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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11651 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-03-19 19:27:16 +00:00
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36
doc/kspace_style.html
View File

@ -200,12 +200,12 @@ angstroms instead of 10 angstroms) provides better MSM accuracy for
both the real space and grid computed forces.
</P>
<P>Currently calculation of the full pressure tensor in MSM is expensive.
Using the <A HREF = "kspace_modify.html">kspace_modify</A>
<I>pressure/scalar yes</I> command provides a less expensive way to compute the
scalar pressure (Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
to run an isotropic barostat. If the full pressure tensor is needed, then
calculating the pressure at every timestep or using a fixed pressure
simulation with MSM will cause the code to run slower.
Using the <A HREF = "kspace_modify.html">kspace_modify</A> <I>pressure/scalar yes</I>
command provides a less expensive way to compute the scalar pressure
(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
to run an isotropic barostat. If the full pressure tensor is needed,
then calculating the pressure at every timestep or using a fixed
pressure simulation with MSM will cause the code to run slower.
</P>
<HR>
@ -223,16 +223,20 @@ to determine the number of K-space vectors for style <I>ewald</I> or the
grid size for style <I>pppm</I> or <I>msm</I>.
</P>
<P>Note that style <I>pppm</I> only computes the grid size at the beginning of
a simulation, so if the length or triclinic tilt of the simulation cell
increases dramatically during the course of the simulation, the accuracy
of the simulation may degrade. For example, for a triclinic system with
all three tilt factors set to the maximum limit, the PPPM grid should be
increased roughly by a factor of 1.5 in the y direction and 2.0 in the z
direction as compared to the same system using a cubic orthogonal simulation
cell. One way to ensure the accuracy requirement is being met is to run a
short simulation at the maximum expected tilt or length, note the required
grid size, and then use the <A HREF = "kspace_modify.html">kspace_modify</A> <I>mesh</I>
command to manually set the PPPM grid size to this value.
a simulation, so if the length or triclinic tilt of the simulation
cell increases dramatically during the course of the simulation, the
accuracy of the simulation may degrade. Likewise, if the
<A HREF = "kspace_modify.html">kspace_modify slab</A> option is used with
shrink-wrap boundaries in the z-dimension, and the box size changes
dramatically in z. For example, for a triclinic system with all three
tilt factors set to the maximum limit, the PPPM grid should be
increased roughly by a factor of 1.5 in the y direction and 2.0 in the
z direction as compared to the same system using a cubic orthogonal
simulation cell. One way to ensure the accuracy requirement is being
met is to run a short simulation at the maximum expected tilt or
length, note the required grid size, and then use the
<A HREF = "kspace_modify.html">kspace_modify</A> <I>mesh</I> command to manually set the
PPPM grid size to this value.
</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

36
doc/kspace_style.txt
View File

@ -193,12 +193,12 @@ angstroms instead of 10 angstroms) provides better MSM accuracy for
both the real space and grid computed forces.
Currently calculation of the full pressure tensor in MSM is expensive.
Using the "kspace_modify"_kspace_modify.html
{pressure/scalar yes} command provides a less expensive way to compute the
scalar pressure (Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
to run an isotropic barostat. If the full pressure tensor is needed, then
calculating the pressure at every timestep or using a fixed pressure
simulation with MSM will cause the code to run slower.
Using the "kspace_modify"_kspace_modify.html {pressure/scalar yes}
command provides a less expensive way to compute the scalar pressure
(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
to run an isotropic barostat. If the full pressure tensor is needed,
then calculating the pressure at every timestep or using a fixed
pressure simulation with MSM will cause the code to run slower.
:line
@ -216,16 +216,20 @@ to determine the number of K-space vectors for style {ewald} or the
grid size for style {pppm} or {msm}.
Note that style {pppm} only computes the grid size at the beginning of
a simulation, so if the length or triclinic tilt of the simulation cell
increases dramatically during the course of the simulation, the accuracy
of the simulation may degrade. For example, for a triclinic system with
all three tilt factors set to the maximum limit, the PPPM grid should be
increased roughly by a factor of 1.5 in the y direction and 2.0 in the z
direction as compared to the same system using a cubic orthogonal simulation
cell. One way to ensure the accuracy requirement is being met is to run a
short simulation at the maximum expected tilt or length, note the required
grid size, and then use the "kspace_modify"_kspace_modify.html {mesh}
command to manually set the PPPM grid size to this value.
a simulation, so if the length or triclinic tilt of the simulation
cell increases dramatically during the course of the simulation, the
accuracy of the simulation may degrade. Likewise, if the
"kspace_modify slab"_kspace_modify.html option is used with
shrink-wrap boundaries in the z-dimension, and the box size changes
dramatically in z. For example, for a triclinic system with all three
tilt factors set to the maximum limit, the PPPM grid should be
increased roughly by a factor of 1.5 in the y direction and 2.0 in the
z direction as compared to the same system using a cubic orthogonal
simulation cell. One way to ensure the accuracy requirement is being
met is to run a short simulation at the maximum expected tilt or
length, note the required grid size, and then use the
"kspace_modify"_kspace_modify.html {mesh} command to manually set the
PPPM grid size to this value.
RMS force errors in real space for {ewald} and {pppm} are estimated
using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as