diff --git a/doc/balance.html b/doc/balance.html
index 3f1244d9a..d1d8a9af5 100644
--- a/doc/balance.html
+++ b/doc/balance.html
@@ -1,232 +1,232 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>balance command
</H3>
<P>NOTE: the fix balance command referred to here for dynamic load
balancing has not yet been released.
</P>
<P><B>Syntax:</B>
</P>
<PRE>balance keyword args ...
</PRE>
<LI>one or more keyword/arg pairs may be appended
</UL>
<LI>keyword = <I>x</I> or <I>y</I> or <I>z</I> or <I>dynamic</I> or <I>out</I>
<PRE> <I>x</I> args = <I>uniform</I> or Px-1 numbers between 0 and 1
<I>uniform</I> = evenly spaced cuts between processors in x dimension
numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
<I>y</I> args = <I>uniform</I> or Py-1 numbers between 0 and 1
<I>uniform</I> = evenly spaced cuts between processors in y dimension
numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
<I>z</I> args = <I>uniform</I> or Pz-1 numbers between 0 and 1
<I>uniform</I> = evenly spaced cuts between processors in z dimension
numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
- <I>dynamic</I> args = disstr Niter thresh
+ <I>dynamic</I> args = dimstr Niter thresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
thresh = stop balancing when this imbalance threshhold is reached
<I>out</I> arg = filename
filename = output file to write each processor's sub-domain to
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>balance x uniform y 0.4 0.5 0.6
balance dynamic xz 5 1.1
balance dynamic x 20 1.0 out tmp.balance
</PRE>
<P><B>Description:</B>
</P>
<P>This command adjusts the size of processor sub-domains within the
simulation box, to attempt to balance the number of particles and thus
the computational cost (load) evenly across processors. The load
balancing is "static" in the sense that this command performs the
balancing once, before or between simulations. The processor
sub-domains will then remain static during the subsequent run. To
perform "dynamic" balancing, see the <A HREF = "fix_balance.html">fix balance</A>
command, which can adjust processor sub-domain sizes on-the-fly during
a <A HREF = "run.html">run</A>.
</P>
<P>Load-balancing is only useful if the particles in the simulation box
have a spatially-varying density distribution. E.g. a model of a
vapor/liquid interface, or a solid with an irregular-shaped geometry
containing void regions. In this case, the LAMMPS default of dividing
the simulation box volume into a regular-spaced grid of processor
sub-domain, with one equal-volume sub-domain per procesor, may assign
very different numbers of particles per processor. This can lead to
poor performance in a scalability sense, when the simulation is run in
parallel.
</P>
<P>Note that the <A HREF = "processors.html">processors</A> command gives you control
over how the box volume is split across processors. Specifically, for
a Px by Py by Pz grid of processors, it chooses or lets you choose Px,
Py, and Pz, subject to the constraint that Px * Py * Pz = P, the total
number of processors. This is sufficient to achieve good load-balance
for many models on many processor counts. However, all the processor
sub-domains will still be the same shape and have the same volume.
</P>
<P>This command does not alter the topology of the Px by Py by Pz grid or
processors. But it shifts the cutting planes between processors (in
3d, or lines in 2d), which adjusts the volume (area in 2d) assigned to
each processor, as in the following 2d diagram. The left diagram is
the default partitioning of the simulation box across processors (one
sub-box for each of 16 processors); the right diagram is after
balancing.
</P>
<CENTER><IMG SRC = "JPG/balance.jpg">
</CENTER>
<P>When the balance command completes, it prints out the final positions
of all cutting planes in each of the 3 dimensions (as fractions of the
box length). It also prints statistics about its results, including
the change in "imbalance factor". This factor is defined as the
maximum number of particles owned by any processor, divided by the
average number of particles per processor. Thus an imbalance factor
of 1.0 is perfect balance. For 10000 particles running on 10
processors, if the most heavily loaded processor has 1200 particles,
then the factor is 1.2, meaning there is a 20% imbalance. The change
in the maximum number of particles (on any processor) is also printed.
</P>
<P>IMPORTANT NOTE: This command attempts to minimize the imbalance
factor, as defined above. But because of the topology constraint that
only the cutting planes (lines) between processors are moved, there
are many irregular distributions of particles, where this factor
cannot be shrunk to 1.0, particuarly in 3d. Also, computational cost
is not strictly proportional to particle count, and changing the
relative size and shape of processor sub-domains may lead to
additional computational and communication overheads, e.g. in the PPPM
solver used via the <A HREF = "kspace_style.html">kspace_style</A> command. Thus
you should benchmark the run times of your simulation before and after
balancing.
