forked from lijiext/lammps
171 lines
6.3 KiB
Plaintext
171 lines
6.3 KiB
Plaintext
.. index:: compute temp/asphere
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compute temp/asphere 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/asphere keyword value ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp/asphere = 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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.. parsed-literal::
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compute 1 all temp/asphere
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compute myTemp mobile temp/asphere bias tempCOM
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compute myTemp mobile temp/asphere 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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aspherical 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 finite-size particles (aspherical or spherical) can be included
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in the group. For 3d finite-size particles, each has 6 degrees of
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freedom (3 translational, 3 rotational). For 2d finite-size
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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
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finite-size aspherical or spherical particles in your model will
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freely rotate, sampling all their rotational dof. It is possible to
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use a combination of interaction potentials and fixes that induce no
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torque or otherwise constrain some of all of your particles so that
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this is not the case. Then there are less dof and you should use the
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:doc:`compute_modify extra <compute_modify>` command to adjust the dof
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accordingly.
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For example, an aspherical particle with all three of its shape
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parameters the same is a sphere. If it does not rotate, then it
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should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
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uniaxial aspherical particle has two of its three shape parameters the
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same. If it does not rotate around the axis perpendicular to its
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circular cross section, then it should have 5 dof instead of 6 in 3d.
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The latter is the case for uniaxial ellipsoids in a :doc:`GayBerne model <pair_gayberne>` since there is no induced torque around the
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optical axis. It will also be the case for biaxial ellipsoids when
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exactly two of the semiaxes have the same length and the corresponding
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relative well depths are equal.
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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 1/2 I w^2, where I is the inertia tensor
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for the aspherical particle and w is its angular velocity, which is
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computed from its angular momentum.
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.. note::
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For :doc:`2d models <dimension>`, particles are treated as
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ellipsoids, not ellipses, meaning their moments of inertia will be the
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same as in 3d.
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A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute. The formula for the components of the
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tensor is the same as the above formula, except that v^2 and w^2 are
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replaced by vx*vy and wx*wy for the xy component, and the appropriate
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elements of the inertia tensor are used. The 6 components of the
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vector are ordered xx, yy, zz, xy, xz, 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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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>` 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* 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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----------
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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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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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This compute is part of the ASPHERE package. It is only enabled if
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LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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This compute requires that atoms store angular momementum and a
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quaternion as defined by the :doc:`atom_style ellipsoid <atom_style>`
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command.
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All particles in the group must be finite-size. They cannot be point
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particles, but they can be aspherical or spherical as defined by their
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shape attribute.
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Related commands
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""""""""""""""""
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:doc:`compute temp <compute_temp>`
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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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