forked from lijiext/lammps
105 lines
3.0 KiB
Plaintext
105 lines
3.0 KiB
Plaintext
.. index:: fix nvt/manifold/rattle
|
|
|
|
fix nvt/manifold/rattle command
|
|
===============================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ...
|
|
|
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
|
* nvt/manifold/rattle = style name of this fix command
|
|
* tol = tolerance to which Newton iteration must converge
|
|
* maxit = maximum number of iterations to perform
|
|
* manifold = name of the manifold
|
|
* manifold-args = parameters for the manifold
|
|
* one or more keyword/value pairs may be appended
|
|
.. parsed-literal::
|
|
|
|
keyword = *temp* or *tchain* or *every*
|
|
*temp* values = Tstart Tstop Tdamp
|
|
Tstart, Tstop = external temperature at start/end of run
|
|
Tdamp = temperature damping parameter (time units)
|
|
*tchain* value = N
|
|
N = length of thermostat chain (1 = single thermostat)
|
|
*every* value = N
|
|
N = print info about iteration every N steps. N = 0 means no output
|
|
|
|
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
This fix combines the RATTLE-based :ref:`(Andersen) <Andersen>` time integrator of :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>` :ref:`(Paquay) <Paquay>` with a Nose-Hoover-chain thermostat to sample the
|
|
canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
|
|
For a list of currently supported manifolds and their parameters, see :doc:`manifolds <manifolds>`
|
|
|
|
|
|
----------
|
|
|
|
|
|
Restart, fix_modify, output, run start/stop, minimize info
|
|
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
|
|
|
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
|
are relevant to this fix. No global or per-atom quantities are stored
|
|
by this fix for access by various :ref:`output commands <howto_15>`. No parameter of this fix can
|
|
be used with the *start/stop* keywords of the :doc:`run <run>` command.
|
|
This fix is not invoked during :doc:`energy minimization <minimize>`.
|
|
|
|
|
|
----------
|
|
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
|
|
This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
|
|
was built with that package. See the :ref:`Making LAMMPS <start_3>`
|
|
section for more info.
|
|
|
|
Only use this with *min_style hftn* or *min_style quickmin*\ . If not, the constraints
|
|
will not be satisfied very well at all. A warning is generated if the *min_style* is
|
|
incompatible but no error.
|
|
|
|
|
|
----------
|
|
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`fix nve/manifold/rattle <fix_nvt_manifold_rattle>`, :doc:`fix manifoldforce <fix_manifoldforce>`
|
|
**Default:** every = 0
|
|
|
|
|
|
----------
|
|
|
|
|
|
.. _Andersen:
|
|
|
|
|
|
|
|
**(Andersen)** Andersen, J. Comp. Phys. 52, 24, (1983).
|
|
|
|
.. _Paquay:
|
|
|
|
|
|
|
|
**(Paquay)** Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
|
|
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|