</P>
<HR>
<P>The <I>x</I>, <I>y</I>, and <I>z</I> keywords adjust the position of cutting planes
between processor sub-domains in a specific dimension. The <I>uniform</I>
argument spaces the planes evenly, as in the left diagram above. The
<I>numeric</I> argument requires you to list Ps-1 numbers that specify the
position of the cutting planes. This requires that you know Ps = Px
or Py or Pz = the number of processors assigned by LAMMPS to the
relevant dimension. This assignment is made (and the Px, Py, Pz
values printed out) when the simulation box is created by the
"create_box" or "read_data" or "read_restart" command and is
influenced by the settings of the "processors" command.
</P>
<P>Each of the numeric values must be between 0 and 1, and they must be
listed in ascending order. They represent the fractional position of
the cutting place. The left (or lower) edge of the box is 0.0, and
the right (or upper) edge is 1.0. Neither of these values is
specified. Only the interior Ps-1 positions are specified. Thus is
there are 2 procesors in the x dimension, you specify a single value
such as 0.75, which would make the left processor's sub-domain 3x
larger than the right processor's sub-domain.
</P>
<HR>
<P>The <I>dynamic</I> keyword changes the cutting planes between processors in
an iterative fashion, seeking to reduce the imbalance factor, similar
to how the <A HREF = "fix_balance.html">fix balance</A> command operates. Note that
this keyword begins its operation from the current processor
partitioning, which could be uniform or the result of a previous
balance command.
</P>
<P>The <I>dimstr</I> argument is a string of characters, each of which must be
an "x" or "y" or "z". Eacn character can appear zero or one time,
since there is no advantage to balancing on a dimension more than
once. You should normally only list dimensions where you expect there
to be a density variation in the particles.
</P>
<P>Balancing proceeds by adjusting the cutting planes in each of the
dimensions listed in <I>dimstr</I>, one dimension at a time. For a single
dimension, the balancing operation (described below) is iterated on up
to <I>Niter</I> times. After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the <I>thresh</I>
criterion is met.
</P>
<P>A rebalance operation in a single dimension is performed using a
recursive multisectioning algorithm, where the position of each
cutting plane (line in 2d) in the dimension is adjusted independently.
This is similar to a recursive bisectioning (RCB) for a single value,
except that the bounds used for each bisectioning take advantage of
information from neighboring cuts if possible. At each iteration, the
count of particles on either side of each plane is tallied. If the
counts do not match the target value for the plane, the position of
the cut is adjusted. As the recustion progresses, the count of
particles on either side of the plane gets closer to the target value.
</P>
<HR>
<P>The <I>out</I> keyword writes a text file to the specified <I>filename</I> with
the results of the balancing operation. The file contains the bounds
of the sub-domain for each processor after the balancing operation
completes. The format of the file is compatible with the
<A HREF = "pizza">Pizza.py</A> <I>mdump</I> tool which has support for manipulating and
visualizing mesh files. An example is show here for a balancing by 4
processors for a 2d problem:
</P>
<PRE>ITEM: TIMESTEP
0
ITEM: NUMBER OF SQUARES
4
ITEM: SQUARES
1 1 1 2 7 6
2 2 2 3 8 7
3 3 3 4 9 8
4 4 4 5 10 9
ITEM: TIMESTEP
0
ITEM: NUMBER OF NODES
10
ITEM: BOX BOUNDS
-153.919 184.703
0 15.3919
-0.769595 0.769595
ITEM: NODES
1 1 -153.919 0 0
2 1 7.45545 0 0
3 1 14.7305 0 0
4 1 22.667 0 0
5 1 184.703 0 0
6 1 -153.919 15.3919 0
7 1 7.45545 15.3919 0
8 1 14.7305 15.3919 0
9 1 22.667 15.3919 0
10 1 184.703 15.3919 0
</PRE>
<P>The "SQUARES" lists the node IDs of the 4 vertices in a rectangle for
each processor (1 to 4). The first SQUARE 1 (for processor 0) is a
rectangle of type 1 (equal to SQUARE ID) and contains vertices
1,2,7,6. The coordinates of all the vertices are listed in the NODES
section. Note that the 4 sub-domains share vertices, so there are
only 10 unique vertices in total.
