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doc/html/_sources/fix_srd.txt
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.. index:: fix srd
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fix srd 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 srd N groupbig-ID Tsrd hgrid seed keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* srd = style name of this fix command
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* N = reset SRD particle velocities every this many timesteps
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* groupbig-ID = ID of group of large particles that SRDs interact with
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* Tsrd = temperature of SRD particles (temperature units)
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* hgrid = grid spacing for SRD grouping (distance units)
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* seed = random # seed (positive integer)
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* zero or more keyword/value pairs may be appended
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* keyword = *lamda* or *collision* or *overlap* or *inside* or *exact* or *radius* or *bounce* or *search* or *cubic* or *shift* or *tstat* or *rescale*
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.. parsed-literal::
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*lamda* value = mean free path of SRD particles (distance units)
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*collision* value = *noslip* or *slip* = collision model
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*overlap* value = *yes* or *no* = whether big particles may overlap
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*inside* value = *error* or *warn* or *ignore* = how SRD particles which end up inside a big particle are treated
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*exact* value = *yes* or *no*
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*radius* value = rfactor = scale collision radius by this factor
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*bounce* value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
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*search* value = sgrid = grid spacing for collision partner searching (distance units)
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*cubic* values = style tolerance
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style = *error* or *warn*
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tolerance = fractional difference allowed (0 <= tol <= 1)
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*shift* values = flag shiftseed
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flag = *yes* or *no* or *possible* = SRD bin shifting for better statistics
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*yes* = perform bin shifting each time SRD velocities are rescaled
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*no* = no shifting
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*possible* = shift depending on mean free path and bin size
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shiftseed = random # seed (positive integer)
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*tstat* value = *yes* or *no* = thermostat SRD particles or not
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*rescale* value = *yes* or *no* or *rotate* or *collide* = rescaling of SRD velocities
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*yes* = rescale during velocity rotation and collisions
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*no* = no rescaling
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*rotate* = rescale during velocity rotation, but not collisions
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*collide* = rescale during collisions, but not velocity rotation
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Examples
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""""""""
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.. parsed-literal::
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fix 1 srd srd 10 big 1.0 0.25 482984
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fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5
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Description
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"""""""""""
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Treat a group of partilces as stochastic rotation dynamics (SRD)
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particles that serve as a background solvent when interacting with big
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(colloidal) particles in groupbig-ID. The SRD formalism is described
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in :ref:`(Hecht) <Hecht>`. The key idea behind using SRD particles as a
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cheap coarse-grained solvent is that SRD particles do not interact
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with each other, but only with the solute particles, which in LAMMPS
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can be spheroids, ellipsoids, or line segments, or triangles, or rigid
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bodies containing multiple spherioids or ellipsoids or line segments
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or triangles. The collision and rotation properties of the model
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imbue the SRD particles with fluid-like properties, including an
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effective viscosity. Thus simulations with large solute particles can
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be run more quickly, to measure solute propoerties like diffusivity
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and viscosity in a background fluid. The usual LAMMPS fixes for such
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simulations, such as :doc:`fix deform <fix_deform>`, :doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
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can be used in conjunction with the SRD model.
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For more details on how the SRD model is implemented in LAMMPS, :ref:`this paper <Petersen>` describes the implementation and usage of pure SRD
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fluids. :ref:`This paper <Lechman>`, which is nearly complete, describes
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the implementation and usage of mixture systems (solute particles in
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an SRD fluid). See the examples/srd directory for sample input
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scripts using SRD particles in both settings.
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This fix does 2 things:
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(1) It advects the SRD particles, performing collisions between SRD
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and big particles or walls every timestep, imparting force and torque
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to the big particles. Collisions also change the position and
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velocity of SRD particles.
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(2) It resets the velocity distribution of SRD particles via random
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rotations every N timesteps.
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SRD particles have a mass, temperature, characteristic timestep
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dt_SRD, and mean free path between collisions (lamda). The
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fundamental equation relating these 4 quantities is
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.. parsed-literal::
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lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
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The mass of SRD particles is set by the :doc:`mass <mass>` command
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elsewhere in the input script. The SRD timestep dt_SRD is N times the
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step dt defined by the :doc:`timestep <timestep>` command. Big
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particles move in the normal way via a time integration :doc:`fix <fix>`
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with a short timestep dt. SRD particles advect with a large timestep
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dt_SRD >= dt.
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If the *lamda* keyword is not specified, the the SRD temperature
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*Tsrd* is used in the above formula to compute lamda. If the *lamda*
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keyword is specified, then the *Tsrd* setting is ignored and the above
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equation is used to compute the SRD temperature.
