diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 66091f497..6d27bb707 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -1,344 +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 kspace_modify command :h3 [Syntax:] kspace_modify keyword value ... :pre one or more keyword/value pairs may be listed :ulb,l keyword = {mesh} or {order} or {order/disp} or {mix/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {fftbench} or {collective} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} or {disp/auto}:l {mesh} value = x y z x,y,z = grid size in each dimension for long-range Coulombics {mesh/disp} value = x y z x,y,z = grid size in each dimension for 1/r^6 dispersion {order} value = N N = extent of Gaussian for PPPM or MSM mapping of charge to grid {order/disp} value = N N = extent of Gaussian for PPPM mapping of dispersion term to grid {mix/disp} value = {pair} or {geom} or {none} {overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor {minorder} value = M M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication {force} value = accuracy (force units) {gewald} value = rinv (1/distance units) rinv = G-ewald parameter for Coulombics {gewald/disp} value = rinv (1/distance units) rinv = G-ewald parameter for dispersion {slab} value = volfactor or {nozforce} volfactor = ratio of the total extended volume used in the 2d approximation compared with the volume of the simulation domain {nozforce} turns off kspace forces in the z direction {compute} value = {yes} or {no} {cutoff/adjust} value = {yes} or {no} {pressure/scalar} value = {yes} or {no} {fftbench} value = {yes} or {no} {collective} value = {yes} or {no} {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode {kmax/ewald} value = kx ky kz kx,ky,kz = number of Ewald sum kspace vectors in each dimension {force/disp/real} value = accuracy (force units) {force/disp/kspace} value = accuracy (force units) {splittol} value = tol tol = relative size of two eigenvalues (see discussion below) {disp/auto} value = yes or no :pre :ule [Examples:] kspace_modify mesh 24 24 30 order 6 kspace_modify slab 3.0 :pre [Description:] Set parameters used by the kspace solvers defined by the "kspace_style"_kspace_style.html command. Not all parameters are relevant to all kspace styles. The {mesh} keyword sets the grid size for kspace style {pppm} or {msm}. In the case of PPPM, this is the FFT mesh, and each dimension must be factorizable into powers of 2, 3, and 5. In the case of MSM, this is the finest scale real-space mesh, and each dimension must be factorizable into powers of 2. When this option is not set, the PPPM or MSM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. The {mesh/disp} keyword sets the grid size for kspace style {pppm/disp}. This is the FFT mesh for long-range dispersion and ach dimension must be factorizable into powers of 2, 3, and 5. When this option is not set, the PPPM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. The {order} keyword determines how many grid spacings an atom's charge extends when it is mapped to the grid in kspace style {pppm} or {msm}. The default for this parameter is 5 for PPPM and 8 for MSM, which means each charge spans 5 or 8 grid cells in each dimension, respectively. For the LAMMPS implementation of MSM, the order can range from 4 to 10 and must be even. For PPPM, the minimum allowed setting is 2 and the maximum allowed setting is 7. The larger the value of this parameter, the smaller that LAMMPS will set the grid size, to achieve the requested accuracy. Conversely, the smaller the order value, the larger the grid size will be. Note that there is an inherent trade-off involved: a small grid will lower the cost of FFTs or MSM direct sum, but a larger order parameter will increase the cost of interpolating charge/fields to/from the grid. The {order/disp} keyword determines how many grid spacings an atom's dispersion term extends when it is mapped to the grid in kspace style {pppm/disp}. It has the same meaning as the {order} setting for Coulombics. The {overlap} keyword can be used in conjunction with the {minorder} keyword with the PPPM styles to adjust the amount of communication that occurs when values on the FFT grid are exchanged between processors. This communication is distinct from the communication inherent in the parallel FFTs themselves, and is required because processors interpolate charge and field values using grid point values owned by neighboring processors (i.e. ghost point communication). If the {overlap} keyword is set to {yes} then this communication is allowed to extend beyond nearest-neighbor processors, e.g. when using lots of processors on a small problem. If it is set to {no} then the communication will be limited to nearest-neighbor processors and the {order} setting will be reduced if necessary, as explained by the {minorder} keyword discussion. The {overlap} keyword is always set to {yes} in MSM. The {minorder} keyword allows LAMMPS to reduce the {order} setting if necessary to keep the communication of ghost grid point limited to exchanges between nearest-neighbor processors. See the discussion of the {overlap} keyword for details. If the {overlap} keyword is set to {yes}, which is the default, this is never needed. If it set to {no} and overlap occurs, then LAMMPS will reduce the order setting, one step at a time, until the ghost grid overlap only extends to nearest neighbor processors. The {minorder} keyword limits how small the {order} setting can become. The minimum allowed value for PPPM is 2, which is the default. If {minorder} is set to