diff --git a/doc/html/_sources/fix_manifoldforce.txt b/doc/html/_sources/fix_manifoldforce.txt new file mode 100644 index 0000000000..75c643e659 --- /dev/null +++ b/doc/html/_sources/fix_manifoldforce.txt @@ -0,0 +1,72 @@ +.. 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 diff --git a/doc/html/_sources/fix_nve_manifold_rattle.txt b/doc/html/_sources/fix_nve_manifold_rattle.txt new file mode 100644 index 0000000000..51e05cf252 --- /dev/null +++ b/doc/html/_sources/fix_nve_manifold_rattle.txt @@ -0,0 +1,124 @@ +.. 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 diff --git a/doc/html/_sources/fix_nvt_manifold_rattle.txt b/doc/html/_sources/fix_nvt_manifold_rattle.txt new file mode 100644 index 0000000000..cbaf93831a --- /dev/null +++ b/doc/html/_sources/fix_nvt_manifold_rattle.txt @@ -0,0 +1,104 @@ +.. 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 diff --git a/doc/html/_sources/manifolds.txt b/doc/html/_sources/manifolds.txt new file mode 100644 index 0000000000..6b2486b8f4 --- /dev/null +++ b/doc/html/_sources/manifolds.txt @@ -0,0 +1,45 @@ +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