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49
doc/README
49
doc/README
@ -1,10 +1,46 @@
|
||||
Generation of LAMMPS Documentation
|
||||
LAMMPS Documentation
|
||||
|
||||
Depending on how you obtained LAMMPS, this directory has 2 or 3
|
||||
sub-directories and optionally 2 PDF files:
|
||||
|
||||
src content files for LAMMPS documentation
|
||||
html HTML version of the LAMMPS manual (see html/Manual.html)
|
||||
tools tools and settings for building the documentation
|
||||
Manual.pdf large PDF version of entire manual
|
||||
Developer.pdf small PDF with info about how LAMMPS is structured
|
||||
|
||||
If you downloaded LAMMPS as a tarball from the web site, all these
|
||||
directories and files should be included.
|
||||
|
||||
If you downloaded LAMMPS from the public SVN or Git repositories, then
|
||||
the HTML and PDF files are not included. Instead you need to create
|
||||
them, in one of three ways:
|
||||
|
||||
(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
|
||||
site. Just type "make fetch". This should create a html_www dir and
|
||||
Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS
|
||||
features have been added more recently than the date of your version,
|
||||
the fetched documentation will include those changes (but your source
|
||||
code will not, unless you update your local repository).
|
||||
|
||||
(b) You can build the HTML and PDF files yourself, by typing "make
|
||||
html" followed by "make pdf". Note that the PDF make requires the
|
||||
HTML files already exist. This requires various tools including
|
||||
Sphinx, which the build process will attempt to download and install
|
||||
on your system, if not already available. See more details below.
|
||||
|
||||
(c) You can genererate an older, simpler, less-fancy style of HTML
|
||||
documentation by typing "make old". This will create an "old"
|
||||
directory. This can be useful if (b) does not work on your box for
|
||||
some reason, or you want to quickly view the HTML version of a doc
|
||||
page you have created or edited yourself within the src directory.
|
||||
E.g. if you are planning to submit a new feature to LAMMPS.
|
||||
|
||||
----------------
|
||||
|
||||
The generation of all documentation is managed by the Makefile in this
|
||||
dir.
|
||||
|
||||
----------------
|
||||
|
||||
Options:
|
||||
|
||||
make html # generate HTML in html dir using Sphinx
|
||||
@ -51,3 +87,10 @@ Once Python 3 is installed, open a Terminal and type
|
||||
pip3 install virtualenv
|
||||
|
||||
This will install virtualenv from the Python Package Index.
|
||||
|
||||
----------------
|
||||
|
||||
Installing prerequisites for PDF build
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="26 Sep 2016 version">
|
||||
<META NAME="docnumber" CONTENT="28 Sep 2016 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -21,7 +21,7 @@
|
||||
<H1></H1>
|
||||
|
||||
LAMMPS Documentation :c,h3
|
||||
26 Sep 2016 version :c,h4
|
||||
28 Sep 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
||||
@ -2123,7 +2123,7 @@ thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
|
||||
run 100000
|
||||
variable v equal (v_v11+v_v22+v_v33)/3.0
|
||||
variable ndens equal count(all)/vol
|
||||
print "average viscosity: $v \[Pa.s/] @ $T K, $\{ndens\} /A^3" :pre
|
||||
print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre
|
||||
|
||||
The fifth method is related to the above Green-Kubo method,
|
||||
but uses the Einstein formulation, analogous to the Einstein
|
||||
|
||||
@ -845,7 +845,7 @@ PYTHON package :link(PYTHON),h5
|
||||
Contents: A "python"_python.html command which allow you to execute
|
||||
Python code from a LAMMPS input script. The code can be in a separate
|
||||
file or embedded in the input script itself. See "Section
|
||||
11.2"_Section_python.html#py-2 for an overview of using Python from
|
||||
11.2"_Section_python.html#py_2 for an overview of using Python from
|
||||
LAMMPS and for other ways to use LAMMPS and Python together.
|
||||
|
||||
Building with the PYTHON package assumes you have a Python shared
|
||||
|
||||
@ -10,7 +10,7 @@ balance command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
balance thresh style args ... keyword value ... :pre
|
||||
balance thresh style args ... keyword args ... :pre
|
||||
|
||||
thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l
|
||||
one style/arg pair can be used (or multiple for {x},{y},{z}) :l
|
||||
@ -32,9 +32,23 @@ style = {x} or {y} or {z} or {shift} or {rcb} :l
|
||||
Niter = # of times to iterate within each dimension of dimstr sequence
|
||||
stopthresh = stop balancing when this imbalance threshhold is reached
|
||||
{rcb} args = none :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {out} :l
|
||||
{out} value = filename
|
||||
zero or more keyword/arg pairs may be appended :l
|
||||
keyword = {weight} or {out} :l
|
||||
{weight} style args = use weighted particle counts for the balancing
|
||||
{style} = {group} or {neigh} or {time} or {var} or {store}
|
||||
{group} args = Ngroup group1 weight1 group2 weight2 ...
|
||||
Ngroup = number of groups with assigned weights
|
||||
group1, group2, ... = group IDs
|
||||
weight1, weight2, ... = corresponding weight factors
|
||||
{neigh} factor = compute weight based on number of neighbors
|
||||
factor = scaling factor (> 0)
|
||||
{time} factor = compute weight based on time spend computing
|
||||
factor = scaling factor (> 0)
|
||||
{var} name = take weight from atom-style variable
|
||||
name = name of the atom-style variable
|
||||
{store} name = store weight in custom atom property defined by "fix property/atom"_fix_property_atom.html command
|
||||
name = atom property name (without d_ prefix)
|
||||
{out} arg = filename
|
||||
filename = write each processor's sub-domain to a file :pre
|
||||
:ule
|
||||
|
||||
@ -44,28 +58,42 @@ balance 0.9 x uniform y 0.4 0.5 0.6
|
||||
balance 1.2 shift xz 5 1.1
|
||||
balance 1.0 shift xz 5 1.1
|
||||
balance 1.1 rcb
|
||||
balance 1.0 shift x 10 1.1 weight group 2 fast 0.5 slow 2.0
|
||||
balance 1.0 shift x 10 1.1 weight time 0.8 weight neigh 0.5 weight store balance
|
||||
balance 1.0 shift x 20 1.0 out tmp.balance :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This command adjusts the size and shape 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
|
||||
within the simulation box, to attempt to balance the number of atoms
|
||||
or particles and thus indirectly the computational cost (load) more
|
||||
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 and shapes on-the-fly during a "run"_run.html.
|
||||
|
||||
Load-balancing is typically 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
|
||||
Load-balancing is typically most useful if the particles in the
|
||||
simulation box have a spatially-varying density distribution or when
|
||||
the computational cost varies signficantly between different
|
||||
particles. E.g. a model of a vapor/liquid interface, or a solid with
|
||||
an irregular-shaped geometry containing void regions, or "hybrid pair
|
||||
style simulations"_pair_hybrid.html which combine pair styles with
|
||||
different computational cost. In these cases, the LAMMPS default of
|
||||
dividing the simulation box volume into a regular-spaced grid of 3d
|
||||
bricks, with one equal-volume sub-domain per procesor, may assign very
|
||||
different numbers of particles per processor. This can lead to poor
|
||||
performance when the simulation is run in parallel.
|
||||
bricks, with one equal-volume sub-domain per procesor, may assign
|
||||
numbers of particles per processor in a way that the computational
|
||||
effort varies significantly. This can lead to poor performance when
|
||||
the simulation is run in parallel.
|
||||
|
||||
The balancing can be performed with or without per-particle weighting.
|
||||
With no weighting, the balancing attempts to assign an equal number of
|
||||
particles to each processor. With weighting, the balancing attempts
|
||||
to assign an equal aggregate computational weight to each processor,
|
||||
which typically inducces a diffrent number of atoms assigned to each
|
||||
processor. Details on the various weighting options and examples for
|
||||
how they can be used are "given below"_#weighted_balance.
|
||||
|
||||
Note that the "processors"_processors.html command allows some control
|
||||
over how the box volume is split across processors. Specifically, for
|
||||
@ -78,9 +106,9 @@ sub-domains will still have the same shape and same volume.
|
||||
The requested load-balancing operation is only performed if the
|
||||
current "imbalance factor" in particles owned by each processor
|
||||
exceeds the specified {thresh} parameter. The imbalance 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.
|
||||
defined as the maximum number of particles (or weight) owned by any
|
||||
processor, divided by the average number of particles (or weight) per
|
||||
processor. Thus an imbalance factor of 1.0 is perfect balance.
|
||||
|
||||
As an example, for 10000 particles running on 10 processors, if the
|
||||
most heavily loaded processor has 1200 particles, then the factor is
|
||||
@ -108,7 +136,7 @@ defined above. But depending on the method a perfect balance (1.0)
|
||||
may not be achieved. For example, "grid" methods (defined below) that
|
||||
create a logical 3d grid cannot achieve perfect balance for many
|
||||
irregular distributions of particles. Likewise, if a portion of the
|
||||
system is a perfect lattice, e.g. the intiial system is generated by
|
||||
system is a perfect lattice, e.g. the initial system is generated by
|
||||
the "create_atoms"_create_atoms.html command, then "grid" methods may
|
||||
be unable to achieve exact balance. This is because entire lattice
|
||||
planes will be owned or not owned by a single processor.
|
||||
@ -134,11 +162,11 @@ The {x}, {y}, {z}, and {shift} styles are "grid" methods which produce
|
||||
a logical 3d grid of processors. They operate by changing the cutting
|
||||
planes (or lines) between processors in 3d (or 2d), to adjust the
|
||||
volume (area in 2d) assigned to each processor, as in the following 2d
|
||||
diagram where processor sub-domains are shown and atoms are colored by
|
||||
the processor that owns them. The leftmost diagram is the default
|
||||
partitioning of the simulation box across processors (one sub-box for
|
||||
each of 16 processors); the middle diagram is after a "grid" method
|
||||
has been applied.
|
||||
diagram where processor sub-domains are shown and particles are
|
||||
colored by the processor that owns them. The leftmost diagram is the
|
||||
default partitioning of the simulation box across processors (one
|
||||
sub-box for each of 16 processors); the middle diagram is after a
|
||||
"grid" method has been applied.
|
||||
|
||||
:image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg)
|
||||
:c
|
||||
@ -146,8 +174,8 @@ has been applied.
|
||||
The {rcb} style is a "tiling" method which does not produce a logical
|
||||
3d grid of processors. Rather it tiles the simulation domain with
|
||||
rectangular sub-boxes of varying size and shape in an irregular
|
||||
fashion so as to have equal numbers of particles in each sub-box, as
|
||||
in the rightmost diagram above.
|
||||
fashion so as to have equal numbers of particles (or weight) in each
|
||||
sub-box, as in the rightmost diagram above.
|
||||
|
||||
The "grid" methods can be used with either of the
|
||||
"comm_style"_comm_style.html command options, {brick} or {tiled}. The
|
||||
@ -230,7 +258,7 @@ counts do not match the target value for the plane, the position of
|
||||
the cut is adjusted to be halfway between a low and high bound. The
|
||||
low and high bounds are adjusted on each iteration, using new count
|
||||
information, so that they become closer together over time. Thus as
|
||||
the recustion progresses, the count of particles on either side of the
|
||||
the recursion progresses, the count of particles on either side of the
|
||||
plane gets closer to the target value.
|
||||
|
||||
Once the rebalancing is complete and final processor sub-domains
|
||||
@ -262,21 +290,129 @@ the longest dimension, leaving one new box on either side of the cut.
|
||||
All the processors are also partitioned into 2 groups, half assigned
|
||||
to the box on the lower side of the cut, and half to the box on the
|
||||
upper side. (If the processor count is odd, one side gets an extra
|
||||
processor.) The cut is positioned so that the number of atoms in the
|
||||
lower box is exactly the number that the processors assigned to that
|
||||
box should own for load balance to be perfect. This also makes load
|
||||
balance for the upper box perfect. The positioning is done
|
||||
iteratively, by a bisectioning method. Note that counting atoms on
|
||||
either side of the cut requires communication between all processors
|
||||
at each iteration.
|
||||
processor.) The cut is positioned so that the number of particles in
|
||||
the lower box is exactly the number that the processors assigned to
|
||||
that box should own for load balance to be perfect. This also makes
|
||||
load balance for the upper box perfect. The positioning is done
|
||||
iteratively, by a bisectioning method. Note that counting particles
|
||||
on either side of the cut requires communication between all
|
||||
processors at each iteration.
|
||||
|
||||
That is the procedure for the first cut. Subsequent cuts are made
|
||||
recursively, in exactly the same manner. The subset of processors
|
||||
assigned to each box make a new cut in the longest dimension of that
|
||||
box, splitting the box, the subset of processsors, and the atoms in
|
||||
the box in two. The recursion continues until every processor is
|
||||
assigned a sub-box of the entire simulation domain, and owns the atoms
|
||||
in that sub-box.
|
||||
box, splitting the box, the subset of processsors, and the particles
|
||||
in the box in two. The recursion continues until every processor is
|
||||
assigned a sub-box of the entire simulation domain, and owns the
|
||||
particles in that sub-box.
|
||||
|
||||
:line
|
||||
|
||||
This sub-section describes how to perform weighted load balancing
|
||||
using the {weight} keyword. :link(weighted_balance)
|
||||
|
||||
By default, all particles have a weight of 1.0, which means each
|
||||
particle is assumed to require the same amount of computation during a
|
||||
timestep. There are, however, scenarios where this is not a good
|
||||
assumption. Measuring the computational cost for each particle
|
||||
accurately would be impractical and slow down the computation.
|
||||
Instead the {weight} keyword implements several ways to influence the
|
||||
per-particle weights empirically by properties readily available or
|
||||
using the user's knowledge of the system. Note that the absolute
|
||||
value of the weights are not important; their ratio is what is used to
|
||||
assign particles to processors. A particle with a weight of 2.5 is
|
||||
assumed to require 5x more computational than a particle with a weight
|
||||
of 0.5.
|
||||
|
||||
Below is a list of possible weight options with a short description of
|
||||
their usage and some example scenarios where they might be applicable.
|
||||
It is possible to apply multiple weight flags and the weightins they
|
||||
induce will be combined through multiplication. Most of the time,
|
||||
however, it is sufficient to use just one method.
|
||||
|
||||
The {group} weight style assigns weight factors to specified
|
||||
"groups"_group.html of particles. The {group} style keyword is
|
||||
followed by the number of groups, then pairs of group IDs and the
|
||||
corresponding weight factor. If a particle belongs to none of the
|
||||
specified groups, its weight is not changed. If it belongs to
|
||||
multiple groups, its weight is the product of the weight factors.
|
||||
|
||||
This weight style is useful in combination with pair style
|
||||
"hybrid"_pair_hybrid.html, e.g. when combining a more costly manybody
|
||||
potential with a fast pair-wise potential. It is also useful when
|
||||
using "run_style respa"_run_style.html where some portions of the
|
||||
system have many bonded interactions and others none. It assumes that
|
||||
the computational cost for each group remains constant over time.
|
||||
This is a purely empirical weighting, so a series test runs to tune
|
||||
the assigned weight factors for optimal performance is recommended.
|
||||
|
||||
The {neigh} weight style assigns a weight to each particle equal to
|
||||
its number of neighbors divided by the avergage number of neighbors
|
||||
for all particles. The {factor} setting is then appied as an overall
|
||||
scale factor to all the {neigh} weights which allows tuning of the
|
||||
impact of this style. A {factor} smaller than 1.0 (e.g. 0.8) often
|
||||
results in the best performance, since the number of neighbors is
|
||||
likely to overestimate the ideal weight.
|
||||
|
||||
This weight style is useful for systems where there are different
|
||||
cutoffs used for different pairs of interations, or the density
|
||||
fluctuates, or a large number of particles are in the vicinity of a
|
||||
wall, or a combination of these effects. If a simulation uses
|
||||
multiple neighbor lists, this weight style will use the first suitable
|
||||
neighbor list it finds. It will not request or compute a new list. A
|
||||
warning will be issued if there is no suitable neighbor list available
|
||||
or if it is not current, e.g. if the balance command is used before a
|
||||
"run"_run.html or "minimize"_minimize.html command is used, in which
|
||||
case the neighbor list may not yet have been built. In this case no
|
||||
weights are computed. Inserting a "run 0 post no"_run.html command
|
||||
before issuing the {balance} command, may be a workaround for this
|
||||
case, as it will induce the neighbor list to be built.
|
||||
|
||||
The {time} weight style uses "timer data"_timer.html to estimate a
|
||||
weight for each particle. It uses the same information as is used for
|
||||
the "MPI task timing breakdown"_Section_start.html#start_8, namely,
|
||||
the timings for sections {Pair}, {Bond}, {Kspace}, and {Neigh}. The
|
||||
time spent in these sections of the timestep are measured for each MPI
|
||||
rank, summed up, then converted into a cost for each MPI rank relative
|
||||
to the average cost over all MPI ranks for the same sections. That
|
||||
cost then evenly distributed over all the particles owned by that
|
||||
rank. Finally, the {factor} setting is then appied as an overall
|
||||
scale factor to all the {time} weights as a way to fine tune the
|
||||
impact of this weight style. Good {factor} values to use are
|
||||
typically between 0.5 and 1.2.
|
||||
|
||||
For the {balance} command the timing data is taken from the preceding
|
||||
run command, i.e. the timings are for the entire previous run. For
|
||||
the {fix balance} command the timing data is for only the timesteps
|
||||
since the last balancing operation was performed. If timing
|
||||
information for the required sections is not available, e.g. at the
|
||||
beginning of a run, or when the "timer"_timer.html command is set to
|
||||
either {loop} or {off}, a warning is issued. In this case no weights
|
||||
are computed.
|
||||
|
||||
This weight style is the most generic one, and should be tried first,
|
||||
if neither the {group} or {neigh} styles are easily applicable.
|
||||
However, since the computed cost function is averaged over all local
|
||||
particles this weight style may not be highly accurate. This style
|
||||
can also be effective as a secondary weight in combination with either
|
||||
{group} or {neigh} to offset some of inaccuracies in either of those
|
||||
heuristics.
|
||||
|
||||
The {var} weight style assigns per-particle weights by evaluating an
|
||||
"atom-style variable"_variable.html specified by {name}. This is
|
||||
provided as a more flexible alternative to the {group} weight style,
|
||||
allowing definition of a more complex heuristics based on information
|
||||
(global and per atom) available inside of LAMMPS. For example,
|
||||
atom-style variables can reference the position of a particle, its
|
||||
velocity, the volume of its Voronoi cell, etc.
|
||||
|
||||
The {store} weight style does not compute a weight factor. Instead it
|
||||
stores the current accumulated weights in a custom per-atom property
|
||||
specified by {name}. This must be a property defined as {d_name} via
|
||||
the "fix property/atom"_fix_property_atom.html command. Note that
|
||||
these custom per-atom properties can be output in a "dump"_dump.html
|
||||
file, so this is a way to examine, debug, or visualize the
|
||||
per-particle weights computed during the load-balancing operation.
|
||||
|
||||
:line
|
||||
|
||||
@ -342,6 +478,7 @@ appear in {dimstr} for the {shift} style.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"processors"_processors.html, "fix balance"_fix_balance.html
|
||||
"group"_group.html, "processors"_processors.html,
|
||||
"fix balance"_fix_balance.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -10,7 +10,7 @@ fix balance command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID balance Nfreq thresh style args keyword value ... :pre
|
||||
fix ID group-ID balance Nfreq thresh style args keyword args ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
balance = style name of this fix command :l
|
||||
@ -21,10 +21,24 @@ style = {shift} or {rcb} :l
|
||||
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
|
||||
stopthresh = stop balancing when this imbalance threshhold is reached
|
||||
rcb args = none :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {out} :l
|
||||
{out} value = filename
|
||||
{rcb} args = none :pre
|
||||
zero or more keyword/arg pairs may be appended :l
|
||||
keyword = {weight} or {out} :l
|
||||
{weight} style args = use weighted particle counts for the balancing
|
||||
{style} = {group} or {neigh} or {time} or {var} or {store}
|
||||
{group} args = Ngroup group1 weight1 group2 weight2 ...
|
||||
Ngroup = number of groups with assigned weights
|
||||
group1, group2, ... = group IDs
|
||||
weight1, weight2, ... = corresponding weight factors
|
||||
{neigh} factor = compute weight based on number of neighbors
|
||||
factor = scaling factor (> 0)
|
||||
{time} factor = compute weight based on time spend computing
|
||||
factor = scaling factor (> 0)
|
||||
{var} name = take weight from atom-style variable
|
||||
name = name of the atom-style variable
|
||||
{store} name = store weight in custom atom property defined by "fix property/atom"_fix_property_atom.html command
|
||||
name = atom property name (without d_ prefix)
|
||||
{out} arg = filename
|
||||
filename = write each processor's sub-domain to a file, at each re-balancing :pre
|
||||
:ule
|
||||
|
||||
@ -32,6 +46,9 @@ keyword = {out} :l
|
||||
|
||||
fix 2 all balance 1000 1.05 shift x 10 1.05
|
||||
fix 2 all balance 100 0.9 shift xy 20 1.1 out tmp.balance
|
||||
fix 2 all balance 100 0.9 shift xy 20 1.1 weight group 3 substrate 3.0 solvent 1.0 solute 0.8 out tmp.balance
|
||||
fix 2 all balance 100 1.0 shift x 10 1.1 weight time 0.8
|
||||
fix 2 all balance 100 1.0 shift xy 5 1.1 weight var myweight weight neigh 0.6 weight store allweight
|
||||
fix 2 all balance 1000 1.1 rcb :pre
|
||||
|
||||
[Description:]
|
||||
@ -44,14 +61,32 @@ rebalancing is performed periodically during the simulation. To
|
||||
perform "static" balancing, before or between runs, see the
|
||||
"balance"_balance.html command.
|
||||
|
||||
Load-balancing is typically 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 3d
|
||||
bricks, with one equal-volume sub-domain per processor, may assign
|
||||
very different numbers of particles per processor. This can lead to
|
||||
poor performance when the simulation is run in parallel.
|
||||
Load-balancing is typically most useful if the particles in the
|
||||
simulation box have a spatially-varying density distribution or
|
||||
where the computational cost varies signficantly between different
|
||||
atoms. E.g. a model of a vapor/liquid interface, or a solid with
|
||||
an irregular-shaped geometry containing void regions, or
|
||||
"hybrid pair style simulations"_pair_hybrid.html which combine
|
||||
pair styles with different computational cost. In these cases, the
|
||||
LAMMPS default of dividing the simulation box volume into a
|
||||
regular-spaced grid of 3d bricks, with one equal-volume sub-domain
|
||||
per procesor, may assign numbers of particles per processor in a
|
||||
way that the computational effort varies significantly. This can
|
||||
lead to poor performance when the simulation is run in parallel.
|
||||
|
||||
The balancing can be performed with or without per-particle weighting.
|
||||
With no weighting, the balancing attempts to assign an equal number of
|
||||
particles to each processor. With weighting, the balancing attempts
|
||||
to assign an equal aggregate computational weight to each processor,
|
||||
which typically inducces a diffrent number of atoms assigned to each
|
||||
processor.
|
||||
|
||||
NOTE: The weighting options listed above are documented with the
|
||||
"balance"_balance.html command in "this section of the balance
|
||||
command"_balance.html#weighted_balance doc page. That section
|
||||
describes the various weighting options and gives a few examples of
|
||||
how they can be used. The weighting options are the same for both the
|
||||
fix balance and "balance"_balance.html commands.
|
||||
|
||||
Note that the "processors"_processors.html command allows some control
|
||||
over how the box volume is split across processors. Specifically, for
|
||||
@ -64,9 +99,9 @@ sub-domains will still have the same shape and same volume.
|
||||
On a particular timestep, a load-balancing operation is only performed
|
||||
if the current "imbalance factor" in particles owned by each processor
|
||||
exceeds the specified {thresh} parameter. The imbalance 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.
|
||||
defined as the maximum number of particles (or weight) owned by any
|
||||
processor, divided by the average number of particles (or weight) per
|
||||
processor. Thus an imbalance factor of 1.0 is perfect balance.
|
||||
|
||||
As an example, for 10000 particles running on 10 processors, if the
|
||||
most heavily loaded processor has 1200 particles, then the factor is
|
||||
@ -117,8 +152,8 @@ applied.
