Homec4science
Diffusion lammps (master) Browse

lammps/doc/_sources/fix_nvt_body.txt
9cf43f2a0b7fmaster

Last Change
Raw File

fix_nvt_body.txt
View Options

.. index:: fix nvt/body
fix nvt/body command
====================
Syntax
""""""
.. parsed-literal::
fix ID group-ID nvt/body keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* nvt/body = style name of this fix command
* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
Examples
""""""""
.. parsed-literal::
fix 1 all nvt/body temp 300.0 300.0 100.0
fix 1 all nvt/body temp 300.0 300.0 100.0 drag 0.2
Description
"""""""""""
Perform constant NVT integration to update position, velocity,
orientation, and angular velocity each timestep for body
particles in the group using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
This fix differs from the :doc:`fix nvt <fix_nh>` command, which
assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational
degrees of freedom for the body particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
Additional parameters affecting the thermostat are specified by
keywords and values documented with the :doc:`fix nvt <fix_nh>`
command. See, for example, discussion of the *temp* and *drag*
keywords.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/body", as if this command
had been issued:
.. parsed-literal::
compute fix-ID_temp group-ID temp/body
See the :doc:`compute temp/body <compute_temp_body>` command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
:doc:`compute_modify <compute_modify>` command or print this temperature
during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
----------
Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
fix. You can use it to assign a :doc:`compute <compute>` you have
defined to this fix which will be used in its thermostatting
procedure.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
This fix computes the same global scalar and global vector of
quantities as does the :doc:`fix nvt <fix_nh>` command.
This fix can ramp its target temperature over multiple runs, using the
*start* and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the BODY package. It is only enabled if LAMMPS
was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the :doc:`atom_style body <atom_style>`
command.
Related commands
""""""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix nve_body <fix_nve_body>`, :doc:`fix npt_body <fix_npt_body>`, :doc:`fix_modify <fix_modify>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help