forked from lijiext/lammps
336 lines
17 KiB
Plaintext
336 lines
17 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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kspace_modify command :h3
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[Syntax:]
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kspace_modify keyword value ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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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
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{mesh} value = x y z
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x,y,z = grid size in each dimension for long-range Coulombics
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{mesh/disp} value = x y z
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x,y,z = grid size in each dimension for 1/r^6 dispersion
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{order} value = N
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N = extent of Gaussian for PPPM or MSM mapping of charge to grid
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{order/disp} value = N
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N = extent of Gaussian for PPPM mapping of dispersion term to grid
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{mix/disp} value = {pair} or {geom} or {none}
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{overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
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{minorder} value = M
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M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
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{force} value = accuracy (force units)
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{gewald} value = rinv (1/distance units)
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rinv = G-ewald parameter for Coulombics
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{gewald/disp} value = rinv (1/distance units)
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rinv = G-ewald parameter for dispersion
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{slab} value = volfactor or {nozforce}
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volfactor = ratio of the total extended volume used in the
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2d approximation compared with the volume of the simulation domain
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{nozforce} turns off kspace forces in the z direction
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{compute} value = {yes} or {no}
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{cutoff/adjust} value = {yes} or {no}
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{pressure/scalar} value = {yes} or {no}
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{fftbench} value = {yes} or {no}
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{collective} value = {yes} or {no}
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{diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
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{kmax/ewald} value = kx ky kz
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kx,ky,kz = number of Ewald sum kspace vectors in each dimension
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{force/disp/real} value = accuracy (force units)
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{force/disp/kspace} value = accuracy (force units)
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{splittol} value = tol
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tol = relative size of two eigenvalues (see discussion below)
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{disp/auto} value = yes or no :pre
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:ule
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[Examples:]
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kspace_modify mesh 24 24 30 order 6
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kspace_modify slab 3.0 :pre
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[Description:]
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Set parameters used by the kspace solvers defined by the
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"kspace_style"_kspace_style.html command. Not all parameters are
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relevant to all kspace styles.
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The {mesh} keyword sets the grid size for kspace style {pppm} or
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{msm}. In the case of PPPM, this is the FFT mesh, and each dimension
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must be factorizable into powers of 2, 3, and 5. In the case of MSM,
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this is the finest scale real-space mesh, and each dimension must be
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factorizable into powers of 2. When this option is not set, the PPPM
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or MSM solver chooses its own grid size, consistent with the
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user-specified accuracy and pairwise cutoff. Values for x,y,z of
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0,0,0 unset the option.
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The {mesh/disp} keyword sets the grid size for kspace style
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{pppm/disp}. This is the FFT mesh for long-range dispersion and ach
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dimension must be factorizable into powers of 2, 3, and 5. When this
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option is not set, the PPPM solver chooses its own grid size,
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consistent with the user-specified accuracy and pairwise cutoff.
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Values for x,y,z of 0,0,0 unset the option.
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The {order} keyword determines how many grid spacings an atom's charge
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extends when it is mapped to the grid in kspace style {pppm} or {msm}.
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The default for this parameter is 5 for PPPM and 8 for MSM, which
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means each charge spans 5 or 8 grid cells in each dimension,
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respectively. For the LAMMPS implementation of MSM, the order can
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range from 4 to 10 and must be even. For PPPM, the minimum allowed
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setting is 2 and the maximum allowed setting is 7. The larger the
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value of this parameter, the smaller that LAMMPS will set the grid
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size, to achieve the requested accuracy. Conversely, the smaller the
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order value, the larger the grid size will be. Note that there is an
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inherent trade-off involved: a small grid will lower the cost of FFTs
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or MSM direct sum, but a larger order parameter will increase the cost
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of interpolating charge/fields to/from the grid.
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The {order/disp} keyword determines how many grid spacings an atom's
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dispersion term extends when it is mapped to the grid in kspace style
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{pppm/disp}. It has the same meaning as the {order} setting for
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Coulombics.
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The {overlap} keyword can be used in conjunction with the {minorder}
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keyword with the PPPM styles to adjust the amount of communication
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that occurs when values on the FFT grid are exchangeed between
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processors. This communication is distinct from the communication
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inherent in the parallel FFTs themselves, and is required because
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processors interpolate charge and field values using grid point values
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owned by neighboring processors (i.e. ghost point communication). If
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the {overlap} keyword is set to {yes} then this communication is
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allowed to extend beyond nearest-neighbor processors, e.g. when using
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lots of processors on a small problem. If it is set to {no} then the
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communication will be limited to nearest-neighbor processors and the
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{order} setting will be reduced if necessary, as explained by the
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{minorder} keyword discussion. The {overlap} keyword is always set to
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{yes} in MSM.