|
||||
The {rcb} style is a "tiling" method which does not produce a logical
|
||||
3d grid of processors. Rather it tiles the simulation domain with
|
||||
rectangular sub-boxes of varying size and shape in an irregular
|
||||
fashion so as to have equal numbers of particles in each sub-box, as
|
||||
in the rightmost diagram above.
|
||||
fashion so as to have equal numbers of particles (or weight) in each
|
||||
sub-box, as in the rightmost diagram above.
|
||||
|
||||
The "grid" methods can be used with either of the
|
||||
"comm_style"_comm_style.html command options, {brick} or {tiled}. The
|
||||
@ -139,12 +174,9 @@ from scratch.
|
||||
|
||||
:line
|
||||
|
||||
The {group-ID} is currently ignored. In the future it may be used to
|
||||
determine what particles are considered for balancing. Normally it
|
||||
would only makes sense to use the {all} group. But in some cases it
|
||||
may be useful to balance on a subset of the particles, e.g. when
|
||||
modeling large nanoparticles in a background of small solvent
|
||||
particles.
|
||||
The {group-ID} is ignored. However the impact of balancing on
|
||||
different groups of atoms can be affected by using the {group} weight
|
||||
style as described below.
|
||||
|
||||
The {Nfreq} setting determines how often a rebalance is performed. If
|
||||
{Nfreq} > 0, then rebalancing will occur every {Nfreq} steps. Each
|
||||
@ -225,7 +257,7 @@ than {Niter} and exit early.
|
||||
|
||||
The {rcb} style invokes a "tiled" method for balancing, as described
|
||||
above. It performs a recursive coordinate bisectioning (RCB) of the
|
||||
simulation domain. The basic idea is as follows.
|
||||
simulation domain. The basic idea is as follows.
|
||||
|
||||
The simulation domain is cut into 2 boxes by an axis-aligned cut in
|
||||
the longest dimension, leaving one new box on either side of the cut.
|
||||
@ -250,10 +282,10 @@ in that sub-box.
|
||||
|
||||
:line
|
||||
|
||||
The {out} keyword writes a text file to the specified {filename} with
|
||||
the results of each rebalancing 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
|
||||
The {out} keyword writes text to the specified {filename} with the
|
||||
results of each rebalancing 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 shown here for a balancing by 4
|
||||
processors for a 2d problem:
|
||||
@ -321,8 +353,8 @@ values in the vector are as follows:
|
||||
3 = imbalance factor right before the last rebalance was performed :ul
|
||||
|
||||
As explained above, the imbalance factor is the ratio of the maximum
|
||||
number of particles on any processor to the average number of
|
||||
particles per processor.
|
||||
number of particles (or total weight) on any processor to the average
|
||||
number of particles (or total weight) per processor.
|
||||
|
||||
These quantities can be accessed by various "output
|
||||
commands"_Section_howto.html#howto_15. The scalar and vector values
|
||||
@ -336,11 +368,11 @@ minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
For 2d simulations, a "z" cannot appear in {dimstr} for the {shift}
|
||||
style.
|
||||
For 2d simulations, the {z} style cannot be used. Nor can a "z"
|
||||
appear in {dimstr} for the {shift} style.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"processors"_processors.html, "balance"_balance.html
|
||||
"group"_group.html, "processors"_processors.html, "balance"_balance.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -56,7 +56,7 @@ CMAP :pre
|
||||
|
||||
1 1 8 10 12 18 20
|
||||
2 5 18 20 22 25 27
|
||||
...
|
||||
\[...\]
|
||||
N 3 314 315 317 318 330 :pre
|
||||
|
||||
The first column is an index from 1 to N to enumerate the CMAP terms;
|
||||
@ -66,7 +66,7 @@ remaining 5 columns are the atom IDs of the atoms in the two 4-atom
|
||||
dihedrals that overlap to create the CMAP 5-body interaction. Note
|
||||
that the "crossterm" and "CMAP" keywords for the header and body
|
||||
sections match those specified in the read_data command following the
|
||||
data file name; see the "read_data"_doc/read_data.html doc page for
|
||||
data file name; see the "read_data"_read_data.html doc page for
|
||||
more details.
|
||||
|
||||
A data file containing CMAP crossterms can be generated from a PDB
|
||||
@ -124,9 +124,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
:line
|
||||
|
||||
(Buck)
|
||||
Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
|
||||
:link(Buck)
|
||||
[(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
|
||||
(2006).
|
||||
|
||||
(Brooks)
|
||||
Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
|
||||
:link(Brooks)
|
||||
[(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
|
||||
|
||||
@ -24,6 +24,7 @@ Fixes :h1
|
||||
fix_bond_create
|
||||
fix_bond_swap
|
||||
fix_box_relax
|
||||
fix_cmap
|
||||
fix_colvars
|
||||
fix_controller
|
||||
fix_deform
|
||||
|
||||
@ -147,6 +147,7 @@ fix_bond_break.html
|
||||
fix_bond_create.html
|
||||
fix_bond_swap.html
|
||||
fix_box_relax.html
|
||||
fix_cmap.html
|
||||
fix_colvars.html
|
||||
fix_controller.html
|
||||
fix_deform.html
|
||||
|
||||
@ -48,17 +48,14 @@ follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA,
|
||||
|
||||
Each replica runs on a partition of one or more processors. Processor
|
||||
partitions are defined at run-time using the -partition command-line
|
||||
switch; see "Section 2.7"_Section_start.html#start_7 of the
|
||||
manual. Note that if you have MPI installed, you can run a
|
||||
multi-replica simulation with more replicas (partitions) than you have
|
||||
physical processors, e.g you can run a 10-replica simulation on just
|
||||
one or two processors. You will simply not get the performance
|
||||
speed-up you would see with one or more physical processors per
|
||||
replica. See "this section"_Section_howto.html#howto_5 of the manual
|
||||
for further discussion.
|
||||
|
||||
NOTE: The current NEB implementation in LAMMPS only allows there to be
|
||||
one processor per replica.
|
||||
switch; see "Section 2.7"_Section_start.html#start_7 of the manual.
|
||||
Note that if you have MPI installed, you can run a multi-replica
|
||||
simulation with more replicas (partitions) than you have physical
|
||||
processors, e.g you can run a 10-replica simulation on just one or two
|
||||
processors. You will simply not get the performance speed-up you
|
||||
would see with one or more physical processors per replica. See
|
||||
"Section 6.5"_Section_howto.html#howto_5 of the manual for further
|
||||
discussion.
|
||||
|
||||
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
|
||||
minimization across all the replicas. The mimimizer uses whatever
|
||||
@ -255,12 +252,6 @@ An atom map must be defined which it is not by default for "atom_style
|
||||
atomic"_atom_style.html problems. The "atom_modify
|
||||
map"_atom_modify.html command can be used to do this.
|
||||
|
||||
The "atom_modify sort 0 0.0" command should be used to turn off atom
|
||||
sorting.
|
||||
|
||||
NOTE: This sorting restriction will be removed in a future version of
|
||||
NEB in LAMMPS.
|
||||
|
||||
The minimizers in LAMMPS operate on all atoms in your system, even
|
||||
non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
|
||||
during the minimization, you should use the "fix
|
||||
|
||||
@ -63,14 +63,14 @@ event to occur.
|
||||
|
||||
Each replica runs on a partition of one or more processors. Processor
|
||||
partitions are defined at run-time using the -partition command-line
|
||||
switch; see "Section 2.7"_Section_start.html#start_7 of the
|
||||
manual. Note that if you have MPI installed, you can run a
|
||||
multi-replica simulation with more replicas (partitions) than you have
|
||||
physical processors, e.g you can run a 10-replica simulation on one or
|
||||
two processors. For PRD, this makes little sense, since this offers
|
||||
no effective parallel speed-up in searching for infrequent events. See
|
||||
"Section 6.5"_Section_howto.html#howto_5 of the manual for further
|
||||
discussion.
|
||||
switch; see "Section 2.7"_Section_start.html#start_7 of the manual.
|
||||
Note that if you have MPI installed, you can run a multi-replica
|
||||
simulation with more replicas (partitions) than you have physical
|
||||
processors, e.g you can run a 10-replica simulation on one or two
|
||||
processors. However for PRD, this makes little sense, since running a
|
||||
replica on virtual instead of physical processors,offers no effective
|
||||
parallel speed-up in searching for infrequent events. See "Section
|
||||
6.5"_Section_howto.html#howto_5 of the manual for further discussion.
|
||||
|
||||
When a PRD simulation is performed, it is assumed that each replica is
|
||||
running the same model, though LAMMPS does not check for this.
|
||||
@ -163,7 +163,7 @@ runs for {N} timesteps. If the {time} value is {clock}, then the
|
||||
simulation runs until {N} aggregate timesteps across all replicas have
|
||||
elapsed. This aggregate time is the "clock" time defined below, which
|
||||
typically advances nearly M times faster than the timestepping on a
|
||||
single replica.
|
||||
single replica, where M is the number of replicas.
|
||||
|
||||
:line
|
||||
|
||||
@ -183,25 +183,26 @@ coincident events, and the replica number of the chosen event.
|
||||
|
||||
The timestep is the usual LAMMPS timestep, except that time does not
|
||||
advance during dephasing or quenches, but only during dynamics. Note
|
||||
that are two kinds of dynamics in the PRD loop listed above. The
|
||||
first is when all replicas are performing independent dynamics,
|
||||
waiting for an event to occur. The second is when correlated events
|
||||
are being searched for and only one replica is running dynamics.
|
||||
that are two kinds of dynamics in the PRD loop listed above that
|
||||
contribute to this timestepping. The first is when all replicas are
|
||||
performing independent dynamics, waiting for an event to occur. The
|
||||
second is when correlated events are being searched for, but only one
|
||||
replica is running dynamics.
|
||||
|
||||
The CPU time is the total processor time since the start of the PRD
|
||||
run.
|
||||
The CPU time is the total elapsed time on each processor, since the
|
||||
start of the PRD run.
|
||||
|
||||
The clock is the same as the timestep except that it advances by M
|
||||
steps every timestep during the first kind of dynamics when the M
|
||||
steps per timestep during the first kind of dynamics when the M
|
||||
replicas are running independently. The clock advances by only 1 step
|
||||
per timestep during the second kind of dynamics, since only a single
|
||||
per timestep during the second kind of dynamics, when only a single
|
||||
replica is checking for a correlated event. Thus "clock" time
|
||||
represents the aggregate time (in steps) that effectively elapses
|
||||
represents the aggregate time (in steps) that has effectively elapsed
|
||||
during a PRD simulation on M replicas. If most of the PRD run is
|
||||
spent in the second stage of the loop above, searching for infrequent
|
||||
events, then the clock will advance nearly M times faster than it
|
||||
would if a single replica was running. Note the clock time between
|
||||
events will be drawn from p(t).
|
||||
successive events should be drawn from p(t).
|
||||
|
||||
The event number is a counter that increments with each event, whether
|
||||
it is uncorrelated or correlated.
|
||||
@ -212,14 +213,15 @@ replicas are running independently. The correlation flag will be 1
|
||||
when a correlated event occurs during the third stage of the loop
|
||||
listed above, i.e. when only one replica is running dynamics.
|
||||
|
||||
When more than one replica detects an event at the end of the second
|
||||
stage, then one of them is chosen at random. The number of coincident
|
||||
events is the number of replicas that detected an event. Normally, we
|
||||
expect this value to be 1. If it is often greater than 1, then either
|
||||
the number of replicas is too large, or {t_event} is too large.
|
||||
When more than one replica detects an event at the end of the same
|
||||
event check (every {t_event} steps) during the the second stage, then
|
||||
one of them is chosen at random. The number of coincident events is
|
||||
the number of replicas that detected an event. Normally, this value
|
||||
should be 1. If it is often greater than 1, then either the number of
|
||||
replicas is too large, or {t_event} is too large.
|
||||
|
||||
The replica number is the ID of the replica (from 0 to M-1) that
|
||||
found the event.
|
||||
The replica number is the ID of the replica (from 0 to M-1) in which
|
||||
the event occurred.
|
||||
|
||||
:line
|
||||
|
||||
@ -286,7 +288,7 @@ This command can only be used if LAMMPS was built with the REPLICA
|
||||
package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info on packages.
|
||||
|
||||
{N} and {t_correlate} settings must be integer multiples of
|
||||
The {N} and {t_correlate} settings must be integer multiples of
|
||||
{t_event}.
|
||||
|
||||
Runs restarted from restart file written during a PRD run will not
|
||||
|
||||
@ -90,3 +90,24 @@ def promote_doc_keywords(content):
|
||||
|
||||
def filter_multiple_horizontal_rules(content):
|
||||
return re.sub(r"----------[\s\n]+----------", '', content)
|
||||
|
||||
|
||||
def merge_preformatted_sections(content):
|
||||
mergable_section_pattern = re.compile(r"\.\. parsed-literal::\n"
|
||||
r"\n"
|
||||
r"(?P<listingA>(( [^\n]+\n)|(^\n))+)\n\s*"
|
||||
r"^\.\. parsed-literal::\n"
|
||||
r"\n"
|
||||
r"(?P<listingB>(( [^\n]+\n)|(^\n))+)\n", re.MULTILINE | re.DOTALL)
|
||||
|
||||
m = mergable_section_pattern.search(content)
|
||||
|
||||
while m:
|
||||
content = mergable_section_pattern.sub(r".. parsed-literal::\n"
|
||||
r"\n"
|
||||
r"\g<listingA>"
|
||||
r"\g<listingB>"
|
||||
r"\n", content)
|
||||
m = mergable_section_pattern.search(content)
|
||||
|
||||
return content
|
||||
|
||||
@ -73,10 +73,13 @@ class RSTMarkup(Markup):
|
||||
def unescape_rst_chars(self, text):
|
||||
text = text.replace('\\*', '*')
|
||||
text = text.replace('\\^', '^')
|
||||
text = text.replace('\\_', '_')
|
||||
text = self.unescape_underscore(text)
|
||||
text = text.replace('\\|', '|')
|
||||
return text
|
||||
|
||||
def unescape_underscore(self, text):
|
||||
return text.replace('\\_', '_')
|
||||
|
||||
def inline_math(self, text):
|
||||
start_pos = text.find("\\(")
|
||||
end_pos = text.find("\\)")
|
||||
@ -136,6 +139,7 @@ class RSTFormatting(Formatting):
|
||||
return content.strip()
|
||||
|
||||
def preformat(self, content):
|
||||
content = self.markup.unescape_underscore(content)
|
||||
if self.indent_level > 0:
|
||||
return self.list_indent("\n.. parsed-literal::\n\n" + self.indent(content.rstrip()), self.indent_level)
|
||||
return "\n.. parsed-literal::\n\n" + self.indent(content.rstrip())
|
||||
@ -355,6 +359,7 @@ class Txt2Rst(TxtParser):
|
||||
self.document_filters.append(lammps_filters.detect_and_add_command_to_index)
|
||||
self.document_filters.append(lammps_filters.filter_multiple_horizontal_rules)
|
||||
self.document_filters.append(lammps_filters.promote_doc_keywords)
|
||||
self.document_filters.append(lammps_filters.merge_preformatted_sections)
|
||||
|
||||
def is_ignored_textblock_begin(self, line):
|
||||
return line.startswith('<!-- HTML_ONLY -->')
|
||||
|
||||
@ -169,6 +169,13 @@ class TestFormatting(unittest.TestCase):
|
||||
" Hello\n"
|
||||
" World\n\n", s)
|
||||
|
||||
def test_preformat_formatting_with_underscore(self):
|
||||
s = self.txt2rst.convert("if MPI.COMM_WORLD.rank == 0:\n"
|
||||
" print(\"Potential energy: \", L.eval(\"pe\")) :pre\n")
|
||||
self.assertEqual("\n.. parsed-literal::\n\n"
|
||||
" if MPI.COMM_WORLD.rank == 0:\n"
|
||||
" print(\"Potential energy: \", L.eval(\"pe\"))\n\n", s)
|
||||
|
||||
def test_header_formatting(self):
|
||||
s = self.txt2rst.convert("Level 1 :h1\n"
|
||||
"Level 2 :h2\n"
|
||||
|
||||
55
examples/balance/in.balance.clock.dynamic
Normal file
55
examples/balance/in.balance.clock.dynamic
Normal file
@ -0,0 +1,55 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
fix 0 all balance 50 1.0 shift x 10 1.0 &
|
||||
weight time 1.0 weight store WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
run 500
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 &
|
||||
weight neigh 0.5 weight time 0.66 weight store WEIGHT
|
||||
run 500
|
||||
run 500
|
||||
|
||||
48
examples/balance/in.balance.clock.static
Normal file
48
examples/balance/in.balance.clock.static
Normal file
@ -0,0 +1,48 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
group fast type 1
|
||||
group slow type 2
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
run 250
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
run 250
|
||||
47
examples/balance/in.balance.group.dynamic
Normal file
47
examples/balance/in.balance.group.dynamic
Normal file
@ -0,0 +1,47 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
group fast type 1
|
||||
group slow type 2
|
||||
balance 1.0 shift x 5 1.1 &
|
||||
weight group 2 fast 1.0 slow ${factor} # out weighted.txt
|
||||
fix 0 all balance 10 1.0 shift x 5 1.1 &
|
||||
weight group 2 fast 1.0 slow ${factor}
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
54
examples/balance/in.balance.group.static
Normal file
54
examples/balance/in.balance.group.static
Normal file
@ -0,0 +1,54 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
balance 1.0 shift x 5 1.1 # out unweighted.txt
|
||||
|
||||
balance 1.0 x uniform
|
||||
|
||||
variable weight atom (type==1)*1.0+(type==2)*v_factor
|
||||
balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
|
||||
|
||||
balance 1.0 x uniform
|
||||
|
||||
group fast type 1
|
||||
group slow type 2
|
||||
balance 1.0 shift x 5 1.1 &
|
||||
weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
47
examples/balance/in.balance.kspace
Normal file
47
examples/balance/in.balance.kspace
Normal file
@ -0,0 +1,47 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
#atom_style charge
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
#set type 1:2 charge 0.0
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/long/coul/long long off 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
kspace_style pppm/disp 1.0e-4
|
||||
kspace_modify gewald/disp 0.1
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
group fast type 1
|
||||
group slow type 2
|
||||
fix 0 all balance 20 1.0 shift x 5 1.0 &
|
||||
weight group 2 fast 1.0 slow 2.0 weight time 0.66
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
53
examples/balance/in.balance.neigh.dynamic
Normal file
53
examples/balance/in.balance.neigh.dynamic
Normal file
