2007-10-17 02:39:08 +08:00
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<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>
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<HR>
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<H3>fix viscosity command
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</H3>
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<P><B>Syntax:</B>
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</P>
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2008-03-28 23:45:51 +08:00
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<PRE>fix ID group-ID viscosity N vdim pdim Nbin keyword value ...
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2007-10-17 02:39:08 +08:00
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</PRE>
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2008-03-28 23:45:51 +08:00
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>viscosity = style name of this fix command
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<LI>N = perform momentum exchange every N steps
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<LI>vdim = <I>x</I> or <I>y</I> or <I>z</I> = which momentum component to exchange
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<LI>pdim = <I>x</I> or <I>y</I> or <I>z</I> = direction of momentum transfer
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2008-06-25 07:22:45 +08:00
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<LI>Nbin = # of layers in pdim direction (must be even number)
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2008-03-28 23:45:51 +08:00
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>swap</I> or <I>target</I>
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<PRE> <I>swap</I> value = Nswap = number of swaps to perform every N steps
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<I>vtarget</I> value = V or INF = target velocity of swap partners (velocity units)
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</PRE>
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2007-10-17 02:39:08 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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2008-03-28 23:45:51 +08:00
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<PRE>fix 1 all viscosity 100 x z 20
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fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5
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2007-10-17 02:39:08 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Use the Muller-Plathe algorithm described in <A HREF = "#Muller-Plathe">this
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paper</A> to exchange momenta between two particles in
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different regions of the simulation box every N steps. This induces a
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shear velocity profile in the system. As described below this enables
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a viscosity of the fluid to be calculated. This algorithm is
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sometimes called a reverse non-equilibrium MD (reverse NEMD) approach
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to computing viscosity. This is because the usual NEMD approach is to
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impose a shear velocity profile on the system and measure the response
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via an off-diagonal component of the stress tensor, which is
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proportional to the momentum flux. In the Muller-Plathe method, the
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momentum flux is imposed, and the shear velocity profile is the
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system's response.
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</P>
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<P>The simulation box is divided into <I>Nbin</I> layers in the <I>pdim</I>
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2008-06-25 07:22:45 +08:00
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direction, where the layer 1 is at the low end of that dimension and
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the layer <I>Nbin</I> is at the high end. Every N steps, Nswap pairs of
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atoms are chosen in the following manner. Only atoms in the fix group
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are considered. Nswap atoms in layer 1 with positive velocity
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components in the <I>vdim</I> direction closest to the target value <I>V</I> are
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selected. Similarly, Nswap atoms in the "middle" layer (see below) with
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negative velocity components in the <I>vdim</I> direction closest to the
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negative of the target value <I>V</I> are selected. The two sets of Nswap
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atoms are paired up and their <I>vdim</I> momenta components are swapped
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within each pair. This resets their velocities, typically in opposite
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directions. Over time, this induces a shear velocity profile in the
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system which can be measured using commands such as the following,
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which writes the profile to the file tmp.profile:
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2007-10-17 02:39:08 +08:00
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</P>
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2008-05-15 05:40:02 +08:00
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<PRE>fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
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file tmp.profile units reduced
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2007-10-17 02:39:08 +08:00
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</PRE>
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2008-03-28 23:45:51 +08:00
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<P>Note that by default, Nswap = 1 and vtarget = INF, though this can be
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changed by the optional <I>swap</I> and <I>vtarget</I> keywords. When vtarget =
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INF, one or more atoms with the most positive and negative velocity
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components are selected. Setting these parameters appropriately, in
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conjunction with the swap rate N, allows the momentum flux rate to be
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adjusted across a wide range of values, and the momenta to be
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exchanged in large chunks or more smoothly.
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</P>
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2008-06-25 07:22:45 +08:00
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<P>The "middle" layer for momenta swapping is defined as the <I>Nbin</I>/2 + 1
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layer. Thus if <I>Nbin</I> = 20, the two swapping layers are 1 and 11.
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This should lead to a symmetric velocity profile since the two layers
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are separated by the same distance in both directions in a periodic
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sense. This is why <I>Nbin</I> is restricted to being an even number.
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</P>
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2007-10-17 02:39:08 +08:00
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<P>As described below, the total momentum transferred by these velocity
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swaps is computed by the fix and can be output. Dividing this
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quantity by time and the cross-sectional area of the simulation box
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yields a momentum flux. The ratio of momentum flux to the slope of
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2012-11-15 00:08:42 +08:00
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the shear velocity profile is proportional to the viscosity of the
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fluid, in appropriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe
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paper</A> for details.
