2016-05-10 01:33:12 +08:00
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
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< li > fix viscous command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< div class = "section" id = "fix-viscous-command" >
< span id = "index-0" > < / span > < h1 > fix viscous command< / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > fix< / span > < span class = "n" > ID< / span > < span class = "n" > group< / span > < span class = "o" > -< / span > < span class = "n" > ID< / span > < span class = "n" > viscous< / span > < span class = "n" > gamma< / span > < span class = "n" > keyword< / span > < span class = "n" > values< / span > < span class = "o" > ...< / span >
< / pre > < / div >
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< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < span class = "doc" > fix< / span > < / a > command< / li >
< li > viscous = style name of this fix command< / li >
< li > gamma = damping coefficient (force/velocity units)< / li >
< li > zero or more keyword/value pairs may be appended< / li >
< / ul >
< pre class = "literal-block" >
keyword = < em > scale< / em >
< em > scale< / em > values = type ratio
type = atom type (1-N)
ratio = factor to scale the damping coefficient by
< / pre >
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< div class = "section" id = "examples" >
< h2 > Examples< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > fix< / span > < span class = "mi" > 1< / span > < span class = "n" > flow< / span > < span class = "n" > viscous< / span > < span class = "mf" > 0.1< / span >
< span class = "n" > fix< / span > < span class = "mi" > 1< / span > < span class = "n" > damp< / span > < span class = "n" > viscous< / span > < span class = "mf" > 0.5< / span > < span class = "n" > scale< / span > < span class = "mi" > 3< / span > < span class = "mf" > 2.5< / span >
< / pre > < / div >
< / div >
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< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > Add a viscous damping force to atoms in the group that is proportional
to the velocity of the atom. The added force can be thought of as a
frictional interaction with implicit solvent, i.e. the no-slip Stokes
drag on a spherical particle. In granular simulations this can be
useful for draining the kinetic energy from the system in a controlled
fashion. If used without additional thermostatting (to add kinetic
energy to the system), it has the effect of slowly (or rapidly)
freezing the system; hence it can also be used as a simple energy
minimization technique.< / p >
< p > The damping force F is given by F = - gamma * velocity. The larger
the coefficient, the faster the kinetic energy is reduced. If the
optional keyword < em > scale< / em > is used, gamma can scaled up or down by the
specified factor for atoms of that type. It can be used multiple
times to adjust gamma for several atom types.< / p >
< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > You should specify gamma in force/velocity units. This is not
the same as mass/time units, at least for some of the LAMMPS
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< a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > options like “ real” or “ metal” that are not
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self-consistent.< / p >
< / div >
< p > In a Brownian dynamics context, gamma = Kb T / D, where Kb =
Boltzmann’ s constant, T = temperature, and D = particle diffusion
coefficient. D can be written as Kb T / (3 pi eta d), where eta =
dynamic viscosity of the frictional fluid and d = diameter of
particle. This means gamma = 3 pi eta d, and thus is proportional to
the viscosity of the fluid and the particle diameter.< / p >
< p > In the current implementation, rather than have the user specify a
viscosity, gamma is specified directly in force/velocity units. If
needed, gamma can be adjusted for atoms of different sizes
(i.e. sigma) by using the < em > scale< / em > keyword.< / p >
< p > Note that Brownian dynamics models also typically include a randomized
force term to thermostat the system at a chosen temperature. The < a class = "reference internal" href = "fix_langevin.html" > < span class = "doc" > fix langevin< / span > < / a > command does this. It has the same
viscous damping term as fix viscous and adds a random force to each
atom. The random force term is proportional to the sqrt of the chosen
thermostatting temperature. Thus if you use fix langevin with a
target T = 0, its random force term is zero, and you are essentially
performing the same operation as fix viscous. Also note that the
gamma of fix viscous is related to the damping parameter of < a class = "reference internal" href = "fix_langevin.html" > < span class = "doc" > fix langevin< / span > < / a > , however the former is specified in units
of force/velocity and the latter in units of time, so that it can more
easily be used as a thermostat.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restart-fix-modify-output-run-start-stop-minimize-info" >
< h2 > Restart, fix_modify, output, run start/stop, minimize info< / h2 >
< p > No information about this fix is written to < a class = "reference internal" href = "restart.html" > < span class = "doc" > binary restart files< / span > < / a > . None of the < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various < a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > output commands< / span > < / a > . No parameter of this fix can
be used with the < em > start/stop< / em > keywords of the < a class = "reference internal" href = "run.html" > < span class = "doc" > run< / span > < / a > command.< / p >
2016-06-18 07:24:05 +08:00
< p > The < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > < em > respa< / em > option is supported by this
fix. This allows to set at which level of the < a class = "reference internal" href = "run_style.html" > < span class = "doc" > r-RESPA< / span > < / a >
integrator the fix is modifying forces. Default is the outermost level.< / p >
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< p > The forces due to this fix are imposed during an energy minimization,
invoked by the < a class = "reference internal" href = "minimize.html" > < span class = "doc" > minimize< / span > < / a > command. This fix should only
be used with damped dynamics minimizers that allow for
non-conservative forces. See the < a class = "reference internal" href = "min_style.html" > < span class = "doc" > min_style< / span > < / a > command
for details.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< / h2 >
< p > < a class = "reference internal" href = "fix_langevin.html" > < span class = "doc" > fix langevin< / span > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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