forked from lijiext/lammps
355 lines
18 KiB
HTML
355 lines
18 KiB
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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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<HR>
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<H3>fix srd 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 srd N groupbig-ID Tsrd hgrid seed keyword value ...
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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>srd = style name of this fix command
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<LI>N = reset SRD particle velocities every this many timesteps
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<LI>groupbig-ID = ID of group of large particles that SRDs interact with
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<LI>Tsrd = temperature of SRD particles (temperature units)
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<LI>hgrid = grid spacing for SRD grouping (distance units)
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<LI>seed = random # seed (positive integer)
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</UL>
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<UL><LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>lamda</I> or <I>collision</I> or <I>overlap</I> or <I>inside</I> or <I>exact</I> or <I>radius</I> or <I>bounce</I> or <I>search</I> or <I>cubic</I> or <I>shift</I> or <I>stream</I>
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<PRE> <I>lamda</I> value = mean free path of SRD particles (distance units)
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<I>collision</I> value = <I>noslip</I> or <I>slip</I> = collision model
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<I>overlap</I> value = <I>yes</I> or <I>no</I> = whether big particles may overlap
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<I>inside</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I> = how SRD particles which end up inside a big particle are treated
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<I>exact</I> value = <I>yes</I> or <I>no</I>
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<I>radius</I> value = rfactor = scale collision radius by this factor
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<I>bounce</I> value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
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<I>search</I> value = sgrid = grid spacing for collision partner searching (distance units)
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<I>cubic</I> values = style tolerance
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style = <I>error</I> or <I>warn</I>
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tolerance = fractional difference allowed (0 <= tol <= 1)
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<I>shift</I> values = style seed
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style = <I>old</I> or <I>no</I> or <I>yes</I> or <I>possible</I>
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seed = random # seed (positive integer)
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<I>stream</I> value = <I>yes</I> or <I>no</I> = whether or not streaming velocity is added for shear deformation
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</PRE>
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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 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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</PRE>
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<P><B>Description:</B>
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</P>
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<P>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 <A HREF = "#Hecht">(Hecht)</A>. 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 rigid bodies containing multiples
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spherioids and ellipsoids. The collision and rotation properties of
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the model imbue the SRD particles with fluid-like properties,
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including an effective viscosity. Thus simulations with large solute
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particles can be run more quickly, to measure solute propoerties like
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diffusivity and viscosity in a background fluid. The usual LAMMPS
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fixes for such simulations, such as <A HREF = "fix_deform.html">fix deform</A>, <A HREF = "fix_viscosity.html">fix
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viscosity</A>, and <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>,
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can be used in conjunction with the SRD model.
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</P>
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<P>For more details on how the SRD model is implemented in LAMMPS, <A HREF = "#Petersen">this
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paper</A> describes the implementation and usage of pure SRD
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fluids. <A HREF = "#Lechman">This paper</A>, 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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</P>
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<P>This fix does 2 things:
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</P>
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<P>(1) It advects the SRD particles, performing collisions between SRD
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and big particles every timestep, imparting force and torque to the
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big particles. Collisions also change the position and velocity of
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SRD particles.
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</P>
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<P>(2) It resets the velocity distribution of SRD particles via random
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rotations every N timesteps.
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</P>
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<P>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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</P>
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<PRE>lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
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</PRE>
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<P>The mass of SRD particles is set by the <A HREF = "mass.html">mass</A> 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 <A HREF = "timestep.html">timestep</A> command. Big
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particles move in the normal way via a time integration <A HREF = "fix.html">fix</A>
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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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</P>
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<P>If the <I>lamda</I> keyword is not specified, the the SRD temperature
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<I>Tsrd</I> is used in the above formula to compute lamda. If the <I>lamda</I>
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keyword is specified, then the <I>Tsrd</I> setting is ignored and the above
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equation is used to compute the SRD temperature.
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</P>
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<P>The characteristic length scale for the SRD fluid is set by <I>hgrid</I>
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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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</P>
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<P>Lamda cannot be smaller than 0.6 * hgrid, else an error is generated.
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The velocities of SRD particles are bounded by Vmax, which is set so
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that an SRD particle will not advect further than Dmax = 4*lamda in
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dt_SRD. This means that roughly speaking, Dmax should not be larger
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than a big particle diameter, else SRDs may pass thru big particles
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without colliding. A warning is generated if this is the case.
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</P>
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<P>SRD/big particle collisions are modeled as a lightweight SRD point
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particle hitting a heavy big particle of given diameter at a point on
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its surface and bouncing off with a new velocity. The collision
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changes the momentum of the SRD particle. It imparts a force and
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torque to the big particle.
