git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14995 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/_sources/fix_nve_manifold_rattle.txt

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+.. index:: fix nve/manifold/rattle
+
+fix nve/manifold/rattle command
+===============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/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 = *every*
+     *every* values = N
+       N = print info about iteration every N steps. N = 0 means no output
+
+
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   fix 1 all nve/manifold/rattle 1e-4 10 sphere 5.0 
+   fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position and velocity for
+atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
+is handled by RATTLE :ref:`(Andersen) <Andersen>` written out for the special case of
+single-particle constraints as explained in :ref:`(Paquay) <Paquay>`.
+V is volume; E is energy. This way, the dynamics of particles constrained to
+curved surfaces can be studied. If combined with :doc:`fix langevin <fix_langevin>`, this generates
+Brownian motion of particles constrained to a curved surface. For a list of currently supported
+manifolds and their parameters, see :doc:`manifolds <manifolds>`.
+
+Note that the particles must initially be close to the manifold in question. If not, RATTLE will
+not be able to iterate until the constraint is satisfied, and an error is generated. For simple
+manifolds this can be achieved with *region* and *create_atoms* commands, but for more complex
+surfaces it might be more useful to write a script.
+
+The manifold args may be equal-style variables, like so:
+
+.. parsed-literal::
+
+   variable R equal "ramp(5.0,3.0)"
+   fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
+
+In this case, the manifold parameter will change in time according to the variable.
+This is not a problem for the time integrator as long as the change of the manifold is slow with respect to the dynamics of the particles.
+Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved.
+
+
+----------
+
+
+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 nvt/manifold/rattle <fix_nvt_manifold_rattle>`, :doc:`fix manifoldforce <fix_manifoldforce>`
+
+**Default:** every = 0, tchain = 3
+
+
+----------
+
+
+.. _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