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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8932 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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pscrozi 2012-10-10 00:35:57 +00:00
parent bf38f77b44
commit 43a5f76cdc
4 changed files with 20 additions and 63 deletions
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25
doc/kspace_modify.html
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@ -24,11 +24,9 @@
<I>mesh/disp</I> value = x y z
x,y,z = grid size in each dimension for 1/r^6 dispersion
<I>order</I> 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
<I>order/disp</I> value = N
N = extent of Gaussian for PPPM mapping of dispersion term to grid
<I>order/split</I> value = N
N = order of Taylor series used to split the potential between different MSM levels
<I>force</I> value = accuracy (force units)
<I>gewald</I> value = rinv (1/distance units)
rinv = G-ewald parameter for Coulombics
@ -45,7 +43,7 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>kspace_modify mesh 24 24 30 order 6 order/split 3
<PRE>kspace_modify mesh 24 24 30 order 6
kspace_modify slab 3.0
</PRE>
<P><B>Description:</B>
@ -88,14 +86,6 @@ dispersion term extends when it is mapped to the grid in kspace style
<I>pppm/disp</I>. It has the same meaning as the <I>order</I> setting for
Coulombics.
</P>
<P>The <I>order/split</I> 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. <A HREF = "#Hardy">(Hardy)</A> recommends that the <I>order/split</I>
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 <I>order/split</I> 5 or 6, though this will
increase the interpolation cost as described above.
</P>
<P>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 <I>pppm</I> variants will be added later.
<P><B>Default:</B>
</P>
<P>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).
</P>
<HR>
@ -189,10 +178,4 @@ diff = ad (MSM).
<P><B>(Yeh)</B> Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
</P>
<A NAME = "Hardy"></A>
<P><B>(Hardy)</B> David, Multilevel Summation for the Fast Evaluation of
Forces for the Simulation of Biomolecules, University of Illinois
at Urbana-Champaign, (2006).
</P>
</HTML>

26
doc/kspace_modify.txt
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@ -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).

17
doc/kspace_style.html
View File

@ -77,7 +77,7 @@ style</A> 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:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD >Pair style </TD><TD > KSpace style </TD></TR>
<TR ALIGN="center"><TD >coul/long </TD><TD > ewald or pppm</TD></TR>
<TR ALIGN="center"><TD >coul/msm </TD><TD > msm</TD></TR>
@ -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.
</P>
<P>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.
</P>
<HR>
@ -184,7 +179,7 @@ smaller than the reference force.
</P>
<P>The accuracy setting is used in conjunction with the pairwise cutoff
to determine the number of K-space vectors for style <I>ewald</I> or the
FFT grid size for style <I>pppm</I> or <I>msm</I>.
grid size for style <I>pppm</I> or <I>msm</I>.
</P>
<P>RMS force errors in real space for <I>ewald</I> and <I>pppm</I> are estimated
using equation 18 of <A HREF = "#Kolafa">(Kolafa)</A>, which is also referenced as

15
doc/kspace_style.txt
View File

@ -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