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Updating kspace docs to reflect changes in MSM allowing non-periodic boundaries.

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9244 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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pscrozi
2013-01-07 23:20:16 +00:00
parent 7886b6f1d1
commit 426ad1c55b
4 changed files with 41 additions and 23 deletions
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12
doc/kspace_modify.html
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@ -168,8 +168,10 @@ must prevent particle migration beyond the initial z-bounds, typically
by providing a wall-style fix. The methodology behind the <I>slab</I> by providing a wall-style fix. The methodology behind the <I>slab</I>
option is explained in the paper by <A HREF = "#Yeh">(Yeh)</A>. An alternative slab option is explained in the paper by <A HREF = "#Yeh">(Yeh)</A>. An alternative slab
option can be invoked with the <I>nozforce</I> keyword in lieu of the option can be invoked with the <I>nozforce</I> keyword in lieu of the
volfactor. This turns off all kspace forces in the z direction. The volfactor. This turns off all kspace forces in the z direction.
<I>slab</I> and <I>nozforce</I> options are not allowed for MSM. The <I>nozforce</I> option is not supported by MSM. For MSM, any combination
of periodic, non-periodic, or shrink-wrapped boundaries can be set
using <A HREF = "boundary.html">boundary</A> (the slab approximation in not needed).
</P> </P>
<P>The <I>compute</I> keyword allows Kspace computations to be turned off, <P>The <I>compute</I> keyword allows Kspace computations to be turned off,
even though a <A HREF = "kspace_style.html">kspace_style</A> is defined. This is even though a <A HREF = "kspace_style.html">kspace_style</A> 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. generate the 3 components of the electric field at each grid point.
This is sometimes referred to as "smoothed" PPPM. This approach This is sometimes referred to as "smoothed" PPPM. This approach
requires a somewhat larger PPPM mesh to achieve the same accuracy as requires a somewhat larger PPPM mesh to achieve the same accuracy as
the <I>ik</I> method. Analogous approaches have been implemented in MSM the <I>ik</I> method. The <I>ad</I> method is always used for MSM.
and can be specified using the same keywords. The <I>ad</I> approach is
the default for MSM.
</P> </P>
<P>IMPORTANT NOTE: Currently, not all PPPM styles support the <I>ad</I> <P>IMPORTANT NOTE: Currently, not all PPPM styles support the <I>ad</I>
option. Support for those PPPM variants will be added later. option. Support for those PPPM variants will be added later.
@ -221,7 +221,7 @@ option. Support for those PPPM variants will be added later.
<P>The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = <P>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, 5 (PPPM), order = 8 (MSM), minorder = 2, overlap = yes, force = -1.0,
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = 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).
</P> </P>
<HR> <HR>

12
doc/kspace_modify.txt
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@ -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} by providing a wall-style fix. The methodology behind the {slab}
option is explained in the paper by "(Yeh)"_#Yeh. An alternative 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 option can be invoked with the {nozforce} keyword in lieu of the
volfactor. This turns off all kspace forces in the z direction. The volfactor. This turns off all kspace forces in the z direction.
{slab} and {nozforce} options are not allowed for MSM. 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, The {compute} keyword allows Kspace computations to be turned off,
even though a "kspace_style"_kspace_style.html is defined. This is 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. generate the 3 components of the electric field at each grid point.
This is sometimes referred to as "smoothed" PPPM. This approach This is sometimes referred to as "smoothed" PPPM. This approach
requires a somewhat larger PPPM mesh to achieve the same accuracy as requires a somewhat larger PPPM mesh to achieve the same accuracy as
the {ik} method. Analogous approaches have been implemented in MSM the {ik} method. The {ad} method is always used for 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} IMPORTANT NOTE: Currently, not all PPPM styles support the {ad}
option. Support for those PPPM variants will be added later. 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 = 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, 5 (PPPM), order = 8 (MSM), minorder = 2, overlap = yes, force = -1.0,
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = 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 :line

21
doc/kspace_style.html
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@ -73,7 +73,7 @@ style</A> to perform consistent short-range pairwise
calculations. This means that the name of the pair style contains a 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: matching keyword to the name of the KSpace style, as in this table:
</P> </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 >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/long </TD><TD > ewald or pppm</TD></TR>
<TR ALIGN="center"><TD >coul/msm </TD><TD > msm</TD></TR> <TR ALIGN="center"><TD >coul/msm </TD><TD > msm</TD></TR>
@ -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 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 FFTs and scales as N. It may therefore be faster than the other
K-space solvers for relatively large problems when running on large 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.
</P> </P>
<P>MSM is most competitive versus Ewald and PPPM when only relatively <P>MSM is most competitive versus Ewald and PPPM when only relatively
low accuracy forces, about 1e-4 relative error or less accurate, 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 angstroms instead of 10 angstroms) provides better MSM accuracy for
both the real space and grid computed forces. both the real space and grid computed forces.
</P> </P>
<P>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.
</P>
<HR> <HR>
<P>The specified <I>accuracy</I> determines the relative RMS error in per-atom <P>The specified <I>accuracy</I> determines the relative RMS error in per-atom
@ -231,10 +236,14 @@ only enabled if LAMMPS was built with that package. See the <A HREF = "Section_
LAMMPS</A> section for more info. Note that LAMMPS</A> section for more info. Note that
the KSPACE package is installed by default. the KSPACE package is installed by default.
</P> </P>
<P>A simulation must be 3d and periodic in all dimensions to use an Ewald <P>For MSM, a simulation must be 3d and one can use any combination of
or PPPM solver. The only exception is if the slab option is set with periodic, non-periodic, or shrink-wrapped boundaries (specified using
<A HREF = "kspace_modify.html">kspace_modify</A>, in which case the xy dimensions the <A HREF = "boundary.html">boundary</A> command).
must be periodic and the z dimension must be non-periodic. </P>
<P>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 <A HREF = "kspace_modify.html">kspace_modify</A>,
in which case the xy dimensions must be periodic and the z dimension must be
non-periodic.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>

19
doc/kspace_style.txt
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@ -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 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 FFTs and scales as N. It may therefore be faster than the other
K-space solvers for relatively large problems when running on large 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 MSM is most competitive versus Ewald and PPPM when only relatively
low accuracy forces, about 1e-4 relative error or less accurate, 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 angstroms instead of 10 angstroms) provides better MSM accuracy for
both the real space and grid computed forces. 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 :line
The specified {accuracy} determines the relative RMS error in per-atom 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 LAMMPS"_Section_start.html#start_3 section for more info. Note that
the KSPACE package is installed by default. the KSPACE package is installed by default.
A simulation must be 3d and periodic in all dimensions to use an Ewald For MSM, a simulation must be 3d and one can use any combination of
or PPPM solver. The only exception is if the slab option is set with periodic, non-periodic, or shrink-wrapped boundaries (specified using
"kspace_modify"_kspace_modify.html, in which case the xy dimensions the "boundary"_boundary.html command).
must be periodic and the z dimension must be non-periodic.
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:] [Related commands:]