From c01aad8ec21c6e790201f3c4a06af4a9f63aea88 Mon Sep 17 00:00:00 2001 From: pscrozi Date: Fri, 5 Oct 2012 16:44:23 +0000 Subject: [PATCH] Minor tweak to docs. git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8914 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/kspace_modify.html | 4 +- doc/kspace_modify.txt | 376 ++++++++++++++++++++--------------------- 2 files changed, 190 insertions(+), 190 deletions(-) diff --git a/doc/kspace_modify.html b/doc/kspace_modify.html index ace17f694a..bb6b3207c4 100644 --- a/doc/kspace_modify.html +++ b/doc/kspace_modify.html @@ -45,7 +45,7 @@

Examples:

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

 
Description:
@@ -92,7 +92,7 @@ Coulombics.
 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 splitorder is 2.  For higher accuracy in
+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.
 

diff --git a/doc/kspace_modify.txt b/doc/kspace_modify.txt
index dd0687aba3..971bc7aa60 100644
--- a/doc/kspace_modify.txt
+++ b/doc/kspace_modify.txt
@@ -1,188 +1,188 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-kspace_modify command :h3
-
-[Syntax:]
-
-kspace_modify keyword value ... :pre
-
-one or more keyword/value pairs may be listed :ulb,l
-keyword = {mesh} or {order} or {gewald} or {slab} or (nozforce} or {compute} or {diff} :l
-  {mesh} value = x y z
-    x,y,z = grid size in each dimension for long-range Coulombics
-  {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
-  {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
-  {gewald/disp} value = rinv (1/distance units)
-    rinv = G-ewald parameter for dispersion
-  {slab} value = volfactor or {nozforce}
-    volfactor = ratio of the total extended volume used in the
-      2d approximation compared with the volume of the simulation domain
-  {nozforce} turns off kspace forces in the z direction
-  {compute} value = {yes} or {no} 
-  {diff} value = {ik} or {ad} :pre
-:ule
-
-[Examples:]
-
-kspace_modify mesh 24 24 30 order 6 splitorder 3
-kspace_modify slab 3.0 :pre
-
-[Description:]
-
-Set parameters used by the kspace solvers defined by the
-"kspace_style"_kspace_style.html command.  Not all parameters are
-relevant to all kspace styles.
-
-The {mesh} keyword sets the grid size for kspace style {pppm} or
-{msm}.  In the case of PPPM, this is the FFT mesh, and each dimension
-must be factorizable into powers of 2, 3, and 5.  In the case of MSM,
-this is the finest scale real-space mesh, and each dimension must be
-factorizable into powers of 2.  When this option is not set, the PPPM
-or MSM 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.
-
-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,
-consistent with the user-specified accuracy and pairwise cutoff.
-Values for x,y,z of 0,0,0 unset the option.
-
-The {order} keyword determines how many grid spacings an atom's charge
-extends when it is mapped to the grid in kspace style {pppm} or {msm}.  
-The default for this parameter is 5 for PPPM and 4 for MSM, which means 
-each charge spans 5 or 4 grid cells in each dimension, respectively.  
-For the LAMMPS implementation of MSM, the order can range from 4 to 10
-and must be even. For PPPM, the minimum allowed setting is 2 and the 
-maximum allowed setting is 7.  The larger the value of this parameter, 
-the smaller the grid will need to be to achieve the requested accuracy.  
-Conversely, the smaller the order value, the larger the grid will be.  
-Note that there is an inherent trade-off involved: a small grid will 
-lower the cost of FFTs or MSM direct sum, but a larger order parameter
-will increase the cost of interpolating charge/fields to/from the grid.
-
-The {order/disp} keyword determines how many grid spacings an atom's
-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 {splitorder} 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
-small problems are run on large numbers of processors.  A warning will
-be generated indicating the order parameter is being reduced to allow
-LAMMPS to run the problem. Automatic reduction of order is not currently
-implemented in MSM, so an error (instead of a warning) will be generated.
-
-The {force} keyword overrides the relative accuracy parameter set by
-the "kspace_style"_kspace_style.html command with an absolute
-accuracy.  The accuracy determines the RMS error in per-atom forces
-calculated by the long-range solver and is thus specified in force
-units.  A negative value for the accuracy setting means to use the
-relative accuracy parameter.  The accuracy setting is used in
-conjunction with the pairwise cutoff to determine the number of
-K-space vectors for style {ewald}, the FFT grid size for style
-{pppm}, or the real space grid size for style {msm}.
