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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2932 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-06-30 21:13:38 +00:00
parent 48c3b0d03f
commit 87c330d436
2 changed files with 46 additions and 38 deletions
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42
doc/fix_viscous.html
View File

@ -43,12 +43,13 @@ fix 1 damp viscous 0.5 scale 3 2.5
</P>
<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. 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 is a simple energy minimization
technique.
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
@ -56,24 +57,27 @@ optional keyword <I>scale</I> 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>
<P>In a Brownian dynamics context, gamma = kT / mD, where k = Boltzmann's
constant, T = temperature, m = particle mass, and D = particle
diffusion coefficient. D can be written as kT / (6 pi eta d), where
eta = viscosity of the frictional fluid and d = diameter of particle.
This means gamma = 6 pi eta d, and thus is proportional to the
viscosity of the fluid and the particle diameter.
<P>In a Brownian dynamics context, gamma = kT / D, where k = Boltzmann's
constant, T = temperature, and D = particle diffusion coefficient. D
can be written as kT / (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 (in centiPoise or some other units), 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 <I>scale</I>
keyword.
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 <I>scale</I> 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 HREF = "fix_langevin.html">fix
langevin</A> command adds both a viscous damping term
and this random force to each atom; hence if using fix <I>langevin</I> you
do not typically need to use fix <I>viscous</I>.
langevin</A> command does this. It has the same
viscous damping term as fix viscous and adds a random force to each
atom. Hence if using fix <I>langevin</I> you do not typically need to use
fix <I>viscous</I>. Also note that the gamma of fix viscous is related to
the damping parameter of <A HREF = "fix_langevin.html">fix langevin</A>, except that
the units of gamma are force/velocity (or mass/time) and the units of
damp are time, so that it can more easily be used as a thermostat.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>

42
doc/fix_viscous.txt
View File

@ -33,12 +33,13 @@ fix 1 damp viscous 0.5 scale 3 2.5 :pre
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. 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 is a simple energy minimization
technique.
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.
The damping force F is given by F = - gamma * velocity. The larger
the coefficient, the faster the kinetic energy is reduced. If the
@ -46,24 +47,27 @@ optional keyword {scale} 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.
In a Brownian dynamics context, gamma = kT / mD, where k = Boltzmann's
constant, T = temperature, m = particle mass, and D = particle
diffusion coefficient. D can be written as kT / (6 pi eta d), where
eta = viscosity of the frictional fluid and d = diameter of particle.
This means gamma = 6 pi eta d, and thus is proportional to the
viscosity of the fluid and the particle diameter.
In a Brownian dynamics context, gamma = kT / D, where k = Boltzmann's
constant, T = temperature, and D = particle diffusion coefficient. D
can be written as kT / (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.
In the current implementation, rather than have the user specify a
viscosity (in centiPoise or some other units), 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 {scale}
keyword.
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 {scale} keyword.
Note that Brownian dynamics models also typically include a randomized
force term to thermostat the system at a chosen temperature. The "fix
langevin"_fix_langevin.html command adds both a viscous damping term
and this random force to each atom; hence if using fix {langevin} you
do not typically need to use fix {viscous}.
langevin"_fix_langevin.html command does this. It has the same
viscous damping term as fix viscous and adds a random force to each
atom. Hence if using fix {langevin} you do not typically need to use
fix {viscous}. Also note that the gamma of fix viscous is related to
the damping parameter of "fix langevin"_fix_langevin.html, except that
the units of gamma are force/velocity (or mass/time) and the units of
damp are time, so that it can more easily be used as a thermostat.
[Restart, fix_modify, output, run start/stop, minimize info:]