fix srd command — LAMMPS documentation

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# fix srd command

## Syntax

    fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ...

- ID, group-ID are documented in fix command

- srd = style name of this fix command

- N = reset SRD particle velocities every this many timesteps

- groupbig-ID = ID of group of large particles that SRDs interact with

- Tsrd = temperature of SRD particles (temperature units)

- hgrid = grid spacing for SRD grouping (distance units)

- seed = random # seed (positive integer)

- zero or more keyword/value pairs may be appended

- keyword = lamda or collision or overlap or inside or exact or radius or bounce or search or cubic or shift or tstat or rescale

      lamda value = mean free path of SRD particles (distance units)
      collision value = noslip or slip = collision model
      overlap value = yes or no = whether big particles may overlap
      inside value = error or warn or ignore = how SRD particles which end up inside a big particle are treated
      exact value = yes or no
      radius value = rfactor = scale collision radius by this factor
      bounce value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
      search value = sgrid = grid spacing for collision partner searching (distance units)
      cubic values = style tolerance
        style = error or warn
        tolerance = fractional difference allowed (0 <= tol <= 1)
      shift values = flag shiftseed
        flag = yes or no or possible = SRD bin shifting for better statistics
          yes = perform bin shifting each time SRD velocities are rescaled
          no = no shifting
          possible = shift depending on mean free path and bin size
        shiftseed = random # seed (positive integer)
      tstat value = yes or no = thermostat SRD particles or not
      rescale value = yes or no or rotate or collide = rescaling of SRD velocities
        yes = rescale during velocity rotation and collisions
        no = no rescaling
        rotate = rescale during velocity rotation, but not collisions
        collide = rescale during collisions, but not velocity rotation

## Examples

    fix 1 srd srd 10 big 1.0 0.25 482984
    fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5

## Description

Treat a group of particles as stochastic rotation dynamics (SRD) particles that serve as a background solvent when interacting with big (colloidal) particles in groupbig-ID. The SRD formalism is described in (Hecht). The key idea behind using SRD particles as a cheap coarse-grained solvent is that SRD particles do not interact with each other, but only with the solute particles, which in LAMMPS can be spheroids, ellipsoids, or line segments, or triangles, or rigid bodies containing multiple spheroids or ellipsoids or line segments or triangles. The collision and rotation properties of the model imbue the SRD particles with fluid-like properties, including an effective viscosity. Thus simulations with large solute particles can be run more quickly, to measure solute properties like diffusivity and viscosity in a background fluid. The usual LAMMPS fixes for such simulations, such as fix deform, fix viscosity, and fix nvt/sllod, can be used in conjunction with the SRD model.

For more details on how the SRD model is implemented in LAMMPS, this paper describes the implementation and usage of pure SRD fluids. This paper, which is nearly complete, describes the implementation and usage of mixture systems (solute particles in an SRD fluid). See the examples/srd directory for sample input scripts using SRD particles in both settings.

This fix does two things:

> 1. It advects the SRD particles, performing collisions between SRD and big particles or walls every timestep, imparting force and torque to the big particles. Collisions also change the position and velocity of SRD particles.

> 2. It resets the velocity distribution of SRD particles via random rotations every N timesteps.

SRD particles have a mass, temperature, characteristic timestep \(dt_{SRD}\), and mean free path between collisions (\(\lambda\)). The fundamental equation relating these 4 quantities is

\[\lambda = dt_{SRD} \sqrt{\frac{k_B T_{SRD}}{m}}\]

The mass m of SRD particles is set by the mass command elsewhere in the input script. The SRD timestep \(dt_{SRD}\) is N times the step dt defined by the timestep command. Big particles move in the normal way via a time integration fix with a short timestep dt. SRD particles advect with a large timestep \(dt_{SRD} \ge dt\).

