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138 lines
5.9 KiB
HTML
<HTML>
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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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<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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<PRE>fix ID group-ID viscosity N vdim pdim Nbin
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</PRE>
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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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<LI>Nbin = # of layers in pdim direction
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all viscosity 100 x z 20
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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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direction. Every N steps, two atoms are chosen in the following
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manner. Only atoms in the fix group are considered. The atom in the
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bottom layer with the most positive momentum component in the <I>vdim</I>
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direction is the first atom. The atom in the middle later with the
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most negative momentum component in the <I>vdim</I> direction is the second
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atom. The <I>vdim</I> momenta components of these two atoms are swapped,
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which resets their velocities, typically in opposite directions. Over
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time, this induces a shear velocity profile in the system which can be
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measured using commands such as the following, which writes the
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profile to the file tmp.profile:
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</P>
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<PRE>compute c1 all attribute/atom vx
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fix f1 all ave/spatial 100 10 1000 z lower 0.05 tmp.profile &
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compute c1 units reduced
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</PRE>
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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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the shear velocity profile is the viscosity of the fluid, in
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appopriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
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details.
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</P>
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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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<P>An alternative method for calculating a viscosity is to run a NEMD
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simulation, as described in <A HREF = "Section_howto.html#4_13">this section</A> of
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the manual. NEMD simulations deform the simmulation box via the <A HREF = "fix_deform.html">fix
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deform</A> command. Thus they cannot be run on a charged
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system using a <A HREF = "kspace_style.html">PPPM solver</A> since PPPM does not
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currently support non-orthogonal boxes. Using fix viscosity keeps the
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box orthogonal; thus it does not suffer from this limitation.
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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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<P>The cummulative momentum transferred between the bottom and middle of
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the simulation box (in the <I>pdim</I> direction) is stored as a scalar
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quantity by this fix. This quantity is zeroed when the fix is defined
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and accumlates thereafter, once every N steps. The units of the
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quantity are momentum = mass*velocity. This quantity can be accessed
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by various <A HREF = "Section_howto.html#4_15">output commands</A>, such as
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<A HREF = "thermo_style.html">thermo_style custom</A>.
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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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<P>If the masses of all exchange partners are the same, then swaps
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conserve both momentum and kinetic energy. Thus you should not need
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to thermostat the system. If you do use a thermostat, you may want to
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apply it only to the non-swapped dimensions (other than <I>vdim</I>).
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</P>
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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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</P>
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<P>When running a simulation with large, massive particles or molecules
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in a background solvent, you may want to only exchange momenta bewteen
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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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<P><A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "fix_nvt_sllod.html">fix
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nvt/sllod</A>
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</P>
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<P><B>Default:</B> none
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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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<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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</HTML>
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