@ -0,0 +1,53 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 &
|
||||
weight neigh 0.8 weight store WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mp4 c_p type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
run 500
|
||||
run 500
|
||||
run 500
|
||||
|
||||
53
examples/balance/in.balance.neigh.rcb
Normal file
53
examples/balance/in.balance.neigh.rcb
Normal file
@ -0,0 +1,53 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
comm_style tiled
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
fix 0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
|
||||
run 250
|
||||
run 250
|
||||
|
||||
51
examples/balance/in.balance.neigh.static
Normal file
51
examples/balance/in.balance.neigh.static
Normal file
@ -0,0 +1,51 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8
|
||||
run 250 post no
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8
|
||||
run 250 post no
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
|
||||
run 250
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
|
||||
run 250
|
||||
|
||||
66
examples/balance/in.balance.var.dynamic
Normal file
66
examples/balance/in.balance.var.dynamic
Normal file
@ -0,0 +1,66 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
|
||||
group fast type 1
|
||||
group slow type 2
|
||||
balance 1.0 shift x 10 1.0 &
|
||||
weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
|
||||
variable lastweight atom c_p
|
||||
|
||||
fix 0 all balance 50 1.0 shift x 10 1.0 &
|
||||
weight var lastweight weight time 0.5 weight store WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
run 500
|
||||
|
||||
balance 1.0 shift x 10 1.0 &
|
||||
weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
|
||||
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 &
|
||||
weight var lastweight weight neigh 0.5 weight store WEIGHT
|
||||
|
||||
run 500
|
||||
run 500
|
||||
@ -1,225 +0,0 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style bond
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 6
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 10.0 1.2
|
||||
|
||||
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
|
||||
|
||||
special_bonds lj/coul 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
1 = max # of special neighbors
|
||||
create_bonds all all 1 1.0 1.5
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Added 1014 bonds, new total = 1014
|
||||
6 = max # of 1-2 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
comm_modify cutoff 7.5
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom (c_1%10)+1
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 7.5
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 4.44301 Mbytes
|
||||
Step Temp E_pair Press 10[3] 10
|
||||
0 25.701528 -2.2032569 3.1039469 1 1
|
||||
100 27.623422 -6.228166 2.6542136 1 1
|
||||
200 33.35302 -15.746749 3.2018248 1 1
|
||||
300 39.17734 -24.1557 4.9116986 1 1
|
||||
400 41.660701 -27.615203 8.6214678 1 1
|
||||
500 37.154935 -24.096962 3.2656162 1 1
|
||||
600 35.061294 -21.52655 2.3693223 1 1
|
||||
700 37.204395 -22.313267 2.7108913 1 1
|
||||
800 39.050704 -24.972147 5.5398741 1 1
|
||||
900 38.37275 -24.777769 3.9291488 1 1
|
||||
1000 39.147816 -26.003699 4.3586203 1 1
|
||||
1100 36.084337 -24.88638 4.5496174 1 1
|
||||
1200 32.404559 -20.810803 6.0760128 1 1
|
||||
1300 32.625538 -19.709411 4.3718289 1 1
|
||||
1400 32.246777 -18.785184 3.435959 1 1
|
||||
1500 29.174368 -17.434726 2.2702916 1 1
|
||||
1600 27.359273 -15.40756 1.033659 1 1
|
||||
1700 26.046626 -14.318045 0.87714473 1 1
|
||||
1800 24.540401 -13.017686 0.84464169 1 1
|
||||
1900 26.259688 -12.777739 0.80954004 1 1
|
||||
2000 27.491023 -13.363863 1.4519188 1 1
|
||||
2100 27.839831 -13.709118 3.0184763 1 1
|
||||
2200 26.669065 -12.710422 1.4560094 1 1
|
||||
2300 26.86742 -12.730386 0.16986139 1 1
|
||||
2400 26.375504 -12.476682 1.907352 1 1
|
||||
2500 26.581263 -12.530908 1.5507765 1 1
|
||||
2600 27.67091 -12.922702 2.0391206 1 1
|
||||
2700 27.158784 -13.306789 3.7355268 1 1
|
||||
2800 25.635671 -13.502047 2.9431633 1 1
|
||||
2900 24.648357 -12.388002 0.44910075 1 1
|
||||
3000 22.988768 -10.685349 0.37214853 1 1
|
||||
3100 21.788719 -10.171928 -0.95734833 1 1
|
||||
3200 22.707514 -9.6682633 -0.32868418 1 1
|
||||
3300 22.907772 -10.612766 -0.024319089 1 1
|
||||
3400 24.276426 -10.802246 0.44731188 1 1
|
||||
3500 25.086959 -10.797849 2.3218091 1 1
|
||||
3600 26.064365 -12.589537 1.2460738 1 1
|
||||
3700 24.656426 -11.956895 0.57862216 1 1
|
||||
3800 22.316856 -11.174148 -0.7567936 1 1
|
||||
3900 22.590299 -9.5928781 0.4127727 1 1
|
||||
4000 22.353461 -9.5887736 -0.34247396 1 1
|
||||
4100 24.103395 -9.76584 0.98989862 1 1
|
||||
4200 23.92261 -10.566828 -0.71536268 1 1
|
||||
4300 24.44409 -11.358378 0.37166197 1 1
|
||||
4400 24.772419 -11.324888 0.26732853 1 1
|
||||
4500 23.150748 -11.309892 -0.43134573 1 1
|
||||
4600 24.008361 -10.212365 0.43277527 1 1
|
||||
4700 25.107401 -9.5753673 0.020406689 1 1
|
||||
4800 23.658604 -8.9131426 0.46554745 1 1
|
||||
4900 22.530251 -9.023311 -0.014405315 1 1
|
||||
5000 23.110692 -9.6567397 0.9033234 1 1
|
||||
5100 23.760144 -9.7623416 0.32059726 1 1
|
||||
5200 25.048012 -9.6748253 0.66411561 1 1
|
||||
5300 24.09835 -9.7867216 0.61128267 1 1
|
||||
5400 22.984982 -9.9464053 0.28096544 1 1
|
||||
5500 22.502003 -9.9294451 -0.53666181 1 1
|
||||
5600 23.712298 -10.054318 0.64334761 1 1
|
||||
5700 23.350796 -10.217344 2.1979894 1 1
|
||||
5800 25.246549 -12.458753 0.055553025 1 1
|
||||
5900 24.422272 -10.641177 0.82506839 1 1
|
||||
6000 22.478315 -10.629525 -0.774321 1 1
|
||||
6100 22.970846 -10.218868 0.59819592 1 1
|
||||
6200 24.500063 -10.355481 0.55427078 1 1
|
||||
6300 22.358071 -9.9041539 0.89500518 1 1
|
||||
6400 23.924951 -11.121442 0.045999129 1 1
|
||||
6500 24.83773 -10.464191 2.0048038 1 1
|
||||
6600 24.752158 -9.9939162 0.53794465 1 1
|
||||
6700 23.073765 -9.3662561 0.38618685 1 1
|
||||
6800 21.940219 -8.4948475 -0.25184019 1 1
|
||||
6900 22.23783 -8.8668868 0.0072863367 1 1
|
||||
7000 25.667836 -10.473211 0.59852886 1 1
|
||||
7100 23.352123 -9.0862268 0.85289283 1 1
|
||||
7200 24.072107 -9.4020576 0.090222808 1 1
|
||||
7300 22.806746 -8.4687857 -0.46892989 1 1
|
||||
7400 24.798425 -9.1144357 -0.38738146 1 1
|
||||
7500 24.748499 -9.1560558 0.94929896 1 1
|
||||
7600 25.364753 -10.176533 0.2649225 1 1
|
||||
7700 25.137988 -9.6617897 1.3920543 1 1
|
||||
7800 25.502583 -10.320832 0.64812816 1 1
|
||||
7900 24.5208 -9.9466543 -0.084071026 1 1
|
||||
8000 24.653522 -10.312942 0.32535023 1 1
|
||||
8100 23.129565 -9.6250435 0.016356303 1 1
|
||||
8200 23.82421 -9.7608023 0.11631418 1 1
|
||||
8300 25.081262 -9.3510452 0.92337854 1 1
|
||||
8400 24.328205 -9.2875396 0.28266968 1 1
|
||||
8500 25.041711 -11.254976 -0.21368615 1 1
|
||||
8600 24.111473 -9.0389585 1.2102938 1 1
|
||||
8700 23.50066 -9.0926498 0.78819229 1 1
|
||||
8800 23.840962 -9.3434474 0.091313007 1 1
|
||||
8900 23.081841 -9.0635966 0.56672001 1 1
|
||||
9000 24.712103 -9.3243213 0.60301629 1 1
|
||||
9100 24.457422 -9.439298 -0.60457515 1 1
|
||||
9200 25.070662 -9.1945782 1.2399235 1 1
|
||||
9300 25.019869 -8.7910068 0.42340497 1 1
|
||||
9400 24.23662 -9.3111098 -0.75379175 1 1
|
||||
9500 24.836827 -8.7324281 0.81857501 1 1
|
||||
9600 24.901993 -8.6624128 0.84890877 1 1
|
||||
9700 24.936686 -8.9869503 1.9627894 1 1
|
||||
9800 25.393368 -9.8538595 0.45344428 1 1
|
||||
9900 25.942336 -9.7854728 0.68352091 1 1
|
||||
10000 24.636319 -9.3369442 0.62793231 1 1
|
||||
Loop time of 1.67474 on 1 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 2579511.004 tau/day, 5971.090 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47884 | 0.47884 | 0.47884 | 0.0 | 28.59
|
||||
Bond | 0.24918 | 0.24918 | 0.24918 | 0.0 | 14.88
|
||||
Neigh | 0.82974 | 0.82974 | 0.82974 | 0.0 | 49.54
|
||||
Comm | 0.01265 | 0.01265 | 0.01265 | 0.0 | 0.76
|
||||
Output | 0.00085878 | 0.00085878 | 0.00085878 | 0.0 | 0.05
|
||||
Modify | 0.075636 | 0.075636 | 0.075636 | 0.0 | 4.52
|
||||
Other | | 0.02783 | | | 1.66
|
||||
|
||||
Nlocal: 361 ave 361 max 361 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2421 ave 2421 max 2421 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2421
|
||||
Ave neighs/atom = 6.70637
|
||||
Ave special neighs/atom = 5.61773
|
||||
Neighbor list builds = 4937
|
||||
Dangerous builds = 5
|
||||
Total wall time: 0:00:01
|
||||
@ -1,225 +0,0 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style bond
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 6
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 10.0 1.2
|
||||
|
||||
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
|
||||
|
||||
special_bonds lj/coul 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
1 = max # of special neighbors
|
||||
create_bonds all all 1 1.0 1.5
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Added 1014 bonds, new total = 1014
|
||||
6 = max # of 1-2 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
comm_modify cutoff 7.5
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom (c_1%10)+1
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 7.5
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 4.49421 Mbytes
|
||||
Step Temp E_pair Press 10[3] 10
|
||||
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
|
||||
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
|
||||
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
|
||||
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
|
||||
400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
|
||||
500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906
|
||||
600 35.059889 -21.524279 2.372849 1.3296399 1.0083102
|
||||
700 36.70516 -21.98396 3.2995108 1.3296399 1.0083102
|
||||
800 39.53521 -25.672748 4.3257712 1.3961219 1.0083102
|
||||
900 38.566797 -24.778382 4.1874914 1.3739612 1.0083102
|
||||
1000 37.506157 -25.381025 5.6634589 1.4182825 1.0193906
|
||||
1100 34.186888 -23.460558 5.2123037 1.2963989 1.0083102
|
||||
1200 33.302788 -22.509552 4.9394032 1.1745152 1.0193906
|
||||
1300 33.271956 -22.831342 4.5519649 1.1966759 1.0083102
|
||||
1400 30.344677 -20.654604 4.1641375 1.0969529 1.0193906
|
||||
1500 27.292624 -18.180523 1.0686706 1.1412742 1.0083102
|
||||
1600 26.787948 -15.907011 1.7236133 1.1745152 1.0193906
|
||||
1700 25.708419 -15.568774 0.73006531 1.1080332 1.0193906
|
||||
1800 26.523196 -14.641077 0.78443231 1.1301939 1.0083102
|
||||
1900 25.151151 -13.927975 1.1760729 1.1080332 1.0193906
|
||||
2000 27.637036 -15.055467 1.5903524 1.1301939 1.0083102
|
||||
2100 27.642772 -14.038356 2.4101976 1.2077562 1.0083102
|
||||
2200 27.178261 -13.277262 1.9252291 1.1745152 1.0193906
|
||||
2300 25.615526 -12.67851 0.88527229 1.1634349 1.0083102
|
||||
2400 24.918218 -13.029669 0.95714212 1.1966759 1.0193906
|
||||
2500 27.302154 -13.02629 1.3556788 1.1080332 1.0193906
|
||||
2600 26.798157 -13.78042 2.703198 1.1855956 1.0083102
|
||||
2700 27.24573 -16.504845 3.1771274 1.1523546 1.0193906
|
||||
2800 24.592313 -14.795322 1.6473982 1.0969529 1.0193906
|
||||
2900 22.803769 -13.043913 0.71978239 1.0969529 1.0083102
|
||||
3000 21.388681 -13.323114 -1.3437735 1.0858726 1.0083102
|
||||
3100 21.929044 -11.627262 -0.38509856 1.1191136 1.0083102
|
||||
3200 22.350115 -10.438826 0.7833392 1.0526316 1.0083102
|
||||
3300 22.619011 -9.9110914 1.4143766 1.1191136 1.0193906
|
||||
3400 24.251234 -11.712256 1.4299187 1.0969529 1.0193906
|
||||
3500 25.633796 -12.609976 1.4809529 1.0969529 1.0083102
|
||||
3600 23.070279 -11.178798 0.35315388 1.1191136 1.0083102
|
||||
3700 22.635771 -10.360523 0.060253018 1.1412742 1.0193906
|
||||
3800 20.746426 -9.7066538 0.24549731 1.0526316 1.0083102
|
||||
3900 22.467121 -10.469368 0.9854352 1.0969529 1.0193906
|
||||
4000 22.658639 -10.781605 0.014232783 1.1191136 1.0083102
|
||||
4100 22.839698 -10.528796 1.3995223 1.0526316 1.0083102
|
||||
4200 23.52621 -12.150065 0.74863439 1.0747922 1.0193906
|
||||
4300 24.401948 -11.703236 0.25019621 1.0637119 1.0193906
|
||||
4400 22.769001 -11.763045 -0.033044917 1.1412742 1.0083102
|
||||
4500 22.170178 -11.572473 -0.40444128 1.0526316 1.0083102
|
||||
4600 22.409231 -10.761099 -0.012942618 1.0747922 1.0083102
|
||||
4700 22.953641 -10.999181 0.17199357 1.0637119 1.0083102
|
||||
4800 22.746977 -10.69943 -0.050664647 1.0526316 1.0083102
|
||||
4900 23.784023 -10.353932 0.55400224 1.0747922 1.0304709
|
||||
5000 23.250563 -11.567067 -0.23735032 1.0637119 1.0083102
|
||||
5100 22.521138 -10.661998 0.50094359 1.0747922 1.0083102
|
||||
5200 21.318659 -9.5996948 0.75683786 1.0637119 1.0193906
|
||||
5300 21.603355 -10.042239 -0.2376815 1.0637119 1.0083102
|
||||
5400 21.350407 -10.181041 -0.87085628 1.1745152 1.0193906
|
||||
5500 22.430002 -10.535576 0.47962005 1.1191136 1.0193906
|
||||
5600 22.459036 -11.914086 0.47719353 1.0858726 1.0193906
|
||||
5700 23.348257 -12.888911 0.55511547 1.0858726 1.0193906
|
||||
5800 23.357742 -12.328566 0.734193 1.0526316 1.0193906
|
||||
5900 24.002277 -11.439187 0.23688862 1.0858726 1.0193906
|
||||
6000 22.398563 -10.682615 0.28777592 1.0747922 1.0193906
|
||||
6100 22.23883 -10.838986 -0.17956279 1.1080332 1.0083102
|
||||
6200 21.930735 -11.182485 0.044031465 1.0526316 1.0193906
|
||||
6300 22.658226 -11.142419 0.060550217 1.0526316 1.0193906
|
||||
6400 22.375935 -11.1764 -0.027267206 1.0526316 1.0193906
|
||||
6500 21.553541 -9.9609653 1.0562139 1.0858726 1.0193906
|
||||
6600 23.339323 -10.988956 0.19462502 1.0526316 1.0083102
|
||||
6700 22.506968 -11.276791 0.50225378 1.0969529 1.0083102
|
||||
6800 22.991741 -10.292043 1.3278137 1.0858726 1.0193906
|
||||
6900 22.716461 -10.540264 1.090723 1.0304709 1.0083102
|
||||
7000 20.88433 -10.566053 -0.47976012 1.0969529 1.0193906
|
||||
7100 22.034864 -10.27774 0.24169213 1.0193906 1.0083102
|
||||
7200 23.107403 -10.304771 0.39888005 1.0969529 1.0304709
|
||||
7300 22.734104 -9.8038963 1.1986757 1.0858726 1.0083102
|
||||
7400 23.566402 -10.560548 1.0213434 1.1080332 1.0193906
|
||||
7500 23.651346 -10.596902 1.290057 1.0969529 1.0083102
|
||||
7600 23.181407 -10.247073 0.80701327 1.0526316 1.0083102
|
||||
7700 23.778698 -10.659208 0.54327672 1.0304709 1.0193906
|
||||
7800 22.655159 -10.183303 0.81382393 1.0747922 1.0193906
|
||||
7900 22.897008 -10.849819 0.56424197 1.0415512 1.0083102
|
||||
8000 23.698074 -10.398048 0.42170034 1.0747922 1.0083102
|
||||
8100 22.726563 -9.8563277 0.30293638 1.0193906 1.0193906
|
||||
8200 23.424699 -10.687885 0.54222367 1.0415512 1.0083102
|
||||
8300 22.921826 -10.919492 0.55264172 1.0747922 1.0083102
|
||||
8400 23.220159 -9.7725217 1.2872547 1.1080332 1.0083102
|
||||
8500 23.606204 -9.7070499 1.0340181 1.0747922 1.0193906
|
||||
8600 23.008166 -10.451507 -0.42524326 1.0747922 1.0083102
|
||||
8700 22.4959 -10.278782 0.19535494 1.0858726 1.0083102
|
||||
8800 25.153658 -10.757 1.5966743 1.0193906 1.0193906
|
||||
8900 23.206798 -10.486994 1.2031737 1.0637119 1.0083102
|
||||
9000 22.726684 -10.406196 0.10165144 1.0858726 1.0304709
|
||||
9100 22.504045 -9.638919 -0.80560991 1.0747922 1.0083102
|
||||
9200 21.431928 -9.073801 0.3773795 1.0415512 1.0193906
|
||||
9300 23.596502 -11.045041 -0.3135787 1.0858726 1.0083102
|
||||
9400 25.308669 -11.931174 1.3143518 1.0526316 1.0193906
|
||||
9500 24.394499 -10.661499 0.82236963 1.0969529 1.0193906
|
||||
9600 21.987451 -9.5632699 0.30728292 1.0858726 1.0193906
|
||||
9700 22.150748 -9.5707928 -0.1239396 1.0526316 1.0193906
|
||||
9800 23.347328 -9.7899306 0.29737715 1.0193906 1.0083102
|
||||
9900 20.310207 -9.4839992 -1.2980277 1.0193906 1.0193906
|
||||
10000 22.978427 -9.9593786 -0.45943368 1.0526316 1.0083102
|
||||
Loop time of 0.815364 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 5298244.819 tau/day, 12264.456 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12547 | 0.13632 | 0.14796 | 2.6 | 16.72
|
||||
Bond | 0.05547 | 0.06023 | 0.064582 | 1.7 | 7.39
|
||||
Neigh | 0.28201 | 0.28972 | 0.298 | 1.1 | 35.53
|
||||
Comm | 0.16858 | 0.19467 | 0.22096 | 4.3 | 23.88
|
||||
Output | 0.0017931 | 0.0019639 | 0.0023253 | 0.5 | 0.24
|
||||
Modify | 0.039718 | 0.040559 | 0.041364 | 0.4 | 4.97
|
||||
Other | | 0.09189 | | | 11.27
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 195.25 ave 202 max 185 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 629.5 ave 731 max 543 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2518
|
||||
Ave neighs/atom = 6.97507
|
||||
Ave special neighs/atom = 5.61773
|
||||
Neighbor list builds = 4874
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,524 +0,0 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
|
||||
# careful not to slam into wall too hard
|
||||
|
||||
variable v index 0.3
|
||||
variable w index 0.08
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style bond
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 6
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 0.3 $w 0 sum yes
|
||||
velocity all set 0.3 0.08 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 10.0 1.2
|
||||
|
||||
create_bonds all all 1 1.0 1.5
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Added 1014 bonds, new total = 1014
|
||||
6 = max # of 1-2 neighbors
|
||||
30 = max # of 1-3 neighbors
|
||||
180 = max # of 1-4 neighbors
|
||||
36 = max # of special neighbors
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom (c_1%10)+1
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 40000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 6.31529 Mbytes
|
||||
Step Temp E_pair Press 10[3] 10
|
||||
0 0.57437856 0 0.26099453 1 1
|
||||
100 0.29756515 0 0.10149401 1 1
|
||||
200 0.35394813 0 0.075159099 1 1
|
||||
300 0.39245849 0 0.033002384 1 1
|
||||
400 0.34078347 0 -0.020825841 1 1
|
||||
500 0.35201095 0 -0.062637506 1 1
|
||||
600 0.34014717 0 -0.11122965 1 1
|
||||
700 0.3323524 0 -0.11598015 1 1
|
||||
800 0.35116047 0 -0.096162395 1 1
|
||||
900 0.35695352 0 -0.01385176 1 1
|
||||
1000 0.36986539 0 0.056772858 1 1
|
||||
1100 0.34584644 0 0.084941323 1 1
|
||||
1200 0.31921435 0 0.10545078 1 1
|
||||
1300 0.32952819 0 0.124902 1 1
|
||||
1400 0.34497365 0 0.12662081 1 1
|
||||
1500 0.33429243 0 0.096230972 1 1
|
||||
1600 0.33765387 0 0.025800542 1 1
|
||||
1700 0.35134464 0 -0.04422593 1 1
|
||||
1800 0.35003859 0 -0.096745576 1 1
|
||||
1900 0.33839618 0 -0.095465943 1 1
|
||||
2000 0.33732078 0 -0.094652802 1 1
|
||||
2100 0.34552238 0 -0.076729261 1 1
|
||||
2200 0.34893142 0 -0.036853228 1 1
|
||||
2300 0.35379341 0 0.021124847 1 1
|
||||
2400 0.34829744 0 0.09230184 1 1
|
||||
2500 0.33038141 0 0.1399855 1 1
|
||||
2600 0.30983019 0 0.12754742 1 1
|
||||
2700 0.32992561 0 0.10485138 1 1
|
||||
2800 0.34604747 0 0.066174138 1 1
|
||||
2900 0.3444791 0 0.036590652 1 1
|
||||
3000 0.34721342 0 -0.023793368 1 1
|
