Syntax: +
+fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ... ++
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 = style seed + style = old or no or yes or possible + seed = random # seed (positive integer) + stream value = yes or no = whether or not streaming velocity is added for shear deformation ++ +
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 partilces 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 rigid bodies containing multiples +spherioids and ellipsoids. 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 propoerties 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 2 things: +
+(1) It advects the SRD particles, performing collisions between SRD +and big particles 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 (lamda). The +fundamental equation relating these 4 quantities is +
+lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) ++
The mass 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 >= dt. +
+If the lamda keyword is not specified, the the SRD temperature +Tsrd is used in the above formula to compute lamda. 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. +
+Lamda cannot be smaller than 0.6 * hgrid, else an error is generated. +The velocities of SRD particles are bounded by Vmax, which is set so +that an SRD particle will not advect further than Dmax = 4*lamda in +dt_SRD. This means that roughly speaking, Dmax should not be larger +than a big particle diameter, else SRDs may pass thru big particles +without colliding. A warning is generated if this is the case. +
+SRD/big particle collisions are modeled as a lightweight SRD point +particle hitting a heavy big particle of given diameter 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. +
+The collision keyword sets the style of SRD/big particle collisions. +The slip style means that the tangential component of the SRD +particle momentum is preserved. Thus a force is imparted to the 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 the 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 +bewteen 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. +
+The search keyword can be used to choose a bin size for identifying +SRD/big particle collisions. The default is to use the hgrid +parameter 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. When the style of the shift keyword is set to +old, there is an additional constraint that there must be an integer +number of bins within each processor's sub-domain. Thus the actual +bin size will depend on the size and shape of the overall simulation +box and, in the case of shift set to old, on the number of +processors assigned to each dimension of the box (see the +processors command). 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. +
+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 +lamda. If lamda 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 seed is used to generate +these vectors. This operation sufficiently randomizes which SRD +particles are in the same bin, even if lamda is small. +
+If the shift style is set to old, then no shifting is performed. +An error will be generated if lamda < 0.6 of the SRD bin size. If the +shift style 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 lamda < 0.6 of the SRD bin size. If the +shift style 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 style is set to yes then +shifting is performed regardless of the magnitude of lamda. +
+The shift seed is not used if the shift style is set to old or +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 stream keyword is used when SRD particles are used with the fix +deform command to perform a simulation undergoing +shear, e.g. to measure a viscosity. If the stream style is set to +yes, then the mean velocity of each bin of SRD particles is set to +the streaming velocity of the deforming box, each time SRD velocities +are reset, every N timesteps. If the stream style is set to no, +then the mean velocity is unchanged, which may mean that it takes a +long time for the SRD fluid to come to equilibrium with a velocity +profile that matches the simulation box deformation. +
+IMPORTANT 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 communicate 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 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 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 thermodyanmic output. +
+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. +
+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: none +
+This command can only be used if LAMMPS was built with the "srd" +package. See the Making LAMMPS section for +more info on packages. +
+This fix can only be used with a fully periodic simulation box. +
+Related commands: none +
+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, stream = 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). +
+:link(Lechman) (Lechman) Lechman, et al, in preparation (2010). +
+ diff --git a/doc/fix_srd.txt b/doc/fix_srd.txt new file mode 100644 index 0000000000..1bb9fe5e98 --- /dev/null +++ b/doc/fix_srd.txt @@ -0,0 +1,344 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix srd command :h3 + +[Syntax:] + +fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html 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) :ul + +zero or more keyword/value pairs may be appended :ulb,l +keyword = {lamda} or {collision} or {overlap} or {inside} or {exact} or {radius} or {bounce} or {search} or {cubic} or {shift} or {stream} :l + {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 = style seed + style = {old} or {no} or {yes} or {possible} + seed = random # seed (positive integer) + {stream} value = {yes} or {no} = whether or not streaming velocity is added for shear deformation :pre +:ule + +[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 :pre + +[Description:] + +Treat a group of partilces 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)"_#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 rigid bodies containing multiples +spherioids and ellipsoids. 