the same value as {order} then no reduction is allowed, and LAMMPS will generate an error if the grid communication is non-nearest-neighbor and {overlap} is set to {no}. The {minorder} keyword is not currently supported in MSM. The PPPM order parameter may be reset by LAMMPS when it sets up the FFT grid if the implied grid stencil extends beyond the grid cells owned by neighboring processors. Typically this will only occur when small problems are run on large numbers of processors. A warning will be generated indicating the order parameter is being reduced to allow LAMMPS to run the problem. Automatic adjustment of the order parameter is not supported in MSM. The {force} keyword overrides the relative accuracy parameter set by the "kspace_style"_kspace_style.html command with an absolute accuracy. The accuracy determines the RMS error in per-atom forces calculated by the long-range solver and is thus specified in force units. A negative value for the accuracy setting means to use the relative accuracy parameter. The accuracy setting is used in conjunction with the pairwise cutoff to determine the number of K-space vectors for style {ewald}, the FFT grid size for style {pppm}, or the real space grid size for style {msm}. The {gewald} keyword sets the value of the Ewald or PPPM G-ewald parameter for charge as {rinv} in reciprocal distance units. Without this setting, LAMMPS chooses the parameter automatically as a function of cutoff, precision, grid spacing, etc. This means it can vary from one simulation to the next which may not be desirable for matching a KSpace solver to a pre-tabulated pairwise potential. This setting can also be useful if Ewald or PPPM fails to choose a good grid spacing and G-ewald parameter automatically. If the value is set to 0.0, LAMMPS will choose the G-ewald parameter automatically. MSM does not use the {gewald} parameter. The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald parameter for dispersion as {rinv} in reciprocal distance units. It has the same meaning as the {gewald} setting for Coulombics. The {slab} keyword allows an Ewald or PPPM solver to be used for a systems that are periodic in x,y but non-periodic in z - a "boundary"_boundary.html setting of "boundary p p f". This is done by treating the system as if it were periodic in z, but inserting empty volume between atom slabs and removing dipole inter-slab interactions so that slab-slab interactions are effectively turned off. The volfactor value sets the ratio of the extended dimension in z divided by the actual dimension in z. The recommended value is 3.0. A larger value is inefficient; a smaller value introduces unwanted slab-slab interactions. The use of fixed boundaries in z means that the user must prevent particle migration beyond the initial z-bounds, typically by providing a wall-style fix. The methodology behind the {slab} option is explained in the paper by "(Yeh)"_#Yeh. The {slab} option is also extended to non-neutral systems "(Ballenegger)"_#Ballenegger. An alternative slab option can be invoked with the {nozforce} keyword in lieu of the volfactor. This turns off all kspace forces in the z direction. The {nozforce} option is not supported by MSM. For MSM, any combination of periodic, non-periodic, or shrink-wrapped boundaries can be set using "boundary"_boundary.html (the slab approximation in not needed). The {slab} keyword is not currently supported by Ewald or PPPM when using a triclinic simulation cell. The slab correction has also been extended to point dipole interactions "(Klapp)"_#Klapp in "kspace_style"_kspace_style.html {ewald/disp}. NOTE: If you wish to apply an electric field in the Z-direction, in conjunction with the {slab} keyword, you should do it by adding explicit charged particles to the +/- Z surfaces. If you do it via the "fix efield"_fix_efield.html command, it will not give the correct dielectric constant due to the Yeh/Berkowitz "(Yeh)"_#Yeh correction not being compatible with how "fix efield"_fix_efield.html works. The {compute} keyword allows Kspace computations to be turned off, even though a "kspace_style"_kspace_style.html is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for computing only partial forces that do not include the Kspace contribution. You can also do this by simply not defining a "kspace_style"_kspace_style.html, but a Kspace-compatible "pair_style"_pair_style.html requires a kspace style to be defined. This keyword gives you that option. The {cutoff/adjust} keyword applies only to MSM. If this option is turned on, the Coulombic cutoff will be automatically adjusted at the beginning of the run to give the desired estimated error. Other cutoffs such as LJ will not be affected. If the grid is not set using the {mesh} command, this command will also attempt to use the optimal grid that minimizes cost using an estimate given by "(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat experimental, and still may not yield the optimal parameters. The {pressure/scalar} keyword applies only to MSM. If this option is turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will be computed, which can be used, for example, to run an isotropic barostat. Computing the full pressure tensor with MSM is expensive, and this option provides a faster alternative. The scalar pressure is computed using a relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer instead of using the virial equation. This option cannot be used to access individual components of the pressure tensor, to compute per-atom virial, or with suffix kspace/pair styles