||||
3100 0.33404314 0 -0.08374223 1 1
|
||||
3200 0.33019355 0 -0.12715599 1 1
|
||||
3300 0.33515177 0 -0.12217394 1 1
|
||||
3400 0.33628481 0 -0.070877624 1 1
|
||||
3500 0.34257038 0 -0.021612062 1 1
|
||||
3600 0.32838009 0 0.030131228 1 1
|
||||
3700 0.34462142 0 0.074586378 1 1
|
||||
3800 0.30891825 0 0.10605673 1 1
|
||||
3900 0.33847951 0 0.13956139 1 1
|
||||
4000 0.32952079 0 0.12688129 1 1
|
||||
4100 0.32646772 0 0.081089042 1 1
|
||||
4200 0.35399503 0 0.013422873 1 1
|
||||
4300 0.33154914 0 -0.050919508 1 1
|
||||
4400 0.34113556 0 -0.083171 1 1
|
||||
4500 0.32651708 0 -0.1063133 1 1
|
||||
4600 0.34359609 0 -0.1076395 1 1
|
||||
4700 0.34973537 0 -0.088231606 1 1
|
||||
4800 0.35198515 0 -0.020901044 1 1
|
||||
4900 0.35187284 0 0.043645941 1 1
|
||||
5000 0.34887336 0 0.095698609 1 1
|
||||
5100 0.30308163 0 0.11649328 1 1
|
||||
5200 0.32401285 0 0.12072411 1 1
|
||||
5300 0.33025072 0 0.10933161 1 1
|
||||
5400 0.33288012 0 0.078356448 1 1
|
||||
5500 0.35142492 0 0.036958063 1 1
|
||||
5600 0.35125368 0 -0.041371343 1 1
|
||||
5700 0.34547744 0 -0.096450846 1 1
|
||||
5800 0.30939887 0 -0.12356656 1 1
|
||||
5900 0.32315628 0 -0.11338676 1 1
|
||||
6000 0.34117485 0 -0.066198961 1 1
|
||||
6100 0.35298043 0 -0.016172816 1 1
|
||||
6200 0.35130653 0 0.027660468 1 1
|
||||
6300 0.35398766 0 0.087221238 1 1
|
||||
6400 0.30963379 0 0.11990957 1 1
|
||||
6500 0.3174541 0 0.14103528 1 1
|
||||
6600 0.31989791 0 0.11575506 1 1
|
||||
6700 0.33811477 0 0.060747353 1 1
|
||||
6800 0.3424043 0 0.010357152 1 1
|
||||
6900 0.34804319 0 -0.042621786 1 1
|
||||
7000 0.35357865 0 -0.067248959 1 1
|
||||
7100 0.33556885 0 -0.10983726 1 1
|
||||
7200 0.33531101 0 -0.112179 1 1
|
||||
7300 0.35742607 0 -0.078405267 1 1
|
||||
7400 0.34577559 0 -0.01985432 1 1
|
||||
7500 0.3498641 0 0.052289439 1 1
|
||||
7600 0.33773715 0 0.092939035 1 1
|
||||
7700 0.33093497 0 0.11924405 1 1
|
||||
7800 0.31435814 0 0.12701724 1 1
|
||||
7900 0.33132217 0 0.10793075 1 1
|
||||
8000 0.33451798 0 0.077993125 1 1
|
||||
8100 0.35188371 0 0.019929977 1 1
|
||||
8200 0.33645742 0 -0.039302079 1 1
|
||||
8300 0.3415632 0 -0.098067982 1 1
|
||||
8400 0.30619282 0 -0.12952879 1 1
|
||||
8500 0.34446484 0 -0.098084709 1 1
|
||||
8600 0.33761673 0 -0.07069818 1 1
|
||||
8700 0.34495452 0 -0.022458056 1 1
|
||||
8800 0.33502983 0 0.027742411 1 1
|
||||
8900 0.35418591 0 0.092390134 1 1
|
||||
9000 0.31648387 0 0.12467398 1 1
|
||||
9100 0.33994825 0 0.14460327 1 1
|
||||
9200 0.33822571 0 0.11273284 1 1
|
||||
9300 0.33260773 0 0.060063671 1 1
|
||||
9400 0.36140305 0 0.021427642 1 1
|
||||
9500 0.34273562 0 -0.034064202 1 1
|
||||
9600 0.33867054 0 -0.089076906 1 1
|
||||
9700 0.32088235 0 -0.12027075 1 1
|
||||
9800 0.3320823 0 -0.11602794 1 1
|
||||
9900 0.33916442 0 -0.080281044 1 1
|
||||
10000 0.34852268 0 -0.01000914 1 1
|
||||
10100 0.32955942 0 0.04258493 1 1
|
||||
10200 0.34487898 0 0.086971308 1 1
|
||||
10300 0.32325593 0 0.11558149 1 1
|
||||
10400 0.30927871 0 0.12239437 1 1
|
||||
10500 0.33176799 0 0.12285937 1 1
|
||||
10600 0.35120027 0 0.084897432 1 1
|
||||
10700 0.33129697 0 0.0053089279 1 1
|
||||
10800 0.36028769 0 -0.04280715 1 1
|
||||
10900 0.35552287 0 -0.084955999 1 1
|
||||
11000 0.3406024 0 -0.096554577 1 1
|
||||
11100 0.33041202 0 -0.10703492 1 1
|
||||
11200 0.32442686 0 -0.084328121 1 1
|
||||
11300 0.35952468 0 -0.020191965 1 1
|
||||
11400 0.34610624 0 0.03440148 1 1
|
||||
11500 0.3415612 0 0.1041929 1 1
|
||||
11600 0.34040042 0 0.13215705 1 1
|
||||
11700 0.33555094 0 0.12738686 1 1
|
||||
11800 0.3458647 0 0.10963398 1 1
|
||||
11900 0.33836678 0 0.067253864 1 1
|
||||
12000 0.34853314 0 0.03201448 1 1
|
||||
12100 0.34600048 0 -0.034833402 1 1
|
||||
12200 0.33145631 0 -0.09865675 1 1
|
||||
12300 0.32848884 0 -0.1248489 1 1
|
||||
12400 0.3321344 0 -0.11266575 1 1
|
||||
12500 0.32622305 0 -0.061634993 1 1
|
||||
12600 0.36213537 0 -0.0090593315 1 1
|
||||
12700 0.34673866 0 0.036734645 1 1
|
||||
12800 0.34606618 0 0.086267678 1 1
|
||||
12900 0.34271431 0 0.12415522 1 1
|
||||
13000 0.31993287 0 0.13879926 1 1
|
||||
13100 0.3422918 0 0.11978905 1 1
|
||||
13200 0.33055236 0 0.062620483 1 1
|
||||
13300 0.34652207 0 0.0043833459 1 1
|
||||
13400 0.33574661 0 -0.04691024 1 1
|
||||
13500 0.33940837 0 -0.074241604 1 1
|
||||
13600 0.32093414 0 -0.1078027 1 1
|
||||
13700 0.34336597 0 -0.10544097 1 1
|
||||
13800 0.35806461 0 -0.072531559 1 1
|
||||
13900 0.35209713 0 -0.018851408 1 1
|
||||
14000 0.35702629 0 0.061046366 1 1
|
||||
14100 0.33234093 0 0.094086465 1 1
|
||||
14200 0.3459466 0 0.12186656 1 1
|
||||
14300 0.3327428 0 0.11396572 1 1
|
||||
14400 0.32409443 0 0.10658903 1 1
|
||||
14500 0.35022184 0 0.083558031 1 1
|
||||
14600 0.34823843 0 0.024605569 1 1
|
||||
14700 0.35298973 0 -0.040418888 1 1
|
||||
14800 0.33679845 0 -0.10067728 1 1
|
||||
14900 0.32790966 0 -0.10925568 1 1
|
||||
15000 0.34208495 0 -0.09568004 1 1
|
||||
15100 0.33647529 0 -0.055652929 1 1
|
||||
15200 0.35328398 0 -0.020236536 1 1
|
||||
15300 0.34252669 0 0.026434179 1 1
|
||||
15400 0.34409435 0 0.094410599 1 1
|
||||
15500 0.32288994 0 0.12034455 1 1
|
||||
15600 0.32109689 0 0.13645185 1 1
|
||||
15700 0.33681572 0 0.098607746 1 1
|
||||
15800 0.33635195 0 0.05570715 1 1
|
||||
15900 0.34289757 0 0.013849092 1 1
|
||||
16000 0.34225547 0 -0.035597548 1 1
|
||||
16100 0.33660991 0 -0.076931881 1 1
|
||||
16200 0.32802152 0 -0.12765884 1 1
|
||||
16300 0.3469374 0 -0.10785455 1 1
|
||||
16400 0.34053641 0 -0.070259853 1 1
|
||||
16500 0.34610591 0 -0.014315306 1 1
|
||||
16600 0.35109001 0 0.041251169 1 1
|
||||
16700 0.34336905 0 0.077996627 1 1
|
||||
16800 0.33277414 0 0.11053634 1 1
|
||||
16900 0.32183338 0 0.11680626 1 1
|
||||
17000 0.34044352 0 0.10806555 1 1
|
||||
17100 0.32967873 0 0.067759786 1 1
|
||||
17200 0.36172278 0 -0.0048631904 1 1
|
||||
17300 0.35619435 0 -0.04215545 1 1
|
||||
17400 0.34540936 0 -0.093994174 1 1
|
||||
17500 0.33193585 0 -0.098831315 1 1
|
||||
17600 0.3544756 0 -0.085660403 1 1
|
||||
17700 0.34505209 0 -0.069640515 1 1
|
||||
17800 0.36291124 0 -0.0063088133 1 1
|
||||
17900 0.34255705 0 0.046794555 1 1
|
||||
18000 0.34163238 0 0.11767705 1 1
|
||||
18100 0.3466445 0 0.1351712 1 1
|
||||
18200 0.33037668 0 0.12703659 1 1
|
||||
18300 0.33677404 0 0.10956306 1 1
|
||||
18400 0.34978954 0 0.087193072 1 1
|
||||
18500 0.33354363 0 0.051095814 1 1
|
||||
18600 0.34651729 0 0.0056245561 1 1
|
||||
18700 0.32622232 0 -0.047319269 1 1
|
||||
18800 0.32978847 0 -0.054929416 1 1
|
||||
18900 0.34192451 0 -0.037252471 1 1
|
||||
19000 0.34061294 0 -0.001167235 1 1
|
||||
19100 0.34194478 0 0.016945224 1 1
|
||||
19200 0.33321765 0 0.050665354 1 1
|
||||
19300 0.33197783 0 0.080470585 1 1
|
||||
19400 0.33284715 0 0.12423599 1 1
|
||||
19500 0.33867856 0 0.12689524 1 1
|
||||
19600 0.36092786 0 0.11417704 1 1
|
||||
19700 0.34270183 0 0.069038291 1 1
|
||||
19800 0.34880695 0 0.042483681 1 1
|
||||
19900 0.33903644 0 0.034788638 1 1
|
||||
20000 0.32590125 0 0.011383785 1 1
|
||||
20100 0.30358859 0 0.0030743554 1 1
|
||||
20200 0.31830224 0 0.017637826 1 1
|
||||
20300 0.34195438 0 0.072811099 1 1
|
||||
20400 0.31249563 0 0.10063541 1 1
|
||||
20500 0.31544938 0 0.1405794 1 1
|
||||
20600 0.30071644 0 0.12763486 1 1
|
||||
20700 0.2890265 0 0.1136651 1 1
|
||||
20800 0.28962296 0 0.094481978 1 1
|
||||
20900 0.29447212 0 0.0967165 1 1
|
||||
21000 0.31159961 0 0.067307231 1 1
|
||||
21100 0.30490648 0 0.017689358 1 1
|
||||
21200 0.30687262 0 -0.016055512 1 1
|
||||
21300 0.30083286 0 -0.0014988997 1 1
|
||||
21400 0.32070426 0 0.015960302 1 1
|
||||
21500 0.31439311 0 0.038170385 1 1
|
||||
21600 0.32617832 0 0.043263788 1 1
|
||||
21700 0.35151793 0 0.066302727 1 1
|
||||
21800 0.35912885 0 0.070099103 1 1
|
||||
21900 0.32451958 0 0.068935768 1 1
|
||||
22000 0.35219298 0 0.067161227 1 1
|
||||
22100 0.34857705 0 0.032731746 1 1
|
||||
22200 0.34750227 0 0.0056917695 1 1
|
||||
22300 0.34766017 0 -0.0027090483 1 1
|
||||
22400 0.33426062 0 -0.023196063 1 1
|
||||
22500 0.34174625 0 -0.025019717 1 1
|
||||
22600 0.3356145 0 -0.029707418 1 1
|
||||
22700 0.3362653 0 -0.035815733 1 1
|
||||
22800 0.33973405 0 -0.0024705835 1 1
|
||||
22900 0.33813085 0 0.0077527467 1 1
|
||||
23000 0.33339981 0 0.028340744 1 1
|
||||
23100 0.34079832 0 0.018521302 1 1
|
||||
23200 0.33074548 0 0.032378405 1 1
|
||||
23300 0.32965664 0 0.035989589 1 1
|
||||
23400 0.30927749 0 0.024581106 1 1
|
||||
23500 0.32890632 0 0.01092479 1 1
|
||||
23600 0.34137438 0 0.0094839745 1 1
|
||||
23700 0.34512638 0 -0.012392771 1 1
|
||||
23800 0.31781354 0 -0.012908449 1 1
|
||||
23900 0.32405513 0 -0.015018071 1 1
|
||||
24000 0.33549728 0 -0.012812915 1 1
|
||||
24100 0.31368736 0 -0.020818372 1 1
|
||||
24200 0.33533836 0 0.0056121057 1 1
|
||||
24300 0.32530627 0 0.018183931 1 1
|
||||
24400 0.31930662 0 0.027446878 1 1
|
||||
24500 0.33540302 0 0.040307455 1 1
|
||||
24600 0.34020431 0 0.027403921 1 1
|
||||
24700 0.3291814 0 0.01204865 1 1
|
||||
24800 0.31552604 0 0.019654111 1 1
|
||||
24900 0.34727253 0 0.01670543 1 1
|
||||
25000 0.35120105 0 0.0038617562 1 1
|
||||
25100 0.32706871 0 -0.021196623 1 1
|
||||
25200 0.32915282 0 -0.017146508 1 1
|
||||
25300 0.32577518 0 -0.01312495 1 1
|
||||
25400 0.33286855 0 0.0014726193 1 1
|
||||
25500 0.33002601 0 0.0080974022 1 1
|
||||
25600 0.34127655 0 0.014296091 1 1
|
||||
25700 0.34048065 0 0.022513032 1 1
|
||||
25800 0.33029079 0 0.038733531 1 1
|
||||
25900 0.33031324 0 0.026156982 1 1
|
||||
26000 0.32967371 0 0.028727383 1 1
|
||||
26100 0.33775718 0 0.015607478 1 1
|
||||
26200 0.35097144 0 0.012291703 1 1
|
||||
26300 0.34303792 0 0.00094823191 1 1
|
||||
26400 0.33632665 0 -0.0026904889 1 1
|
||||
26500 0.33580127 0 -0.0074168555 1 1
|
||||
26600 0.33063188 0 -0.020378601 1 1
|
||||
26700 0.33581846 0 -0.00084397268 1 1
|
||||
26800 0.32998532 0 0.015932208 1 1
|
||||
26900 0.33825444 0 0.010428603 1 1
|
||||
27000 0.32081518 0 0.019818223 1 1
|
||||
27100 0.31448098 0 0.020093416 1 1
|
||||
27200 0.32643684 0 0.021934917 1 1
|
||||
27300 0.33289466 0 0.023713072 1 1
|
||||
27400 0.32310744 0 0.024110945 1 1
|
||||
27500 0.33115619 0 0.0025776713 1 1
|
||||
27600 0.33295887 0 -0.010710764 1 1
|
||||
27700 0.32968876 0 -0.0064595905 1 1
|
||||
27800 0.34064581 0 -0.0086519116 1 1
|
||||
27900 0.33559187 0 -0.0055753593 1 1
|
||||
28000 0.32300727 0 -0.0004153384 1 1
|
||||
28100 0.32147461 0 -0.0058543412 1 1
|
||||
28200 0.35532383 0 0.013646951 1 1
|
||||
28300 0.31507942 0 0.026532255 1 1
|
||||
28400 0.32711006 0 0.033214981 1 1
|
||||
28500 0.34472462 0 0.028050837 1 1
|
||||
28600 0.33708059 0 0.019115676 1 1
|
||||
28700 0.34478087 0 0.023743689 1 1
|
||||
28800 0.34546686 0 0.0081772997 1 1
|
||||
28900 0.34004886 0 0.017771865 1 1
|
||||
29000 0.33604232 0 -0.010505671 1 1
|
||||
29100 0.33541374 0 -0.016273261 1 1
|
||||
29200 0.34347489 0 -0.010002306 1 1
|
||||
29300 0.34083904 0 0.0089701784 1 1
|
||||
29400 0.34846892 0 0.020765104 1 1
|
||||
29500 0.3416255 0 0.022650856 1 1
|
||||
29600 0.33725496 0 0.020693083 1 1
|
||||
29700 0.34480638 0 0.024317128 1 1
|
||||
29800 0.31459471 0 0.023097895 1 1
|
||||
29900 0.33014448 0 0.03114046 1 1
|
||||
30000 0.33741498 0 0.015624314 1 1
|
||||
30100 0.32598657 0 -0.0018860541 1 1
|
||||
30200 0.34855815 0 0.0017983372 1 1
|
||||
30300 0.33375921 0 0.0010991235 1 1
|
||||
30400 0.35008944 0 -0.0027316177 1 1
|
||||
30500 0.33279729 0 -0.0035788551 1 1
|
||||
30600 0.33868746 0 -0.0016249482 1 1
|
||||
30700 0.33597034 0 -0.0014524001 1 1
|
||||
30800 0.3227257 0 0.016353457 1 1
|
||||
30900 0.32676516 0 0.027396654 1 1
|
||||
31000 0.34083982 0 0.031606413 1 1
|
||||
31100 0.32165238 0 0.013583368 1 1
|
||||
31200 0.3428492 0 0.020486611 1 1
|
||||
31300 0.32372541 0 0.01215566 1 1
|
||||
31400 0.32734692 0 0.016229397 1 1
|
||||
31500 0.33089262 0 0.0060426618 1 1
|
||||
31600 0.34273493 0 -0.013456537 1 1
|
||||
31700 0.32723905 0 -0.019243766 1 1
|
||||
31800 0.33636488 0 0.0027814902 1 1
|
||||
31900 0.32834805 0 0.00706877 1 1
|
||||
32000 0.33995148 0 0.0018383309 1 1
|
||||
32100 0.33412282 0 0.0076455933 1 1
|
||||
32200 0.34334884 0 0.023586129 1 1
|
||||
32300 0.32778925 0 0.020564321 1 1
|
||||
32400 0.33163443 0 0.038878463 1 1
|
||||
32500 0.32290345 0 0.022247461 1 1
|
||||
32600 0.34113954 0 0.010966365 1 1
|
||||
32700 0.33390633 0 0.0037777555 1 1
|
||||
32800 0.34385341 0 0.010556575 1 1
|
||||
32900 0.32137047 0 0.00022027143 1 1
|
||||
33000 0.32079172 0 -0.017261272 1 1
|
||||
33100 0.33570882 0 -0.0051942206 1 1
|
||||
33200 0.34320894 0 -0.011515281 1 1
|
||||
33300 0.32794746 0 -0.0018153673 1 1
|
||||
33400 0.33060982 0 0.027118146 1 1
|
||||
33500 0.33641809 0 0.02143035 1 1
|
||||
33600 0.33643061 0 0.020833068 1 1
|
||||
33700 0.3485949 0 0.030918751 1 1
|
||||
33800 0.3283985 0 0.01947613 1 1
|
||||
33900 0.31959761 0 0.021128147 1 1
|
||||
34000 0.33897984 0 0.015270986 1 1
|
||||
34100 0.32392267 0 0.0020130852 1 1
|
||||
34200 0.33084514 0 -0.024316708 1 1
|
||||
34300 0.3342259 0 -0.0059047764 1 1
|
||||
34400 0.33385098 0 0.0063818721 1 1
|
||||
34500 0.33255603 0 -0.01023837 1 1
|
||||
34600 0.34766173 0 0.0056703013 1 1
|
||||
34700 0.339822 0 0.0061648559 1 1
|
||||
34800 0.33902329 0 0.030037037 1 1
|
||||
34900 0.3216153 0 0.027996689 1 1
|
||||
35000 0.32701056 0 0.024778517 1 1
|
||||
35100 0.3124942 0 0.011316548 1 1
|
||||
35200 0.34486416 0 0.011670127 1 1
|
||||
35300 0.33275353 0 0.020491246 1 1
|
||||
35400 0.33618763 0 0.014678874 1 1
|
||||
35500 0.32352282 0 -0.018568683 1 1
|
||||
35600 0.32617903 0 -0.012796912 1 1
|
||||
35700 0.32378048 0 -0.021318585 1 1
|
||||
35800 0.3371086 0 -0.0023678632 1 1
|
||||
35900 0.33818476 0 0.011197742 1 1
|
||||
36000 0.35142144 0 0.022520935 1 1
|
||||
36100 0.35147297 0 0.020277852 1 1
|
||||
36200 0.33489465 0 0.014564878 1 1
|
||||
36300 0.33841515 0 0.036439962 1 1
|
||||
36400 0.32301096 0 0.019966746 1 1
|
||||
36500 0.35612028 0 0.036509556 1 1
|
||||
36600 0.33841597 0 -0.0042180605 1 1
|
||||
36700 0.34477654 0 -0.0052770853 1 1
|
||||
36800 0.33804317 0 -0.013751733 1 1
|
||||
36900 0.35003816 0 -0.0021184393 1 1
|
||||
37000 0.32965041 0 -0.020900951 1 1
|
||||
37100 0.34653095 0 -0.013667977 1 1
|
||||
37200 0.35019871 0 -0.0071740923 1 1
|
||||
37300 0.34859745 0 0.02006041 1 1
|
||||
37400 0.35739859 0 0.020892822 1 1
|
||||
37500 0.34128859 0 0.041072111 1 1
|
||||
37600 0.33781905 0 0.023376738 1 1
|
||||
37700 0.32961874 0 0.030953741 1 1
|
||||
37800 0.343987 0 0.029579795 1 1
|
||||
37900 0.33610448 0 0.036836828 1 1
|
||||
38000 0.32757228 0 0.020902031 1 1
|
||||
38100 0.32735808 0 0.019544751 1 1
|
||||
38200 0.35646953 0 0.044607528 1 1
|
||||
38300 0.32509773 0 0.03610738 1 1
|
||||
38400 0.32111741 0 0.034474043 1 1
|
||||
38500 0.30590608 0 0.053461212 1 1
|
||||
38600 0.32322402 0 0.053453832 1 1
|
||||
38700 0.33843057 0 0.076264534 1 1
|
||||
38800 0.31350741 0 0.064733869 1 1
|
||||
38900 0.31943061 0 0.067836769 1 1
|
||||
39000 0.33775583 0 0.0788316 1 1
|
||||
39100 0.34256036 0 0.075874935 1 1
|
||||
39200 0.33128527 0 0.071610976 1 1
|
||||
39300 0.34519653 0 0.046257301 1 1
|
||||
39400 0.34351844 0 0.052422917 1 1
|
||||
39500 0.35716037 0 0.048916058 1 1
|
||||
39600 0.34000737 0 0.016149089 1 1
|
||||
39700 0.34587892 0 0.021619621 1 1
|
||||
39800 0.34878036 0 0.0092881327 1 1
|
||||
39900 0.35225411 0 -0.011341599 1 1
|
||||
40000 0.36309266 0 0.0050869295 1 1
|
||||
Loop time of 1.94553 on 1 procs for 40000 steps with 361 atoms
|
||||
|
||||
Performance: 8881898.790 tau/day, 20559.951 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.068658 | 0.068658 | 0.068658 | 0.0 | 3.53
|
||||
Bond | 0.9979 | 0.9979 | 0.9979 | 0.0 | 51.29
|
||||
Neigh | 0.50428 | 0.50428 | 0.50428 | 0.0 | 25.92
|
||||
Comm | 0.015341 | 0.015341 | 0.015341 | 0.0 | 0.79
|
||||
Output | 0.0029466 | 0.0029466 | 0.0029466 | 0.0 | 0.15
|
||||
Modify | 0.28324 | 0.28324 | 0.28324 | 0.0 | 14.56
|
||||
Other | | 0.07317 | | | 3.76
|
||||
|
||||
Nlocal: 361 ave 361 max 361 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 31.0249
|
||||
Neighbor list builds = 3079
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,202 +0,0 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 2.47688 Mbytes
|
||||
Step Temp E_pair Press 10[3] 10
|
||||
0 25.701528 -29.143179 -1.2407285 1 1
|
||||
100 26.269576 -29.713313 7.9052334 1 1
|
||||
200 26.368336 -29.809962 1.6412462 1 1
|
||||
300 26.479082 -29.920083 2.3678653 1 1
|
||||
400 26.522239 -29.965537 6.6787858 1 1
|
||||
500 25.725591 -29.168034 0.67065285 1 1
|
||||
600 26.247693 -29.692706 7.9887712 1 1
|
||||
700 26.237368 -29.676926 1.5987214 1 1
|
||||
800 25.889643 -29.431589 4.6160859 1 1
|
||||
900 23.635295 -27.372963 9.029962 1 1
|
||||
1000 22.571904 -25.87422 1.8936085 1 1
|
||||
1100 17.493795 -21.447274 9.502619 1 1
|
||||
1200 17.214459 -20.726964 6.3578933 1 1
|
||||
1300 16.424366 -19.75746 3.9025348 1 1
|
||||
1400 15.09282 -18.172384 1.7966088 1 1
|
||||
1500 13.669129 -16.736191 1.3320876 1 1
|
||||
1600 13.518191 -16.481254 2.2474968 1 1
|
||||
1700 13.840191 -16.808798 1.848689 1 1
|
||||
1800 12.705797 -15.654395 2.6658475 1 1
|
||||
1900 12.560112 -15.376796 1.6651246 1 1
|
||||
2000 12.11219 -14.943991 1.2347207 1 1
|
||||
2100 11.681161 -14.453803 1.1856253 1 1
|
||||
2200 11.380134 -14.15437 1.0983288 1 1
|
||||
2300 11.404137 -14.206989 1.0886428 1 1
|
||||
2400 11.267361 -14.00915 1.1353313 1 1
|
||||
2500 11.086288 -13.866685 1.5189761 1 1
|
||||
2600 11.241757 -14.031809 1.6088858 1 1
|
||||
2700 10.741715 -13.522752 1.2648051 1 1
|
||||
2800 10.594219 -13.461001 1.2068865 1 1
|
||||
2900 10.497917 -13.243311 0.90549881 1 1
|
||||
3000 9.8887944 -12.633322 1.2014467 1 1
|
||||
3100 10.046064 -12.757462 0.72911664 1 1
|
||||
3200 9.8202521 -12.544235 0.85793687 1 1
|
||||
3300 9.9932983 -12.729524 1.3692879 1 1
|
||||
3400 9.4389164 -12.132571 0.83559817 1 1
|
||||
3500 9.4456791 -12.154808 1.2415677 1 1
|
||||
3600 9.4291752 -12.13391 1.1892815 1 1
|
||||
3700 9.2656145 -11.994284 0.93597208 1 1
|
||||
3800 9.6833674 -12.407022 1.4696321 1 1
|
||||
3900 9.2075262 -11.996657 1.0201833 1 1
|
||||
4000 8.704708 -11.395839 1.5366945 1 1
|
||||
4100 8.496226 -11.160512 0.98385093 1 1
|
||||
4200 8.5566638 -11.241219 0.84428298 1 1
|
||||
4300 8.3079987 -10.963542 0.96552044 1 1
|
||||
4400 8.0878014 -10.695296 0.9598929 1 1
|
||||
4500 7.8974753 -10.510996 0.67253552 1 1
|
||||
4600 7.9008492 -10.511956 0.80200878 1 1
|
||||
4700 7.8469401 -10.46341 0.91408186 1 1
|
||||
4800 7.8237062 -10.478701 0.80709563 1 1
|
||||
4900 7.9248576 -10.569715 0.93955604 1 1
|
||||
5000 7.8285795 -10.450559 0.72760696 1 1
|
||||
