From 43a5f76cdcfe8db3256e7ee55b163293adbf9dc6 Mon Sep 17 00:00:00 2001 From: pscrozi Date: Wed, 10 Oct 2012 00:35:57 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8932 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/kspace_modify.html | 25 ++++--------------------- doc/kspace_modify.txt | 26 +++++--------------------- doc/kspace_style.html | 17 ++++++----------- doc/kspace_style.txt | 15 +++++---------- 4 files changed, 20 insertions(+), 63 deletions(-) diff --git a/doc/kspace_modify.html b/doc/kspace_modify.html index bb6b3207c4..5b934c4d3a 100644 --- a/doc/kspace_modify.html +++ b/doc/kspace_modify.html @@ -24,11 +24,9 @@ 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 + 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 - 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 @@ -45,7 +43,7 @@

Examples:

-
kspace_modify mesh 24 24 30 order 6 order/split 3
+
kspace_modify mesh 24 24 30 order 6
 kspace_modify slab 3.0 
 

 
Description:
@@ -88,14 +86,6 @@ 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) 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
@@ -179,9 +169,8 @@ option.  Support for those pppm variants will be added later.
 
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).
+5 (PPPM), order = 4 (MSM), force = -1.0, gewald = gewald/disp = 0.0, 
+slab = 1.0, compute = yes, and diff = ik (PPPM), diff = ad (MSM).
 

 

 
@@ -189,10 +178,4 @@ diff = ad (MSM).
 
 
(Yeh) Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
 

-
-
-
(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/kspace_modify.txt b/doc/kspace_modify.txt
index 815e2dc75b..b0078dcabd 100644
--- a/doc/kspace_modify.txt
+++ b/doc/kspace_modify.txt
@@ -19,11 +19,9 @@ keyword = {mesh} or {order} or {gewald} or {slab} or (nozforce} or {compute} or
   {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
+    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
-  {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
@@ -39,7 +37,7 @@ keyword = {mesh} or {order} or {gewald} or {slab} or (nozforce} or {compute} or
 
 [Examples:]
 
-kspace_modify mesh 24 24 30 order 6 order/split 3
+kspace_modify mesh 24 24 30 order 6
 kspace_modify slab 3.0 :pre
 
 [Description:]
@@ -60,7 +58,7 @@ user-specified accuracy and pairwise cutoff.  Values for x,y,z of
 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,
+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.
 
@@ -82,14 +80,6 @@ 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
@@ -173,16 +163,10 @@ option.  Support for those {pppm} variants will be added later.
 [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).
+5 (PPPM), order = 4 (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/kspace_style.html b/doc/kspace_style.html
index 70451136eb..f21546e197 100644
--- a/doc/kspace_style.html
+++ b/doc/kspace_style.html
@@ -77,7 +77,7 @@ 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:
 

-

+

@@ -161,15 +161,10 @@ as N. It may therefore be faster than the other K-space solvers for
 relatively large problems when running on large core counts.
 
MSM is most competitive versus Ewald and PPPM when only relatively 
-low accuracy forces, about 1% relative error or higher, are needed.
-Note that MSM speed will be poor for large MSM meshes 
-(i.e. 64 x 64 x 64 or larger).  Also 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. 
-Beware that the error estimation method for MSM is not very accurate,
-so you should probably set your own mesh size and ensure that you are
-getting adequate force accuracy by doing an energy conservation test 
-or comparison versus the Ewald method.
+low accuracy forces, about 1e-4 relative error or less accurate, 
+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.
 

 
@@ -184,7 +179,7 @@ smaller than the reference force.
 
The accuracy setting is used in conjunction with the pairwise cutoff
 to determine the number of K-space vectors for style ewald or the
-FFT grid size for style pppm or msm.
+grid size for style pppm or msm.
 
RMS force errors in real space for ewald and pppm are estimated
 using equation 18 of (Kolafa), which is also referenced as
diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt
index ddd4b34a92..9773d60adf 100644
--- a/doc/kspace_style.txt
+++ b/doc/kspace_style.txt
@@ -154,15 +154,10 @@ as N. It may therefore be faster than the other K-space solvers for
 relatively large problems when running on large core counts.
 
 MSM is most competitive versus Ewald and PPPM when only relatively 
-low accuracy forces, about 1% relative error or higher, are needed.
-Note that MSM speed will be poor for large MSM meshes 
-(i.e. 64 x 64 x 64 or larger).  Also 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. 
-Beware that the error estimation method for MSM is not very accurate,
-so you should probably set your own mesh size and ensure that you are
-getting adequate force accuracy by doing an energy conservation test 
-or comparison versus the Ewald method.
+low accuracy forces, about 1e-4 relative error or less accurate, 
+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.
 
 :line
 
@@ -177,7 +172,7 @@ smaller than the reference force.
 
 The accuracy setting is used in conjunction with the pairwise cutoff
 to determine the number of K-space vectors for style {ewald} or the
-FFT grid size for style {pppm} or {msm}.
+grid size for style {pppm} or {msm}.
 
 RMS force errors in real space for {ewald} and {pppm} are estimated
 using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as


 
Pair style  KSpace style 

 
coul/long  ewald or pppm

 
coul/msm  msm