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

doc/html/_sources/fix_manifoldforce.txt

+.. index:: fix manifoldforce
+
+fix manifoldforce command
+=========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID manifoldforce manifold manifold-args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* manifold = name of the manifold
+* manifold-args = parameters for the manifold
+
+
+Examples
+""""""""
+
+fix constrain all manifoldforce sphere 5.0
+
+Description
+"""""""""""
+
+This fix subtracts each time step from the force the component along the normal of the specified :doc:`manifold <manifolds>`.
+This can be used in combination with :doc:`minimize <minimize>` to remove overlap between particles while
+keeping them (roughly) constrained to the given manifold, e.g. to set up a run with :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`.
+I have found that only *hftn* and *quickmin* with a very small time step perform adequately though.
+
+
+----------
+
+
+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 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_nve_manifold_rattle>`, :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm

doc/html/_sources/fix_nve_manifold_rattle.txt

+.. 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

doc/html/_sources/fix_nvt_manifold_rattle.txt

+.. 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

doc/html/_sources/manifolds.txt

+Description
+"""""""""""
+
+Below is a list of currently supported manifolds, their parameters and a short description of them.
+The parameters listed here are in the same order as they should be passed to the relevant fixes.
+
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| *manifold*    | *parameters*   | *equation*                                                                                                                 | *description*                                                                                                                      |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| cylinder      | R              | x^2 + y^2 - R^2 = 0                                                                                                        | Cylinder along z-axis, axis going through (0,0,0)                                                                                  |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| cylinder_dent | R l a          | x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise                                       | A cylinder with a dent around z = 0                                                                                                |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| dumbbell      | a A B c        | -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0                                                             | A dumbbell                                                                                                                         |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| ellipsoid     | a  b c         | (x/a)^2 + (y/b)^2 + (z/c)^2 = 0                                                                                            | An ellipsoid                                                                                                                       |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| plane         | a b c x0 y0 z0 | a*(x-x0) + b*(y-y0) + c*(z-z0) = 0                                                                                         | A plane with normal (a,b,c) going through point (x0,y0,z0)                                                                         |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| plane_wiggle  | a w            | z - a*sin(w*x) = 0                                                                                                         | A plane with a sinusoidal modulation on z along x.                                                                                 |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| sphere        | R              | x^2 + y^2 + z^2 - R^2 = 0                                                                                                  | A sphere of radius R                                                                                                               |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| supersphere   | R q            | |x|^q + |y|^q + |z|^q - R^q = 0                                                                                            | A supersphere of hyperradius R                                                                                                     |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| spine         | a, A, B, B2, c | -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | An approximation to a dendtritic spine                                                                                             |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| spine_two     | a, A, B, B2, c | -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendtritic spine                                                                                        |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| thylakoid     | wB LB lB       | Various, see :ref:`(Paquay) <Paquay>`                                                                                      | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+| torus         | R r            | (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2                                                                                     | A torus with large radius R and small radius r, centered on (0,0,0)                                                                |  |
++---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
+
+.. _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