5100 7.8176003 -10.433727 1.0046395 1 1
|
||||
5200 7.930586 -10.543139 1.1883254 1 1
|
||||
5300 7.4014327 -10.200353 1.2717149 1 1
|
||||
5400 7.3398704 -9.9377313 0.8277383 1 1
|
||||
5500 7.9323894 -10.544566 0.58409181 1 1
|
||||
5600 7.8256391 -10.452111 0.8371735 1 1
|
||||
5700 7.5744223 -10.225985 0.56633204 1 1
|
||||
5800 7.5149231 -10.128901 0.8877957 1 1
|
||||
5900 7.2696456 -9.868796 1.0183026 1 1
|
||||
6000 8.172964 -10.8046 0.82048799 1 1
|
||||
6100 7.569911 -10.224271 0.85335085 1 1
|
||||
6200 7.5498129 -10.158173 0.69550695 1 1
|
||||
6300 7.0906227 -9.664124 0.38267058 1 1
|
||||
6400 6.9720876 -9.556043 0.74772365 1 1
|
||||
6500 7.2708269 -9.8393843 0.87493485 1 1
|
||||
6600 7.0968522 -9.7557969 0.66499003 1 1
|
||||
6700 7.1122649 -9.7305659 1.3152794 1 1
|
||||
6800 6.9990684 -9.5808587 0.25569509 1 1
|
||||
6900 7.2436468 -9.8205382 0.94441711 1 1
|
||||
7000 7.0592104 -9.6306985 0.62683684 1 1
|
||||
7100 6.7457928 -9.3199995 0.92851433 1 1
|
||||
7200 7.0005278 -9.645515 0.79975493 1 1
|
||||
7300 7.0106928 -9.5922649 0.78131757 1 1
|
||||
7400 6.9425198 -9.5718261 0.3016744 1 1
|
||||
7500 7.4193009 -9.9953487 0.55537513 1 1
|
||||
7600 7.1870399 -9.7798145 0.94155142 1 1
|
||||
7700 6.8261504 -9.3693292 0.78601298 1 1
|
||||
7800 6.8794916 -9.4362689 0.9335562 1 1
|
||||
7900 7.0068635 -9.5490666 0.53210657 1 1
|
||||
8000 6.641609 -9.181226 0.80726821 1 1
|
||||
8100 6.9290677 -9.4788963 1.1195905 1 1
|
||||
8200 6.6497084 -9.197688 0.45616164 1 1
|
||||
8300 6.6000864 -9.207368 0.46307403 1 1
|
||||
8400 6.7434835 -9.3226196 0.78570419 1 1
|
||||
8500 7.0766248 -9.5981608 0.48778261 1 1
|
||||
8600 6.8206587 -9.3646115 0.76420951 1 1
|
||||
8700 7.2009315 -9.7629817 0.69026433 1 1
|
||||
8800 7.0581986 -9.636327 0.54467209 1 1
|
||||
8900 7.2337543 -9.8210795 0.61604427 1 1
|
||||
9000 6.7053026 -9.2552306 0.24196123 1 1
|
||||
9100 6.7919694 -9.3561383 0.34320213 1 1
|
||||
9200 6.8518231 -9.4142511 0.73735875 1 1
|
||||
9300 6.5891178 -9.1414615 0.45262773 1 1
|
||||
9400 6.4724853 -9.0217877 0.54837629 1 1
|
||||
9500 6.3569528 -8.9201793 0.19617724 1 1
|
||||
9600 6.3765498 -8.947548 0.85408461 1 1
|
||||
9700 6.5652079 -9.1101844 0.74478711 1 1
|
||||
9800 6.5099709 -9.0677449 0.69826809 1 1
|
||||
9900 6.1773299 -8.7085595 0.69981004 1 1
|
||||
10000 6.3999463 -8.9423632 0.42668066 1 1
|
||||
Loop time of 0.675636 on 1 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 6393974.952 tau/day, 14800.868 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.29845 | 0.29845 | 0.29845 | 0.0 | 44.17
|
||||
Neigh | 0.26869 | 0.26869 | 0.26869 | 0.0 | 39.77
|
||||
Comm | 0.006007 | 0.006007 | 0.006007 | 0.0 | 0.89
|
||||
Output | 0.00076938 | 0.00076938 | 0.00076938 | 0.0 | 0.11
|
||||
Modify | 0.077204 | 0.077204 | 0.077204 | 0.0 | 11.43
|
||||
Other | | 0.02452 | | | 3.63
|
||||
|
||||
Nlocal: 361 ave 361 max 361 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1191 ave 1191 max 1191 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1191
|
||||
Ave neighs/atom = 3.29917
|
||||
Neighbor list builds = 3609
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,202 +0,0 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 2.48839 Mbytes
|
||||
Step Temp E_pair Press 10[3] 10
|
||||
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
|
||||
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
|
||||
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
|
||||
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
|
||||
400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102
|
||||
500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
|
||||
600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
|
||||
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
|
||||
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
|
||||
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
|
||||
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
|
||||
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
|
||||
1200 17.214459 -20.726965 6.3578917 1.0304709 1.0193906
|
||||
1300 16.424154 -19.757386 3.9027133 1.1191136 1.0083102
|
||||
1400 15.04233 -18.126227 1.7539398 1.0858726 1.0193906
|
||||
1500 13.749022 -16.839766 1.4654778 1.0747922 1.0083102
|
||||
1600 13.888812 -16.855703 1.8972035 1.0858726 1.0304709
|
||||
1700 13.647879 -16.652436 1.5110481 1.0526316 1.0304709
|
||||
1800 12.61308 -15.580445 2.1861667 1.0083102 1.0083102
|
||||
1900 12.700272 -15.594505 1.6395684 1.0304709 1.0083102
|
||||
2000 12.204319 -15.16754 1.6302417 1.1080332 1.0083102
|
||||
2100 11.921129 -14.774621 1.4311256 1.0858726 1.0083102
|
||||
2200 11.959274 -14.797326 1.4920985 1.0415512 1.0083102
|
||||
2300 11.633606 -14.455284 1.4447243 1.1412742 1.0193906
|
||||
2400 12.180014 -14.719121 1.4582702 1.0304709 1.0083102
|
||||
2500 11.779995 -14.293633 1.2961686 1.0304709 1.0083102
|
||||
2600 11.86013 -14.272853 1.1970414 1.0415512 1.0193906
|
||||
2700 11.360658 -13.772549 1.192957 1.0526316 1.0083102
|
||||
2800 11.045632 -13.438591 1.2007074 1.0083102 1.0193906
|
||||
2900 10.689472 -13.127138 0.94544611 1.0193906 1.0193906
|
||||
3000 10.445298 -12.809325 1.3035047 1.0304709 1.0193906
|
||||
3100 10.22325 -12.599858 1.7838342 1.0304709 1.0083102
|
||||
3200 10.226845 -12.602391 0.91456469 1.0304709 1.0193906
|
||||
3300 9.8906692 -12.204654 1.4538962 1.0415512 1.0193906
|
||||
3400 9.0246858 -11.627057 1.1929498 1.0304709 1.0193906
|
||||
3500 9.4549317 -11.747347 0.92966653 1.0193906 1.0193906
|
||||
3600 9.2467281 -11.534358 0.94959796 1.0415512 1.0083102
|
||||
3700 9.1099307 -11.381318 1.2963887 1.0193906 1.0083102
|
||||
3800 9.2236074 -11.483205 1.3510186 1.1080332 1.0193906
|
||||
3900 8.6105519 -10.877844 1.3591509 1.0304709 1.0083102
|
||||
4000 8.588698 -10.846126 0.76473884 1.0415512 1.0083102
|
||||
4100 8.5960453 -10.831229 0.93758423 1.0747922 1.0193906
|
||||
4200 8.1049344 -10.436054 0.74947412 1.0526316 1.0083102
|
||||
4300 8.2606129 -10.471049 0.64465155 1.0193906 1.0193906
|
||||
4400 8.0777962 -10.288476 1.1145052 1.0193906 1.0083102
|
||||
4500 7.9202904 -10.10427 0.49016698 1.0304709 1.0083102
|
||||
4600 8.2366755 -10.434942 0.65930769 1.0193906 1.0083102
|
||||
4700 7.9313531 -10.13685 1.097861 1.0304709 1.0083102
|
||||
4800 7.8637296 -10.085957 0.56015483 1.0304709 1.0193906
|
||||
4900 7.3410322 -9.5357686 0.89340163 1.0304709 1.0193906
|
||||
5000 7.6647481 -9.8529515 0.8283225 1.0193906 1.0193906
|
||||
5100 7.4114006 -9.5917802 0.64812231 1.0083102 1.0193906
|
||||
5200 7.6261959 -9.8178843 0.90517452 1.0193906 1.0083102
|
||||
5300 7.6501619 -9.8428477 1.028077 1.0304709 1.0083102
|
||||
5400 7.4694373 -9.6434672 0.38259983 1.0193906 1.0083102
|
||||
5500 7.3111918 -9.4803007 0.47921149 1.0193906 1.0193906
|
||||
5600 7.2132446 -9.3694039 0.71282856 1.0193906 1.0083102
|
||||
5700 6.8349744 -9.0018958 0.85688618 1.0193906 1.0083102
|
||||
5800 7.1978042 -9.3667457 0.61717818 1.0304709 1.0193906
|
||||
5900 7.1441033 -9.3263118 0.32840394 1.0193906 1.0083102
|
||||
6000 7.0943691 -9.2621241 1.3099316 1.0083102 1.0083102
|
||||
6100 6.9547586 -9.1026607 0.44492974 1.0193906 1.0083102
|
||||
6200 7.0932682 -9.2934579 0.93444691 1.0415512 1.0083102
|
||||
6300 7.0536275 -9.2562193 0.57578551 1.0193906 1.0193906
|
||||
6400 6.8839921 -9.0513091 0.65690774 1.0193906 1.0083102
|
||||
6500 6.7618431 -8.9037814 0.6011838 1.0304709 1.0193906
|
||||
6600 6.6600729 -8.7979286 0.73495903 1.0193906 1.0193906
|
||||
6700 6.6544136 -8.8089155 0.41206297 1.0304709 1.0193906
|
||||
6800 6.7935502 -8.9405122 1.022055 1.0193906 1.0083102
|
||||
6900 6.6603594 -8.8085894 0.4271189 1.0526316 1.0193906
|
||||
7000 6.4894888 -8.6794785 0.64389173 1.0526316 1.0193906
|
||||
7100 6.6252776 -8.776746 1.3915989 1.0193906 1.0193906
|
||||
7200 6.6680717 -8.8468379 0.60275261 1.0193906 1.0193906
|
||||
7300 6.697874 -8.8458161 0.50887488 1.0637119 1.0083102
|
||||
7400 6.2112277 -8.340139 0.45211042 1.0415512 1.0193906
|
||||
7500 6.4923853 -8.6255862 0.79982162 1.0083102 1.0193906
|
||||
7600 6.2922271 -8.4027197 0.33603817 1.0304709 1.0083102
|
||||
7700 6.5744688 -8.7079756 0.51620003 1.0415512 1.0083102
|
||||
7800 6.6730316 -8.8278613 1.2334484 1.0304709 1.0083102
|
||||
7900 6.3831791 -8.4878853 0.49555781 1.0415512 1.0193906
|
||||
8000 6.690559 -8.7918607 0.88102021 1.0415512 1.0083102
|
||||
8100 6.5390375 -8.6612074 0.45605815 1.0304709 1.0193906
|
||||
8200 6.6957638 -8.8406262 0.45001955 1.0193906 1.0083102
|
||||
8300 6.8684401 -9.0293678 0.64215355 1.0083102 1.0083102
|
||||
8400 6.4416293 -8.5841829 0.53513285 1.0193906 1.0193906
|
||||
8500 6.6854101 -8.8269391 0.81750487 1.0637119 1.0083102
|
||||
8600 6.588469 -8.7315753 0.33201251 1.0083102 1.0083102
|
||||
8700 6.2974312 -8.4104697 0.57054382 1.0083102 1.0083102
|
||||
8800 6.4691853 -8.5985479 0.95554418 1.0415512 1.0083102
|
||||
8900 6.7437807 -8.8949865 0.69067866 1.0415512 1.0083102
|
||||
9000 6.5681473 -8.6984555 0.88464065 1.0193906 1.0083102
|
||||
9100 6.6158471 -8.7398687 0.72347757 1.0193906 1.0083102
|
||||
9200 6.4521137 -8.6048511 0.75093363 1.0193906 1.0193906
|
||||
9300 6.4179685 -8.5582051 1.0072192 1.0083102 1.0083102
|
||||
9400 6.580258 -8.7234535 0.56842466 1.0193906 1.0193906
|
||||
9500 6.4125418 -8.56348 0.36394135 1.0304709 1.0193906
|
||||
9600 6.6723409 -8.8402798 0.56711277 1.0304709 1.0193906
|
||||
9700 6.4522736 -8.594767 0.43495668 1.0193906 1.0083102
|
||||
9800 6.2127437 -8.3329761 0.68977311 1.0304709 1.0193906
|
||||
9900 6.4360513 -8.5839262 1.1702062 1.0304709 1.0193906
|
||||
10000 6.3393653 -8.4396274 0.46277884 1.0304709 1.0193906
|
||||
Loop time of 0.389322 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 11096205.412 tau/day, 25685.661 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.061902 | 0.074659 | 0.098288 | 5.1 | 19.18
|
||||
Neigh | 0.061993 | 0.067136 | 0.078793 | 2.6 | 17.24
|
||||
Comm | 0.10335 | 0.13334 | 0.15511 | 5.6 | 34.25
|
||||
Output | 0.0017662 | 0.0020409 | 0.0027893 | 1.0 | 0.52
|
||||
Modify | 0.037374 | 0.038055 | 0.038669 | 0.2 | 9.77
|
||||
Other | | 0.07409 | | | 19.03
|
||||
|
||||
Nlocal: 90.25 ave 92 max 88 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 36 ave 38 max 34 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 276.75 ave 448 max 153 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1107
|
||||
Ave neighs/atom = 3.06648
|
||||
Neighbor list builds = 3472
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
225
examples/balance/log.27Sep16.balance.bond.fast.g++.4
Normal file
225
examples/balance/log.27Sep16.balance.bond.fast.g++.4
Normal file
@ -0,0 +1,225 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style bond
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 6
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 10.0 1.2
|
||||
|
||||
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
|
||||
|
||||
special_bonds lj/coul 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
1 = max # of special neighbors
|
||||
create_bonds all all 1 1.0 1.5
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Added 1014 bonds, new total = 1014
|
||||
6 = max # of 1-2 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
comm_modify cutoff 7.5
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom (c_1%10)+1
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 7.5
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 4.49421 Mbytes
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
|
||||
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
|
||||
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
|
||||
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
|
||||
400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
|
||||
500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906
|
||||
600 35.059889 -21.524278 2.3728491 1.3296399 1.0083102
|
||||
700 36.70511 -21.983922 3.299538 1.3296399 1.0083102
|
||||
800 39.54394 -25.667546 4.3058382 1.3961219 1.0083102
|
||||
900 37.868974 -24.379807 5.3176538 1.3518006 1.0083102
|
||||
1000 36.721328 -23.341363 5.8700266 1.3407202 1.0083102
|
||||
1100 35.646239 -23.3255 3.3762843 1.1855956 1.0083102
|
||||
1200 31.452912 -20.792985 5.4901357 1.1966759 1.0083102
|
||||
1300 32.276549 -21.245929 6.4153084 1.2077562 1.0193906
|
||||
1400 29.452751 -20.724401 2.174752 1.1855956 1.0083102
|
||||
1500 28.014757 -18.893532 1.7482766 1.1634349 1.0083102
|
||||
1600 26.222645 -16.78953 0.93944237 1.1966759 1.0304709
|
||||
1700 25.711888 -15.792639 0.20021405 1.0969529 1.0083102
|
||||
1800 24.412639 -13.217606 0.7091708 1.1966759 1.0083102
|
||||
1900 25.644324 -13.020594 1.3661224 1.1412742 1.0083102
|
||||
2000 24.556667 -13.580087 0.80121134 1.0637119 1.0083102
|
||||
2100 25.23657 -13.560862 1.2349706 1.1191136 1.0193906
|
||||
2200 26.456985 -13.804729 1.27046 1.1412742 1.0193906
|
||||
2300 26.416685 -13.212452 1.4096744 1.1412742 1.0083102
|
||||
2400 25.472914 -12.472527 1.5408641 1.1412742 1.0083102
|
||||
2500 25.216305 -12.597474 0.84328282 1.1412742 1.0083102
|
||||
2600 24.107024 -12.455199 1.5587978 1.2409972 1.0193906
|
||||
2700 26.840175 -15.533209 1.2944973 1.1745152 1.0083102
|
||||
2800 26.149759 -14.83948 4.0371126 1.0747922 1.0083102
|
||||
2900 24.651151 -14.934342 2.7634302 1.0747922 1.0193906
|
||||
3000 21.873123 -13.366381 -0.18605935 1.1301939 1.0083102
|
||||
3100 19.974658 -10.620844 -0.16366371 1.0637119 1.0193906
|
||||
3200 20.926558 -10.336663 -0.73116364 1.1080332 1.0083102
|
||||
3300 20.473772 -10.588752 -0.66017168 1.0858726 1.0304709
|
||||
3400 22.476649 -11.87982 1.0141731 1.0747922 1.0083102
|
||||
3500 24.02361 -12.532787 1.4116935 1.1191136 1.0083102
|
||||
3600 22.922792 -12.328391 -0.27783338 1.0969529 1.0083102
|
||||
3700 21.772971 -10.716922 0.95739835 1.1523546 1.0083102
|
||||
3800 21.597174 -10.839031 0.67958603 1.1191136 1.0193906
|
||||
3900 21.883448 -11.258422 -0.40592732 1.0637119 1.0193906
|
||||
4000 22.815486 -10.891868 1.6123322 1.1301939 1.0193906
|
||||
4100 23.276599 -11.400134 0.65653972 1.0415512 1.0193906
|
||||
4200 22.543441 -11.530245 0.074132899 1.1523546 1.0193906
|
||||
4300 22.863379 -10.809451 0.27552824 1.1412742 1.0193906
|
||||
4400 22.475073 -11.125735 1.7708547 1.1191136 1.0193906
|
||||
4500 23.500125 -11.680919 0.91347563 1.0858726 1.0083102
|
||||
4600 21.1812 -11.767353 0.095659263 1.1191136 1.0193906
|
||||
4700 22.950759 -12.108158 0.083009642 1.1966759 1.0083102
|
||||
4800 22.12306 -11.455893 0.47932308 1.1080332 1.0083102
|
||||
4900 23.297573 -11.823246 0.93733479 1.0969529 1.0083102
|
||||
5000 22.98743 -12.014836 0.36186604 1.1080332 1.0083102
|
||||
5100 23.081456 -11.54226 0.73473004 1.0747922 1.0193906
|
||||
5200 20.980311 -11.493036 -0.71555187 1.0637119 1.0193906
|
||||
5300 21.468406 -11.18497 0.54579843 1.0304709 1.0193906
|
||||
5400 22.75839 -10.856825 0.94407228 1.1191136 1.0083102
|
||||
5500 22.705652 -12.112469 0.4753399 1.1412742 1.0083102
|
||||
5600 22.391177 -12.530712 1.0180383 1.1412742 1.0083102
|
||||
5700 21.832834 -11.368512 0.88281166 1.0415512 1.0083102
|
||||
5800 22.850002 -11.948876 -0.46874747 1.0747922 1.0083102
|
||||
5900 21.135991 -12.358431 -0.48932559 1.0526316 1.0193906
|
||||
6000 22.071115 -11.433484 0.49653696 1.0747922 1.0304709
|
||||
6100 21.91427 -11.458553 -0.030708226 1.0637119 1.0193906
|
||||
6200 24.173206 -13.110269 -0.13661363 1.1412742 1.0083102
|
||||
6300 22.204413 -11.373556 1.6254012 1.0747922 1.0304709
|
||||
6400 23.259022 -11.634614 1.4472592 1.1412742 1.0193906
|
||||
6500 22.185287 -11.606998 0.66488201 1.0415512 1.0083102
|
||||
6600 21.329653 -10.989853 0.31700842 1.1301939 1.0083102
|
||||
6700 21.903749 -10.335477 1.3749575 1.0637119 1.0083102
|
||||
6800 21.188714 -10.545014 1.3448408 1.0415512 1.0083102
|
||||
6900 22.683005 -11.254371 0.5048545 1.1523546 1.0193906
|
||||
7000 21.224439 -9.7325551 0.71666112 1.0637119 1.0083102
|
||||
7100 21.712624 -10.594397 0.3657261 1.0858726 1.0193906
|
||||
7200 22.115857 -10.479237 0.95528164 1.0969529 1.0193906
|
||||
7300 22.075732 -11.255 -0.35340754 1.0526316 1.0193906
|
||||
7400 21.659767 -10.238454 -0.063639729 1.1523546 1.0083102
|
||||
7500 21.966354 -10.654264 0.36298903 1.0747922 1.0083102
|
||||
7600 21.541195 -11.151416 0.96453416 1.1080332 1.0193906
|
||||
7700 23.517228 -12.266781 0.49603585 1.1523546 1.0193906
|
||||
7800 21.665911 -11.832323 0.47104209 1.1080332 1.0083102
|
||||
7900 23.469372 -12.358423 -0.757413 1.0747922 1.0193906
|
||||
8000 21.699467 -11.462824 -0.73009236 1.0415512 1.0083102
|
||||
8100 21.583783 -10.21474 0.98837038 1.0969529 1.0193906
|
||||
8200 21.804998 -10.916922 -0.53268178 1.0858726 1.0083102
|
||||
8300 21.291145 -10.875356 0.81277146 1.0858726 1.0193906
|
||||
8400 21.939964 -10.726547 0.95830844 1.0415512 1.0193906
|
||||
8500 23.600157 -11.041255 -0.14583876 1.0747922 1.0083102
|
||||
8600 22.37787 -10.946852 1.0360646 1.0415512 1.0083102
|
||||
8700 23.591205 -11.524803 1.1877377 1.0526316 1.0304709
|
||||
8800 22.567007 -11.4629 0.4360461 1.0526316 1.0083102
|
||||
8900 22.11289 -11.772849 -0.019132631 1.0304709 1.0193906
|
||||
9000 22.814946 -11.705633 0.59029789 1.0747922 1.0083102
|
||||
9100 22.58487 -11.431283 0.9884223 1.1634349 1.0083102
|
||||
9200 23.283939 -11.825534 0.68358625 1.0637119 1.0083102
|
||||
9300 23.292444 -11.365494 0.78631005 1.0526316 1.0083102
|
||||
9400 21.748634 -10.16176 0.59185916 1.0969529 1.0083102
|
||||
9500 21.644797 -10.00944 1.1450108 1.0637119 1.0304709
|
||||
9600 23.01957 -10.683211 1.5735291 1.0637119 1.0193906
|
||||
9700 21.207989 -10.344668 0.34401867 1.0969529 1.0083102
|
||||
9800 22.035363 -10.849581 -0.14118639 1.0304709 1.0083102
|
||||
9900 21.839653 -10.008407 0.96570633 1.0526316 1.0193906
|
||||
10000 22.845561 -10.238723 0.74236932 1.0858726 1.0083102
|
||||
Loop time of 0.812716 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 5315508.362 tau/day, 12304.418 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12434 | 0.13482 | 0.14506 | 2.5 | 16.59
|
||||
Bond | 0.053339 | 0.058165 | 0.062916 | 1.9 | 7.16
|
||||
Neigh | 0.28554 | 0.29233 | 0.29933 | 0.9 | 35.97
|
||||
Comm | 0.16602 | 0.19226 | 0.21833 | 4.3 | 23.66
|
||||
Output | 0.0017536 | 0.0019155 | 0.0022504 | 0.4 | 0.24
|
||||
Modify | 0.040126 | 0.040341 | 0.04054 | 0.1 | 4.96
|
||||
Other | | 0.09288 | | | 11.43
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 198.25 ave 206 max 191 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 667.75 ave 751 max 627 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2671
|
||||
Ave neighs/atom = 7.39889
|
||||
Ave special neighs/atom = 5.61773
|
||||
Neighbor list builds = 4832
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
@ -91,7 +91,7 @@ Neighbor list info ...
