forked from lijiext/lammps
133 lines
5.5 KiB
Plaintext
133 lines
5.5 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix viscosity command :h3
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[Syntax:]
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fix ID group-ID viscosity N vdim pdim Nbin :pre
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ID, group-ID are documented in "fix"_fix.html command
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viscosity = style name of this fix command
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N = perform momentum exchange every N steps
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vdim = {x} or {y} or {z} = which momentum component to exchange
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pdim = {x} or {y} or {z} = direction of momentum transfer
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Nbin = # of layers in pdim direction :ul
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[Examples:]
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fix 1 all viscosity 100 x z 20 :pre
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[Description:]
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Use the Muller-Plathe algorithm described in "this
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paper"_#Muller-Plathe 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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The simulation box is divided into {Nbin} layers in the {pdim}
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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 {vdim}
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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 {vdim} direction is the second
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atom. The {vdim} 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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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 :pre
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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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appropriate units. See the "Muller-Plathe paper"_#Muller-Plathe for
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details.
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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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An alternative method for calculating a viscosity is to run a NEMD
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simulation, as described in "this section"_Section_howto.html#4_13 of
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the manual. NEMD simulations deform the simulation box via the "fix
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deform"_fix_deform.html command. Thus they cannot be run on a charged
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system using a "PPPM solver"_kspace_style.html 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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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix.
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The cumulative momentum transferred between the bottom and middle of
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the simulation box (in the {pdim} 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 accumulates 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 "output commands"_Section_howto.html#4_15, such as
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"thermo_style custom"_thermo_style.html. The scalar value calculated
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by this fix is "intensive", meaning it is independent of the number of
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atoms in the simulation.
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command. This fix is not invoked during "energy
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minimization"_minimize.html.
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[Restrictions:]
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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 {vdim}).
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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 "fix
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shake"_fix_shake.html or "fix rigid"_fix_rigid.html. 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 "Maginn paper"_#Maginn for an example of using this algorithm
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in a computation of alcohol molecule properties.
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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 between
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solvent particles.
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[Related commands:]
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"fix ave/spatial"_fix_ave_spatial.html, "fix
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nvt/sllod"_fix_nvt_sllod.html
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[Default:] none
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:line
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:link(Muller-Plathe)
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[(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
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:link(Maginn)
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[(Maginn)] Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
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260, 218-231 (2007).
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