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</P>
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<P>IMPORTANT NOTE: If your system is periodic in the direction of the
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momentum flux, then the flux is going in 2 directions. This means the
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effective momentum flux in one direction is reduced by a factor of 2.
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You will see this in the equations for viscosity in the Muller-Plathe
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paper. LAMMPS is simply tallying momentum which does not account for
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whether or not your system is periodic; you must use the value
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appropriately to yield a viscosity for your system.
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2007-10-17 02:39:08 +08:00
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</P>
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2007-10-19 06:02:20 +08:00
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<P>IMPORTANT NOTE: After equilibration, if the velocity profile you
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observe is not linear, then you are likely swapping momentum too
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frequently and are not in a regime of linear response. In this case
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you cannot accurately infer a viscosity and should try increasing
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the Nevery parameter.
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</P>
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2007-10-17 02:39:08 +08:00
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<P>An alternative method for calculating a viscosity is to run a NEMD
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2011-12-14 04:43:36 +08:00
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simulation, as described in <A HREF = "Section_howto.html#howto_13">Section_howto
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13</A> of the manual. NEMD simulations
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deform the simmulation box via the <A HREF = "fix_deform.html">fix deform</A>
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command. Thus they cannot be run on a charged system using a <A HREF = "kspace_style.html">PPPM
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solver</A> since PPPM does not currently support
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non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
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thus it does not suffer from this limitation.
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2007-10-17 02:39:08 +08:00
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix.
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</P>
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2010-04-03 00:51:06 +08:00
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<P>This fix computes a global scalar which can be accessed by various
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2011-08-26 01:01:01 +08:00
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<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
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2010-04-03 00:51:06 +08:00
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cummulative momentum transferred between the bottom and middle of the
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simulation box (in the <I>pdim</I> direction) is stored as a scalar
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2007-10-17 02:39:08 +08:00
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quantity by this fix. This quantity is zeroed when the fix is defined
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2008-03-28 23:45:51 +08:00
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and accumlates thereafter, once every N steps. The units of the
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2010-04-03 00:51:06 +08:00
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quantity are momentum = mass*velocity. The scalar value calculated by
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this fix is "intensive".
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2007-10-17 02:39:08 +08:00
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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2013-07-26 06:38:11 +08:00
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<P>This fix is part of the MISC package. It is only enabled if LAMMPS
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was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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2010-07-16 08:14:20 +08:00
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<P>Swaps conserve both momentum and kinetic energy, even if the masses of
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the swapped atoms are not equal. Thus you should not need to
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thermostat the system. If you do use a thermostat, you may want to
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2007-10-17 03:08:11 +08:00
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apply it only to the non-swapped dimensions (other than <I>vdim</I>).
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2007-10-17 02:39:08 +08:00
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</P>
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2007-10-17 02:49:13 +08:00
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<P>LAMMPS does not check, but you should not use this fix to swap
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velocities of atoms that are in constrained molecules, e.g. via <A HREF = "fix_shake.html">fix
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shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is because
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application of the constraints will alter the amount of transferred
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momentum. You should, however, be able to use flexible molecules.
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See the <A HREF = "#Maginn">Maginn paper</A> for an example of using this algorithm
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in a computation of alcohol molecule properties.
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2007-10-17 02:39:08 +08:00
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</P>
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<P>When running a simulation with large, massive particles or molecules
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2008-03-28 23:45:51 +08:00
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in a background solvent, you may want to only exchange momenta bewteen
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2007-10-17 02:39:08 +08:00
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solvent particles.
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</P>
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<P><B>Related commands:</B>
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</P>
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2008-05-16 03:42:47 +08:00
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<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "fix_thermal_conductivity.html">fix
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thermal/conductivity</A>
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2007-10-17 02:39:08 +08:00
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</P>
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2008-03-28 23:45:51 +08:00
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<P><B>Default:</B>
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</P>
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<P>The option defaults are swap = 1 and vtarget = INF.
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2007-10-17 02:39:08 +08:00
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</P>
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<HR>
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<A NAME = "Muller-Plathe"></A>
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<P><B>(Muller-Plathe)</B> Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
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</P>
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2007-10-17 02:49:13 +08:00
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<A NAME = "Maginn"></A>
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<P><B>(Maginn)</B> Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
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260, 218-231 (2007).
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</P>
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2007-10-17 02:39:08 +08:00
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</HTML>
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