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 6.41878 Mbytes
|
||||
Step Temp E_pair Press 10[3] 10
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 0.57437856 0 0.26099453 3.2354571 1.0526316
|
||||
100 0.29756515 0 0.10149401 1.0193906 1.0083102
|
||||
200 0.35394813 0 0.075159099 1.0304709 1.0083102
|
||||
@ -108,9 +108,9 @@ Step Temp E_pair Press 10[3] 10
|
||||
1300 0.32952819 0 0.124902 1.0083102 1.0083102
|
||||
1400 0.34497365 0 0.12662081 1.0193906 1.0083102
|
||||
1500 0.33429243 0 0.096230972 1.0526316 1.0193906
|
||||
1600 0.33765387 0 0.025800542 1.0304709 1.0083102
|
||||
1700 0.35134464 0 -0.04422593 1.0415512 1.0193906
|
||||
1800 0.35003859 0 -0.096745576 1.0304709 1.0193906
|
||||
1600 0.33765387 0 0.025800542 1.0304709 1.0193906
|
||||
1700 0.35134464 0 -0.04422593 1.0415512 1.0083102
|
||||
1800 0.35003859 0 -0.096745576 1.0304709 1.0083102
|
||||
1900 0.33839618 0 -0.095465943 1.0193906 1.0083102
|
||||
2000 0.33732078 0 -0.094652802 1.0083102 1.0083102
|
||||
2100 0.34552238 0 -0.076729261 1.0304709 1.0083102
|
||||
@ -179,7 +179,7 @@ Step Temp E_pair Press 10[3] 10
|
||||
8400 0.30619282 0 -0.12952879 1.0193906 1.0193906
|
||||
8500 0.34446484 0 -0.098084709 1.0083102 1.0083102
|
||||
8600 0.33761673 0 -0.07069818 1.0193906 1.0083102
|
||||
8700 0.34495452 0 -0.022458056 1.0193906 1.0083102
|
||||
8700 0.34495452 0 -0.022458056 1.0193906 1.0193906
|
||||
8800 0.33502983 0 0.027742411 1.0304709 1.0083102
|
||||
8900 0.35418591 0 0.092390134 1.0083102 1.0193906
|
||||
9000 0.31648387 0 0.12467398 1.0193906 1.0083102
|
||||
@ -192,12 +192,12 @@ Step Temp E_pair Press 10[3] 10
|
||||
9700 0.32088235 0 -0.12027075 1.0193906 1.0083102
|
||||
9800 0.3320823 0 -0.11602794 1.0415512 1.0083102
|
||||
9900 0.33916442 0 -0.080281044 1.0083102 1.0083102
|
||||
10000 0.34852268 0 -0.01000914 1.0193906 1.0193906
|
||||
10000 0.34852268 0 -0.01000914 1.0193906 1.0083102
|
||||
10100 0.32955942 0 0.04258493 1.0083102 1.0083102
|
||||
10200 0.34487898 0 0.086971308 1.0304709 1.0193906
|
||||
10200 0.34487898 0 0.086971308 1.0304709 1.0083102
|
||||
10300 0.32325593 0 0.11558149 1.0304709 1.0193906
|
||||
10400 0.30927871 0 0.12239437 1.0083102 1.0083102
|
||||
10500 0.33176799 0 0.12285937 1.0193906 1.0193906
|
||||
10500 0.33176799 0 0.12285937 1.0193906 1.0083102
|
||||
10600 0.35120027 0 0.084897432 1.0083102 1.0083102
|
||||
10700 0.33129697 0 0.0053089279 1.0193906 1.0193906
|
||||
10800 0.36028769 0 -0.04280715 1.0193906 1.0083102
|
||||
@ -214,7 +214,7 @@ Step Temp E_pair Press 10[3] 10
|
||||
11900 0.33836678 0 0.067253864 1.0193906 1.0193906
|
||||
12000 0.34853314 0 0.03201448 1.0193906 1.0083102
|
||||
12100 0.34600048 0 -0.034833402 1.0304709 1.0083102
|
||||
12200 0.33145631 0 -0.09865675 1.0193906 1.0193906
|
||||
12200 0.33145631 0 -0.09865675 1.0193906 1.0083102
|
||||
12300 0.32848884 0 -0.1248489 1.0193906 1.0193906
|
||||
12400 0.3321344 0 -0.11266575 1.0083102 1.0083102
|
||||
12500 0.32622305 0 -0.061634993 1.0304709 1.0083102
|
||||
@ -225,11 +225,11 @@ Step Temp E_pair Press 10[3] 10
|
||||
13000 0.31993287 0 0.13879926 1.0193906 1.0193906
|
||||
13100 0.3422918 0 0.11978905 1.0083102 1.0083102
|
||||
13200 0.33055236 0 0.062620483 1.0193906 1.0083102
|
||||
13300 0.34652207 0 0.0043833459 1.0304709 1.0193906
|
||||
13300 0.34652207 0 0.0043833459 1.0304709 1.0083102
|
||||
13400 0.33574661 0 -0.04691024 1.0304709 1.0083102
|
||||
13500 0.33940837 0 -0.074241604 1.0304709 1.0083102
|
||||
13600 0.32093414 0 -0.1078027 1.0193906 1.0083102
|
||||
13700 0.34336597 0 -0.10544097 1.0193906 1.0083102
|
||||
13600 0.32093414 0 -0.1078027 1.0193906 1.0193906
|
||||
13700 0.34336597 0 -0.10544097 1.0193906 1.0193906
|
||||
13800 0.35806461 0 -0.072531559 1.0193906 1.0083102
|
||||
13900 0.35209713 0 -0.018851408 1.0083102 1.0083102
|
||||
14000 0.35702629 0 0.061046366 1.0083102 1.0083102
|
||||
@ -243,13 +243,13 @@ Step Temp E_pair Press 10[3] 10
|
||||
14800 0.33679845 0 -0.10067728 1.0193906 1.0193906
|
||||
14900 0.32790966 0 -0.10925568 1.0193906 1.0083102
|
||||
15000 0.34208495 0 -0.09568004 1.0193906 1.0083102
|
||||
15100 0.33647529 0 -0.055652929 1.0083102 1.0193906
|
||||
15100 0.33647529 0 -0.055652929 1.0083102 1.0083102
|
||||
15200 0.35328398 0 -0.020236536 1.0193906 1.0193906
|
||||
15300 0.34252669 0 0.026434179 1.0083102 1.0193906
|
||||
15400 0.34409435 0 0.094410599 1.0304709 1.0083102
|
||||
15500 0.32288994 0 0.12034455 1.0415512 1.0193906
|
||||
15600 0.32109689 0 0.13645185 1.0193906 1.0193906
|
||||
15700 0.33681572 0 0.098607746 1.0415512 1.0083102
|
||||
15600 0.32109689 0 0.13645185 1.0193906 1.0083102
|
||||
15700 0.33681572 0 0.098607746 1.0415512 1.0193906
|
||||
15800 0.33635195 0 0.05570715 1.0193906 1.0193906
|
||||
15900 0.34289757 0 0.013849092 1.0304709 1.0083102
|
||||
16000 0.34225547 0 -0.035597548 1.0304709 1.0083102
|
||||
@ -261,7 +261,7 @@ Step Temp E_pair Press 10[3] 10
|
||||
16600 0.35109001 0 0.041251169 1.0304709 1.0083102
|
||||
16700 0.34336905 0 0.077996627 1.0193906 1.0083102
|
||||
16800 0.33277414 0 0.11053634 1.0083102 1.0083102
|
||||
16900 0.32183338 0 0.11680626 1.0193906 1.0083102
|
||||
16900 0.32183338 0 0.11680626 1.0193906 1.0193906
|
||||
17000 0.34044352 0 0.10806555 1.0193906 1.0083102
|
||||
17100 0.32967873 0 0.067759786 1.0304709 1.0193906
|
||||
17200 0.36172278 0 -0.0048631904 1.0304709 1.0083102
|
||||
@ -293,17 +293,17 @@ Step Temp E_pair Press 10[3] 10
|
||||
19800 0.34880695 0 0.042483681 1.0193906 1.0083102
|
||||
19900 0.33903644 0 0.034788638 1.0083102 1.0193906
|
||||
20000 0.32590125 0 0.011383785 1.0193906 1.0083102
|
||||
20100 0.30358859 0 0.0030743554 1.0526316 1.0083102
|
||||
20100 0.30358859 0 0.0030743554 1.0526316 1.0193906
|
||||
20200 0.31830224 0 0.017637826 1.0193906 1.0193906
|
||||
20300 0.34195438 0 0.072811099 1.0304709 1.0193906
|
||||
20400 0.31249563 0 0.10063541 1.0415512 1.0083102
|
||||
20500 0.31544938 0 0.1405794 1.0083102 1.0083102
|
||||
20600 0.30071644 0 0.12763486 1.0193906 1.0193906
|
||||
20700 0.2890265 0 0.1136651 1.0083102 1.0083102
|
||||
20700 0.2890265 0 0.1136651 1.0083102 1.0193906
|
||||
20800 0.28962296 0 0.094481978 1.0193906 1.0083102
|
||||
20900 0.29447212 0 0.0967165 1.0193906 1.0193906
|
||||
21000 0.31159961 0 0.067307231 1.0083102 1.0193906
|
||||
21100 0.30490648 0 0.017689358 1.0083102 1.0304709
|
||||
21000 0.31159961 0 0.067307231 1.0083102 1.0083102
|
||||
21100 0.30490648 0 0.017689358 1.0083102 1.0193906
|
||||
21200 0.30687262 0 -0.016055512 1.0193906 1.0193906
|
||||
21300 0.30083286 0 -0.0014988997 1.0193906 1.0083102
|
||||
21400 0.32070426 0 0.015960302 1.0083102 1.0083102
|
||||
@ -314,7 +314,7 @@ Step Temp E_pair Press 10[3] 10
|
||||
21900 0.32451958 0 0.068935768 1.0304709 1.0193906
|
||||
22000 0.35219298 0 0.067161227 1.0193906 1.0193906
|
||||
22100 0.34857705 0 0.032731746 1.0193906 1.0083102
|
||||
22200 0.34750227 0 0.0056917695 1.0193906 1.0083102
|
||||
22200 0.34750227 0 0.0056917695 1.0193906 1.0193906
|
||||
22300 0.34766017 0 -0.0027090483 1.0193906 1.0083102
|
||||
22400 0.33426062 0 -0.023196063 1.0304709 1.0193906
|
||||
22500 0.34174625 0 -0.025019717 1.0083102 1.0083102
|
||||
@ -328,11 +328,11 @@ Step Temp E_pair Press 10[3] 10
|
||||
23300 0.32965664 0 0.035989589 1.0193906 1.0083102
|
||||
23400 0.30927749 0 0.024581106 1.0193906 1.0083102
|
||||
23500 0.32890632 0 0.01092479 1.0304709 1.0193906
|
||||
23600 0.34137438 0 0.0094839745 1.0193906 1.0083102
|
||||
23600 0.34137438 0 0.0094839745 1.0193906 1.0193906
|
||||
23700 0.34512638 0 -0.012392771 1.0304709 1.0193906
|
||||
23800 0.31781354 0 -0.012908449 1.0193906 1.0193906
|
||||
23900 0.32405513 0 -0.015018071 1.0415512 1.0193906
|
||||
24000 0.33549728 0 -0.012812915 1.0193906 1.0083102
|
||||
23900 0.32405513 0 -0.015018071 1.0415512 1.0083102
|
||||
24000 0.33549728 0 -0.012812915 1.0193906 1.0193906
|
||||
24100 0.31368736 0 -0.020818372 1.0304709 1.0193906
|
||||
24200 0.33533836 0 0.0056121057 1.0083102 1.0193906
|
||||
24300 0.32530627 0 0.018183931 1.0415512 1.0083102
|
||||
@ -352,12 +352,12 @@ Step Temp E_pair Press 10[3] 10
|
||||
25700 0.34048065 0 0.022513032 1.0193906 1.0193906
|
||||
25800 0.33029079 0 0.038733531 1.0193906 1.0083102
|
||||
25900 0.33031324 0 0.026156982 1.0304709 1.0193906
|
||||
26000 0.32967371 0 0.028727383 1.0083102 1.0083102
|
||||
26000 0.32967371 0 0.028727383 1.0083102 1.0193906
|
||||
26100 0.33775718 0 0.015607478 1.0083102 1.0193906
|
||||
26200 0.35097144 0 0.012291703 1.0083102 1.0083102
|
||||
26300 0.34303792 0 0.00094823191 1.0083102 1.0193906
|
||||
26400 0.33632665 0 -0.0026904889 1.0193906 1.0193906
|
||||
26500 0.33580127 0 -0.0074168555 1.0193906 1.0193906
|
||||
26500 0.33580127 0 -0.0074168555 1.0193906 1.0083102
|
||||
26600 0.33063188 0 -0.020378601 1.0083102 1.0193906
|
||||
26700 0.33581846 0 -0.00084397268 1.0083102 1.0193906
|
||||
26800 0.32998532 0 0.015932208 1.0304709 1.0193906
|
||||
@ -375,12 +375,12 @@ Step Temp E_pair Press 10[3] 10
|
||||
28000 0.32300727 0 -0.0004153384 1.0304709 1.0083102
|
||||
28100 0.32147461 0 -0.0058543412 1.0083102 1.0083102
|
||||
28200 0.35532383 0 0.013646951 1.0304709 1.0083102
|
||||
28300 0.31507942 0 0.026532255 1.0415512 1.0193906
|
||||
28300 0.31507942 0 0.026532255 1.0415512 1.0083102
|
||||
28400 0.32711006 0 0.033214981 1.0193906 1.0083102
|
||||
28500 0.34472462 0 0.028050837 1.0304709 1.0193906
|
||||
28600 0.33708059 0 0.019115676 1.0083102 1.0083102
|
||||
28700 0.34478087 0 0.023743689 1.0304709 1.0083102
|
||||
28800 0.34546686 0 0.0081772997 1.0304709 1.0193906
|
||||
28700 0.34478087 0 0.023743689 1.0304709 1.0193906
|
||||
28800 0.34546686 0 0.0081772997 1.0304709 1.0083102
|
||||
28900 0.34004886 0 0.017771865 1.0415512 1.0193906
|
||||
29000 0.33604232 0 -0.010505671 1.0304709 1.0193906
|
||||
29100 0.33541374 0 -0.016273261 1.0083102 1.0083102
|
||||
@ -411,14 +411,14 @@ Step Temp E_pair Press 10[3] 10
|
||||
31600 0.34273493 0 -0.013456537 1.0083102 1.0083102
|
||||
31700 0.32723905 0 -0.019243766 1.0193906 1.0083102
|
||||
31800 0.33636488 0 0.0027814902 1.0083102 1.0083102
|
||||
31900 0.32834805 0 0.00706877 1.0083102 1.0083102
|
||||
31900 0.32834805 0 0.00706877 1.0083102 1.0193906
|
||||
32000 0.33995148 0 0.0018383309 1.0193906 1.0193906
|
||||
32100 0.33412282 0 0.0076455933 1.0083102 1.0083102
|
||||
32200 0.34334884 0 0.023586129 1.0083102 1.0083102
|
||||
32300 0.32778925 0 0.020564321 1.0193906 1.0083102
|
||||
32400 0.33163443 0 0.038878463 1.0193906 1.0083102
|
||||
32500 0.32290345 0 0.022247461 1.0193906 1.0193906
|
||||
32600 0.34113954 0 0.010966365 1.0304709 1.0083102
|
||||
32600 0.34113954 0 0.010966365 1.0304709 1.0193906
|
||||
32700 0.33390633 0 0.0037777555 1.0193906 1.0083102
|
||||
32800 0.34385341 0 0.010556575 1.0193906 1.0193906
|
||||
32900 0.32137047 0 0.00022027143 1.0526316 1.0193906
|
||||
@ -443,15 +443,15 @@ Step Temp E_pair Press 10[3] 10
|
||||
34800 0.33902329 0 0.030037037 1.0415512 1.0193906
|
||||
34900 0.3216153 0 0.027996689 1.0304709 1.0083102
|
||||
35000 0.32701056 0 0.024778517 1.0193906 1.0193906
|
||||
35100 0.3124942 0 0.011316548 1.0193906 1.0304709
|
||||
35100 0.3124942 0 0.011316548 1.0193906 1.0193906
|
||||
35200 0.34486416 0 0.011670127 1.0193906 1.0193906
|
||||
35300 0.33275353 0 0.020491246 1.0193906 1.0193906
|
||||
35400 0.33618763 0 0.014678874 1.0083102 1.0083102
|
||||
35400 0.33618763 0 0.014678874 1.0083102 1.0193906
|
||||
35500 0.32352282 0 -0.018568683 1.0193906 1.0193906
|
||||
35600 0.32617903 0 -0.012796912 1.0193906 1.0193906
|
||||
35700 0.32378048 0 -0.021318585 1.0193906 1.0083102
|
||||
35800 0.3371086 0 -0.0023678632 1.0193906 1.0193906
|
||||
35900 0.33818476 0 0.011197742 1.0193906 1.0193906
|
||||
35900 0.33818476 0 0.011197742 1.0193906 1.0083102
|
||||
36000 0.35142144 0 0.022520935 1.0083102 1.0193906
|
||||
36100 0.35147297 0 0.020277852 1.0193906 1.0083102
|
||||
36200 0.33489465 0 0.014564878 1.0415512 1.0083102
|
||||
@ -464,10 +464,10 @@ Step Temp E_pair Press 10[3] 10
|
||||
36900 0.35003816 0 -0.0021184393 1.0083102 1.0193906
|
||||
37000 0.32965041 0 -0.020900951 1.0193906 1.0083102
|
||||
37100 0.34653095 0 -0.013667977 1.0193906 1.0083102
|
||||
37200 0.35019871 0 -0.0071740923 1.0083102 1.0304709
|
||||
37200 0.35019871 0 -0.0071740923 1.0083102 1.0193906
|
||||
37300 0.34859745 0 0.02006041 1.0304709 1.0083102
|
||||
37400 0.35739859 0 0.020892822 1.0193906 1.0083102
|
||||
37500 0.34128859 0 0.041072111 1.0193906 1.0193906
|
||||
37500 0.34128859 0 0.041072111 1.0193906 1.0083102
|
||||
37600 0.33781905 0 0.023376738 1.0193906 1.0083102
|
||||
37700 0.32961874 0 0.030953741 1.0193906 1.0083102
|
||||
37800 0.343987 0 0.029579795 1.0083102 1.0083102
|
||||
@ -481,7 +481,7 @@ Step Temp E_pair Press 10[3] 10
|
||||
38600 0.32322402 0 0.053453832 1.0193906 1.0304709
|
||||
38700 0.33843057 0 0.076264534 1.0083102 1.0193906
|
||||
38800 0.31350741 0 0.064733869 1.0415512 1.0083102
|
||||
38900 0.31943061 0 0.067836769 1.0304709 1.0193906
|
||||
38900 0.31943061 0 0.067836769 1.0304709 1.0083102
|
||||
39000 0.33775583 0 0.0788316 1.0193906 1.0193906
|
||||
39100 0.34256036 0 0.075874935 1.0083102 1.0193906
|
||||
39200 0.33128527 0 0.071610976 1.0193906 1.0083102
|
||||
@ -491,23 +491,23 @@ Step Temp E_pair Press 10[3] 10
|
||||
39600 0.34000737 0 0.016149089 1.0304709 1.0083102
|
||||
39700 0.34587892 0 0.021619621 1.0526316 1.0083102
|
||||
39800 0.34878036 0 0.0092881327 1.0083102 1.0193906
|
||||
39900 0.35225411 0 -0.011341599 1.0083102 1.0083102
|
||||
39900 0.35225411 0 -0.011341599 1.0083102 1.0193906
|
||||
40000 0.36309266 0 0.0050869295 1.0304709 1.0083102
|
||||
Loop time of 1.06031 on 4 procs for 40000 steps with 361 atoms
|
||||
Loop time of 1.07961 on 4 procs for 40000 steps with 361 atoms
|
||||
|
||||
Performance: 16297104.069 tau/day, 37724.778 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 16005824.195 tau/day, 37050.519 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.019866 | 0.021036 | 0.024189 | 1.3 | 1.98
|
||||
Bond | 0.21436 | 0.24183 | 0.27259 | 5.1 | 22.81
|
||||
Neigh | 0.16022 | 0.16068 | 0.16101 | 0.1 | 15.15
|
||||
Comm | 0.2742 | 0.31331 | 0.3498 | 5.6 | 29.55
|
||||
Output | 0.0070348 | 0.0075188 | 0.0087383 | 0.8 | 0.71
|
||||
Modify | 0.14238 | 0.14861 | 0.15484 | 1.3 | 14.02
|
||||
Other | | 0.1673 | | | 15.78
|
||||
Pair | 0.019289 | 0.021061 | 0.024797 | 1.5 | 1.95
|
||||
Bond | 0.21005 | 0.23732 | 0.26838 | 5.0 | 21.98
|
||||
Neigh | 0.15978 | 0.16143 | 0.16328 | 0.4 | 14.95
|
||||
Comm | 0.2817 | 0.32626 | 0.36457 | 5.8 | 30.22
|
||||
Output | 0.0069985 | 0.0075181 | 0.0087821 | 0.8 | 0.70
|
||||
Modify | 0.1463 | 0.15235 | 0.16128 | 1.5 | 14.11
|
||||
Other | | 0.1737 | | | 16.09
|
||||
|
||||
Nlocal: 90.25 ave 91 max 89 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
221
examples/balance/log.27Sep16.balance.clock.dynamic.g++.4
Normal file
221
examples/balance/log.27Sep16.balance.clock.dynamic.g++.4
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 weight store WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
Memory usage per processor = 3.0442 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||||
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
|
||||
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
|
||||
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
Loop time of 2.31899 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 93143.824 tau/day, 215.611 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1238 | 1.43 | 1.6724 | 19.4 | 61.66
|
||||
Neigh | 0.26414 | 0.3845 | 0.55604 | 20.2 | 16.58
|
||||
Comm | 0.36444 | 0.48475 | 0.61759 | 15.3 | 20.90
|
||||
Output | 0.00027871 | 0.00032145 | 0.00035334 | 0.2 | 0.01
|
||||
Modify | 0.0064867 | 0.0086303 | 0.011487 | 2.3 | 0.37
|
||||
Other | | 0.01078 | | | 0.46
|
||||
|
||||
Nlocal: 1000 ave 1565 max 584 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8752 ave 9835 max 8078 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149308 ave 161748 max 133300 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 597231
|
||||
Ave neighs/atom = 149.308
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
|
||||
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
|
||||
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
|
||||
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
|
||||
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
|
||||
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
|
||||
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
|
||||
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
|
||||
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
|
||||
Loop time of 2.32391 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 92946.753 tau/day, 215.155 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1054 | 1.4081 | 1.6402 | 19.8 | 60.59
|
||||
Neigh | 0.28061 | 0.4047 | 0.57291 | 19.7 | 17.41
|
||||
Comm | 0.38485 | 0.4918 | 0.62503 | 15.5 | 21.16
|
||||
Output | 0.00028014 | 0.00031483 | 0.00032997 | 0.1 | 0.01
|
||||
Modify | 0.0064781 | 0.0084658 | 0.011106 | 2.2 | 0.36
|
||||
Other | | 0.01051 | | | 0.45
|
||||
|
||||
Nlocal: 1000 ave 1560 max 593 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8716.25 ave 9788 max 8009 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150170 ave 164293 max 129469 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 600678
|
||||
Ave neighs/atom = 150.169
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
|
||||
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
|
||||
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
|
||||
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
|
||||
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
|
||||
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
|
||||
1300 0.54134321 -6.2590728 0 -5.447261 -1.9170271 4738.2137
|
||||
1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
|
||||
1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
|
||||
1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
|
||||
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
|
||||
Loop time of 2.13659 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 101095.806 tau/day, 234.018 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3372 | 1.3773 | 1.4155 | 2.5 | 64.46
|
||||
Neigh | 0.22376 | 0.37791 | 0.57496 | 25.4 | 17.69
|
||||
Comm | 0.20357 | 0.36123 | 0.52777 | 25.5 | 16.91
|
||||
Output | 0.00029254 | 0.00034094 | 0.00039411 | 0.2 | 0.02
|
||||
Modify | 0.0056622 | 0.0082379 | 0.01147 | 2.9 | 0.39
|
||||
Other | | 0.01156 | | | 0.54
|
||||
|
||||
Nlocal: 1000 ave 1629 max 525 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 8647.25 ave 9725 max 7935 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150494 ave 161009 max 143434 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 601974
|
||||
Ave neighs/atom = 150.494
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
|
||||
1550 0.55327017 -6.2750125 0 -5.4453148 -1.9506584 4738.2137
|
||||
1600 0.54419003 -6.2612622 0 -5.4451812 -1.8559437 4738.2137
|
||||
1650 0.54710034 -6.2661978 0 -5.4457525 -1.8882831 4738.2137
|
||||
1700 0.53665689 -6.2504958 0 -5.4457117 -1.8068004 4738.2137
|
||||
1750 0.54864706 -6.2681124 0 -5.4453476 -1.8662646 4738.2137
|
||||
1800 0.54476202 -6.2615083 0 -5.4445696 -1.8352824 4738.2137
|
||||
1850 0.54142953 -6.2555505 0 -5.4436093 -1.8005654 4738.2137
|
||||
1900 0.53992431 -6.254135 0 -5.444451 -1.7768688 4738.2137
|
||||
1950 0.54665954 -6.2640971 0 -5.4443128 -1.7947032 4738.2137
|
||||
2000 0.54557798 -6.2625416 0 -5.4443793 -1.8072514 4738.2137
|
||||
Loop time of 2.17499 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 99310.978 tau/day, 229.887 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3333 | 1.3705 | 1.397 | 2.0 | 63.01
|
||||
Neigh | 0.24071 | 0.41014 | 0.62928 | 26.6 | 18.86
|
||||
Comm | 0.19069 | 0.37486 | 0.53972 | 26.6 | 17.23
|
||||
Output | 0.00031614 | 0.00035483 | 0.00040388 | 0.2 | 0.02
|
||||
Modify | 0.0057304 | 0.0083074 | 0.01159 | 2.8 | 0.38
|
||||
Other | | 0.01083 | | | 0.50
|
||||
|
||||
Nlocal: 1000 ave 1628 max 523 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 8641.5 ave 9769 max 7941 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Neighs: 151654 ave 163181 max 145045 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 606616
|
||||
Ave neighs/atom = 151.654
|
||||
Neighbor list builds = 56
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:09
|
||||
188
examples/balance/log.27Sep16.balance.clock.static.g++.4
Normal file
188
examples/balance/log.27Sep16.balance.clock.static.g++.4
Normal file
@ -0,0 +1,188 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
group fast type 1
|
||||
2600 atoms in group fast
|
||||
group slow type 2
|
||||
1400 atoms in group slow
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000447989 seconds
|
||||
iteration count = 2
|
||||
time weight factor: 1
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
x cuts: 0 0.25 0.5 0.6875 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Memory usage per processor = 2.77892 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358
|
||||
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778
|
||||
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
Loop time of 1.42972 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 75539.346 tau/day, 174.860 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.34009 | 0.65732 | 1.1925 | 42.3 | 45.98
|
||||
Neigh | 0.1324 | 0.17067 | 0.19962 | 6.6 | 11.94
|
||||
Comm | 0.03502 | 0.5933 | 0.88766 | 45.1 | 41.50
|
||||
Output | 0.0001173 | 0.00012749 | 0.00013947 | 0.1 | 0.01
|
||||
Modify | 0.0024164 | 0.0032778 | 0.0040991 | 1.0 | 0.23
|
||||
Other | | 0.00502 | | | 0.35
|
||||
|
||||
Nlocal: 1000 ave 1263 max 712 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 8711.5 ave 9045 max 8325 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 149325 ave 275165 max 77227 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 597299
|
||||
Ave neighs/atom = 149.325
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
rebalancing time: 0.000354052 seconds
|
||||
iteration count = 4
|
||||
time weight factor: 1
|
||||
initial/final max load/proc = 1673.83 1097.18
|
||||
initial/final imbalance factor = 1.67383 1.09718
|
||||
x cuts: 0 0.296875 0.453125 0.605469 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842
|
||||
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
|
||||
Loop time of 1.10579 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 97667.971 tau/day, 226.083 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47383 | 0.65917 | 0.86391 | 21.2 | 59.61
|
||||
Neigh | 0.12071 | 0.17144 | 0.23972 | 11.6 | 15.50
|
||||
Comm | 0.10061 | 0.26652 | 0.39924 | 24.8 | 24.10
|
||||
Output | 0.00012779 | 0.00014991 | 0.00018096 | 0.2 | 0.01
|
||||
Modify | 0.0021801 | 0.0032307 | 0.0047314 | 1.8 | 0.29
|
||||
Other | | 0.005272 | | | 0.48
|
||||
|
||||
Nlocal: 1000 ave 1479 max 635 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 8759.5 ave 9918 max 7969 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149356 ave 195930 max 110209 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 597424
|
||||
Ave neighs/atom = 149.356
|
||||
Neighbor list builds = 24
|
||||
Dangerous builds = 0
|
||||
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
|
||||
rebalancing time: 0.000221968 seconds
|
||||
iteration count = 4
|
||||
time weight factor: 1
|
||||
initial/final max load/proc = 1200.06 1176.79
|
||||
initial/final imbalance factor = 1.20006 1.17679
|
||||
x cuts: 0 0.306641 0.443359 0.595947 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
|
||||
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834
|
||||
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993
|
||||
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672
|
||||
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967
|
||||
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
|
||||
Loop time of 1.10659 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 97597.325 tau/day, 225.920 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.59596 | 0.67205 | 0.81576 | 10.9 | 60.73
|
||||
Neigh | 0.098 | 0.18193 | 0.2707 | 16.7 | 16.44
|
||||
Comm | 0.15524 | 0.24375 | 0.40352 | 19.4 | 22.03
|
||||
Output | 0.00013709 | 0.00017041 | 0.00020695 | 0.2 | 0.02
|
||||
Modify | 0.0016487 | 0.0032793 | 0.0050011 | 2.4 | 0.30
|
||||
Other | | 0.005414 | | | 0.49
|
||||
|
||||
Nlocal: 1000 ave 1580 max 493 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 8736.5 ave 9808 max 8009 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149124 ave 178715 max 132100 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 596497
|
||||
Ave neighs/atom = 149.124
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
202
examples/balance/log.27Sep16.balance.g++.4
Normal file
202
examples/balance/log.27Sep16.balance.g++.4
Normal file
@ -0,0 +1,202 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
#dump 2 all custom 50 tmp.dump id v_p x y z
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 42 29 1
|
||||
Memory usage per processor = 2.48839 Mbytes
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
|
||||
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
|
||||
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
|
||||
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
|
||||
400 26.522239 -29.965537 6.6787858 1.1855956 1.0193906
|
||||
500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
|
||||
600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
|
||||
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
|
||||
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
|
||||
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
|
||||
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
|
||||
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
|
||||
1200 17.214459 -20.726965 6.3578917 1.0304709 1.0193906
|
||||
1300 16.424084 -19.757322 3.9028131 1.1191136 1.0083102
|
||||
1400 15.026954 -18.109911 1.7623684 1.0858726 1.0193906
|
||||
1500 13.640678 -16.740794 1.5347425 1.0858726 1.0193906
|
||||
