git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14997 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
61
doc/src/fix_manifoldforce.txt
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61
doc/src/fix_manifoldforce.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix manifoldforce command :h3
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[Syntax:]
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fix ID group-ID manifoldforce manifold manifold-args ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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manifold = name of the manifold :l
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manifold-args = parameters for the manifold :l
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:ule
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[Examples:]
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fix constrain all manifoldforce sphere 5.0
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[Description:]
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This fix subtracts each time step from the force the component along the normal of the specified "manifold"_manifolds.html.
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This can be used in combination with "minimize"_minimize.html to remove overlap between particles while
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keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html.
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I have found that only {hftn} and {quickmin} with a very small time step perform adequately though.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various "output
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commands"_Section_howto.html#howto_15. No parameter of this fix can
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be used with the {start/stop} keywords of the "run"_run.html command.
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This fix is invoked during "energy minimization"_minimize.html.
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:line
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[Restrictions:]
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This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
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was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
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will not be satisfied very well at all. A warning is generated if the {min_style} is
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incompatible but no error.
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:line
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[Related commands:]
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"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
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100
doc/src/fix_nve_manifold_rattle.txt
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100
doc/src/fix_nve_manifold_rattle.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix nve/manifold/rattle command :h3
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[Syntax:]
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fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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nve/manifold/rattle = style name of this fix command :l
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tol = tolerance to which Newton iteration must converge :l
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maxit = maximum number of iterations to perform :l
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manifold = name of the manifold :l
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manifold-args = parameters for the manifold :l
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one or more keyword/value pairs may be appended :l
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keyword = {every}
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{every} values = N
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N = print info about iteration every N steps. N = 0 means no output :pre
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:ule
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[Examples:]
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fix 1 all nve/manifold/rattle 1e-4 10 sphere 5.0
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fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25 :pre
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[Description:]
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Perform constant NVE integration to update position and velocity for
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atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
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is handled by RATTLE "(Andersen)"_#Andersen written out for the special case of
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single-particle constraints as explained in "(Paquay)"_#Paquay.
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V is volume; E is energy. This way, the dynamics of particles constrained to
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curved surfaces can be studied. If combined with "fix langevin"_fix_langevin.html, this generates
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Brownian motion of particles constrained to a curved surface. For a list of currently supported
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manifolds and their parameters, see "manifolds"_manifolds.html.
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Note that the particles must initially be close to the manifold in question. If not, RATTLE will
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not be able to iterate until the constraint is satisfied, and an error is generated. For simple
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manifolds this can be achieved with {region} and {create_atoms} commands, but for more complex
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surfaces it might be more useful to write a script.
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The manifold args may be equal-style variables, like so:
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variable R equal "ramp(5.0,3.0)"
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fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R :pre
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In this case, the manifold parameter will change in time according to the variable.
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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.
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Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various "output
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commands"_Section_howto.html#howto_15. No parameter of this fix can
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be used with the {start/stop} keywords of the "run"_run.html command.
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This fix is not invoked during "energy minimization"_minimize.html.
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:line
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[Restrictions:]
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This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
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was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
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will not be satisfied very well at all. A warning is generated if the {min_style} is
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incompatible but no error.
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:line
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[Related commands:]
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"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
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[Default:] every = 0, tchain = 3
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:line
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:link(Andersen)
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[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
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:link(Paquay)
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[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
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preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
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85
doc/src/fix_nvt_manifold_rattle.txt
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85
doc/src/fix_nvt_manifold_rattle.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix nvt/manifold/rattle command :h3
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[Syntax:]
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fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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nvt/manifold/rattle = style name of this fix command :l
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tol = tolerance to which Newton iteration must converge :l
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maxit = maximum number of iterations to perform :l
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manifold = name of the manifold :l
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manifold-args = parameters for the manifold :l
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one or more keyword/value pairs may be appended :l
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keyword = {temp} or {tchain} or {every}
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{temp} values = Tstart Tstop Tdamp
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Tstart, Tstop = external temperature at start/end of run
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Tdamp = temperature damping parameter (time units)
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{tchain} value = N
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N = length of thermostat chain (1 = single thermostat)
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{every} value = N
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N = print info about iteration every N steps. N = 0 means no output :pre
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:ule
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[Examples:]
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fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
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[Description:]
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This fix combines the RATTLE-based "(Andersen)"_#Andersen time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay with a Nose-Hoover-chain thermostat to sample the
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canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
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For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various "output
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commands"_Section_howto.html#howto_15. No parameter of this fix can
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be used with the {start/stop} keywords of the "run"_run.html command.
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This fix is not invoked during "energy minimization"_minimize.html.
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:line
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[Restrictions:]
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This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
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was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
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will not be satisfied very well at all. A warning is generated if the {min_style} is
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incompatible but no error.
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:line
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[Related commands:]
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"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
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[Default:] every = 0
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:line
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:link(Andersen)
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[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
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:link(Paquay)
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[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
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preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
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31
doc/src/manifolds.txt
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31
doc/src/manifolds.txt
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@ -0,0 +1,31 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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[Description:]
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Below is a list of currently supported manifolds, their parameters and a short description of them.
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The parameters listed here are in the same order as they should be passed to the relevant fixes.
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{manifold} || {parameters} || {equation} || {description}
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cylinder || R || x^2 + y^2 - R^2 = 0 || Cylinder along z-axis, axis going through (0,0,0)
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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
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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 ||
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ellipsoid || a b c || (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 || An ellipsoid
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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)
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plane_wiggle || a w || z - a*sin(w*x) = 0 || A plane with a sinusoidal modulation on z along x.
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sphere || R || x^2 + y^2 + z^2 - R^2 = 0 || A sphere of radius R
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supersphere || R q || |x|^q + |y|^q + |z|^q - R^q = 0 || A supersphere of hyperradius R
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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
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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
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thylakoid || wB LB lB || Various, see "(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
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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) :tb(s=||)
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:link(Paquay)
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[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
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preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
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