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The {minorder} keyword allows LAMMPS to reduce the {order} setting if
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necessary to keep the communication of ghost grid point limited to
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exchanges between nearest-neighbor processors. See the discussion of
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the {overlap} keyword for details. If the {overlap} keyword is set to
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{yes}, which is the default, this is never needed. If it set to {no}
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and overlap occurs, then LAMMPS will reduce the order setting, one
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step at a time, until the ghost grid overlap only extends to nearest
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neighbor processors. The {minorder} keyword limits how small the
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{order} setting can become. The minimum allowed value for PPPM is 2,
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which is the default. If {minorder} is set to the same value as
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{order} then no reduction is allowed, and LAMMPS will generate an
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error if the grid communcation is non-nearest-neighbor and {overlap}
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is set to {no}. The {minorder} keyword is not currently supported in
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MSM.
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The PPPM order parameter may be reset by LAMMPS when it sets up the
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FFT grid if the implied grid stencil extends beyond the grid cells
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owned by neighboring processors. Typically this will only occur when
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small problems are run on large numbers of processors. A warning will
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be generated indicating the order parameter is being reduced to allow
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LAMMPS to run the problem. Automatic adjustment of the order parameter
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is not supported in MSM.
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The {force} keyword overrides the relative accuracy parameter set by
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the "kspace_style"_kspace_style.html command with an absolute
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accuracy. The accuracy determines the RMS error in per-atom forces
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calculated by the long-range solver and is thus specified in force
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units. A negative value for the accuracy setting means to use the
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relative accuracy parameter. The accuracy setting is used in
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conjunction with the pairwise cutoff to determine the number of
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K-space vectors for style {ewald}, the FFT grid size for style
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{pppm}, or the real space grid size for style {msm}.
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The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
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parameter for charge as {rinv} in reciprocal distance units. Without
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this setting, LAMMPS chooses the parameter automatically as a function
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of cutoff, precision, grid spacing, etc. This means it can vary from
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one simulation to the next which may not be desirable for matching a
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KSpace solver to a pre-tabulated pairwise potential. This setting can
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also be useful if Ewald or PPPM fails to choose a good grid spacing
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and G-ewald parameter automatically. If the value is set to 0.0,
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LAMMPS will choose the G-ewald parameter automatically. MSM does not
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use the {gewald} parameter.
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The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
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parameter for dispersion as {rinv} in reciprocal distance units. It
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has the same meaning as the {gewald} setting for Coulombics.
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The {slab} keyword allows an Ewald or PPPM solver to be used for a
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systems that are periodic in x,y but non-periodic in z - a
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"boundary"_boundary.html setting of "boundary p p f". This is done by
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treating the system as if it were periodic in z, but inserting empty
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volume between atom slabs and removing dipole inter-slab interactions
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so that slab-slab interactions are effectively turned off. The
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volfactor value sets the ratio of the extended dimension in z divided
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by the actual dimension in z. The recommended value is 3.0. A larger
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value is inefficient; a smaller value introduces unwanted slab-slab
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interactions. The use of fixed boundaries in z means that the user
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must prevent particle migration beyond the initial z-bounds, typically
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by providing a wall-style fix. The methodology behind the {slab}
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option is explained in the paper by "(Yeh)"_#Yeh. The {slab} option
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is also extended to non-neutral systems
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"(Ballenegger)"_#Ballenegger. An alternative slab option can be
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invoked with the {nozforce} keyword in lieu of the volfactor. This
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turns off all kspace forces in the z direction. The {nozforce} option
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is not supported by MSM. For MSM, any combination of periodic,
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non-periodic, or shrink-wrapped boundaries can be set using
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"boundary"_boundary.html (the slab approximation in not needed). The
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{slab} keyword is not currently supported by Ewald or PPPM when using
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a triclinic simulation cell. The slab correction has also been
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extended to point dipole interactions "(Klapp)"_#Klapp in
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"kspace_style"_kspace_style.html {ewald/disp}.
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The {compute} keyword allows Kspace computations to be turned off,
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even though a "kspace_style"_kspace_style.html is defined. This is
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not useful for running a real simulation, but can be useful for
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debugging purposes or for computing only partial forces that do not
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include the Kspace contribution. You can also do this by simply not
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defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
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"pair_style"_pair_style.html requires a kspace style to be defined.
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This keyword gives you that option.
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The {cutoff/adjust} keyword applies only to MSM. If this option is
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turned on, the Coulombic cutoff will be automatically adjusted at the
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beginning of the run to give the desired estimated error. Other
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cutoffs such as LJ will not be affected. If the grid is not set using
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the {mesh} command, this command will also attempt to use the optimal
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grid that minimizes cost using an estimate given by
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"(Hardy)"_#Hardy. Note that this cost estimate is not exact, somewhat
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experimental, and still may not yield the optimal parameters.
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The {pressure/scalar} keyword applies only to MSM. If this option is
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turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
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be computed, which can be used, for example, to run an isotropic barostat.
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Computing the full pressure tensor with MSM is expensive, and this option
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provides a faster alternative. The scalar pressure is computed using a
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relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer
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instead of using the virial equation. This option cannot be used to access
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individual components of the pressure tensor, to compute per-atom virial,
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or with suffix kspace/pair styles of MSM, like OMP or GPU.