1600 13.618211 -16.610276 1.9480883 1.0747922 1.0083102
|
||||
1700 13.266465 -16.300632 1.6890777 1.0637119 1.0193906
|
||||
1800 12.178444 -15.175544 2.1018989 1.0304709 1.0083102
|
||||
1900 12.131633 -15.075269 2.0174899 1.0526316 1.0193906
|
||||
2000 12.290785 -15.185923 1.8747772 1.0415512 1.0193906
|
||||
2100 12.02255 -14.947108 1.086185 1.0747922 1.0083102
|
||||
2200 11.733238 -14.620414 0.93934447 1.0526316 1.0193906
|
||||
2300 12.180779 -15.092283 1.1969416 1.0526316 1.0083102
|
||||
2400 11.721247 -14.503377 1.3759878 1.1080332 1.0083102
|
||||
2500 11.609116 -14.371603 2.0315139 1.0747922 1.0083102
|
||||
2600 11.712503 -14.494711 1.7236598 1.0415512 1.0193906
|
||||
2700 10.932816 -13.665751 1.2772732 1.0415512 1.0083102
|
||||
2800 10.418752 -13.183889 1.2940564 1.0415512 1.0193906
|
||||
2900 10.668297 -13.404525 0.90378659 1.0304709 1.0083102
|
||||
3000 10.562215 -13.581566 1.0507999 1.0083102 1.0193906
|
||||
3100 10.283188 -13.016565 1.0685664 1.0526316 1.0193906
|
||||
3200 10.424678 -13.136756 1.4038511 1.0193906 1.0083102
|
||||
3300 10.207304 -12.901323 1.3077174 1.0415512 1.0193906
|
||||
3400 10.143301 -12.802915 1.2776266 1.0415512 1.0193906
|
||||
3500 9.8449452 -12.507639 1.5455496 1.0637119 1.0083102
|
||||
3600 9.5629038 -12.204164 0.84971204 1.0304709 1.0083102
|
||||
3700 9.1851938 -11.809431 1.0102805 1.0304709 1.0193906
|
||||
3800 9.3305969 -11.989086 0.69923461 1.0193906 1.0083102
|
||||
3900 9.2415243 -11.880498 1.2471235 1.0637119 1.0193906
|
||||
4000 8.8240051 -11.417696 0.60781901 1.0304709 1.0083102
|
||||
4100 8.9126422 -11.503716 0.96900558 1.0083102 1.0083102
|
||||
4200 8.3738185 -10.93925 0.84927158 1.0193906 1.0083102
|
||||
4300 8.2401487 -10.90291 0.97775564 1.0083102 1.0083102
|
||||
4400 8.061288 -10.722169 1.4106859 1.0193906 1.0193906
|
||||
4500 7.8900038 -10.422818 0.67651486 1.0193906 1.0193906
|
||||
4600 7.8306694 -10.363812 0.83437455 1.0193906 1.0193906
|
||||
4700 8.1116499 -10.712008 0.58885383 1.0304709 1.0193906
|
||||
4800 8.0508103 -10.576232 0.52562827 1.0193906 1.0083102
|
||||
4900 7.8161815 -10.368333 0.89724847 1.0415512 1.0083102
|
||||
5000 7.4940002 -9.9763835 1.215446 1.0304709 1.0083102
|
||||
5100 7.9981403 -10.510786 1.0948502 1.0304709 1.0193906
|
||||
5200 7.7674668 -10.259031 0.81850586 1.0304709 1.0193906
|
||||
5300 7.9627913 -10.465018 0.75004253 1.0304709 1.0083102
|
||||
5400 7.8093696 -10.371624 0.75451812 1.0193906 1.0083102
|
||||
5500 8.1189569 -10.623288 0.91908416 1.0304709 1.0083102
|
||||
5600 7.5970957 -10.070305 0.84265844 1.0415512 1.0083102
|
||||
5700 7.4322203 -9.9176252 0.32608772 1.0304709 1.0083102
|
||||
5800 7.8210607 -10.311444 0.95696619 1.0304709 1.0083102
|
||||
5900 7.6181913 -10.111225 1.1341946 1.0193906 1.0083102
|
||||
6000 7.2217555 -9.7122281 0.75858423 1.0637119 1.0083102
|
||||
6100 7.3643302 -9.851242 0.5240439 1.0193906 1.0193906
|
||||
6200 7.0281589 -9.4834454 0.59523945 1.0526316 1.0193906
|
||||
6300 7.1383115 -9.6099868 0.87558078 1.0193906 1.0193906
|
||||
6400 7.2136999 -9.6965877 0.88426542 1.0304709 1.0083102
|
||||
6500 7.1710521 -9.7082917 1.2055959 1.0415512 1.0193906
|
||||
6600 7.4150515 -9.9376614 0.48201097 1.0304709 1.0083102
|
||||
6700 6.8701427 -9.3844769 0.72785561 1.0526316 1.0193906
|
||||
6800 6.8486978 -9.3256413 0.93231327 1.0193906 1.0083102
|
||||
6900 6.583533 -9.0068813 0.51281911 1.0193906 1.0193906
|
||||
7000 6.7199396 -9.1773668 0.12636874 1.0193906 1.0083102
|
||||
7100 6.5193695 -8.9553058 1.0423295 1.0083102 1.0193906
|
||||
7200 6.4868896 -8.9090695 0.49867926 1.0083102 1.0193906
|
||||
7300 6.2975635 -8.7775483 0.49072731 1.0415512 1.0083102
|
||||
7400 6.4966155 -8.9410837 0.52952897 1.0193906 1.0083102
|
||||
7500 6.7100139 -9.166691 0.82930078 1.0193906 1.0083102
|
||||
7600 6.3569418 -8.7843554 0.93473251 1.0193906 1.0083102
|
||||
7700 6.122789 -8.5434369 0.33725874 1.0526316 1.0083102
|
||||
7800 6.0249595 -8.4453069 0.52784464 1.0193906 1.0083102
|
||||
7900 6.6673238 -9.1166487 0.93753595 1.0193906 1.0083102
|
||||
8000 6.4177253 -8.8896071 0.57421674 1.0193906 1.0193906
|
||||
8100 5.965959 -8.3655023 0.42043964 1.0304709 1.0193906
|
||||
8200 6.3325216 -8.758339 0.76723151 1.0193906 1.0193906
|
||||
8300 6.4992751 -8.943922 0.86331769 1.0526316 1.0193906
|
||||
8400 6.1834495 -8.6059885 0.43133079 1.0415512 1.0193906
|
||||
8500 6.2567239 -8.6758815 0.8551113 1.0083102 1.0193906
|
||||
8600 6.1232623 -8.5905174 0.6014726 1.0304709 1.0083102
|
||||
8700 6.6650376 -9.0949995 0.46866086 1.0637119 1.0193906
|
||||
8800 6.6103957 -9.0116868 0.84371859 1.0083102 1.0193906
|
||||
8900 5.8867946 -8.3162884 0.64216189 1.0415512 1.0193906
|
||||
9000 5.685369 -8.0652138 0.32067903 1.0304709 1.0083102
|
||||
9100 6.2783881 -8.6826466 0.36419567 1.0415512 1.0304709
|
||||
9200 6.0162211 -8.4584809 0.58707128 1.0083102 1.0083102
|
||||
9300 5.9900511 -8.3949266 0.62037401 1.0304709 1.0193906
|
||||
9400 6.2686573 -8.6713334 0.81204427 1.0415512 1.0083102
|
||||
9500 6.0317917 -8.4325112 0.63221293 1.0304709 1.0193906
|
||||
9600 5.8217003 -8.256407 0.816143 1.0304709 1.0083102
|
||||
9700 5.6011023 -7.9966077 0.4114902 1.0304709 1.0193906
|
||||
9800 5.6339982 -8.0317639 0.32315576 1.0083102 1.0083102
|
||||
9900 5.8044743 -8.1942271 0.62892477 1.0193906 1.0083102
|
||||
10000 6.1722678 -8.5642925 0.80423557 1.0304709 1.0083102
|
||||
Loop time of 0.39332 on 4 procs for 10000 steps with 361 atoms
|
||||
|
||||
Performance: 10983420.832 tau/day, 25424.585 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.067888 | 0.075593 | 0.091022 | 3.3 | 19.22
|
||||
Neigh | 0.071147 | 0.075568 | 0.085203 | 2.1 | 19.21
|
||||
Comm | 0.10841 | 0.12918 | 0.14463 | 4.0 | 32.84
|
||||
Output | 0.0017445 | 0.001877 | 0.0022032 | 0.4 | 0.48
|
||||
Modify | 0.038837 | 0.039568 | 0.040469 | 0.3 | 10.06
|
||||
Other | | 0.07153 | | | 18.19
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 22.25 ave 27 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 268.25 ave 400 max 133 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1073
|
||||
Ave neighs/atom = 2.9723
|
||||
Neighbor list builds = 3611
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
103
examples/balance/log.27Sep16.balance.group.dynamic.g++.4
Normal file
103
examples/balance/log.27Sep16.balance.group.dynamic.g++.4
Normal file
@ -0,0 +1,103 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
group fast type 1
|
||||
2600 atoms in group fast
|
||||
group slow type 2
|
||||
1400 atoms in group slow
|
||||
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted.txt
|
||||
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000452042 seconds
|
||||
iteration count = 2
|
||||
group weights: fast=1 slow=1
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
x cuts: 0 0.25 0.5 0.6875 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor}
|
||||
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Memory usage per processor = 2.9192 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||||
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
|
||||
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
Loop time of 1.48606 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 72675.623 tau/day, 168.231 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.23243 | 0.67 | 1.2235 | 47.4 | 45.09
|
||||
Neigh | 0.17043 | 0.18781 | 0.21572 | 4.1 | 12.64
|
||||
Comm | 0.036635 | 0.61802 | 1.0727 | 51.6 | 41.59
|
||||
Output | 0.00011992 | 0.00013161 | 0.00015426 | 0.1 | 0.01
|
||||
Modify | 0.005506 | 0.0055596 | 0.0056329 | 0.1 | 0.37
|
||||
Other | | 0.004531 | | | 0.30
|
||||
|
||||
Nlocal: 1000 ave 1001 max 999 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 8727 ave 8761 max 8674 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 149349 ave 260848 max 51191 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 597396
|
||||
Ave neighs/atom = 149.349
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
139
examples/balance/log.27Sep16.balance.group.static.g++.4
Normal file
139
examples/balance/log.27Sep16.balance.group.static.g++.4
Normal file
@ -0,0 +1,139 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
balance 1.0 shift x 5 1.1 # out unweighted.txt
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000433922 seconds
|
||||
iteration count = 2
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
x cuts: 0 0.25 0.5 0.6875 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
balance 1.0 x uniform
|
||||
rebalancing time: 0.000152826 seconds
|
||||
iteration count = 0
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
x cuts: 0 0.25 0.5 0.75 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
variable weight atom (type==1)*1.0+(type==2)*v_factor
|
||||
balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
|
||||
rebalancing time: 0.000287056 seconds
|
||||
iteration count = 2
|
||||
weight variable: weight
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
x cuts: 0 0.25 0.5 0.6875 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
balance 1.0 x uniform
|
||||
rebalancing time: 0.00011611 seconds
|
||||
iteration count = 0
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
x cuts: 0 0.25 0.5 0.75 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
group fast type 1
|
||||
2600 atoms in group fast
|
||||
group slow type 2
|
||||
1400 atoms in group slow
|
||||
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt
|
||||
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
|
||||
rebalancing time: 0.000248909 seconds
|
||||
iteration count = 2
|
||||
group weights: fast=1 slow=1
|
||||
initial/final max load/proc = 1200 1200
|
||||
initial/final imbalance factor = 1.2 1.2
|
||||
x cuts: 0 0.25 0.5 0.6875 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Memory usage per processor = 2.77892 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358
|
||||
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778
|
||||
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
Loop time of 1.41033 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 76577.913 tau/day, 177.264 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.33785 | 0.6592 | 1.1713 | 41.7 | 46.74
|
||||
Neigh | 0.14133 | 0.17129 | 0.19681 | 5.6 | 12.15
|
||||
Comm | 0.039078 | 0.57085 | 0.87566 | 45.3 | 40.48
|
||||
Output | 0.00022721 | 0.00024492 | 0.00026417 | 0.1 | 0.02
|
||||
Modify | 0.0025113 | 0.0033261 | 0.0040808 | 1.0 | 0.24
|
||||
Other | | 0.005427 | | | 0.38
|
||||
|
||||
Nlocal: 1000 ave 1263 max 712 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 8711.5 ave 9045 max 8325 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 149325 ave 275165 max 77227 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 597299
|
||||
Ave neighs/atom = 149.325
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
110
examples/balance/log.27Sep16.balance.kspace.g++.4
Normal file
110
examples/balance/log.27Sep16.balance.kspace.g++.4
Normal file
@ -0,0 +1,110 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
#atom_style charge
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
#set type 1:2 charge 0.0
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/long/coul/long long off 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
kspace_style pppm/disp 1.0e-4
|
||||
kspace_modify gewald/disp 0.1
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
group fast type 1
|
||||
2600 atoms in group fast
|
||||
group slow type 2
|
||||
1400 atoms in group slow
|
||||
fix 0 all balance 20 1.0 shift x 5 1.0 weight group 2 fast 1.0 slow 2.0 weight time 0.66
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
PPPMDisp initialization ...
|
||||
Dispersion G vector (1/distance) = 0.1
|
||||
Dispersion grid = 2 2 2
|
||||
Dispersion stencil order = 5
|
||||
Dispersion estimated absolute RMS force accuracy = 1.01251
|
||||
Dispersion estimated absolute real space RMS force accuracy = 1.01251
|
||||
Dispersion estimated absolute kspace RMS force accuracy = 7.29446e-07
|
||||
Disperion estimated relative force accuracy = 1.01251
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc dispersion = 294 4
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
Memory usage per processor = 3.32692 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 52.148338 0 53.647963 94.09503 4738.2137
|
||||
50 17.850656 42.620113 0 69.389403 142.80556 4738.2137
|
||||
100 9.4607189 49.700118 0 63.887649 117.51739 4738.2137
|
||||
150 13.992056 47.731988 0 68.714825 140.56926 4738.2137
|
||||
200 11.617635 52.509395 0 69.931491 142.6933 4738.2137
|
||||
250 13.536262 48.330072 0 68.629389 133.91619 4738.2137
|
||||
300 12.619724 50.326376 0 69.25123 132.46494 4738.2137
|
||||
350 14.513005 50.110693 0 71.874758 143.39284 4738.2137
|
||||
400 12.429702 49.690909 0 68.3308 130.0808 4738.2137
|
||||
450 13.928225 50.969523 0 71.856637 144.44675 4738.2137
|
||||
500 13.286368 50.355522 0 70.280091 137.2389 4738.2137
|
||||
Loop time of 4.79482 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 45048.596 tau/day, 104.279 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.85927 | 1.571 | 2.2092 | 51.0 | 32.76
|
||||
Kspace | 0.61247 | 1.982 | 3.2697 | 85.3 | 41.34
|
||||
Neigh | 0.2976 | 0.98099 | 1.8525 | 68.1 | 20.46
|
||||
Comm | 0.090759 | 0.23335 | 0.34356 | 22.4 | 4.87
|
||||
Output | 0.00027442 | 0.00034857 | 0.0004065 | 0.3 | 0.01
|
||||
Modify | 0.013081 | 0.016089 | 0.0201 | 2.3 | 0.34
|
||||
Other | | 0.01104 | | | 0.23
|
||||
|
||||
Nlocal: 1000 ave 1853 max 359 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 7773.5 ave 9196 max 6355 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 127368 ave 180948 max 71698 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 509471
|
||||
Ave neighs/atom = 127.368
|
||||
Neighbor list builds = 124
|
||||
Dangerous builds = 97
|
||||
Total wall time: 0:00:04
|
||||
221
examples/balance/log.27Sep16.balance.neigh.dynamic.g++.4
Normal file
221
examples/balance/log.27Sep16.balance.neigh.dynamic.g++.4
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.8 weight store WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mp4 c_p type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
WARNING: No suitable neighbor list found. Neighbor weighted balancing skipped (../imbalance_neigh.cpp:65)
|
||||
Memory usage per processor = 3.0442 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||||
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
|
||||
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
|
||||
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
Loop time of 2.27598 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 94904.173 tau/day, 219.686 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1158 | 1.4132 | 1.6545 | 19.0 | 62.09
|
||||
Neigh | 0.25541 | 0.38197 | 0.55281 | 20.3 | 16.78
|
||||
Comm | 0.33626 | 0.46086 | 0.58471 | 14.7 | 20.25
|
||||
Output | 0.00030327 | 0.00033396 | 0.0003922 | 0.2 | 0.01
|
||||
Modify | 0.0061643 | 0.0082641 | 0.011169 | 2.4 | 0.36
|
||||
Other | | 0.01137 | | | 0.50
|
||||
|
||||
Nlocal: 1000 ave 1551 max 604 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8754.75 ave 9849 max 8074 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 149308 ave 163995 max 129030 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 597231
|
||||
Ave neighs/atom = 149.308
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
|
||||
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
|
||||
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
|
||||
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
|
||||
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
|
||||
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
|
||||
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
|
||||
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
|
||||
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
|
||||
Loop time of 2.14853 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 100533.652 tau/day, 232.717 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1688 | 1.3591 | 1.5126 | 13.1 | 63.26
|
||||
Neigh | 0.24981 | 0.38774 | 0.57835 | 22.5 | 18.05
|
||||
Comm | 0.36101 | 0.38157 | 0.41179 | 3.0 | 17.76
|
||||
Output | 0.00031686 | 0.00034499 | 0.00040627 | 0.2 | 0.02
|
||||
Modify | 0.0059092 | 0.0082516 | 0.011432 | 2.6 | 0.38
|
||||
Other | | 0.01149 | | | 0.53
|
||||
|
||||
Nlocal: 1000 ave 1559 max 601 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8717.25 ave 9789 max 8011 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150170 ave 165071 max 129263 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 600678
|
||||
Ave neighs/atom = 150.169
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
|
||||
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
|
||||
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
|
||||
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
|
||||
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
|
||||
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
|
||||
1300 0.54134321 -6.2590728 0 -5.447261 -1.9170271 4738.2137
|
||||
1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
|
||||
1400 0.53726925 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
|
||||
1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
|
||||
1500 0.54223342 -6.2591056 0 -5.4459588 -1.886698 4738.2137
|
||||
Loop time of 2.13806 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 101026.160 tau/day, 233.857 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1911 | 1.3674 | 1.5133 | 12.4 | 63.95
|
||||
Neigh | 0.2394 | 0.37334 | 0.55622 | 22.2 | 17.46
|
||||
Comm | 0.36084 | 0.37761 | 0.409 | 3.0 | 17.66
|
||||
Output | 0.00030899 | 0.00033534 | 0.00039768 | 0.2 | 0.02
|
||||
Modify | 0.0060141 | 0.0083458 | 0.011389 | 2.6 | 0.39
|
||||
Other | | 0.01105 | | | 0.52
|
||||
|
||||
Nlocal: 1000 ave 1545 max 604 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8704 ave 9801 max 7983 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 150494 ave 165851 max 129789 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 601974
|
||||
Ave neighs/atom = 150.494
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.06519 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1500 0.54223342 -6.2591056 0 -5.4459588 -1.886698 4738.2137
|
||||
1550 0.55327017 -6.2750125 0 -5.4453147 -1.9506581 4738.2137
|
||||
1600 0.54419032 -6.2612626 0 -5.4451812 -1.8559458 4738.2137
|
||||
1650 0.54710059 -6.2661984 0 -5.4457527 -1.8882842 4738.2137
|
||||
1700 0.53665689 -6.2504959 0 -5.4457118 -1.8067985 4738.2137
|
||||
1750 0.54864916 -6.2681196 0 -5.4453516 -1.8662894 4738.2137
|
||||
1800 0.54476391 -6.2615108 0 -5.4445692 -1.8352746 4738.2137
|
||||
1850 0.54142945 -6.2555553 0 -5.4436142 -1.8005732 4738.2137
|
||||
1900 0.53992253 -6.2541407 0 -5.4444594 -1.7768992 4738.2137
|
||||
1950 0.54663678 -6.2640967 0 -5.4443465 -1.7945736 4738.2137
|
||||
2000 0.54563235 -6.2626431 0 -5.4443992 -1.807693 4738.2137
|
||||
Loop time of 2.18212 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 98986.300 tau/day, 229.135 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1776 | 1.3712 | 1.5256 | 13.4 | 62.84
|
||||
Neigh | 0.26314 | 0.4065 | 0.59956 | 22.6 | 18.63
|
||||
Comm | 0.36859 | 0.3845 | 0.41286 | 2.7 | 17.62
|
||||
Output | 0.00031281 | 0.00033575 | 0.00039792 | 0.2 | 0.02
|
||||
Modify | 0.0058827 | 0.0082896 | 0.011639 | 2.7 | 0.38
|
||||
Other | | 0.01133 | | | 0.52
|
||||
|
||||
Nlocal: 1000 ave 1544 max 605 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8676.25 ave 9831 max 7985 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Neighs: 151653 ave 166956 max 130753 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 606611
|
||||
Ave neighs/atom = 151.653
|
||||
Neighbor list builds = 56
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:08
|
||||
134
examples/balance/log.27Sep16.balance.neigh.rcb.g++.4
Normal file
134
examples/balance/log.27Sep16.balance.neigh.rcb.g++.4
Normal file
@ -0,0 +1,134 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
comm_style tiled
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
fix 0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
WARNING: No suitable neighbor list found. Neighbor weighted balancing skipped (../imbalance_neigh.cpp:65)
|
||||
Memory usage per processor = 2.90262 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||||
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
|
||||
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
Loop time of 0.943947 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 114413.252 tau/day, 264.845 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.64601 | 0.66027 | 0.67403 | 1.2 | 69.95
|
||||
Neigh | 0.18111 | 0.18828 | 0.1953 | 1.2 | 19.95
|
||||
Comm | 0.072217 | 0.084395 | 0.096822 | 3.4 | 8.94
|
||||
Output | 0.00016904 | 0.00018668 | 0.00020409 | 0.1 | 0.02
|
||||
Modify | 0.005301 | 0.0055165 | 0.0056343 | 0.2 | 0.58
|
||||
Other | | 0.005294 | | | 0.56
|
||||
|
||||
Nlocal: 1000 ave 1004 max 996 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 7674 ave 7678 max 7668 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 149349 ave 150214 max 148735 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 597396
|
||||
Ave neighs/atom = 149.349
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
run 250
|
||||
Memory usage per processor = 2.9031 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
|
||||
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
|
||||
Loop time of 0.886707 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 121798.994 tau/day, 281.942 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.6277 | 0.63292 | 0.64433 | 0.8 | 71.38
|
||||
Neigh | 0.1778 | 0.17937 | 0.18309 | 0.5 | 20.23
|
||||
Comm | 0.05461 | 0.06445 | 0.070518 | 2.3 | 7.27
|
||||
Output | 0.00015926 | 0.00017142 | 0.00018311 | 0.1 | 0.02
|
||||
Modify | 0.0050013 | 0.0050754 | 0.0051844 | 0.1 | 0.57
|
||||
Other | | 0.004719 | | | 0.53
|
||||
|
||||
Nlocal: 1000 ave 1008 max 990 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 7665.5 ave 7675 max 7650 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 149308 ave 149883 max 148467 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 597231
|
||||
Ave neighs/atom = 149.308
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
207
examples/balance/log.27Sep16.balance.neigh.static.g++.4
Normal file
207
examples/balance/log.27Sep16.balance.neigh.static.g++.4
Normal file
@ -0,0 +1,207 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
variable factor index 1.0
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
WARNING: No suitable neighbor list found. Neighbor weighted balancing skipped (../imbalance_neigh.cpp:65)
|
||||
rebalancing time: 0.00040102 seconds
|
||||
iteration count = 3
|
||||
neigh weight factor: 0.8
|
||||
initial/final max load/proc = 1200 1000
|
||||
initial/final imbalance factor = 1.2 1
|
||||
x cuts: 0 0.25 0.5 0.71875 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250 post no
|
||||
Memory usage per processor = 2.77892 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358
|
||||
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778
|
||||
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606
|
||||
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
|
||||
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
Loop time of 1.42566 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8
|
||||
rebalancing time: 0.000426054 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
initial/final max load/proc = 1687.06 1002.87
|
||||
initial/final imbalance factor = 1.68662 1.0026
|
||||
x cuts: 0 0.306885 0.452881 0.599335 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250 post no
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
|
||||
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842
|
||||
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056
|
||||
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594
|
||||
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
|
||||
Loop time of 1.02512 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8
|
||||
rebalancing time: 0.000252008 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
initial/final max load/proc = 1054.41 1008.56
|
||||
initial/final imbalance factor = 1.05567 1.00976
|
||||
x cuts: 0 0.303588 0.449887 0.597189 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250 post no
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
|
||||
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834
|
||||
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993
|
||||
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672
|
||||
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967
|
||||
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
|
||||
Loop time of 1.03672 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
|
||||
rebalancing time: 0.000267982 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
time weight factor: 0.6
|
||||
initial/final max load/proc = 1393.27 1116.61
|
||||
initial/final imbalance factor = 1.25201 1.0034
|
||||
x cuts: 0 0.337163 0.448601 0.555904 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
|
||||
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922
|
||||
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329
|
||||
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122
|
||||
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466
|
||||
Loop time of 1.07042 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 100895.237 tau/day, 233.554 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.56894 | 0.64706 | 0.72522 | 8.1 | 60.45
|
||||
Neigh | 0.091286 | 0.17756 | 0.29256 | 20.9 | 16.59
|
||||
Comm | 0.042178 | 0.23721 | 0.40194 | 31.6 | 22.16
|
||||
Output | 0.00012493 | 0.0001505 | 0.00017571 | 0.1 | 0.01
|
||||
Modify | 0.0016253 | 0.0032219 | 0.0054028 | 2.9 | 0.30
|
||||
Other | | 0.005214 | | | 0.49
|
||||
|
||||
Nlocal: 1000 ave 1695 max 489 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 8733.5 ave 10199 max 7650 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 150170 ave 166473 max 132232 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 600681
