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rLAMMPS lammps
fix_viscosity.html
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<HTML>
<CENTER><A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
-
<A
HREF =
"Manual.html"
>
LAMMPS Documentation
</A>
-
<A
HREF =
"Section_commands.html#comm"
>
LAMMPS Commands
</A>
</CENTER>
<HR>
<H3>
fix viscosity command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
fix ID group-ID viscosity N vdim pdim Nbin
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"fix.html"
>
fix
</A>
command
<LI>
viscosity = style name of this fix command
<LI>
N = perform momentum exchange every N steps
<LI>
vdim =
<I>
x
</I>
or
<I>
y
</I>
or
<I>
z
</I>
= which momentum component to exchange
<LI>
pdim =
<I>
x
</I>
or
<I>
y
</I>
or
<I>
z
</I>
= direction of momentum transfer
<LI>
Nbin = # of layers in pdim direction
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
fix 1 all viscosity 100 x z 20
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Use the Muller-Plathe algorithm described in
<A
HREF =
"#Muller-Plathe"
>
this
paper
</A>
to exchange momenta between two particles in
different regions of the simulation box every N steps. This induces a
shear velocity profile in the system. As described below this enables
a viscosity of the fluid to be calculated. This algorithm is
sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
to computing viscosity. This is because the usual NEMD approach is to
impose a shear velocity profile on the system and measure the response
via an off-diagonal component of the stress tensor, which is
proportional to the momentum flux. In the Muller-Plathe method, the
momentum flux is imposed, and the shear velocity profile is the
system's response.
</P>
<P>
The simulation box is divided into
<I>
Nbin
</I>
layers in the
<I>
pdim
</I>
direction. Every N steps, two atoms are chosen in the following
manner. Only atoms in the fix group are considered. The atom in the
bottom layer with the most positive momentum component in the
<I>
vdim
</I>
direction is the first atom. The atom in the middle later with the
most negative momentum component in the
<I>
vdim
</I>
direction is the second
atom. The
<I>
vdim
</I>
momenta components of these two atoms are swapped,
which resets their velocities, typically in opposite directions. Over
time, this induces a shear velocity profile in the system which can be
measured using commands such as the following, which writes the
profile to the file tmp.profile:
</P>
<PRE>
compute c1 all attribute/atom vx
fix f1 all ave/spatial 100 10 1000 z lower 0.05 tmp.profile
&
compute c1 units reduced
</PRE>
<P>
As described below, the total momentum transferred by these velocity
swaps is computed by the fix and can be output. Dividing this
quantity by time and the cross-sectional area of the simulation box
yields a momentum flux. The ratio of momentum flux to the slope of
the shear velocity profile is the viscosity of the fluid, in
appropriate units. See the
<A
HREF =
"#Muller-Plathe"
>
Muller-Plathe paper
</A>
for
details.
</P>
<P>
IMPORTANT NOTE: After equilibration, if the velocity profile you
observe is not linear, then you are likely swapping momentum too
frequently and are not in a regime of linear response. In this case
you cannot accurately infer a viscosity and should try increasing
the Nevery parameter.
</P>
<P>
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in
<A
HREF =
"Section_howto.html#4_13"
>
this section
</A>
of
the manual. NEMD simulations deform the simulation box via the
<A
HREF =
"fix_deform.html"
>
fix
deform
</A>
command. Thus they cannot be run on a charged
system using a
<A
HREF =
"kspace_style.html"
>
PPPM solver
</A>
since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the
box orthogonal; thus it does not suffer from this limitation.
</P>
<P><B>
Restart, fix_modify, output, run start/stop, minimize info:
</B>
</P>
<P>
No information about this fix is written to
<A
HREF =
"restart.html"
>
binary restart
files
</A>
. None of the
<A
HREF =
"fix_modify.html"
>
fix_modify
</A>
options
are relevant to this fix.
</P>
<P>
The cumulative momentum transferred between the bottom and middle of
the simulation box (in the
<I>
pdim
</I>
direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
and accumulates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. This quantity can be accessed
by various
<A
HREF =
"Section_howto.html#4_15"
>
output commands
</A>
, such as
<A
HREF =
"thermo_style.html"
>
thermo_style custom
</A>
. The scalar value calculated
by this fix is "intensive", meaning it is independent of the number of
atoms in the simulation.
</P>
<P>
No parameter of this fix can be used with the
<I>
start/stop
</I>
keywords of
the
<A
HREF =
"run.html"
>
run
</A>
command. This fix is not invoked during
<A
HREF =
"minimize.html"
>
energy
minimization
</A>
.
</P>
<P><B>
Restrictions:
</B>
</P>
<P>
If the masses of all exchange partners are the same, then swaps
conserve both momentum and kinetic energy. Thus you should not need
to thermostat the system. If you do use a thermostat, you may want to
apply it only to the non-swapped dimensions (other than
<I>
vdim
</I>
).
</P>
<P>
LAMMPS does not check, but you should not use this fix to swap
velocities of atoms that are in constrained molecules, e.g. via
<A
HREF =
"fix_shake.html"
>
fix
shake
</A>
or
<A
HREF =
"fix_rigid.html"
>
fix rigid
</A>
. This is because
application of the constraints will alter the amount of transferred
momentum. You should, however, be able to use flexible molecules.
See the
<A
HREF =
"#Maginn"
>
Maginn paper
</A>
for an example of using this algorithm
in a computation of alcohol molecule properties.
</P>
<P>
When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta between
solvent particles.
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"fix_ave_spatial.html"
>
fix ave/spatial
</A>
,
<A
HREF =
"fix_nvt_sllod.html"
>
fix
nvt/sllod
</A>
</P>
<P><B>
Default:
</B>
none
</P>
<HR>
<A
NAME =
"Muller-Plathe"
></A>
<P><B>
(Muller-Plathe)
</B>
Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
</P>
<A
NAME =
"Maginn"
></A>
<P><B>
(Maginn)
</B>
Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
260, 218-231 (2007).
</P>
</HTML>
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