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The {fftbench} keyword applies only to PPPM. It is on by default. If
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this option is turned off, LAMMPS will not take the time at the end
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of a run to give FFT benchmark timings, and will finish a few seconds
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faster than it would if this option were on.
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The {collective} keyword applies only to PPPM. It is set to {no} by
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default, except on IBM BlueGene machines. If this option is set to
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{yes}, LAMMPS will use MPI collective operations to remap data for
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3d-FFT operations instead of the default point-to-point communication.
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This is faster on IBM BlueGene machines, and may also be faster on
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other machines if they have an efficient implementation of MPI
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collective operations and adequate hardware.
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The {diff} keyword specifies the differentiation scheme used by the
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PPPM method to compute forces on particles given electrostatic
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potentials on the PPPM mesh. The {ik} approach is the default for
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PPPM and is the original formulation used in "(Hockney)"_#Hockney. It
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performs differentiation in Kspace, and uses 3 FFTs to transfer each
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component of the computed fields back to real space for total of 4
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FFTs per timestep.
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The analytic differentiation {ad} approach uses only 1 FFT to transfer
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information back to real space for a total of 2 FFTs per timestep. It
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then performs analytic differentiation on the single quantity to
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generate the 3 components of the electric field at each grid point.
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This is sometimes referred to as "smoothed" PPPM. This approach
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requires a somewhat larger PPPM mesh to achieve the same accuracy as
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the {ik} method. Currently, only the {ik} method (default) can be
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used for a triclinic simulation cell with PPPM. The {ad} method is
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always used for MSM.
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IMPORTANT NOTE: Currently, not all PPPM styles support the {ad}
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option. Support for those PPPM variants will be added later.
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The {kmax/ewald} keyword sets the number of kspace vectors in each
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dimension for kspace style {ewald}. The three values must be positive
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integers, or else (0,0,0), which unsets the option. When this option
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is not set, the Ewald sum scheme chooses its own kspace vectors,
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consistent with the user-specified accuracy and pairwise cutoff. In
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any case, if kspace style {ewald} is invoked, the values used are
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printed to the screen and the log file at the start of the run.
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With the {mix/disp} keyword one can select the mixing rule for the
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dispersion coefficients. With {pair}, the dispersion coefficients of
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unlike types are computed as indicated with
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"pair_modify"_pair_modify.html. With {geom}, geometric mixing is
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enforced on the dispersion coefficients in the kspace
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coefficients. When using the arithmetic mixing rule, this will
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speed-up the simulations but introduces some error in the force
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computations, as shown in "(Wennberg)"_#Wennberg. With {none}, it is
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assumed that no mixing rule is applicable. Splitting of the dispersion
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coefficients will be performed as described in
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"(Isele-Holder)"_#Isele-Holder. This splitting can be influenced with
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the {splittol} keywords. Only the eigenvalues that are larger than tol
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compared to the largest eigenvalues are included. Using this keywords
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the original matrix of dispersion coefficients is approximated. This
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leads to faster computations, but the accuracy in the reciprocal space
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computations of the dispersion part is decreased.
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The {force/disp/real} and {force/disp/kspace} keywords set the force
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accuracy for the real and space computations for the dispersion part
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of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder, optimal
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performance and accuracy in the results is obtained when these values
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are different.
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The {disp/auto} option controlls whether the pppm/disp is allowed to
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generate PPPM parameters automatically. If set to {no}, parameters have
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to be specified using the {gewald/disp}, {mesh/disp},
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{force/disp/real} or {force/disp/kspace} keywords, or
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the code will stop with an error message. When this option is set to
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{yes}, the error message will not appear and the simulation will start.
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For a typical application, using the automatic parameter generation will provide
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simulations that are either inaccurate or slow. Using this option is thus not
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recommended. For guidelines on how to obtain good parameters, see the "How-To"_Section_howto.html#howto_23 discussion.
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[Restrictions:] none
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[Related commands:]
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"kspace_style"_kspace_style.html, "boundary"_boundary.html
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[Default:]
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The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
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5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
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gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
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yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
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(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
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split = 0, tol = 1.0e-6, and disp/auto = no.
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:line
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:link(Hockney)
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[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
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Adam Hilger, NY (1989).
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:link(Yeh)
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[(Yeh)] Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
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:link(Ballenegger)
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[(Ballenegger)] Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
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(2009).
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:link(Klapp)
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[(Klapp)] Klapp, Schoen, J Chem Phys, 117, 8050 (2002).
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:link(Hardy)
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[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
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Evaluation of Forces for the Simulation of Biomolecules, University of
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Illinois at Urbana-Champaign, (2006).
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:link(Hummer)
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[(Hummer)] Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
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:link(Isele-Holder)
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[(Isele-Holder)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
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Chem Theory Comput, 9, 5412 (2013).
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:link(Wennberg)
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[(Wennberg)] Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
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9, 3527 (2013).
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