If the lamda keyword is not specified, the SRD temperature \(T_{SRD}\) is used in the above formula to compute \(\lambda\). If the lamda keyword is specified, then the Tsrd setting is ignored and the above equation is used to compute the SRD temperature.

The characteristic length scale for the SRD fluid is set by hgrid which is used to bin SRD particles for purposes of resetting their velocities. Normally hgrid is set to be 1/4 of the big particle diameter or smaller, to adequately resolve fluid properties around the big particles.

\(\lambda\) cannot be smaller than 0.6 * hgrid, else an error is generated (unless the shift keyword is used, see below). The velocities of SRD particles are bounded by Vmax, which is set so that an SRD particle will not advect further than \(D_{max} = 4 \lambda\) in \(dt_{SRD}\). This means that roughly speaking, \(D_{max}\) should not be larger than a big particle diameter, else SRDs may pass through big particles without colliding. A warning is generated if this is the case.

Collisions between SRD particles and big particles or walls are modeled as a lightweight SRD point particle hitting a heavy big particle of given diameter or a wall at a point on its surface and bouncing off with a new velocity. The collision changes the momentum of the SRD particle. It imparts a force and torque to the big particle. It imparts a force to a wall. Static or moving SRD walls are setup via the fix wall/srd command. For the remainder of this doc page, a collision of an SRD particle with a wall can be viewed as a collision with a big particle of infinite radius and mass.

The collision keyword sets the style of collisions. The slip style means that the tangential component of the SRD particle momentum is preserved. Thus a force is imparted to a big particle, but no torque. The normal component of the new SRD velocity is sampled from a Gaussian distribution at temperature Tsrd.

For the noslip style, both the normal and tangential components of the new SRD velocity are sampled from a Gaussian distribution at temperature Tsrd. Additionally, a new tangential direction for the SRD velocity is chosen randomly. This collision style imparts torque to a big particle. Thus a time integrator fix that rotates the big particles appropriately should be used.

The overlap keyword should be set to yes if two (or more) big particles can ever overlap. This depends on the pair potential interaction used for big-big interactions, or could be the case if multiple big particles are held together as rigid bodies via the fix rigid command. If the overlap keyword is no and big particles do in fact overlap, then SRD/big collisions can generate an error if an SRD ends up inside two (or more) big particles at once. How this error is treated is determined by the inside keyword. Running with overlap set to no allows for faster collision checking, so it should only be set to yes if needed.

The inside keyword determines how a collision is treated if the computation determines that the timestep started with the SRD particle already inside a big particle. If the setting is error then this generates an error message and LAMMPS stops. If the setting is warn then this generates a warning message and the code continues. If the setting is ignore then no message is generated. One of the output quantities logged by the fix (see below) tallies the number of such events, so it can be monitored. Note that once an SRD particle is inside a big particle, it may remain there for several steps until it drifts outside the big particle.

The exact keyword determines how accurately collisions are computed. A setting of yes computes the time and position of each collision as SRD and big particles move together. A setting of no estimates the position of each collision based on the end-of-timestep positions of the SRD and big particle. If overlap is set to yes, the setting of the exact keyword is ignored since time-accurate collisions are needed.

The radius keyword scales the effective size of big particles. If big particles will overlap as they undergo dynamics, then this keyword can be used to scale down their effective collision radius by an amount rfactor, so that SRD particle will only collide with one big particle at a time. For example, in a Lennard-Jones system at a temperature of 1.0 (in reduced LJ units), the minimum separation between two big particles is as small as about 0.88 sigma. Thus an rfactor value of 0.85 should prevent dual collisions.

The bounce keyword can be used to limit the maximum number of collisions an SRD particle undergoes in a single timestep as it bounces between nearby big particles. Note that if the limit is reached, the SRD can be left inside a big particle. A setting of 0 is the same as no limit.

There are 2 kinds of bins created and maintained when running an SRD simulation. The first are “SRD bins” which are used to bin SRD particles and reset their velocities, as discussed above. The second are “search bins” which are used to identify SRD/big particle collisions.