</P>
<P>For a 3d problem, the syntax is similar with "SQUARES" replaced by
"CUBES", and 8 vertices listed for each processor, instead of 4.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The <I>dynamic</I> keyword cannot be used with the <I>x</I>, <I>y</I>, or <I>z</I>
arguments.
</P>
<P>For 2d simulations, the <I>z</I> keyword cannot be used. Nor can a "z"
appear in <I>dimstr</I> for the <I>dynamic</I> keyword.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "processors.html">processors</A>, <A HREF = "fix_balance.html">fix balance</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/balance.txt b/doc/balance.txt
index a0b037bd0..cfbaeeec8 100644
--- a/doc/balance.txt
+++ b/doc/balance.txt
@@ -1,224 +1,224 @@
"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
balance command :h3
NOTE: the fix balance command referred to here for dynamic load
balancing has not yet been released.
[Syntax:]
balance keyword args ... :pre
one or more keyword/arg pairs may be appended :ule,l
keyword = {x} or {y} or {z} or {dynamic} or {out} :l
{x} args = {uniform} or Px-1 numbers between 0 and 1
{uniform} = evenly spaced cuts between processors in x dimension
numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
{y} args = {uniform} or Py-1 numbers between 0 and 1
{uniform} = evenly spaced cuts between processors in y dimension
numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
{z} args = {uniform} or Pz-1 numbers between 0 and 1
{uniform} = evenly spaced cuts between processors in z dimension
numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
- {dynamic} args = disstr Niter thresh
+ {dynamic} args = dimstr Niter thresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
thresh = stop balancing when this imbalance threshhold is reached
{out} arg = filename
filename = output file to write each processor's sub-domain to :pre
:ule
[Examples:]
balance x uniform y 0.4 0.5 0.6
balance dynamic xz 5 1.1
balance dynamic x 20 1.0 out tmp.balance :pre
[Description:]
This command adjusts the size of processor sub-domains within the
simulation box, to attempt to balance the number of particles and thus
the computational cost (load) evenly across processors. The load
balancing is "static" in the sense that this command performs the
balancing once, before or between simulations. The processor
sub-domains will then remain static during the subsequent run. To
perform "dynamic" balancing, see the "fix balance"_fix_balance.html
command, which can adjust processor sub-domain sizes on-the-fly during
a "run"_run.html.
Load-balancing is only useful if the particles in the simulation box
have a spatially-varying density distribution. E.g. a model of a
vapor/liquid interface, or a solid with an irregular-shaped geometry
containing void regions. In this case, the LAMMPS default of dividing
the simulation box volume into a regular-spaced grid of processor
sub-domain, with one equal-volume sub-domain per procesor, may assign
very different numbers of particles per processor. This can lead to
poor performance in a scalability sense, when the simulation is run in
parallel.
Note that the "processors"_processors.html command gives you control
over how the box volume is split across processors. Specifically, for
a Px by Py by Pz grid of processors, it chooses or lets you choose Px,
Py, and Pz, subject to the constraint that Px * Py * Pz = P, the total
number of processors. This is sufficient to achieve good load-balance
for many models on many processor counts. However, all the processor
sub-domains will still be the same shape and have the same volume.
This command does not alter the topology of the Px by Py by Pz grid or
processors. But it shifts the cutting planes between processors (in
3d, or lines in 2d), which adjusts the volume (area in 2d) assigned to
each processor, as in the following 2d diagram. The left diagram is
the default partitioning of the simulation box across processors (one
sub-box for each of 16 processors); the right diagram is after
balancing.
:c,image(JPG/balance.jpg)
When the balance command completes, it prints out the final positions
of all cutting planes in each of the 3 dimensions (as fractions of the
box length). It also prints statistics about its results, including
the change in "imbalance factor". This factor is defined as the
maximum number of particles owned by any processor, divided by the
average number of particles per processor. Thus an imbalance factor
of 1.0 is perfect balance. For 10000 particles running on 10
processors, if the most heavily loaded processor has 1200 particles,
then the factor is 1.2, meaning there is a 20% imbalance. The change
in the maximum number of particles (on any processor) is also printed.
IMPORTANT NOTE: This command attempts to minimize the imbalance
factor, as defined above. But because of the topology constraint that
only the cutting planes (lines) between processors are moved, there
are many irregular distributions of particles, where this factor
cannot be shrunk to 1.0, particuarly in 3d. Also, computational cost
is not strictly proportional to particle count, and changing the
relative size and shape of processor sub-domains may lead to
additional computational and communication overheads, e.g. in the PPPM
solver used via the "kspace_style"_kspace_style.html command. Thus
you should benchmark the run times of your simulation before and after
balancing.
