103 lines
3.5 KiB
Plaintext
103 lines
3.5 KiB
Plaintext
"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
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timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen1
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written out for the special case of single-particle constraints as
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explained in "(Paquay)"_#Paquay2. V is volume; E is energy. This way,
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the dynamics of particles constrained to curved surfaces can be
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studied. If combined with "fix langevin"_fix_langevin.html, this
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generates Brownian motion of particles constrained to a curved
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surface. For a list of currently supported manifolds and their
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parameters, see "manifolds"_manifolds.html.
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Note that the particles must initially be close to the manifold in
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question. If not, RATTLE will not be able to iterate until the
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constraint is satisfied, and an error is generated. For simple
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manifolds this can be achieved with {region} and {create_atoms}
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commands, but for more complex surfaces it might be more useful to
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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
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the variable. This is not a problem for the time integrator as long
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as the change of the manifold is slow with respect to the dynamics of
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the particles. Note that if the manifold has to exert work on the
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particles because of these changes, the total energy might not be
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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
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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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
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manifoldforce"_fix_manifoldforce.html
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[Default:] every = 0, tchain = 3
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:line
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:link(Andersen1)
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[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
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:link(Paquay2)
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[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016).
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preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
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