From 7feb074d6678f6c15421574154c9a88a50a302ea Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 9 Oct 2012 14:51:20 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8924 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/kspace_modify.txt | 376 +++++++++++++++++++++--------------------- doc/pair_lj_long.html | 14 +- doc/pair_lj_long.txt | 14 +- 3 files changed, 202 insertions(+), 202 deletions(-) diff --git a/doc/kspace_modify.txt b/doc/kspace_modify.txt index 971bc7aa60..815e2dc75b 100644 --- a/doc/kspace_modify.txt +++ b/doc/kspace_modify.txt @@ -1,188 +1,188 @@ -"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 {gewald} or {slab} or (nozforce} or {compute} or {diff} :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 = gridextent 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 - {order/split} value = N - N = order of Taylor series used to split the potential between different MSM levels - {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} - {diff} value = {ik} or {ad} :pre -:ule - -[Examples:] - -kspace_modify mesh 24 24 30 order 6 order/split 3 -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 4 for MSM, which means -each charge spans 5 or 4 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 the grid will need to be to achieve the requested accuracy. -Conversely, the smaller the order value, the larger the grid 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 {order/split} keyword determines the order of the Taylor series -used to split the potential between different MSM grid levels, and can -range from 2 and 6. "(Hardy)"_#Hardy recommends that the {order/split} -be roughly half of the order parameter. For example, the default MSM -order is 4 and the default split order is 2. For higher accuracy in -MSM, one can use order 10 and {order/split} 5 or 6, though this will -increase the interpolation cost as described above. - -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 reduction of order is not currently -implemented in MSM, so an error (instead of a warning) will be generated. - -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. 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 -{slab} and {nozforce} options are not allowed for MSM. - -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 {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. It performs differentiation in Kspace, but uses 3 FFTs to -transfer the computed fields back to real space (total of 4 FFTs per -timestep). The analytic differentiation, or {ad} approach uses only 1 -FFT to transfer the computed fields back to real space (total of 2 -FFTs per timestep), but requires a somewhat larger PPPM mesh to -achieve the same accuracy as the {ik} approach. Analogous approaches -have been implemented in MSM and can be specified using the same -keywords. The {ad} approach is the default for MSM. - -IMPORTANT NOTE: Currently, not all {pppm} styles support the {ad} -option. Support for those {pppm} variants will be added later. - -[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 = 4 (MSM), order/split = 2 (MSM), force = -1.0, gewald -= gewald/disp = 0.0, slab = 1.0, compute = yes, and diff = ik (PPPM), -diff = ad (MSM). - -:line - -:link(Yeh) -[(Yeh)] Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999). - -:link(Hardy) -[(Hardy)] David, Multilevel Summation for the Fast Evaluation of -Forces for the Simulation of Biomolecules, University of Illinois -at Urbana-Champaign, (2006). +"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 {gewald} or {slab} or (nozforce} or {compute} or {diff} :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 = gridextent 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 + {order/split} value = N + N = order of Taylor series used to split the potential between different MSM levels + {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} + {diff} value = {ik} or {ad} :pre +:ule + +[Examples:] + +kspace_modify mesh 24 24 30 order 6 order/split 3 +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 4 for MSM, which means +each charge spans 5 or 4 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 the grid will need to be to achieve the requested accuracy. +Conversely, the smaller the order value, the larger the grid 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 {order/split} keyword determines the order of the Taylor series +used to split the potential between different MSM grid levels, and can +range from 2 and 6. "(Hardy)"_#Hardy recommends that the {order/split} +be roughly half of the order parameter. For example, the default MSM +order is 4 and the default split order is 2. For higher accuracy in +MSM, one can use order 10 and {order/split} 5 or 6, though this will +increase the interpolation cost as described above. + +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 reduction of order is not currently +implemented in MSM, so an error (instead of a warning) will be generated. + +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. 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 +{slab} and {nozforce} options are not allowed for MSM. + +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 {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. It performs differentiation in Kspace, but uses 3 FFTs to +transfer the computed fields back to real space (total of 4 FFTs per +timestep). The analytic differentiation, or {ad} approach uses only 1 +FFT to transfer the computed fields back to real space (total of 2 +FFTs per timestep), but requires a somewhat larger PPPM mesh to +achieve the same accuracy as the {ik} approach. Analogous approaches +have been implemented in MSM and can be specified using the same +keywords. The {ad} approach is the default for MSM. + +IMPORTANT NOTE: Currently, not all {pppm} styles support the {ad} +option. Support for those {pppm} variants will be added later. + +[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 = 4 (MSM), order/split = 2 (MSM), force = -1.0, gewald += gewald/disp = 0.0, slab = 1.0, compute = yes, and diff = ik (PPPM), +diff = ad (MSM). + +:line + +:link(Yeh) +[(Yeh)] Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999). + +:link(Hardy) +[(Hardy)] David, Multilevel Summation for the Fast Evaluation of +Forces for the Simulation of Biomolecules, University of Illinois +at Urbana-Champaign, (2006). diff --git a/doc/pair_lj_long.html b/doc/pair_lj_long.html index 59748b8688..25a50e772b 100644 --- a/doc/pair_lj_long.html +++ b/doc/pair_lj_long.html @@ -13,13 +13,13 @@

pair_style lj/long/coul/long/omp command

-

pair_style lj/long/coul/long/tip4p command +

pair_style lj/long/tip4p/long command

Syntax: 

pair_style style args
-