-
-The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
-parameter for charge as {rinv} in reciprocal distance units.  Without
-this setting, LAMMPS chooses the parameter automatically as a function
-of cutoff, precision, grid spacing, etc.  This means it can vary from
-one simulation to the next which may not be desirable for matching a
-KSpace solver to a pre-tabulated pairwise potential.  This setting can
-also be useful if Ewald or PPPM fails to choose a good grid spacing
-and G-ewald parameter automatically.  If the value is set to 0.0,
-LAMMPS will choose the G-ewald parameter automatically.  MSM does not
-use the {gewald} parameter.
-
-The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
-parameter for dispersion as {rinv} in reciprocal distance units.  It
-has the same meaning as the {gewald} setting for Coulombics.
-
-The {slab} keyword allows an Ewald or PPPM solver to be used for a
-systems that are periodic in x,y but non-periodic in z - a
-"boundary"_boundary.html setting of "boundary p p f".  This is done by
-treating the system as if it were periodic in z, but inserting empty
-volume between atom slabs and removing dipole inter-slab interactions
-so that slab-slab interactions are effectively turned off.  The
-volfactor value sets the ratio of the extended dimension in z divided
-by the actual dimension in z.  The recommended value is 3.0.  A larger
-value is inefficient; a smaller value introduces unwanted slab-slab
-interactions.  The use of fixed boundaries in z means that the user
-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.
-
-The {compute} keyword allows Kspace computations to be turned off,
-even though a "kspace_style"_kspace_style.html is defined.  This is
-not useful for running a real simulation, but can be useful for
-debugging purposes or for computing only partial forces that do not
-include the Kspace contribution.  You can also do this by simply not
-defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
-"pair_style"_pair_style.html requires a kspace style to be defined.
-This keyword gives you that option.
-
-The {diff} keyword specifies the differentiation scheme used by the
-PPPM method to compute forces on particles given electrostatic
-potentials on the PPPM mesh.  The {ik} approach is the default for
-PPPM.  It performs differentiation in Kspace, but uses 3 FFTs to
-transfer the computed fields back to real space (total of 4 FFTs per
-timestep). The analytic differentiation, or {ad} approach uses only 1
-FFT to transfer the computed fields back to real space (total of 2
-FFTs per timestep), but requires a somewhat larger PPPM mesh to
-achieve the same accuracy as the {ik} approach. Analogous approaches
-have been implemented in 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}
-option.  Support for those {pppm} variants will be added later.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"kspace_style"_kspace_style.html, "boundary"_boundary.html
-
-[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).
-
-: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).
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+kspace_modify command :h3
+
+[Syntax:]
+
+kspace_modify keyword value ... :pre
+
+one or more keyword/value pairs may be listed :ulb,l
+keyword = {mesh} or {order} or {gewald} or {slab} or (nozforce} or {compute} or {diff} :l
+  {mesh} value = x y z
+    x,y,z = grid size in each dimension for long-range Coulombics
+  {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
+  {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
+  {gewald/disp} value = rinv (1/distance units)
+    rinv = G-ewald parameter for dispersion
+  {slab} value = volfactor or {nozforce}
+    volfactor = ratio of the total extended volume used in the
+      2d approximation compared with the volume of the simulation domain
+  {nozforce} turns off kspace forces in the z direction
+  {compute} value = {yes} or {no} 
+  {diff} value = {ik} or {ad} :pre
+:ule
+
+[Examples:]
+
+kspace_modify mesh 24 24 30 order 6 order/split 3
+kspace_modify slab 3.0 :pre
+
+[Description:]
+
+Set parameters used by the kspace solvers defined by the
+"kspace_style"_kspace_style.html command.  Not all parameters are
+relevant to all kspace styles.
+
+The {mesh} keyword sets the grid size for kspace style {pppm} or
+{msm}.  In the case of PPPM, this is the FFT mesh, and each dimension
+must be factorizable into powers of 2, 3, and 5.  In the case of MSM,
+this is the finest scale real-space mesh, and each dimension must be
+factorizable into powers of 2.  When this option is not set, the PPPM
+or MSM 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.
+
+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,
+consistent with the user-specified accuracy and pairwise cutoff.
