108 lines
4.9 KiB
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108 lines
4.9 KiB
ReStructuredText
Thermostats
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===========
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Thermostatting means controlling the temperature of particles in an MD
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simulation. :doc:`Barostatting <Howto_barostat>` means controlling the
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pressure. Since the pressure includes a kinetic component due to
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particle velocities, both these operations require calculation of the
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temperature. Typically a target temperature (T) and/or pressure (P)
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is specified by the user, and the thermostat or barostat attempts to
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equilibrate the system to the requested T and/or P.
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Thermostatting in LAMMPS is performed by :doc:`fixes <fix>`, or in one
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case by a pair style. Several thermostatting fixes are available:
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Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
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(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
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can be invoked via the *dpd/tstat* pair style:
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* :doc:`fix nvt <fix_nh>`
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* :doc:`fix nvt/sphere <fix_nvt_sphere>`
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* :doc:`fix nvt/asphere <fix_nvt_asphere>`
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* :doc:`fix nvt/sllod <fix_nvt_sllod>`
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* :doc:`fix temp/berendsen <fix_temp_berendsen>`
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* :doc:`fix temp/csvr <fix_temp_csvr>`
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* :doc:`fix langevin <fix_langevin>`
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* :doc:`fix temp/rescale <fix_temp_rescale>`
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* :doc:`pair_style dpd/tstat <pair_dpd>`
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:doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
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particles. :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
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that it subtracts out a velocity bias due to a deforming box and
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integrates the SLLOD equations of motion. See the :doc:`Howto nemd <Howto_nemd>` doc page for further details. :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
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velocities but also rotational velocities for spherical and aspherical
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particles.
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.. note::
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A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-thermostat>`
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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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DPD thermostatting alters pairwise interactions in a manner analogous
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to the per-particle thermostatting of :doc:`fix langevin <fix_langevin>`.
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Any of the thermostatting fixes can be instructed to use custom temperature
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computes that remove bias which has two effects: first, the current
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calculated temperature, which is compared to the requested target temperature,
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is calculated with the velocity bias removed; second, the thermostat adjusts
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only the thermal temperature component of the particle's velocities, which are
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the velocities with the bias removed. The removed bias is then added back
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to the adjusted velocities. See the doc pages for the individual
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fixes and for the :doc:`fix_modify <fix_modify>` command for
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instructions on how to assign a temperature compute to a
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thermostatting fix. For example, you can apply a thermostat to only
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the x and z components of velocity by using it in conjunction with
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:doc:`compute temp/partial <compute_temp_partial>`. Of you could
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thermostat only the thermal temperature of a streaming flow of
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particles without affecting the streaming velocity, by using
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:doc:`compute temp/profile <compute_temp_profile>`.
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Below is a list of some custom temperature computes that can be used like that:
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* :doc:`compute_temp_asphere`
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* :doc:`compute_temp_body`
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* :doc:`compute_temp_chunk`
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* :doc:`compute_temp_com`
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* :doc:`compute_temp_deform`
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* :doc:`compute_temp_partial`
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* :doc:`compute_temp_profile`
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* :doc:`compute_temp_ramp`
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* :doc:`compute_temp_region`
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* :doc:`compute_temp_rotate`
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* :doc:`compute_temp_sphere`
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.. note::
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Only the nvt fixes perform time integration, meaning they update
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the velocities and positions of particles due to forces and velocities
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respectively. The other thermostat fixes only adjust velocities; they
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do NOT perform time integration updates. Thus they should be used in
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conjunction with a constant NVE integration fix such as these:
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* :doc:`fix nve <fix_nve>`
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* :doc:`fix nve/sphere <fix_nve_sphere>`
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* :doc:`fix nve/asphere <fix_nve_asphere>`
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Thermodynamic output, which can be setup via the
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:doc:`thermo_style <thermo_style>` command, often includes temperature
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values. As explained on the doc page for the
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:doc:`thermo_style <thermo_style>` command, the default temperature is
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setup by the thermo command itself. It is NOT the temperature
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associated with any thermostatting fix you have defined or with any
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compute you have defined that calculates a temperature. The doc pages
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for the thermostatting fixes explain the ID of the temperature compute
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they create. Thus if you want to view these temperatures, you need to
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specify them explicitly via the :doc:`thermo_style custom <thermo_style>` command. Or you can use the
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:doc:`thermo_modify <thermo_modify>` command to re-define what
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temperature compute is used for default thermodynamic output.
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----------
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.. _Daivis-thermostat:
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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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