:doc:`compute pressue <compute_pressure>` command. The formula for
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the components of the tensor is the same as the above expression for
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:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
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the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
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:math:`xy` component, and so on. Note that because it lacks the 1/2
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factor, these tensor components are twice those of the traditional
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kinetic energy tensor. The six components of the vector are ordered
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:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
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:math:`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>`,
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:doc:`fix temp/berendsen <fix_temp_berendsen>`, and
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: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 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
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<fix_rigid>`. This is because those degrees of freedom (e.g., a
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constrained bond) could apply to sets of atoms that straddle the
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region boundary, and hence the concept is somewhat ill-defined. If
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needed the number of subtracted degrees of freedom can be set
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explicitly using the *extra* option of the :doc:`compute_modify
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<compute_modify>` command.
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See the :doc:`Howto thermostat <Howto_thermostat>` page for a
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discussion of different ways to compute temperature and perform
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thermostatting.
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Output info
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"""""""""""
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This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (symmetric tensor), which can be accessed by
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indices 1--6. These values can be used by any command that uses
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global scalar or vector values from a compute as input. See the
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:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
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output 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 is in temperature :doc:`units <units>`. The vector
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values are 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
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"""""""
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none
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