From 426ad1c55bd8908fc099309d44da4b5fb7fa1925 Mon Sep 17 00:00:00 2001 From: pscrozi Date: Mon, 7 Jan 2013 23:20:16 +0000 Subject: [PATCH] Updating kspace docs to reflect changes in MSM allowing non-periodic boundaries. git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9244 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/kspace_modify.html | 12 ++++++------ doc/kspace_modify.txt | 12 ++++++------ doc/kspace_style.html | 21 +++++++++++++++------ doc/kspace_style.txt | 19 ++++++++++++++----- 4 files changed, 41 insertions(+), 23 deletions(-) diff --git a/doc/kspace_modify.html b/doc/kspace_modify.html index d3fa736a4e..3da9a66b4f 100644 --- a/doc/kspace_modify.html +++ b/doc/kspace_modify.html @@ -168,8 +168,10 @@ 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). 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. +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 (the slab approximation in not needed).

The compute keyword allows Kspace computations to be turned off, even though a kspace_style is defined. This is @@ -203,9 +205,7 @@ 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. Analogous approaches have been implemented in MSM -and can be specified using the same keywords. The ad approach is -the default for MSM. +the ik method. The ad method is always used for MSM.

IMPORTANT NOTE: Currently, not all PPPM styles support the ad option. Support for those PPPM variants will be added later. @@ -221,7 +221,7 @@ option. Support for those PPPM variants will be added later.

The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = 5 (PPPM), order = 8 (MSM), minorder = 2, overlap = yes, force = -1.0, gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes, and diff = ik (PPPM), diff = ad (MSM). +yes (MSM), and diff = ik (PPPM).

diff --git a/doc/kspace_modify.txt b/doc/kspace_modify.txt index 158d710655..3a21672458 100644 --- a/doc/kspace_modify.txt +++ b/doc/kspace_modify.txt @@ -162,8 +162,10 @@ 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. +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 {compute} keyword allows Kspace computations to be turned off, even though a "kspace_style"_kspace_style.html is defined. This is @@ -197,9 +199,7 @@ 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. Analogous approaches have been implemented in MSM -and can be specified using the same keywords. The {ad} approach is -the default for MSM. +the {ik} method. The {ad} method is always used for MSM. IMPORTANT NOTE: Currently, not all PPPM styles support the {ad} option. Support for those PPPM variants will be added later. @@ -215,7 +215,7 @@ option. Support for those PPPM variants will be added later. The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = 5 (PPPM), order = 8 (MSM), minorder = 2, overlap = yes, force = -1.0, gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes, and diff = ik (PPPM), diff = ad (MSM). +yes (MSM), and diff = ik (PPPM). :line diff --git a/doc/kspace_style.html b/doc/kspace_style.html index 06ae1a674d..c12340b364 100644 --- a/doc/kspace_style.html +++ b/doc/kspace_style.html @@ -73,7 +73,7 @@ style to perform consistent short-range pairwise calculations. This means that the name of the pair style contains a matching keyword to the name of the KSpace style, as in this table:

-
+
@@ -159,7 +159,8 @@ mesh, and uses a multi-level hierarchy of coarser and coarser meshes on which direct coulomb solves are done. This method does not use FFTs and scales as N. It may therefore be faster than the other K-space solvers for relatively large problems when running on large -core counts. +core counts. MSM can also be used for non-periodic boundary conditions and +for mixed periodic and non-periodic boundaries.

MSM is most competitive versus Ewald and PPPM when only relatively low accuracy forces, about 1e-4 relative error or less accurate, @@ -167,6 +168,10 @@ are needed. Note that use of a larger coulomb cutoff (i.e. 15 angstroms instead of 10 angstroms) provides better MSM accuracy for both the real space and grid computed forces.

+

Currently the pressure calculation in MSM is expensive, +so calculating the pressure at every timestep or using a fixed pressure +simulation with MSM will cause the code to run slower. +

The specified accuracy determines the relative RMS error in per-atom @@ -231,10 +236,14 @@ only enabled if LAMMPS was built with that package. See the kspace_modify, in which case the xy dimensions -must be periodic and the z dimension must be non-periodic. +

For MSM, a simulation must be 3d and one can use any combination of +periodic, non-periodic, or shrink-wrapped boundaries (specified using +the boundary command). +

+

For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions. +The only exception is if the slab option is set with kspace_modify, +in which case the xy dimensions must be periodic and the z dimension must be +non-periodic.

Related commands:

diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt index 68fc97deb2..6f3be625dd 100644 --- a/doc/kspace_style.txt +++ b/doc/kspace_style.txt @@ -152,7 +152,8 @@ mesh, and uses a multi-level hierarchy of coarser and coarser meshes on which direct coulomb solves are done. This method does not use FFTs and scales as N. It may therefore be faster than the other K-space solvers for relatively large problems when running on large -core counts. +core counts. MSM can also be used for non-periodic boundary conditions and +for mixed periodic and non-periodic boundaries. MSM is most competitive versus Ewald and PPPM when only relatively low accuracy forces, about 1e-4 relative error or less accurate, @@ -160,6 +161,10 @@ are needed. Note that use of a larger coulomb cutoff (i.e. 15 angstroms instead of 10 angstroms) provides better MSM accuracy for both the real space and grid computed forces. +Currently the pressure calculation in MSM is expensive, +so calculating the pressure at every timestep or using a fixed pressure +simulation with MSM will cause the code to run slower. + :line The specified {accuracy} determines the relative RMS error in per-atom @@ -224,10 +229,14 @@ only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. Note that the KSPACE package is installed by default. -A simulation must be 3d and periodic in all dimensions to use an Ewald -or PPPM solver. The only exception is if the slab option is set with -"kspace_modify"_kspace_modify.html, in which case the xy dimensions -must be periodic and the z dimension must be non-periodic. +For MSM, a simulation must be 3d and one can use any combination of +periodic, non-periodic, or shrink-wrapped boundaries (specified using +the "boundary"_boundary.html command). + +For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions. +The only exception is if the slab option is set with "kspace_modify"_kspace_modify.html, +in which case the xy dimensions must be periodic and the z dimension must be +non-periodic. [Related commands:]
Pair style KSpace style
coul/long ewald or pppm
coul/msm msm