:line
The {x}, {y}, and {z} keywords adjust the position of cutting planes
between processor sub-domains in a specific dimension. The {uniform}
argument spaces the planes evenly, as in the left diagram above. The
{numeric} argument requires you to list Ps-1 numbers that specify the
position of the cutting planes. This requires that you know Ps = Px
or Py or Pz = the number of processors assigned by LAMMPS to the
relevant dimension. This assignment is made (and the Px, Py, Pz
values printed out) when the simulation box is created by the
"create_box" or "read_data" or "read_restart" command and is
influenced by the settings of the "processors" command.
Each of the numeric values must be between 0 and 1, and they must be
listed in ascending order. They represent the fractional position of
the cutting place. The left (or lower) edge of the box is 0.0, and
the right (or upper) edge is 1.0. Neither of these values is
specified. Only the interior Ps-1 positions are specified. Thus is
there are 2 procesors in the x dimension, you specify a single value
such as 0.75, which would make the left processor's sub-domain 3x
larger than the right processor's sub-domain.
:line
The {dynamic} keyword changes the cutting planes between processors in
an iterative fashion, seeking to reduce the imbalance factor, similar
to how the "fix balance"_fix_balance.html command operates. Note that
this keyword begins its operation from the current processor
partitioning, which could be uniform or the result of a previous
balance command.
The {dimstr} argument is a string of characters, each of which must be
an "x" or "y" or "z". Eacn character can appear zero or one time,
since there is no advantage to balancing on a dimension more than
once. You should normally only list dimensions where you expect there
to be a density variation in the particles.
Balancing proceeds by adjusting the cutting planes in each of the
dimensions listed in {dimstr}, one dimension at a time. For a single
dimension, the balancing operation (described below) is iterated on up
to {Niter} times. After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the {thresh}
criterion is met.
A rebalance operation in a single dimension is performed using a
recursive multisectioning algorithm, where the position of each
cutting plane (line in 2d) in the dimension is adjusted independently.
This is similar to a recursive bisectioning (RCB) for a single value,
except that the bounds used for each bisectioning take advantage of
information from neighboring cuts if possible. At each iteration, the
count of particles on either side of each plane is tallied. If the
counts do not match the target value for the plane, the position of
the cut is adjusted. As the recustion progresses, the count of
particles on either side of the plane gets closer to the target value.
:line
The {out} keyword writes a text file to the specified {filename} with
the results of the balancing operation. The file contains the bounds
of the sub-domain for each processor after the balancing operation
completes. The format of the file is compatible with the
"Pizza.py"_pizza {mdump} tool which has support for manipulating and
visualizing mesh files. An example is show here for a balancing by 4
processors for a 2d problem:
ITEM: TIMESTEP
0
ITEM: NUMBER OF SQUARES
4
ITEM: SQUARES
1 1 1 2 7 6
2 2 2 3 8 7
3 3 3 4 9 8
4 4 4 5 10 9
ITEM: TIMESTEP
0
ITEM: NUMBER OF NODES
10
ITEM: BOX BOUNDS
-153.919 184.703
0 15.3919
-0.769595 0.769595
ITEM: NODES
1 1 -153.919 0 0
2 1 7.45545 0 0
3 1 14.7305 0 0
4 1 22.667 0 0
5 1 184.703 0 0
6 1 -153.919 15.3919 0
7 1 7.45545 15.3919 0
8 1 14.7305 15.3919 0
9 1 22.667 15.3919 0
10 1 184.703 15.3919 0 :pre
The "SQUARES" lists the node IDs of the 4 vertices in a rectangle for
each processor (1 to 4). The first SQUARE 1 (for processor 0) is a
rectangle of type 1 (equal to SQUARE ID) and contains vertices
1,2,7,6. The coordinates of all the vertices are listed in the NODES
section. Note that the 4 sub-domains share vertices, so there are
only 10 unique vertices in total.
For a 3d problem, the syntax is similar with "SQUARES" replaced by
"CUBES", and 8 vertices listed for each processor, instead of 4.
:line
[Restrictions:]
The {dynamic} keyword cannot be used with the {x}, {y}, or {z}
arguments.
For 2d simulations, the {z} keyword cannot be used. Nor can a "z"
appear in {dimstr} for the {dynamic} keyword.
[Related commands:]
"processors"_processors.html, "fix balance"_fix_balance.html
[Default:] none