123 lines
3.9 KiB
ReStructuredText
123 lines
3.9 KiB
ReStructuredText
.. index:: compute temp
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.. index:: compute temp/kk
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compute temp command
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====================
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Accelerator Variants: *temp/kk*
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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
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* temp = style name of this compute command
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all temp
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compute myTemp mobile temp
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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. A compute of this style can be used by any command that
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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>`,
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etc.
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The temperature is calculated by the formula
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.. math::
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T = \frac{2 E_\mathrm{kin}}{N_\mathrm{DOF} k_B} \quad \mathrm{with} \quad
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E_\mathrm{kin} = \sum^{N_\mathrm{atoms}}_{i=1} \frac{1}{2} m_i v^2_i \quad \mathrm{and} \quad
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N_\mathrm{DOF} = n_\mathrm{dim} N_\mathrm{atoms} - n_\mathrm{dim} - N_\mathrm{fix DOFs}
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where :math:`E_\mathrm{kin}` is the total kinetic energy of the group of
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atoms, :math:`n_\mathrm{dim}` is the dimensionality of the simulation
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(i.e. either 2 or 3), :math:`N_\mathrm{atoms}` is the number of atoms in
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the group, :math:`N_\mathrm{fix DOFs}` is the number of degrees of
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freedom removed by fix commands (see below), :math:`k_B` is the
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Boltzmann constant, and :math:`T` is the resulting computed temperature.
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A kinetic energy tensor, stored as a six-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 the
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above expression for :math:`E_\mathrm{kin}`, except that :math:`v_i^2` is
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replaced by :math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on.
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The six components of the vector are ordered :math:`xx`, :math:`yy`,
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:math:`zz`, :math:`xy`, :math:`xz`, :math:`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 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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By default this *extra* component is initialized to
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:math:`n_\mathrm{dim}` (as shown in the formula above) to represent the
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degrees of freedom removed from a system due to its translation
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invariance due to periodic boundary conditions.
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A compute of this style with the ID of "thermo_temp" is created when
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LAMMPS starts up, as if this command were in the input script:
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.. code-block:: LAMMPS
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compute thermo_temp all temp
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See the "thermo_style" command for more details.
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See the :doc:`Howto thermostat <Howto_thermostat>` page for a
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discussion of different ways to compute temperature and perform
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thermostatting.
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----------
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.. include:: accel_styles.rst
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----------
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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 six (KE tensor), which can be accessed by indices
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1--6. These values can be used by any command that uses global scalar
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or vector values from a compute as input. See the :doc:`Howto output
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<Howto_output>` page for an overview of LAMMPS output 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/partial <compute_temp_partial>`,
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:doc:`compute temp/region <compute_temp_region>`,
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:doc:`compute pressure <compute_pressure>`
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Default
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"""""""
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none
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