135 lines
5.0 KiB
ReStructuredText
135 lines
5.0 KiB
ReStructuredText
.. index:: fix nvt/body
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fix nvt/body command
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====================
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID nvt/body keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* nvt/body = 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/body temp 300.0 300.0 100.0
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fix 1 all nvt/body 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 position, velocity,
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orientation, and angular velocity each timestep for body
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particles 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 fix differs from the :doc:`fix nvt <fix_nh>` command, which
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assumes point particles and only updates their position and velocity.
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The thermostat is applied to both the translational and rotational
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degrees of freedom for the body particles, assuming a compute is
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used which calculates a temperature that includes the rotational
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degrees of freedom (see below). The translational degrees of freedom
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can also have a bias velocity removed from them before thermostatting
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takes place; see the description below.
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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/body", as if this command
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had been issued:
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.. code-block:: LAMMPS
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compute fix-ID_temp group-ID temp/body
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See the :doc:`compute temp/body <compute_temp_body>` 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 = *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 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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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 is part of the BODY package. It is only enabled if LAMMPS
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was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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This fix requires that atoms store torque and angular momentum and a
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quaternion as defined by the :doc:`atom_style body <atom_style>`
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command.
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Related commands
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""""""""""""""""
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:doc:`fix nvt <fix_nh>`, :doc:`fix nve_body <fix_nve_body>`, :doc:`fix npt_body <fix_npt_body>`, :doc:`fix_modify <fix_modify>`
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Default
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"""""""
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none
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