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The characteristic length scale for the SRD fluid is set by *hgrid*
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which is used to bin SRD particles for purposes of resetting their
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velocities. Normally hgrid is set to be 1/4 of the big particle
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diameter or smaller, to adequately resolve fluid properties around the
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big particles.
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Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
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(unless the *shift* keyword is used, see below). The velocities of
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SRD particles are bounded by Vmax, which is set so that an SRD
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particle will not advect further than Dmax = 4*lamda in dt_SRD. This
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means that roughly speaking, Dmax should not be larger than a big
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particle diameter, else SRDs may pass thru big particles without
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colliding. A warning is generated if this is the case.
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Collisions between SRD particles and big particles or walls are
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modeled as a lightweight SRD point particle hitting a heavy big
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particle of given diameter or a wall at a point on its surface and
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bouncing off with a new velocity. The collision changes the momentum
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of the SRD particle. It imparts a force and torque to the big
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particle. It imparts a force to a wall. Static or moving SRD walls
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are setup via the :doc:`fix wall/srd <fix_wall_srd>` command. For the
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remainder of this doc page, a collision of an SRD particle with a wall
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can be viewed as a collision with a big particle of infinite radius
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and mass.
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The *collision* keyword sets the style of collisions. The *slip*
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style means that the tangential component of the SRD particle momentum
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is preserved. Thus a force is imparted to a big particle, but no
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torque. The normal component of the new SRD velocity is sampled from
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a Gaussian distribution at temperature *Tsrd*\ .
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For the *noslip* style, both the normal and tangential components of
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the new SRD velocity are sampled from a Gaussian distribution at
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temperature *Tsrd*\ . Additionally, a new tangential direction for the
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SRD velocity is chosen randomly. This collision style imparts torque
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to a big particle. Thus a time integrator :doc:`fix <fix>` that rotates
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the big particles appropriately should be used.
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----------
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The *overlap* keyword should be set to *yes* if two (or more) big
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particles can ever overlap. This depends on the pair potential
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interaction used for big-big interactions, or could be the case if
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multiple big particles are held together as rigid bodies via the :doc:`fix rigid <fix_rigid>` command. If the *overlap* keyword is *no* and
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big particles do in fact overlap, then SRD/big collisions can generate
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an error if an SRD ends up inside two (or more) big particles at once.
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How this error is treated is determined by the *inside* keyword.
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Running with *overlap* set to *no* allows for faster collision
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checking, so it should only be set to *yes* if needed.
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The *inside* keyword determines how a collision is treated if the
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computation determines that the timestep started with the SRD particle
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already inside a big particle. If the setting is *error* then this
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generates an error message and LAMMPS stops. If the setting is *warn*
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then this generates a warning message and the code continues. If the
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setting is *ignore* then no message is generated. One of the output
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quantities logged by the fix (see below) tallies the number of such
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events, so it can be monitored. Note that once an SRD particle is
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inside a big particle, it may remain there for several steps until it
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drifts outside the big particle.
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The *exact* keyword determines how accurately collisions are computed.
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A setting of *yes* computes the time and position of each collision as
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SRD and big particles move together. A setting of *no* estimates the
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position of each collision based on the end-of-timestep positions of
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the SRD and big particle. If *overlap* is set to yes, the setting of
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the *exact* keyword is ignored since time-accurate collisions are
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needed.
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The *radius* keyword scales the effective size of big particles. If
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big particles will overlap as they undergo dynamics, then this keyword
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can be used to scale down their effective collision radius by an
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amount *rfactor*\ , so that SRD particle will only collide with one big
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particle at a time. For example, in a Lennard-Jones system at a
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temperature of 1.0 (in reduced LJ units), the minimum separation
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bewteen two big particles is as small as about 0.88 sigma. Thus an
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*rfactor* value of 0.85 should prevent dual collisions.
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The *bounce* keyword can be used to limit the maximum number of
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collisions an SRD particle undergoes in a single timestep as it
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bounces between nearby big particles. Note that if the limit is
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reached, the SRD can be left inside a big particle. A setting of 0 is
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the same as no limit.
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||||
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----------
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||||
There are 2 kinds of bins created and maintained when running an SRD
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simulation. The first are "SRD bins" which are used to bin SRD
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particles and reset their velocities, as discussed above. The second
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are "search bins" which are used to identify SRD/big particle
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collisions.
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The *search* keyword can be used to choose a search bin size for
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identifying SRD/big particle collisions. The default is to use the
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*hgrid* parameter for SRD bins as the search bin size. Choosing a
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smaller or large value may be more efficient, depending on the
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problem. But, in a statistical sense, it should not change the
|
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simulation results.