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 propoerties like +diffusivity and viscosity in a background fluid. The usual LAMMPS +fixes for such simulations, such as "fix deform"_fix_deform.html, "fix +viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html, +can be used in conjunction with the SRD model. + +For more details on how the SRD model is implemented in LAMMPS, "this +paper"_#Petersen describes the implementation and usage of pure SRD +fluids. "This paper"_#Lechman, 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 2 things: + +(1) It advects the SRD particles, performing collisions between SRD +and big particles 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 (lamda). The +fundamental equation relating these 4 quantities is + +lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) :pre + +The mass of SRD particles is set by the "mass"_mass.html command +elsewhere in the input script. The SRD timestep dt_SRD is N times the +step dt defined by the "timestep"_timestep.html command. Big +particles move in the normal way via a time integration "fix"_fix.html +with a short timestep dt. SRD particles advect with a large timestep +dt_SRD >= dt. + +If the {lamda} keyword is not specified, the the SRD temperature +{Tsrd} is used in the above formula to compute lamda. 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. + +Lamda cannot be smaller than 0.6 * hgrid, else an error is generated. +The velocities of SRD particles are bounded by Vmax, which is set so +that an SRD particle will not advect further than Dmax = 4*lamda in +dt_SRD. This means that roughly speaking, Dmax should not be larger +than a big particle diameter, else SRDs may pass thru big particles +without colliding. A warning is generated if this is the case. + +SRD/big particle collisions are modeled as a lightweight SRD point +particle hitting a heavy big particle of given diameter 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. + +The {collision} keyword sets the style of SRD/big particle collisions. +The {slip} style means that the tangential component of the SRD +particle momentum is preserved. Thus a force is imparted to the 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 the big particle. Thus a time integrator "fix"_fix.html that +rotates the big particles appropriately should be used. + +:line + +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"_fix_rigid.html 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 +bewteen 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. + +:line + +The {search} keyword can be used to choose a bin size for identifying +SRD/big particle collisions. The default is to use the {hgrid} +parameter 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. When the style of the {shift} keyword is set to +{old}, there is an additional constraint that there must be an integer +number of bins within each processor's sub-domain. Thus the actual +bin size will depend on the size and shape of the overall simulation +box and, in the case of {shift} set to {old}, on the number of +processors assigned to each dimension of the box (see the +"processors"_processors.html command). 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. + +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 +lamda. If lamda 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 seed is used to generate +these vectors. This operation sufficiently randomizes which SRD +particles are in the same bin, even if lamda is small. + +If the {shift} style is set to {old}, then no shifting is performed. +An error will be generated if lamda < 0.6 of the SRD bin size. If the +{shift} style 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 lamda < 0.6 of the SRD bin size. If the +{shift} style 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} style is set to {yes} then +shifting is performed regardless of the magnitude of lamda. + +The shift seed is not used if the {shift} style is set to {old} or +{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 {stream} keyword is used when SRD particles are used with the "fix +deform"_fix_deform.html command to perform a simulation undergoing +shear, e.g. to measure a viscosity. If the {stream} style is set to +{yes}, then the mean velocity of each bin of SRD particles is set to +the streaming velocity of the deforming box, each time SRD velocities +are reset, every N timesteps. If the {stream} style is set to {no}, +then the mean velocity is unchanged, which may mean that it takes a +long time for the SRD fluid to come to equilibrium with a velocity +profile that matches the simulation box deformation. + +:line + +IMPORTANT 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"_atom_modify.html, "neigh_modify +include"_neigh_modify.html, and "communicate group"_communicate.html +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"_pair_style.html for big/big particle +interactions is specified, the "pair_coeff"_pair_coeff.html 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. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html 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"_Section_howto.html#4_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 the last three 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 dues to SRD particles moving too far :ul + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] none + +This command can only be used if LAMMPS was built with the "srd" +package. See the "Making LAMMPS"_Section_start.html#2_3 section for +more info on packages. + +This fix can only be used with a fully periodic simulation box. + +[Related commands:] none + +[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, stream = yes. + +:line + +:link(Hecht) +[(Hecht)] Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005). + +:link(Petersen) +[(Petersen)] Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J +Chem Phys, 132, 174106 (2010). + +:link(Lechman) [(Lechman)] Lechman, et al, in preparation (2010).