194 lines
7.4 KiB
ReStructuredText
194 lines
7.4 KiB
ReStructuredText
.. index:: fix nvt/sllod
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.. index:: fix nvt/sllod/intel
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.. index:: fix nvt/sllod/omp
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.. index:: fix nvt/sllod/kk
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fix nvt/sllod command
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=====================
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Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp*, *nvt/sllod/kk*
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID nvt/sllod keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* nvt/sllod = style name of this fix command
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* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all nvt/sllod temp 300.0 300.0 100.0
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fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2
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Description
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"""""""""""
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Perform constant NVT integration to update positions and velocities
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each timestep for atoms in the group using a Nose/Hoover temperature
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thermostat. V is volume; T is temperature. This creates a system
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trajectory consistent with the canonical ensemble.
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This thermostat is used for a simulation box that is changing size
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and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
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The size/shape change is induced by use of the :doc:`fix deform
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<fix_deform>` command, so each point in the simulation box can be
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thought of as having a "streaming" velocity. This position-dependent
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streaming velocity is subtracted from each atom's actual velocity to
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yield a thermal velocity which is used for temperature computation and
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thermostatting. For example, if the box is being sheared in x,
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relative to y, then points at the bottom of the box (low y) have a
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small x velocity, while points at the top of the box (hi y) have a
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large x velocity. These velocities do not contribute to the thermal
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"temperature" of the atom.
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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. To use
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fix nvt/sllod, fix deform should NOT remap atom positions, because fix
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nvt/sllod adjusts the atom positions and velocities to create a
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velocity profile that matches the changing box size/shape. Fix deform
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SHOULD remap atom velocities when atoms cross periodic boundaries
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since that is consistent with maintaining the velocity profile created
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by fix nvt/sllod. LAMMPS will give an error if this setting is not
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consistent.
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The SLLOD equations of motion, originally proposed by Hoover and Ladd
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(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be
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equivalent to Newton's equations of motion for shear flow by
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:ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
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the desired velocity gradient and the correct production of work by
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stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
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<Daivis>`.
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The LAMMPS implementation corresponds to the p-SLLOD variant
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of SLLOD. :ref:`(Edwards) <Edwards>`.
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The equations of motion are coupled to a
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Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
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following the implementation used for the :doc:`fix nvt <fix_nh>`
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command.
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.. note::
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A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-sllod>`
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discusses use of the SLLOD method and non-equilibrium MD (NEMD)
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thermostatting generally, for both simple and complex fluids,
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e.g. molecular systems. The latter can be tricky to do correctly.
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Additional parameters affecting the thermostat are specified by
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keywords and values documented with the :doc:`fix nvt <fix_nh>`
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command. See, for example, discussion of the *temp* and *drag*
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keywords.
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This fix computes a temperature each timestep. To do this, the fix
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creates its own compute of style "temp/deform", as if this command had
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been issued:
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.. code-block:: LAMMPS
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compute fix-ID_temp group-ID temp/deform
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See the :doc:`compute temp/deform <compute_temp_deform>` command for
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details. Note that the ID of the new compute is the fix-ID +
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underscore + "temp", and the group for the new compute is the same as
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the fix group.
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Note that this is NOT the compute used by thermodynamic output (see
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the :doc:`thermo_style <thermo_style>` command) with ID =
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*thermo_temp*. This means you can change the attributes of this fix's
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temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
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<compute_modify>` command or print this temperature during
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thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
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command using the appropriate compute-ID. It also means that changing
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attributes of *thermo_temp* will have no effect on this fix.
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Like other fixes that perform thermostatting, this fix can be used
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with :doc:`compute commands <compute>` that remove a "bias" from the
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atom velocities. E.g. to apply the thermostat only to atoms within a
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spatial :doc:`region <region>`, or to remove the center-of-mass
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velocity from a group of atoms, or to remove the x-component of
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velocity from the calculation.
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This is not done by default, but only if the :doc:`fix_modify
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<fix_modify>` command is used to assign a temperature compute to this
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fix that includes such a bias term. See the doc pages for individual
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:doc:`compute temp commands <compute>` to determine which ones include
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a bias. In this case, the thermostat works in the following manner:
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bias is removed from each atom, thermostatting is performed on the
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remaining thermal degrees of freedom, and the bias is added back in.
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----------
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.. include:: accel_styles.rst
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the state of the Nose/Hoover thermostat to
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:doc:`binary restart files <restart>`. See the :doc:`read_restart
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<read_restart>` command for info on how to re-specify a fix in an
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input script that reads a restart file, so that the operation of the
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fix continues in an uninterrupted fashion.
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The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
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fix. You can use it to assign a :doc:`compute <compute>` you have
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defined to this fix which will be used in its thermostatting
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procedure.
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The cumulative energy change in the system imposed by this fix is
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included in the :doc:`thermodynamic output <thermo_style>` keywords
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*ecouple* and *econserve*. See the :doc:`thermo_style <thermo_style>`
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doc page for details.
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This fix computes the same global scalar and global vector of
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quantities as does the :doc:`fix nvt <fix_nh>` command.
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This fix can ramp its target temperature over multiple runs, using the
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*start* and *stop* keywords of the :doc:`run <run>` command. See the
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:doc:`run <run>` command for details of how to do this.
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This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix works best without Nose-Hoover chain thermostats, i.e. using
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tchain = 1. Setting tchain to larger values can result in poor
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equilibration.
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Related commands
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""""""""""""""""
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:doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix langevin <fix_langevin>`,
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:doc:`fix_modify <fix_modify>`, :doc:`compute temp/deform <compute_temp_deform>`
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Default
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"""""""
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Same as :doc:`fix nvt <fix_nh>`, except tchain = 1.
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----------
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.. _Evans3:
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**(Evans and Morriss)** Evans and Morriss, Phys Rev A, 30, 1528 (1984).
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.. _Daivis:
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**(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006).
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.. _Edwards:
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**(Edwards)** Edwards, Baig, and Keffer, J Chem Phys 124, 194104 (2006).
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.. _Daivis-sllod:
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**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
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Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
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