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The *cubic* keyword can be used to generate an error or warning when
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the bin size chosen by LAMMPS creates SRD bins that are non-cubic or
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different than the requested value of *hgrid* by a specified
|
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*tolerance*\ . Note that using non-cubic SRD bins can lead to
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undetermined behavior when rotating the velocities of SRD particles,
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hence LAMMPS tries to protect you from this problem.
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LAMMPS attempts to set the SRD bin size to exactly *hgrid*\ . However,
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there must be an integer number of bins in each dimension of the
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simulation box. Thus the actual bin size will depend on the size and
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shape of the overall simulation box. The actual bin size is printed
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as part of the SRD output when a simulation begins.
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If the actual bin size in non-cubic by an amount exceeding the
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tolerance, an error or warning is printed, depending on the style of
|
||||
the *cubic* keyword. Likewise, if the actual bin size differs from
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||||
the requested *hgrid* value by an amount exceeding the tolerance, then
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||||
an error or warning is printed. The *tolerance* is a fractional
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||||
difference. E.g. a tolerance setting of 0.01 on the shape means that
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if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an
|
||||
error or warning is generated. Similarly, if the ratio of any bin
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||||
dimension with *hgrid* exceeds (1 +/- tolerance), then an error or
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||||
warning is generated.
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||||
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.. note::
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The fix srd command can be used with simluations the size and/or
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shape of the simulation box changes. This can be due to non-periodic
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boundary conditions or the use of fixes such as the :doc:`fix deform <fix_deform>` or :doc:`fix wall/srd <fix_wall_srd>` commands
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to impose a shear on an SRD fluid or an interaction with an external
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wall. If the box size changes then the size of SRD bins must be
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recalculated every reneighboring. This is not necessary if only the
|
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box shape changes. This re-binning is always done so as to fit an
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integer number of bins in the current box dimension, whether it be a
|
||||
fixed, shrink-wrapped, or periodic boundary, as set by the
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:doc:`boundary <boundary>` command. If the box size or shape changes,
|
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then the size of the search bins must be recalculated avery
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reneighboring. Note that changing the SRD bin size may alter the
|
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properties of the SRD fluid, such as its viscosity.
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||||
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The *shift* keyword determines whether the coordinates of SRD
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particles are randomly shifted when binned for purposes of rotating
|
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their velocities. When no shifting is performed, SRD particles are
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binned and the velocity distribution of the set of SRD particles in
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each bin is adjusted via a rotation operator. This is a statistically
|
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valid operation if SRD particles move sufficiently far between
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successive rotations. This is determined by their mean-free path
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lamda. If lamda is less than 0.6 of the SRD bin size, then shifting
|
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is required. A shift means that all of the SRD particles are shifted
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by a vector whose coordinates are chosen randomly in the range [-1/2
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bin size, 1/2 bin size]. Note that all particles are shifted by the
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same vector. The specified random number *shiftseed* is used to
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generate these vectors. This operation sufficiently randomizes which
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SRD particles are in the same bin, even if lamda is small.
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If the *shift* flag is set to *no*\ , then no shifting is performed, but
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||||
bin data will be communicated if bins overlap processor boundaries.
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An error will be generated if lamda < 0.6 of the SRD bin size. If the
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*shift* flag is set to *possible*\ , then shifting is performed only if
|
||||
lamda < 0.6 of the SRD bin size. A warning is generated to let you
|
||||
know this is occurring. If the *shift* flag is set to *yes* then
|
||||
shifting is performed regardless of the magnitude of lamda. Note that
|
||||
the *shiftseed* is not used if the *shift* flag is set to *no*\ , but
|
||||
must still be specified.
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||||
|
||||
Note that shifting of SRD coordinates requires extra communication,
|
||||
hence it should not normally be enabled unless required.
|
||||
|
||||
The *tstat* keyword will thermostat the SRD particles to the specified
|
||||
*Tsrd*\ . This is done every N timesteps, during the velocity rotation
|
||||
operation, by rescaling the thermal velocity of particles in each SRD
|
||||
bin to the desired temperature. If there is a streaming velocity
|
||||
associated with the system, e.g. due to use of the :doc:`fix deform <fix_deform>` command to perform a simulation undergoing
|
||||
shear, then that is also accounted for. The mean velocity of each bin
|
||||
of SRD particles is set to the position-dependent streaming velocity,
|
||||
based on the coordinates of the center of the SRD bin. Note that
|
||||
collisions of SRD particles with big particles or walls has a
|
||||
thermostatting effect on the colliding particles, so it may not be
|
||||
necessary to thermostat the SRD particles on a bin by bin basis in
|
||||
that case. Also note that for streaming simulations, if no
|
||||
thermostatting is performed (the default), then it may take a long
|
||||
time for the SRD fluid to come to equilibrium with a velocity profile
|
||||
that matches the simulation box deformation.
