forked from lijiext/lammps
189 lines
7.6 KiB
Plaintext
189 lines
7.6 KiB
Plaintext
.. index:: fix viscosity
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fix viscosity command
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=====================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID viscosity N vdim pdim Nbin keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` 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 (must be even number)
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* zero or more keyword/value pairs may be appended
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* keyword = *swap* or *target*
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.. parsed-literal::
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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)
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Examples
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""""""""
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.. parsed-literal::
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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
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Description
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"""""""""""
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Use the Muller-Plathe algorithm described in :ref:`this 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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.. parsed-literal::
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compute layers all chunk/atom bin/1d z lower 0.05 units reduced
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fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile
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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 :ref:`Muller-Plathe paper <Muller-Plathe>` for details.
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.. note::
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If your system is periodic in the direction of the momentum
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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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.. note::
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After equilibration, if the velocity profile you observe is not
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linear, then you are likely swapping momentum too frequently and are
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not in a regime of linear response. In this case you cannot
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accurately infer a viscosity and should try increasing the Nevery
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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 :ref:`Section_howto 13 <howto_13>` of the manual. NEMD simulations
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deform the simmulation box via the :doc:`fix deform <fix_deform>`
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command. Thus they cannot be run on a charged system using a :doc:`PPPM solver <kspace_style>` 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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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` 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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:ref:`output commands <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 :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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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 :ref:`Making LAMMPS <start_3>` section for more info.
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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 :doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`. 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 :ref:`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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""""""""""""""""
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:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix thermal/conductivity <fix_thermal_conductivity>`
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Default
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"""""""
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The option defaults are swap = 1 and vtarget = INF.
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----------
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.. _Muller-Plathe:
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**(Muller-Plathe)** Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
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.. _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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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