git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14950 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/_sources/compute_temp_body.txt

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+.. index:: compute temp/body
+
+compute temp/body command
+=========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID temp/body keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* temp/body = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *bias* or *dof*
+.. parsed-literal::
+
+     *bias* value = bias-ID
+       bias-ID = ID of a temperature compute that removes a velocity bias
+     *dof* value = *all* or *rotate*
+       all = compute temperature of translational and rotational degrees of freedom
+       rotate = compute temperature of just rotational degrees of freedom
+
+
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   compute 1 all temp/body
+   compute myTemp mobile temp/body bias tempCOM
+   compute myTemp mobile temp/body dof rotate
+
+Description
+"""""""""""
+
+Define a computation that calculates the temperature of a group of
+body particles, including a contribution from both their
+translational and rotational kinetic energy.  This differs from the
+usual :doc:`compute temp <compute_temp>` command, which assumes point
+particles with only translational kinetic energy.
+
+Only body particles can be included in the group.  For 3d particles,
+each has 6 degrees of freedom (3 translational, 3 rotational).  For 2d
+body particles, each has 3 degrees of freedom (2 translational, 1
+rotational).
+
+.. note::
+
+   This choice for degrees of freedom (dof) assumes that all body
+   particles in your model will freely rotate, sampling all their
+   rotational dof.  It is possible to use a combination of interaction
+   potentials and fixes that induce no torque or otherwise constrain some
+   of all of your particles so that this is not the case.  Then there are
+   less dof and you should use the :doc:`compute_modify extra <compute_modify>` command to adjust the dof accordingly.
+
+The translational kinetic energy is computed the same as is described
+by the :doc:`compute temp <compute_temp>` command.  The rotational
+kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
+for the aspherical particle and w is its angular velocity, which is
+computed from its angular momentum.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute.  The formula for the components of the
+tensor is the same as the above formula, except that v^2 and w^2 are
+replaced by vx*vy and wx*wy for the xy component, and the appropriate
+elements of the inertia tensor are used.  The 6 components of the
+vector are ordered xx, yy, zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute_modify <compute_modify>` command if this is not the case.
+
+This compute subtracts out translational degrees-of-freedom due to
+fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`.  This means the
+temperature of groups of atoms that include these constraints will be
+computed correctly.  If needed, the subtracted degrees-of-freedom can
+be altered using the *extra* option of the
+:doc:`compute_modify <compute_modify>` command.
+
+See :ref:`this howto section <howto_16>` of the manual for
+a discussion of different ways to compute temperature and perform
+thermostatting.
+
+
+----------
+
+
+The keyword/value option pairs are used in the following ways.
+
+For the *bias* keyword, *bias-ID* refers to the ID of a temperature
+compute that removes a "bias" velocity from each atom.  This allows
+compute temp/sphere to compute its thermal temperature after the
+translational kinetic energy components have been altered in a
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
+that use this compute will work with this bias term.  See the doc
+pages for individual computes that calculate a temperature and the doc
+pages for fixes that perform thermostatting for more details.
+
+For the *dof* keyword, a setting of *all* calculates a temperature
+that includes both translational and rotational degrees of freedom.  A
+setting of *rotate* calculates a temperature that includes only
+rotational degrees of freedom.
+
+
+----------
+
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See :ref:`this section <howto_15>` for an overview of LAMMPS output
+options.
+
+The scalar value calculated by this compute is "intensive".  The
+vector values are "extensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+vector values will be in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+
+This compute is part of the BODY package.  It is only enabled if
+LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.
+
+This compute requires that atoms store angular momementum and a
+quaternion as defined by the :doc:`atom_style body <atom_style>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute temp <compute_temp>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm