mirror of https://github.com/lammps/lammps.git
141 lines
6.2 KiB
Plaintext
141 lines
6.2 KiB
Plaintext
.. index:: compute temp/deform
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compute temp/deform 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/deform
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp/deform = 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 myTemp all temp/deform
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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 a streaming velocity induced by the
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simulation box changing size and/or shape, for example in a
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non-equilibrium MD (NEMD) simulation. The size/shape change is
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induced by use of the :doc:`fix deform <fix_deform>` command. A compute
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of this style is created by the :doc:`fix nvt/sllod <fix_nvt_sllod>`
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command to compute the thermal temperature of atoms for thermostatting
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purposes. A compute of this style can also be used by any command
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that computes a temperature, e.g. :doc:`thermo_modify <thermo_modify>`,
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:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
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The deformation fix changes the box size and/or shape over time, so
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each atom in the simulation box can be thought of as having a
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"streaming" velocity. For example, if the box is being sheared in x,
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relative to y, then atoms at the bottom of the box (low y) have a
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small x velocity, while atoms at the top of the box (hi y) have a
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large x velocity. This position-dependent streaming velocity is
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subtracted from each atom's actual velocity to yield a thermal
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velocity which is used to compute the temperature.
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.. note::
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:doc:`Fix deform <fix_deform>` has an option for remapping either
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atom coordinates or velocities to the changing simulation box. When
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using this compute in conjunction with a deforming box, fix deform
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should NOT remap atom positions, but rather should let atoms respond
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to the changing box by adjusting their own velocities (or let :doc:`fix deform <fix_deform>` remap the atom velocities, see it's remap
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option). If fix deform does remap atom positions, then they appear to
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move with the box but their velocity is not changed, and thus they do
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NOT have the streaming velocity assumed by this compute. LAMMPS will
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warn you if fix deform is defined and its remap setting is not
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consistent with this compute.
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After the streaming velocity has been subtracted from each atom, the
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temperature is calculated by the formula KE = dim/2 N k T, where KE =
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total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
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or 3 = dimensionality of the simulation, N = number of atoms in the
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group, k = Boltzmann constant, and T = temperature. Note that v in
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the kinetic energy formula is the atom's thermal velocity.
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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 box deformation velocity component by this fix is
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essentially computing the temperature after a "bias" has been removed
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from the velocity of the atoms. If this compute is used with a fix
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command that performs thermostatting then this bias will be subtracted
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from each atom, thermostatting of the remaining thermal velocity will
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be performed, and the bias will be added back in. Thermostatting
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fixes 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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.. note::
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The temperature calculated by this compute is only accurate if
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the atoms are indeed moving with a stream velocity profile that
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matches the box deformation. If not, then the compute will subtract
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off an incorrect stream velocity, yielding a bogus thermal
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temperature. You should NOT assume that your atoms are streaming at
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the same rate the box is deforming. Rather, you should monitor their
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velocity profile, e.g. via the :doc:`fix ave/chunk <fix_ave_chunk>`
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command. And you can compare the results of this compute to :doc:`compute temp/profile <compute_temp_profile>`, which actually calculates the
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stream profile before subtracting it. If the two computes do not give
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roughly the same temperature, then your atoms are not streaming
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consistent with the box deformation. See the :doc:`fix deform <fix_deform>` command for more details on ways to get atoms
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to stream consistently with the box deformation.
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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/ramp <compute_temp_ramp>`, :doc:`compute temp/profile <compute_temp_profile>`, :doc:`fix deform <fix_deform>`,
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:doc:`fix nvt/sllod <fix_nvt_sllod>`
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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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