forked from lijiext/lammps
176 lines
6.8 KiB
Plaintext
176 lines
6.8 KiB
Plaintext
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.. index:: fix temp/berendsen
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fix temp/berendsen command
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==========================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID temp/berendsen Tstart Tstop Tdamp
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* temp/berendsen = style name of this fix command
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* Tstart,Tstop = desired temperature at start/end of run
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.. parsed-literal::
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Tstart can be a variable (see below)
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* Tdamp = temperature damping parameter (time units)
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Examples
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""""""""
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.. parsed-literal::
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fix 1 all temp/berendsen 300.0 300.0 100.0
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Description
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"""""""""""
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Reset the temperature of a group of atoms by using a Berendsen
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thermostat :ref:`(Berendsen) <Berendsen>`, which rescales their velocities
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every timestep.
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The thermostat is applied to only the translational degrees of freedom
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for the particles, which is an important consideration for finite-size
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particles which have rotational degrees of freedom are being
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thermostatted with this fix. The translational degrees of freedom can
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also have a bias velocity removed from them before thermostatting
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takes place; see the description below.
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The desired temperature at each timestep is a ramped value during the
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run from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in
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time units and determines how rapidly the temperature is relaxed. For
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example, a value of 100.0 means to relax the temperature in a timespan
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of (roughly) 100 time units (tau or fmsec or psec - see the
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:doc:`units <units>` command).
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*Tstart* can be specified as an equal-style :doc:`variable <variable>`.
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In this case, the *Tstop* setting is ignored. If the value is a
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variable, it should be specified as v_name, where name is the variable
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name. In this case, the variable will be evaluated each timestep, and
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its value used to determine the target temperature.
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Equal-style variables can specify formulas with various mathematical
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functions, and include :doc:`thermo_style <thermo_style>` command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent temperature.
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.. note::
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Unlike the :doc:`fix nvt <fix_nh>` command which performs
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Nose/Hoover thermostatting AND time integration, this fix does NOT
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perform time integration. It only modifies velocities to effect
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thermostatting. Thus you must use a separate time integration fix,
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like :doc:`fix nve <fix_nve>` to actually update the positions of atoms
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using the modified velocities. Likewise, this fix should not normally
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be used on atoms that also have their temperature controlled by
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another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` commands.
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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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This fix computes a temperature each timestep. To do this, the fix
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creates its own compute of style "temp", as if this command had been
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issued:
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.. parsed-literal::
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compute fix-ID_temp group-ID temp
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See the :doc:`compute temp <compute_temp>` command for details. Note
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that the ID of the new compute is the fix-ID + underscore + "temp",
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and the group for the new compute is the same as 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 = *thermo_temp*\ .
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This means you can change the attributes of this fix's temperature
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(e.g. its degrees-of-freedom) via the
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:doc:`compute_modify <compute_modify>` command or print this temperature
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during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
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It also means that changing attributes of *thermo_temp* will have no
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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 calculate a temperature
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after removing a "bias" from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
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default, but only if the :doc:`fix_modify <fix_modify>` command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
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this case, the thermostat works in the following manner: the current
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temperature is calculated taking the bias into account, bias is
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removed from each atom, thermostatting is performed on the remaining
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thermal degrees of freedom, and the bias is added back in.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`.
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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 temperature :doc:`compute <compute>`
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you have defined to this fix which will be used in its thermostatting
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procedure, as described above. For consistency, the group used by
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this fix and by the compute should be the same.
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
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fix to add the energy change implied by a velocity rescaling to the
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system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
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This fix computes a global scalar which can be accessed by various
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:ref:`output commands <howto_15>`. The scalar is the
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cummulative energy change due to this fix. The scalar value
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calculated by this fix is "extensive".
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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 can be used with dynamic groups as defined by the
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:doc:`group <group>` command. Likewise it can be used with groups to
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which atoms are added or deleted over time, e.g. a deposition
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simulation. However, the conservation properties of the thermostat
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and barostat are defined for systems with a static set of atoms. You
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may observe odd behavior if the atoms in a group vary dramatically
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over time or the atom count becomes very small.
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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 <compute_temp>`,
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:doc:`fix press/berendsen <fix_press_berendsen>`
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**Default:** none
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----------
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.. _Berendsen:
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**(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
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Phys, 81, 3684 (1984).
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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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