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</P>
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<P>The <I>collision</I> keyword sets the style of SRD/big particle collisions.
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The <I>slip</I> style means that the tangential component of the SRD
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particle momentum is preserved. Thus a force is imparted to the big
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particle, but no torque. The normal component of the new SRD velocity
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is sampled from a Gaussian distribution at temperature <I>Tsrd</I>.
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</P>
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<P>For the <I>noslip</I> 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 <I>Tsrd</I>. 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 the big particle. Thus a time integrator <A HREF = "fix.html">fix</A> that
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rotates the big particles appropriately should be used.
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</P>
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<HR>
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<P>The <I>overlap</I> keyword should be set to <I>yes</I> 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 <A HREF = "fix_rigid.html">fix
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rigid</A> command. If the <I>overlap</I> keyword is <I>no</I> 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 <I>inside</I> keyword.
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Running with <I>overlap</I> set to <I>no</I> allows for faster collision
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checking, so it should only be set to <I>yes</I> if needed.
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</P>
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<P>The <I>inside</I> 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 <I>error</I> then this
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generates an error message and LAMMPS stops. If the setting is <I>warn</I>
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then this generates a warning message and the code continues. If the
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setting is <I>ignore</I> 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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</P>
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<P>The <I>exact</I> keyword determines how accurately collisions are computed.
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A setting of <I>yes</I> computes the time and position of each collision as
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SRD and big particles move together. A setting of <I>no</I> 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 <I>overlap</I> is set to yes, the setting of
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the <I>exact</I> keyword is ignored since time-accurate collisions are
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needed.
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</P>
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<P>The <I>radius</I> 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 <I>rfactor</I>, 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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<I>rfactor</I> value of 0.85 should prevent dual collisions.
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</P>
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<P>The <I>bounce</I> 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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</P>
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<HR>
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<P>The <I>search</I> keyword can be used to choose a bin size for identifying
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SRD/big particle collisions. The default is to use the <I>hgrid</I>
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parameter as the search bin size. Choosing a smaller or large value
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may be more efficient, depending on the problem. But, in a
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statistical sense, it should not change the simulation results.
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</P>
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<P>The <I>cubic</I> 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 <I>hgrid</I> by a specified
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<I>tolerance</I>. 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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</P>
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<P>LAMMPS attempts to set the SRD bin size to exactly <I>hgrid</I>. However,
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there must be an integer number of bins in each dimension of the
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simulation box. When the style of the <I>shift</I> keyword is set to
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<I>old</I>, there is an additional constraint that there must be an integer
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number of bins within each processor's sub-domain. Thus the actual
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bin size will depend on the size and shape of the overall simulation
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box and, in the case of <I>shift</I> set to <I>old</I>, on the number of
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processors assigned to each dimension of the box (see the
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<A HREF = "processors.html">processors</A> command). The actual bin size is printed
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as part of the SRD output when a simulation begins.
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</P>
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<P>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
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the <I>cubic</I> keyword. Likewise, if the actual bin size differs from
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the requested <I>hgrid</I> value by an amount exceeding the tolerance, then
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an error or warning is printed. The <I>tolerance</I> 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
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error or warning is generated. Similarly, if the ratio of any bin
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dimension with <I>hgrid</I> exceeds (1 +/- tolerance), then an error or
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warning is generated.
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</P>
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<P>The <I>shift</I> 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 <B>-1/2
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bin size, 1/2 bin size</B>. Note that all particles are shifted by the
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same vector. The specified random number seed is used to generate
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these vectors. This operation sufficiently randomizes which SRD
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particles are in the same bin, even if lamda is small.
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</P>
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<P>If the <I>shift</I> style is set to <I>old</I>, then no shifting is performed.
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An error will be generated if lamda < 0.6 of the SRD bin size. If the
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<I>shift</I> style is set to <I>no</I>, then no shifting is performed, but bin
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data will be communicated if bins overlap processor boundaries. An
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error will be generated if lamda < 0.6 of the SRD bin size. If the
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<I>shift</I> style is set to <I>possible</I>, then shifting is performed only if
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lamda < 0.6 of the SRD bin size. A warning is generated to let you
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know this is occurring. If the <I>shift</I> style is set to <I>yes</I> then
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shifting is performed regardless of the magnitude of lamda.
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</P>
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<P>The shift seed is not used if the <I>shift</I> style is set to <I>old</I> or
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<I>no</I>, but must still be specified.
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</P>
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<P>Note that shifting of SRD coordinates requires extra communication,
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hence it should not normally be enabled unless required.
