2007-10-17 02:39:08 +08:00
|
|
|
<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
|
|
|
|
|
appopriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
|
|
|
|
|
details.
|
|
|
|
|
</P>
|
2007-10-19 06:02:20 +08:00
|
|
|
<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>
|
2007-10-17 02:39:08 +08:00
|
|
|
<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 simmulation 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 cummulative momentum transferred between the bottom and middle of
|
2007-10-17 03:08:11 +08:00
|
|
|
the simulation box (in the <I>pdim</I> direction) is stored as a scalar
|
2007-10-17 02:39:08 +08:00
|
|
|
quantity by this fix. This quantity is zeroed when the fix is defined
|
|
|
|
|
and accumlates thereafter, once every N steps. The units of the
|
2007-10-17 03:08:11 +08:00
|
|
|
quantity are momentum = mass*velocity. This quantity can be accessed
|
|
|
|
|
by various <A HREF = "Section_howto.html#4_15">output commands</A>, such as
|
2007-10-17 02:39:08 +08:00
|
|
|
<A HREF = "thermo_style.html">thermo_style custom</A>.
|
|
|
|
|
</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>
|
2007-10-17 03:08:11 +08:00
|
|
|
<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>).
|
2007-10-17 02:39:08 +08:00
|
|
|
</P>
|
2007-10-17 02:49:13 +08:00
|
|
|
<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.
|
2007-10-17 02:39:08 +08:00
|
|
|
</P>
|
|
|
|
|
<P>When running a simulation with large, massive particles or molecules
|
|
|
|
|
in a background solvent, you may want to only exchange momenta bewteen
|
|
|
|
|
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>
|
2007-10-17 02:49:13 +08:00
|
|
|
<A NAME = "Maginn"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Maginn)</B> Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
|
|
|
|
|
260, 218-231 (2007).
|
|
|
|
|
</P>
|
2007-10-17 02:39:08 +08:00
|
|
|
</HTML>
|
