115 lines
4.2 KiB
ReStructuredText
115 lines
4.2 KiB
ReStructuredText
.. index:: compute temp/rotate
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compute temp/rotate 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/rotate
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp/rotate = style name of this compute command
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute Tbead bead temp/rotate
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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, after subtracting out the center-of-mass velocity and angular velocity
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of the group. This is useful if the group is expected to have a non-zero net
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velocity and/or global rotation motion for some reason. A compute of this
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style can be used by any command that computes a temperature
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(e.g., :doc:`thermo_modify <thermo_modify>`,
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:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`).
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After the center-of-mass velocity and angular velocity has been subtracted from
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each atom, 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 the group, :math:`k_B` is the Boltzmann
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constant, and :math:`T` is the absolute 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 assumed to be
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constant for the duration of the run; use the *dynamic* option of the
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:doc:`compute_modify <compute_modify>` command if this is not the case.
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The removal of the center-of-mass velocity and angular velocity by this fix is
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essentially computing the temperature after a "bias" has been removed from the
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velocity of the atoms. If this compute is used with a fix command
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that performs thermostatting then this bias will be subtracted from
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each atom, thermostatting of the remaining thermal velocity will be
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performed, and the bias will be added back in. Thermostatting fixes
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that work in this way include :doc:`fix nvt <fix_nh>`,
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: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>`.
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This compute subtracts out degrees-of-freedom due to fixes that
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constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
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:doc:`fix rigid <fix_rigid>`. This means the temperature of groups of
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atoms that include these constraints will be computed correctly. If
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needed, the subtracted degrees-of-freedom can be altered using the
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*extra* option of the :doc:`compute_modify <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 global
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scalar or vector values from a compute as input. See the :doc:`Howto
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output <Howto_output>` page for an overview of LAMMPS 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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This compute is part of the EXTRA-COMPUTE package. It is only enabled if
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LAMMPS was built with that package.
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See the :doc:`Build package <Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`compute temp <compute_temp>`
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Default
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"""""""
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none
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