151 lines
5.6 KiB
ReStructuredText
151 lines
5.6 KiB
ReStructuredText
.. index:: compute temp/body
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compute temp/body 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/body keyword value ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp/body = style name of this compute command
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* zero or more keyword/value pairs may be appended
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* keyword = *bias* or *dof*
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.. parsed-literal::
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*bias* value = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias
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*dof* value = *all* or *rotate*
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all = compute temperature of translational and rotational degrees of freedom
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rotate = compute temperature of just rotational degrees of freedom
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all temp/body
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compute myTemp mobile temp/body bias tempCOM
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compute myTemp mobile temp/body dof 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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body particles, including a contribution from both their
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translational and rotational kinetic energy. This differs from the
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usual :doc:`compute temp <compute_temp>` command, which assumes point
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particles with only translational kinetic energy.
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Only body particles can be included in the group. For 3d particles,
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each has 6 degrees of freedom (3 translational, 3 rotational). For 2d
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body particles, each has 3 degrees of freedom (2 translational, 1
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rotational).
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.. note::
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This choice for degrees of freedom (DOF) assumes that all body
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particles in your model will freely rotate, sampling all their
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rotational DOF. It is possible to use a combination of interaction
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potentials and fixes that induce no torque or otherwise constrain
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some of all of your particles so that this is not the case. Then
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there are less DOF and you should use the :doc:`compute_modify
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extra/dof <compute_modify>` command to adjust the DOF accordingly.
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The translational kinetic energy is computed the same as is described
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by the :doc:`compute temp <compute_temp>` command. The rotational
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kinetic energy is computed as :math:`\frac12 I \omega^2`, where :math:`I`
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is the moment of inertia tensor for the aspherical particle and :math:`\omega`
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is its angular velocity, which is computed from its angular momentum.
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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` and :math:`\omega^2` are replaced by :math:`v_x v_y`
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and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on.
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And the appropriate elements of the moment of inertia tensor are used.
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Note that because it lacks the 1/2 factor, these tensor components are
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twice those of the traditional kinetic energy tensor. The six
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components of the vector are ordered :math:`xx`, :math:`yy`,
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:math:`zz`, :math:`xy`, :math:`xz`, :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/dof* option of
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the :doc:`compute_modify <compute_modify>` command if this is not the
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case.
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This compute subtracts out translational degrees-of-freedom due to
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fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>`
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and :doc:`fix rigid <fix_rigid>`. This means the
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temperature of groups of atoms that include these constraints will be
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computed correctly. If needed, the subtracted degrees-of-freedom can
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be altered using the *extra/dof* option of the
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: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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----------
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The keyword/value option pairs are used in the following ways.
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For the *bias* keyword, *bias-ID* refers to the ID of a temperature
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compute that removes a "bias" velocity from each atom. This allows
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compute temp/sphere to compute its thermal temperature after the
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translational kinetic energy components have been altered in a
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prescribed way (e.g., to remove a flow velocity profile). Thermostats
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that use this compute will work with this bias term. See the doc
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pages for individual computes that calculate a temperature and the doc
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pages for fixes that perform thermostatting for more details.
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For the *dof* keyword, a setting of *all* calculates a temperature
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that includes both translational and rotational degrees of freedom. A
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setting of *rotate* calculates a temperature that includes only
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rotational degrees of freedom.
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----------
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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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This compute is part of the BODY 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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This compute requires that atoms store angular momentum and a
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quaternion as defined by the :doc:`atom_style body <atom_style>`
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command.
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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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