diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html index dbcf0a248..3f7633ded 100644 --- a/doc/html/fix_nve_manifold_rattle.html +++ b/doc/html/fix_nve_manifold_rattle.html @@ -1,272 +1,269 @@ fix nve/manifold/rattle command — LAMMPS documentation

fix nve/manifold/rattle command

Syntax

fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ...
  • ID, group-ID are documented in 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
 keyword = every
   every values = N
     N = print info about iteration every N steps. N = 0 means no output

Examples

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 (Andersen) written out for the special case of -single-particle constraints as explained in (Paquay). +single-particle constraints as explained in (Paquay). V is volume; E is energy. This way, the dynamics of particles constrained to curved surfaces can be studied. If combined with fix langevin, this generates Brownian motion of particles constrained to a curved surface. For a list of currently supported manifolds and their parameters, see 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:

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 binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS 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.

\ No newline at end of file diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html index 98dd61224..35e6ea613 100644 --- a/doc/html/fix_nvt_manifold_rattle.html +++ b/doc/html/fix_nvt_manifold_rattle.html @@ -1,257 +1,254 @@ fix nvt/manifold/rattle command — LAMMPS documentation

fix nvt/manifold/rattle command

Syntax

fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ...
  • ID, group-ID are documented in 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
 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 (Andersen) time integrator of fix nve/manifold/rattle (Paquay) with a Nose-Hoover-chain thermostat to sample the +

This fix combines the RATTLE-based (Andersen) time integrator of fix nve/manifold/rattle (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 manifolds

Restart, fix_modify, output, run start/stop, minimize info

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS 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.

\ No newline at end of file diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt index 8d0eb8e57..a35c234e6 100644 --- a/doc/src/fix_nve_manifold_rattle.txt +++ b/doc/src/fix_nve_manifold_rattle.txt @@ -1,100 +1,96 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line fix nve/manifold/rattle command :h3 [Syntax:] fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l nve/manifold/rattle = style name of this fix command :l tol = tolerance to which Newton iteration must converge :l maxit = maximum number of iterations to perform :l manifold = name of the manifold :l manifold-args = parameters for the manifold :l one or more keyword/value pairs may be appended :l keyword = {every} {every} values = N N = print info about iteration every N steps. N = 0 means no output :pre :ule [Examples:] 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 :pre [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 "(Andersen)"_#Andersen written out for the special case of single-particle constraints as explained in "(Paquay)"_#Paquay. V is volume; E is energy. This way, the dynamics of particles constrained to curved surfaces can be studied. If combined with "fix langevin"_fix_langevin.html, this generates Brownian motion of particles constrained to a curved surface. For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html. 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: variable R equal "ramp(5.0,3.0)" fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R :pre 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. :line [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. :line [Restrictions:] This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#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. - :line [Related commands:] "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html [Default:] every = 0, tchain = 3 :line :link(Andersen) [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). :link(Paquay) -[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published, +[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt index f117d10eb..42a06d4ed 100644 --- a/doc/src/fix_nvt_manifold_rattle.txt +++ b/doc/src/fix_nvt_manifold_rattle.txt @@ -1,85 +1,81 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line fix nvt/manifold/rattle command :h3 [Syntax:] fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l nvt/manifold/rattle = style name of this fix command :l tol = tolerance to which Newton iteration must converge :l maxit = maximum number of iterations to perform :l manifold = name of the manifold :l manifold-args = parameters for the manifold :l one or more keyword/value pairs may be appended :l 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 :pre :ule [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 "(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 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 "manifolds"_manifolds.html :line [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. :line [Restrictions:] This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#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. - :line [Related commands:] "fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html [Default:] every = 0 :line :link(Andersen) [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). :link(Paquay) -[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published, +[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.