+Values for x,y,z of 0,0,0 unset the option.
+
+The {order} keyword determines how many grid spacings an atom's charge
+extends when it is mapped to the grid in kspace style {pppm} or {msm}.  
+The default for this parameter is 5 for PPPM and 4 for MSM, which means 
+each charge spans 5 or 4 grid cells in each dimension, respectively.  
+For the LAMMPS implementation of MSM, the order can range from 4 to 10
+and must be even. For PPPM, the minimum allowed setting is 2 and the 
+maximum allowed setting is 7.  The larger the value of this parameter, 
+the smaller the grid will need to be to achieve the requested accuracy.  
+Conversely, the smaller the order value, the larger the grid will be.  
+Note that there is an inherent trade-off involved: a small grid will 
+lower the cost of FFTs or MSM direct sum, but a larger order parameter
+will increase the cost of interpolating charge/fields to/from the grid.
+
+The {order/disp} keyword determines how many grid spacings an atom's
+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
+small problems are run on large numbers of processors.  A warning will
+be generated indicating the order parameter is being reduced to allow
+LAMMPS to run the problem. Automatic reduction of order is not currently
+implemented in MSM, so an error (instead of a warning) will be generated.
+
+The {force} keyword overrides the relative accuracy parameter set by
+the "kspace_style"_kspace_style.html command with an absolute
+accuracy.  The accuracy determines the RMS error in per-atom forces
+calculated by the long-range solver and is thus specified in force
+units.  A negative value for the accuracy setting means to use the
+relative accuracy parameter.  The accuracy setting is used in
+conjunction with the pairwise cutoff to determine the number of
+K-space vectors for style {ewald}, the FFT grid size for style
+{pppm}, or the real space grid size for style {msm}.
+
+The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
+parameter for charge as {rinv} in reciprocal distance units.  Without
+this setting, LAMMPS chooses the parameter automatically as a function
+of cutoff, precision, grid spacing, etc.  This means it can vary from
+one simulation to the next which may not be desirable for matching a
+KSpace solver to a pre-tabulated pairwise potential.  This setting can
+also be useful if Ewald or PPPM fails to choose a good grid spacing
+and G-ewald parameter automatically.  If the value is set to 0.0,
+LAMMPS will choose the G-ewald parameter automatically.  MSM does not
+use the {gewald} parameter.
+
+The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
+parameter for dispersion as {rinv} in reciprocal distance units.  It
+has the same meaning as the {gewald} setting for Coulombics.
+
+The {slab} keyword allows an Ewald or PPPM solver to be used for a
+systems that are periodic in x,y but non-periodic in z - a
+"boundary"_boundary.html setting of "boundary p p f".  This is done by
+treating the system as if it were periodic in z, but inserting empty
+volume between atom slabs and removing dipole inter-slab interactions
+so that slab-slab interactions are effectively turned off.  The
+volfactor value sets the ratio of the extended dimension in z divided
+by the actual dimension in z.  The recommended value is 3.0.  A larger
+value is inefficient; a smaller value introduces unwanted slab-slab
+interactions.  The use of fixed boundaries in z means that the user
+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.
+
+The {compute} keyword allows Kspace computations to be turned off,
+even though a "kspace_style"_kspace_style.html is defined.  This is
+not useful for running a real simulation, but can be useful for
+debugging purposes or for computing only partial forces that do not
+include the Kspace contribution.  You can also do this by simply not
+defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
+"pair_style"_pair_style.html requires a kspace style to be defined.
+This keyword gives you that option.
+
+The {diff} keyword specifies the differentiation scheme used by the
+PPPM method to compute forces on particles given electrostatic
+potentials on the PPPM mesh.  The {ik} approach is the default for
+PPPM.  It performs differentiation in Kspace, but uses 3 FFTs to
+transfer the computed fields back to real space (total of 4 FFTs per
+timestep). The analytic differentiation, or {ad} approach uses only 1
+FFT to transfer the computed fields back to real space (total of 2
+FFTs per timestep), but requires a somewhat larger PPPM mesh to
+achieve the same accuracy as the {ik} approach. Analogous approaches
+have been implemented in 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}
+option.  Support for those {pppm} variants will be added later.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"kspace_style"_kspace_style.html, "boundary"_boundary.html
+
+[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).
+
+: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).