forked from lijiext/lammps
99 lines
3.6 KiB
Plaintext
99 lines
3.6 KiB
Plaintext
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.. index:: compute temp/com
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compute temp/com 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/com
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp/com = style name of this compute command
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Examples
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""""""""
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.. parsed-literal::
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compute 1 all temp/com
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compute myTemp mobile temp/com
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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 of the group.
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This is useful if the group is expected to have a non-zero net
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velocity for some reason. A compute of this style can be used by any
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command that computes a temperature,
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e.g. :doc:`thermo_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
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After the center-of-mass velocity has been subtracted from each atom,
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the temperature is calculated by the formula KE = dim/2 N k T, where
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KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
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dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
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in the group, k = Boltzmann constant, and T = temperature.
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A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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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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The removal of the center-of-mass velocity by this fix is essentially
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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>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :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 :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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**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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none
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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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