134 lines
5.1 KiB
ReStructuredText
134 lines
5.1 KiB
ReStructuredText
.. index:: compute temp/cs
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compute temp/cs 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/cs group1 group2
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp/cs = style name of this compute command
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* group1 = group-ID of either cores or shells
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* group2 = group-ID of either shells or cores
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute oxygen_c-s all temp/cs O_core O_shell
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compute core_shells all temp/cs cores shells
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Description
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"""""""""""
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Define a computation that calculates the temperature of a system based
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on the center-of-mass velocity of atom pairs that are bonded to each
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other. This compute is designed to be used with the adiabatic
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core/shell model of :ref:`(Mitchell and Finchham) <MitchellFinchham1>`.
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See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
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the model as implemented in LAMMPS. Specifically, this compute
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enables correct temperature calculation and thermostatting of
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core/shell pairs where it is desirable for the internal degrees of
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freedom of the core/shell pairs to not be influenced by a thermostat.
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A compute of this style can be used by any command that computes a
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temperature via :doc:`fix_modify <fix_modify>`
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(e.g., :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`).
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Note that this compute does not require all ions to be polarized,
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hence defined as core/shell pairs. One can mix core/shell pairs and
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ions without a satellite particle if desired. The compute will
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consider the non-polarized ions according to the physical system.
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For this compute, core and shell particles are specified by two
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respective group IDs, which can be defined using the
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:doc:`group <group>` command. The number of atoms in the two groups
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must be the same and there should be one bond defined between a pair
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of atoms in the two groups. Non-polarized ions which might also be
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included in the treated system should not be included into either of
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these groups, they are taken into account by the *group-ID* (second
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argument) of the compute.
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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. Note that
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the velocity of each core or shell atom used in the KE calculation is
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the velocity of the center-of-mass (COM) of the core/shell pair the
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atom is part of.
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A kinetic energy tensor, stored as a six-element vector, is also calculated by
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this compute for use in the computation of a pressure tensor. The formula for
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the components of the tensor is the same as the above formula, except that
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:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and so
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on. The six components of the vector are ordered :math:`xx`, :math:`yy`,
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:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. In contrast to the temperature,
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the velocity of each core or shell atom is taken individually.
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The change this fix makes to core/shell atom velocities is essentially
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computing the temperature after a "bias" has been removed from the velocity of
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the atoms. This "bias" is the velocity of the atom relative to the
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center-of-mass velocity of the core/shell pair. If this compute is used with a
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fix command that performs thermostatting then this bias will be subtracted from
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each atom, thermostatting of the remaining center-of-mass velocity will be
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performed, and the bias will be added back in. This means the thermostatting
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will effectively be performed on the core/shell pairs, instead of on the
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individual core and shell atoms. Thermostatting fixes that work in this way
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include :doc:`fix nvt <fix_nh>`, :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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The internal energy of core/shell pairs can be calculated by the
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:doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are defined
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as core/shell pairs. See the :doc:`Howto coreshell <Howto_coreshell>` doc
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page for more discussion on how to do this.
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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 (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.
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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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The number of core/shell pairs contributing to the temperature is
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assumed to be constant for the duration of the run. No fixes should
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be used which generate new molecules or atoms during a simulation.
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Related commands
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""""""""""""""""
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:doc:`compute temp <compute_temp>`,
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:doc:`compute temp/chunk <compute_temp_chunk>`
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Default
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"""""""
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none
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----------
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.. _MitchellFinchham1:
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**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
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5, 1031-1038 (1993).
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