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</P>
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<P>The <I>stream</I> keyword is used when SRD particles are used with the <A HREF = "fix_deform.html">fix
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deform</A> command to perform a simulation undergoing
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shear, e.g. to measure a viscosity. If the <I>stream</I> style is set to
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<I>yes</I>, then the mean velocity of each bin of SRD particles is set to
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the streaming velocity of the deforming box, each time SRD velocities
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are reset, every N timesteps. If the <I>stream</I> style is set to <I>no</I>,
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then the mean velocity is unchanged, which may mean that it takes a
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long time for the SRD fluid to come to equilibrium with a velocity
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profile that matches the simulation box deformation.
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</P>
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<HR>
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<P>IMPORTANT NOTE: This fix is normally used for simulations with a huge
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number of SRD particles relative to the number of big particles,
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e.g. 100 to 1. In this scenario, computations that involve only big
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particles (neighbor list creation, communication, time integration)
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can slow down dramatically due to the large number of background SRD
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particles.
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</P>
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<P>Three other input script commands will largely overcome this effect,
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speeding up an SRD simulation by a significant amount. These are the
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<A HREF = "atom_modify.html">atom_modify first</A>, <A HREF = "neigh_modify.html">neigh_modify
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include</A>, and <A HREF = "communicate.html">communicate group</A>
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commands. Each takes a group-ID as an argument, which in this case
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should be the group-ID of the big solute particles.
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</P>
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<P>Additionally, when a <A HREF = "pair_style.html">pair_style</A> for big/big particle
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interactions is specified, the <A HREF = "pair_coeff.html">pair_coeff</A> command
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should be used to turn off big/SRD interactions, e.g. by setting their
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epsilon or cutoff length to 0.0.
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</P>
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<P>The "delete_atoms overlap" command may be useful in setting up an SRD
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simulation to insure there are no initial overlaps between big and SRD
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particles.
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</P>
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<HR>
|
||
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||
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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
|
||
|
|
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||
|
|
are relevant to this fix.
|
||
|
|
</P>
|
||
|
|
<P>This fix tabulates several SRD statistics which are stored in a vector
|
||
|
|
of length 12, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
|
||
|
|
commands</A>. 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.
|
||
|
|
</P>
|
||
|
|
<P>These are the 12 quantities. All are values for the current timestep,
|
||
|
|
except the last three which are cummulative quantities since the
|
||
|
|
beginning of the run.
|
||
|
|
</P>
|
||
|
|
<UL><LI>(1) # of SRD/big collision checks performed
|
||
|
|
<LI>(2) # of SRDs which had a collision
|
||
|
|
<LI>(3) # of SRD/big colllisions (including multiple bounces)
|
||
|
|
<LI>(4) # of SRD particles inside a big particle
|
||
|
|
<LI>(5) # of SRD particles whose velocity was rescaled to be < Vmax
|
||
|
|
<LI>(6) # of bins for collision searching
|
||
|
|
<LI>(7) # of bins for SRD velocity rotation
|
||
|
|
<LI>(8) # of bins in which SRD temperature was computed
|
||
|
|
<LI>(9) SRD temperature
|
||
|
|
<LI>(10) # of SRD particles which have undergone max # of bounces
|
||
|
|
<LI>(11) max # of bounces any SRD particle has had in a single step
|
||
|
|
<LI>(12) # of reneighborings dues to SRD particles moving too far
|
||
|
|
</UL>
|
||
|
|
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
||
|
|
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
||
|
|
minimization</A>.
|
||
|
|
</P>
|
||
|
|
<P><B>Restrictions:</B> none
|
||
|
|
</P>
|
||
|
|
<P>This command can only be used if LAMMPS was built with the "srd"
|
||
|
|
package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
|
||
|
|
more info on packages.
|
||
|
|
</P>
|
||
|
|
<P>This fix can only be used with a fully periodic simulation box.
|
||
|
|
</P>
|
||
|
|
<P><B>Related commands:</B> none
|
||
|
|
</P>
|
||
|
|
<P><B>Default:</B>
|
||
|
|
</P>
|
||
|
|
<P>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, stream = yes.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<A NAME = "Hecht"></A>
|
||
|
|
|
||
|
|
<P><B>(Hecht)</B> Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).
|
||
|
|
</P>
|
||
|
|
<A NAME = "Petersen"></A>
|
||
|
|
|
||
|
|
<P><B>(Petersen)</B> Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
|
||
|
|
Chem Phys, 132, 174106 (2010).
|
||
|
|
</P>
|
||
|
|
<P>:link(Lechman) <B>(Lechman)</B> Lechman, et al, in preparation (2010).
|
||
|
|
</P>
|
||
|
|
</HTML>
|