of MSM, like OMP or GPU. -The {fftbench} keyword applies only to PPPM. It is on by default. If -this option is turned off, LAMMPS will not take the time at the end -of a run to give FFT benchmark timings, and will finish a few seconds -faster than it would if this option were on. +The {fftbench} keyword applies only to PPPM. It is off by default. If +this option is turned on, LAMMPS will perform a short FFT benchmark +computation and report its timings, and will thus finish a some seconds +later than it would if this option were off. The {collective} keyword applies only to PPPM. It is set to {no} by default, except on IBM BlueGene machines. If this option is set to {yes}, LAMMPS will use MPI collective operations to remap data for 3d-FFT operations instead of the default point-to-point communication. This is faster on IBM BlueGene machines, and may also be faster on other machines if they have an efficient implementation of MPI collective operations and adequate hardware. The {diff} keyword specifies the differentiation scheme used by the PPPM method to compute forces on particles given electrostatic potentials on the PPPM mesh. The {ik} approach is the default for PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It performs differentiation in Kspace, and uses 3 FFTs to transfer each component of the computed fields back to real space for total of 4 FFTs per timestep. The analytic differentiation {ad} approach uses only 1 FFT to transfer information back to real space for a total of 2 FFTs per timestep. It then performs analytic differentiation on the single quantity to generate the 3 components of the electric field at each grid point. This is sometimes referred to as "smoothed" PPPM. This approach requires a somewhat larger PPPM mesh to achieve the same accuracy as the {ik} method. Currently, only the {ik} method (default) can be used for a triclinic simulation cell with PPPM. The {ad} method is always used for MSM. NOTE: Currently, not all PPPM styles support the {ad} option. Support for those PPPM variants will be added later. The {kmax/ewald} keyword sets the number of kspace vectors in each dimension for kspace style {ewald}. The three values must be positive integers, or else (0,0,0), which unsets the option. When this option is not set, the Ewald sum scheme chooses its own kspace vectors, consistent with the user-specified accuracy and pairwise cutoff. In any case, if kspace style {ewald} is invoked, the values used are printed to the screen and the log file at the start of the run. With the {mix/disp} keyword one can select the mixing rule for the dispersion coefficients. With {pair}, the dispersion coefficients of unlike types are computed as indicated with "pair_modify"_pair_modify.html. With {geom}, geometric mixing is enforced on the dispersion coefficients in the kspace coefficients. When using the arithmetic mixing rule, this will speed-up the simulations but introduces some error in the force computations, as shown in "(Wennberg)"_#Wennberg. With {none}, it is assumed that no mixing rule is applicable. Splitting of the dispersion coefficients will be performed as described in "(Isele-Holder)"_#Isele-Holder1. This splitting can be influenced with the {splittol} keywords. Only the eigenvalues that are larger than tol compared to the largest eigenvalues are included. Using this keywords the original matrix of dispersion coefficients is approximated. This leads to faster computations, but the accuracy in the reciprocal space computations of the dispersion part is decreased. The {force/disp/real} and {force/disp/kspace} keywords set the force accuracy for the real and space computations for the dispersion part of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal performance and accuracy in the results is obtained when these values are different. The {disp/auto} option controls whether the pppm/disp is allowed to generate PPPM parameters automatically. If set to {no}, parameters have to be specified using the {gewald/disp}, {mesh/disp}, {force/disp/real} or {force/disp/kspace} keywords, or the code will stop with an error message. When this option is set to {yes}, the error message will not appear and the simulation will start. For a typical application, using the automatic parameter generation will provide simulations that are either inaccurate or slow. Using this option is thus not recommended. For guidelines on how to obtain good parameters, see the "How-To"_Section_howto.html#howto_24 discussion. [Restrictions:] none [Related commands:] "kspace_style"_kspace_style.html, "boundary"_boundary.html [Default:] The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = 5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0, gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik +yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order = order/disp = 7. :line :link(Hockney1) [(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles, Adam Hilger, NY (1989). :link(Yeh) [(Yeh)] Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999). :link(Ballenegger) [(Ballenegger)] Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009). :link(Klapp) [(Klapp)] Klapp, Schoen, J Chem Phys, 117, 8050 (2002). :link(Hardy1) [(Hardy)] David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006). :link(Hummer) [(Hummer)] Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998) :link(Isele-Holder1) [(Isele-Holder)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory Comput, 9, 5412 (2013). :link(Wennberg) [(Wennberg)] Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013).