forked from lijiext/lammps
166 lines
7.2 KiB
Plaintext
166 lines
7.2 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 keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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viscosity = style name of this fix command :l
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N = perform momentum exchange every N steps :l
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vdim = {x} or {y} or {z} = which momentum component to exchange :l
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pdim = {x} or {y} or {z} = direction of momentum transfer :l
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Nbin = # of layers in pdim direction (must be even number) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {swap} or {target} :l
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{swap} value = Nswap = number of swaps to perform every N steps
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{vtarget} value = V or INF = target velocity of swap partners (velocity units) :pre
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:ule
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[Examples:]
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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 :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, where the layer 1 is at the low end of that dimension and
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the layer {Nbin} 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 {vdim} direction closest to the target value {V} 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 {vdim} direction closest to the
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negative of the target value {V} are selected. The two sets of Nswap
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atoms are paired up and their {vdim} 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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fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
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file tmp.profile units reduced :pre
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Note that by default, Nswap = 1 and vtarget = INF, though this can be
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changed by the optional {swap} and {vtarget} 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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The "middle" layer for momenta swapping is defined as the {Nbin}/2 + 1
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layer. Thus if {Nbin} = 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 {Nbin} is restricted to being an even number.
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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 proportional to the viscosity of the
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fluid, in appropriate units. See the "Muller-Plathe
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paper"_#Muller-Plathe for details.
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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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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 "Section_howto
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13"_Section_howto.html#howto_13 of the manual. NEMD simulations
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deform the simmulation box via the "fix deform"_fix_deform.html
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command. Thus they cannot be run on a charged system using a "PPPM
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solver"_kspace_style.html 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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[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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This fix computes a global scalar which can be accessed by various
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"output commands"_Section_howto.html#howto_15. The scalar is the
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cummulative momentum transferred between the bottom and middle of the
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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 accumlates thereafter, once every N steps. The units of the
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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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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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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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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 bewteen
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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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thermal/conductivity"_fix_thermal_conductivity.html
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[Default:]
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The option defaults are swap = 1 and vtarget = INF.
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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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