The search keyword can be used to choose a search bin size for identifying SRD/big particle collisions. The default is to use the hgrid parameter for SRD bins as the search bin size. Choosing a smaller or large value may be more efficient, depending on the problem. But, in a statistical sense, it should not change the simulation results.

The cubic keyword can be used to generate an error or warning when the bin size chosen by LAMMPS creates SRD bins that are non-cubic or different than the requested value of hgrid by a specified tolerance. Note that using non-cubic SRD bins can lead to undetermined behavior when rotating the velocities of SRD particles, hence LAMMPS tries to protect you from this problem.

LAMMPS attempts to set the SRD bin size to exactly hgrid. However, there must be an integer number of bins in each dimension of the simulation box. Thus the actual bin size will depend on the size and shape of the overall simulation box. The actual bin size is printed as part of the SRD output when a simulation begins.

If the actual bin size in non-cubic by an amount exceeding the tolerance, an error or warning is printed, depending on the style of the cubic keyword. Likewise, if the actual bin size differs from the requested hgrid value by an amount exceeding the tolerance, then an error or warning is printed. The tolerance is a fractional difference. E.g. a tolerance setting of 0.01 on the shape means that 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 dimension with hgrid exceeds (1 +/- tolerance), then an error or warning is generated.

Note

The fix srd command can be used with simulations where the size and/or shape of the simulation box changes. This can be due to non-periodic boundary conditions or the use of fixes such as the fix deform or fix wall/srd commands to impose a shear on an SRD fluid or an interaction with an external wall. If the box size changes then the size of SRD bins must be recalculated every reneighboring. This is not necessary if only the box shape changes. This re-binning is always done so as to fit an integer number of bins in the current box dimension, whether it be a fixed, shrink-wrapped, or periodic boundary, as set by the boundary command. If the box size or shape changes, then the size of the search bins must be recalculated every reneighboring. Note that changing the SRD bin size may alter the properties of the SRD fluid, such as its viscosity.

The shift keyword determines whether the coordinates of SRD particles are randomly shifted when binned for purposes of rotating their velocities. When no shifting is performed, SRD particles are binned and the velocity distribution of the set of SRD particles in each bin is adjusted via a rotation operator. This is a statistically valid operation if SRD particles move sufficiently far between successive rotations. This is determined by their mean-free path \(\lambda\). If \(\lambda\) is less than 0.6 of the SRD bin size, then shifting is required. A shift means that all of the SRD particles are shifted by a vector whose coordinates are chosen randomly in the range [-1/2 bin size, 1/2 bin size]. Note that all particles are shifted by the same vector. The specified random number shiftseed is used to generate these vectors. This operation sufficiently randomizes which SRD particles are in the same bin, even if \(lambda\) is small.

If the shift flag is set to no, then no shifting is performed, but bin data will be communicated if bins overlap processor boundaries. An error will be generated if \(\lambda < 0.6\) of the SRD bin size. If the shift flag is set to possible, then shifting is performed only if \(\lambda < 0.6\) 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 \(\lambda\). Note that the shiftseed is not used if the shift flag is set to no, but must still be specified.

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 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 atom_modify first, neigh_modify include, and comm_modify group 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 pair_style for big/big particle interactions is specified, the 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 ensure 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 binary restart files. None of the 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 output commands. 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 thermodynamic 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 cumulative 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 collisions (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 run command. This fix is not invoked during energy minimization.

## Restrictions

This command can only be used if LAMMPS was built with the SRD package. See the Build package doc page for more info.

## Related commands

fix wall/srd

## Default

The option defaults are: lamda (\(\lambda\)) is 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, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).

(Petersen) Petersen, Lechman, Plimpton, Grest, in’ t Veld, Schunk, J Chem Phys, 132, 174106 (2010).

(Lechman) Lechman, et al, in preparation (2010).