|
||||
|
||||
The *rescale* keyword enables rescaling of an SRD particle's velocity
|
||||
if it would travel more than 4 mean-free paths in an SRD timestep. If
|
||||
an SRD particle exceeds this velocity it is possible it will be lost
|
||||
when migrating to other processors or that collisions with big
|
||||
particles will be missed, either of which will generate errors. Thus
|
||||
the safest mode is to run with rescaling enabled. However rescaling
|
||||
removes kinetic energy from the system (the particle's velocity is
|
||||
reduced). The latter will not typically be a problem if
|
||||
thermostatting is enabled via the *tstat* keyword or if SRD collisions
|
||||
with big particles or walls effectively thermostat the system. If you
|
||||
wish to turn off rescaling (on is the default), e.g. for a pure SRD
|
||||
system with no thermostatting so that the temperature does not decline
|
||||
over time, the *rescale* keyword can be used. The *no* value turns
|
||||
rescaling off during collisions and the per-bin velocity rotation
|
||||
operation. The *collide* and *rotate* values turn it on for
|
||||
one of the operations and off for the other.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. note::
|
||||
|
||||
This fix is normally used for simulations with a huge number of
|
||||
SRD particles relative to the number of big particles, e.g. 100 to 1.
|
||||
In this scenario, computations that involve only big particles
|
||||
(neighbor list creation, communication, time integration) can slow
|
||||
down dramatically due to the large number of background SRD particles.
|
||||
|
||||
Three other input script commands will largely overcome this effect,
|
||||
speeding up an SRD simulation by a significant amount. These are the
|
||||
:doc:`atom_modify first <atom_modify>`, :doc:`neigh_modify include <neigh_modify>`, and :doc:`comm_modify group <comm_modify>`
|
||||
commands. Each takes a group-ID as an argument, which in this case
|
||||
should be the group-ID of the big solute particles.
|
||||
|
||||
Additionally, when a :doc:`pair_style <pair_style>` for big/big particle
|
||||
interactions is specified, the :doc:`pair_coeff <pair_coeff>` command
|
||||
should be used to turn off big/SRD interactions, e.g. by setting their
|
||||
epsilon or cutoff length to 0.0.
|
||||
|
||||
The "delete_atoms overlap" command may be useful in setting up an SRD
|
||||
simulation to insure there are no initial overlaps between big and SRD
|
||||
particles.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
||||
are relevant to this fix.
|
||||
|
||||
This fix tabulates several SRD statistics which are stored in a vector
|
||||
of length 12, which can be accessed by various :ref:`output commands <howto_15>`. The vector values calculated
|
||||
by this fix are "intensive", meaning they do not scale with the size
|
||||
of the simulation. Technically, the first 8 do scale with the size of
|
||||
the simulation, but treating them as intensive means they are not
|
||||
scaled when printed as part of thermodyanmic output.
|
||||
|
||||
These are the 12 quantities. All are values for the current timestep,
|
||||
except for quantity 5 and the last three, each of which are
|
||||
cummulative quantities since the beginning of the run.
|
||||
|
||||
* (1) # of SRD/big collision checks performed
|
||||
* (2) # of SRDs which had a collision
|
||||
* (3) # of SRD/big colllisions (including multiple bounces)
|
||||
* (4) # of SRD particles inside a big particle
|
||||
* (5) # of SRD particles whose velocity was rescaled to be < Vmax
|
||||
* (6) # of bins for collision searching
|
||||
* (7) # of bins for SRD velocity rotation
|
||||
* (8) # of bins in which SRD temperature was computed
|
||||
* (9) SRD temperature
|
||||
* (10) # of SRD particles which have undergone max # of bounces
|
||||
* (11) max # of bounces any SRD particle has had in a single step
|
||||
* (12) # of reneighborings due to SRD particles moving too far
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
This command can only be used if LAMMPS was built with the SRD
|
||||
package. See the :ref:`Making LAMMPS <start_3>` section
|
||||
for more info on packages.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix wall/srd <fix_wall_srd>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are lamda inferred from Tsrd, collision = noslip,
|
||||
overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
|
||||
search = hgrid, cubic = error 0.01, shift = no, tstat = no, and
|
||||
rescale = yes.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. _Hecht:
|
||||
|
||||
|
||||
|
||||
**(Hecht)** Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).
|
||||
|
||||
.. _Petersen:
|
||||
|
||||
|
||||
|
||||
**(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
|
||||
Chem Phys, 132, 174106 (2010).
|
||||
|
||||
.. _Lechman:
|
||||
|
||||
|
||||
|
||||
**(Lechman)** Lechman, et al, in preparation (2010).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
Reference in New Issue
Block a user