|
||||
Ave neighs/atom = 150.17
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
|
||||
rebalancing time: 0.000238895 seconds
|
||||
iteration count = 10
|
||||
neigh weight factor: 0.8
|
||||
time weight factor: 0.6
|
||||
initial/final max load/proc = 1167.62 1095.43
|
||||
initial/final imbalance factor = 1.07395 1.00755
|
||||
x cuts: 0 0.345978 0.449963 0.551398 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
run 250
|
||||
Memory usage per processor = 2.7999 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466
|
||||
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821
|
||||
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027
|
||||
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678
|
||||
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178
|
||||
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797
|
||||
Loop time of 1.11596 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 96777.859 tau/day, 224.023 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.56315 | 0.66085 | 0.76319 | 10.9 | 59.22
|
||||
Neigh | 0.085606 | 0.18033 | 0.29805 | 21.9 | 16.16
|
||||
Comm | 0.044225 | 0.2661 | 0.4596 | 35.4 | 23.84
|
||||
Output | 0.00015068 | 0.0001756 | 0.00020194 | 0.1 | 0.02
|
||||
Modify | 0.0015557 | 0.0032289 | 0.0054245 | 3.0 | 0.29
|
||||
Other | | 0.005279 | | | 0.47
|
||||
|
||||
Nlocal: 1000 ave 1694 max 462 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 8755.25 ave 10227 max 7675 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 149995 ave 173733 max 125545 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 599979
|
||||
Ave neighs/atom = 149.995
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:05
|
||||
250
examples/balance/log.27Sep16.balance.var.dynamic.g++.2
Normal file
250
examples/balance/log.27Sep16.balance.var.dynamic.g++.2
Normal file
@ -0,0 +1,250 @@
|
||||
LAMMPS (26 Sep 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
processors * 1 1
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
region long block 3 6 0 10 0 10
|
||||
set region long type 2
|
||||
1400 settings made for type
|
||||
|
||||
velocity all create 1.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_coeff * 2 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
fix p all property/atom d_WEIGHT
|
||||
compute p all property/atom d_WEIGHT
|
||||
|
||||
group fast type 1
|
||||
2600 atoms in group fast
|
||||
group slow type 2
|
||||
1400 atoms in group slow
|
||||
balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65 -> bins = 7 7 7
|
||||
rebalancing time: 0.000465155 seconds
|
||||
iteration count = 10
|
||||
group weights: fast=0.8 slow=2.5
|
||||
storing weight in atom property d_WEIGHT
|
||||
initial/final max load/proc = 2960 3120
|
||||
initial/final imbalance factor = 1.06093 1.11828
|
||||
x cuts: 0 0.449707 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
variable lastweight atom c_p
|
||||
|
||||
fix 0 all balance 50 1.0 shift x 10 1.0 weight var lastweight weight time 0.5 weight store WEIGHT
|
||||
variable maximb equal f_0[1]
|
||||
variable iter equal f_0[2]
|
||||
variable prev equal f_0[3]
|
||||
variable final equal f_0
|
||||
|
||||
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
Memory usage per processor = 3.23652 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||||
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
|
||||
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
|
||||
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
|
||||
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
|
||||
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
|
||||
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
|
||||
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
|
||||
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
|
||||
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
|
||||
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
|
||||
Loop time of 3.69088 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 58522.605 tau/day, 135.469 timesteps/s
|
||||
99.7% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.3504 | 2.5517 | 2.7529 | 12.6 | 69.13
|
||||
Neigh | 0.64397 | 0.73493 | 0.82589 | 10.6 | 19.91
|
||||
Comm | 0.084433 | 0.37799 | 0.67156 | 47.7 | 10.24
|
||||
Output | 0.00024199 | 0.00026727 | 0.00029254 | 0.2 | 0.01
|
||||
Modify | 0.013371 | 0.014984 | 0.016598 | 1.3 | 0.41
|
||||
Other | | 0.01102 | | | 0.30
|
||||
|
||||
Nlocal: 2000 ave 2358 max 1642 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10463 ave 11178 max 9748 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 298070 ave 345748 max 250391 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 596139
|
||||
Ave neighs/atom = 149.035
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.24081 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
|
||||
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
|
||||
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
|
||||
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
|
||||
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
|
||||
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
|
||||
800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
|
||||
850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
|
||||
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
|
||||
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
|
||||
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
|
||||
Loop time of 4.04546 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 53393.133 tau/day, 123.595 timesteps/s
|
||||
99.4% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0718 | 2.5709 | 3.0701 | 31.1 | 63.55
|
||||
Neigh | 0.58891 | 0.73311 | 0.87732 | 16.8 | 18.12
|
||||
Comm | 0.068946 | 0.71436 | 1.3598 | 76.4 | 17.66
|
||||
Output | 0.00024986 | 0.00027978 | 0.00030971 | 0.2 | 0.01
|
||||
Modify | 0.012742 | 0.015146 | 0.01755 | 2.0 | 0.37
|
||||
Other | | 0.01163 | | | 0.29
|
||||
|
||||
Nlocal: 2000 ave 2384 max 1616 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10412.5 ave 11172 max 9653 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 300836 ave 358757 max 242914 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 601671
|
||||
Ave neighs/atom = 150.418
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
|
||||
balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
|
||||
rebalancing time: 0.000392914 seconds
|
||||
iteration count = 10
|
||||
group weights: fast=0.8 slow=2.5
|
||||
storing weight in atom property d_WEIGHT
|
||||
initial/final max load/proc = 3464.4 2800.6
|
||||
initial/final imbalance factor = 1.24172 1.0038
|
||||
x cuts: 0 0.454927 1
|
||||
y cuts: 0 1
|
||||
z cuts: 0 1
|
||||
|
||||
fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT
|
||||
|
||||
run 500
|
||||
Memory usage per processor = 3.24081 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
|
||||
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
|
||||
1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
|
||||
1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
|
||||
1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
|
||||
1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137
|
||||
1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
|
||||
1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
|
||||
1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
|
||||
1450 0.54218439 -6.2574683 0 -5.444395 -1.7901189 4738.2137
|
||||
1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
|
||||
Loop time of 3.50707 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 61589.821 tau/day, 142.569 timesteps/s
|
||||
99.8% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.4976 | 2.5822 | 2.6669 | 5.3 | 73.63
|
||||
Neigh | 0.69706 | 0.73285 | 0.76865 | 4.2 | 20.90
|
||||
Comm | 0.11878 | 0.16671 | 0.21464 | 11.7 | 4.75
|
||||
Output | 0.00026321 | 0.00028443 | 0.00030565 | 0.1 | 0.01
|
||||
Modify | 0.013662 | 0.014432 | 0.015203 | 0.6 | 0.41
|
||||
Other | | 0.01054 | | | 0.30
|
||||
|
||||
Nlocal: 2000 ave 2113 max 1887 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10348.5 ave 10873 max 9824 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 302958 ave 314826 max 291091 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 605917
|
||||
Ave neighs/atom = 151.479
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
run 500
|
||||
Memory usage per processor = 3.24081 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
|
||||
1550 0.5371361 -6.250403 0 -5.4449003 -1.7647032 4738.2137
|
||||
1600 0.54679572 -6.2646443 0 -5.4446558 -1.8115723 4738.2137
|
||||
1650 0.53806586 -6.2519009 0 -5.4450039 -1.7409151 4738.2137
|
||||
1700 0.53479442 -6.2469034 0 -5.4449123 -1.7162447 4738.2137
|
||||
1750 0.53714075 -6.2506513 0 -5.4451416 -1.7340207 4738.2137
|
||||
1800 0.52750518 -6.2358818 0 -5.4448219 -1.6875359 4738.2137
|
||||
1850 0.54585315 -6.2629365 0 -5.4443615 -1.7758587 4738.2137
|
||||
1900 0.53011039 -6.238762 0 -5.4437952 -1.6381988 4738.2137
|
||||
1950 0.54287744 -6.2583143 0 -5.4442018 -1.7367676 4738.2137
|
||||
2000 0.52770954 -6.2349628 0 -5.4435964 -1.5593554 4738.2137
|
||||
Loop time of 3.46214 on 2 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 62389.230 tau/day, 144.420 timesteps/s
|
||||
99.9% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5495 | 2.5809 | 2.6123 | 2.0 | 74.55
|
||||
Neigh | 0.68762 | 0.72466 | 0.7617 | 4.4 | 20.93
|
||||
Comm | 0.12518 | 0.13173 | 0.13829 | 1.8 | 3.80
|
||||
Output | 0.00024581 | 0.00026357 | 0.00028133 | 0.1 | 0.01
|
||||
Modify | 0.013486 | 0.014313 | 0.015139 | 0.7 | 0.41
|
||||
Other | | 0.01028 | | | 0.30
|
||||
|
||||
Nlocal: 2000 ave 2135 max 1865 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 10311.5 ave 10838 max 9785 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 303996 ave 309135 max 298857 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 607992
|
||||
Ave neighs/atom = 151.998
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:14
|
||||
@ -1,12 +1,18 @@
|
||||
Run these examples as:
|
||||
|
||||
mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop1
|
||||
mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop2
|
||||
mpirun -np 3 lmp_linux -partition 3x1 -in in.neb.sivac
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
|
||||
mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
|
||||
|
||||
Create dump files to do visualization from via Python tools:
|
||||
(see lammps/tools/README and lammps/tools/python/README
|
||||
for more info on these Python scripts)
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
|
||||
mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac
|
||||
mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac
|
||||
|
||||
If you uncomment the dump command lines in the input scripts, you can
|
||||
create dump files to do visualization from via Python tools: (see
|
||||
lammps/tools/README and lammps/tools/python/README for more info on
|
||||
these Python scripts)
|
||||
|
||||
python ~/lammps/tools/python/neb_combine.py -o dump.hop1.combine
|
||||
-b dump.nonneb.1
|
||||
|
||||
@ -14,10 +14,13 @@ variable u uloop 20
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass * 1.0
|
||||
#create_box 3 box
|
||||
#create_atoms 1 box
|
||||
#mass * 1.0
|
||||
#write_data initial.hop1
|
||||
|
||||
read_data initial.hop1
|
||||
|
||||
# LJ potentials
|
||||
|
||||
|
||||
@ -15,11 +15,14 @@ variable u uloop 20
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 11 -0.25 0.25
|
||||
region box1 block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1 region box1
|
||||
create_atoms 1 single 11.5 10.5 0
|
||||
|
||||
mass * 1.0
|
||||
#create_box 3 box
|
||||
#create_atoms 1 region box1
|
||||
#create_atoms 1 single 11.5 10.5 0
|
||||
#mass * 1.0
|
||||
#write_data initial.hop2
|
||||
|
||||
read_data initial.hop2
|
||||
|
||||
# LJ potentials
|
||||
|
||||
|
||||
@ -30,17 +30,20 @@ lattice custom $a &
|
||||
region myreg block 0 4 &
|
||||
0 4 &
|
||||
0 4
|
||||
create_box 1 myreg
|
||||
create_atoms 1 region myreg
|
||||
|
||||
mass 1 28.06
|
||||
#create_box 1 myreg
|
||||
#create_atoms 1 region myreg
|
||||
#mass 1 28.06
|
||||
#write_data initial.sivac
|
||||
|
||||
group Si type 1
|
||||
read_data initial.sivac
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group Si type 1
|
||||
|
||||
group del id 300
|
||||
delete_atoms group del
|
||||
delete_atoms group del compress no
|
||||
group vacneigh id 174 175 301 304 306 331 337
|
||||
|
||||
# choose potential
|
||||
@ -54,7 +57,7 @@ variable u uloop 20
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
|
||||
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
|
||||
|
||||
# initial minimization to relax vacancy
|
||||
|
||||
@ -72,5 +75,4 @@ thermo 100
|
||||
timestep 0.01
|
||||
min_style quickmin
|
||||
|
||||
neb 0.0 0.01 50 100 10 final final.sivac
|
||||
|
||||
neb 0.0 0.01 100 100 10 final final.sivac
|
||||
|
||||
860
examples/neb/initial.hop1
Normal file
860
examples/neb/initial.hop1
Normal file
@ -0,0 +1,860 @@
|
||||
LAMMPS data file via write_data, version 27 Sep 2016, timestep = 0
|
||||
|
||||
420 atoms
|
||||
3 atom types
|
||||
|
||||
0.0000000000000000e+00 2.2653923264628304e+01 xlo xhi
|
||||
-1.9618873042551413e-03 1.9620834929855668e+01 ylo yhi
|
||||
-2.8317404080785380e-01 2.8317404080785380e-01 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
|
||||
Atoms # atomic
|
||||
|
||||
1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
2 1 5.6634808161570760e-01 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
3 1 1.1326961632314152e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
4 1 1.6990442448471228e+00 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
5 1 2.2653923264628304e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
6 1 2.8317404080785380e+00 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
7 1 3.3980884896942456e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
8 1 3.9644365713099532e+00 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
9 1 4.5307846529256608e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
10 1 5.0971327345413684e+00 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
11 1 5.6634808161570760e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
12 1 6.2298288977727836e+00 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
13 1 6.7961769793884912e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
14 1 7.3625250610041988e+00 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
15 1 7.9288731426199064e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
16 1 8.4952212242356140e+00 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
24 1 1.3026005877161275e+01 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
33 1 1.8123138611702643e+01 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
|
||||
34 1 1.8689486693318351e+01 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
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|
||||
36 1 1.9822182856549766e+01 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
|
||||
37 1 2.0388530938165474e+01 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
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||||
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|
||||
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||||
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||||
41 1 0.0000000000000000e+00 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
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|
||||
43 1 1.1326961632314152e+00 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
50 1 5.0971327345413684e+00 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
|
||||
51 1 5.6634808161570760e+00 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
|
||||
52 1 6.2298288977727836e+00 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
|
||||
53 1 6.7961769793884912e+00 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
|
||||
54 1 7.3625250610041988e+00 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
55 1 7.9288731426199064e+00 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
56 1 8.4952212242356140e+00 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
57 1 9.0615693058513216e+00 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
58 1 9.6279173874670292e+00 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
59 1 1.0194265469082737e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
|
||||
60 1 1.0760613550698444e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
|
||||
61 1 1.1326961632314152e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
62 1 1.1893309713929860e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
63 1 1.2459657795545567e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
64 1 1.3026005877161275e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
65 1 1.3592353958776982e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
66 1 1.4158702040392690e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
67 1 1.4725050122008398e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
|
||||
68 1 1.5291398203624105e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
|
||||
69 1 1.5857746285239813e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
70 1 1.6424094366855520e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
|
||||
71 1 1.6990442448471228e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
|
||||
72 1 1.7556790530086936e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
|
||||
73 1 1.8123138611702643e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
74 1 1.8689486693318351e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
75 1 1.9255834774934058e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
76 1 1.9822182856549766e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
77 1 2.0388530938165474e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
78 1 2.0954879019781181e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
79 1 2.1521227101396889e+01 1.9618873042551415e+00 0.0000000000000000e+00 0 0 0
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||||
80 1 2.2087575183012596e+01 2.9428309563827124e+00 0.0000000000000000e+00 0 0 0
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||||
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||||
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||||
83 1 1.1326961632314152e+00 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
84 1 1.6990442448471228e+00 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
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||||
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||||
87 1 3.3980884896942456e+00 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
88 1 3.9644365713099532e+00 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
89 1 4.5307846529256608e+00 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
90 1 5.0971327345413684e+00 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
91 1 5.6634808161570760e+00 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
92 1 6.2298288977727836e+00 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
93 1 6.7961769793884912e+00 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
94 1 7.3625250610041988e+00 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
95 1 7.9288731426199064e+00 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
96 1 8.4952212242356140e+00 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
97 1 9.0615693058513216e+00 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
98 1 9.6279173874670292e+00 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
99 1 1.0194265469082737e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
100 1 1.0760613550698444e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
101 1 1.1326961632314152e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
102 1 1.1893309713929860e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
103 1 1.2459657795545567e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
104 1 1.3026005877161275e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
105 1 1.3592353958776982e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
106 1 1.4158702040392690e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
107 1 1.4725050122008398e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
108 1 1.5291398203624105e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
109 1 1.5857746285239813e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
110 1 1.6424094366855520e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
111 1 1.6990442448471228e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
112 1 1.7556790530086936e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
113 1 1.8123138611702643e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
114 1 1.8689486693318351e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
115 1 1.9255834774934058e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
116 1 1.9822182856549766e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
117 1 2.0388530938165474e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
118 1 2.0954879019781181e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
119 1 2.1521227101396889e+01 3.9237746085102829e+00 0.0000000000000000e+00 0 0 0
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||||
120 1 2.2087575183012596e+01 4.9047182606378534e+00 0.0000000000000000e+00 0 0 0
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||||
121 1 0.0000000000000000e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
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||||
122 1 5.6634808161570760e-01 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
123 1 1.1326961632314152e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
124 1 1.6990442448471228e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
125 1 2.2653923264628304e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
126 1 2.8317404080785380e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
127 1 3.3980884896942456e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
128 1 3.9644365713099532e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
129 1 4.5307846529256608e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
130 1 5.0971327345413684e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
131 1 5.6634808161570760e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
132 1 6.2298288977727836e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
133 1 6.7961769793884912e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
134 1 7.3625250610041988e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
135 1 7.9288731426199064e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
136 1 8.4952212242356140e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
137 1 9.0615693058513216e+00 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
|
||||
138 1 9.6279173874670292e+00 6.8666055648929953e+00 0.0000000000000000e+00 0 0 0
|
||||
139 1 1.0194265469082737e+01 5.8856619127654248e+00 0.0000000000000000e+00 0 0 0
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862
examples/neb/initial.hop2
Normal file
862
examples/neb/initial.hop2
Normal file
@ -0,0 +1,862 @@
|
||||
LAMMPS data file via write_data, version 27 Sep 2016, timestep = 0
|
||||
|
||||
421 atoms
|
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3 atom types
|
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|
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0.0000000000000000e+00 2.2653923264628304e+01 xlo xhi
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-2.1580760346806556e-03 2.0601974770713667e+01 ylo yhi
|
||||
-2.8317404080785380e-01 2.8317404080785380e-01 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1
|
||||
2 1
|
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3 1
|
||||
|
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Atoms # atomic
|
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|
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1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
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2 1 5.6634808161570760e-01 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
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330 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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357 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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360 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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361 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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362 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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370 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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415 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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416 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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417 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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418 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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419 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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1042
examples/neb/initial.sivac
Normal file
1042
examples/neb/initial.sivac
Normal file
File diff suppressed because it is too large
Load Diff
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (27 Sep 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
|
||||
10
examples/neb/log.28Sep16.neb.hop1.g++.8
Normal file
10
examples/neb/log.28Sep16.neb.hop1.g++.8
Normal file
@ -0,0 +1,10 @@
|
||||
LAMMPS (27 Sep 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
|
||||
100 0.10482171 0.085218406 0.014588234 0.066178435 0.19602242 0.0070900401 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.639876 -3.0465067 1 -3.0487759
|
||||
111 0.096708718 0.078036984 0.013922966 0.054175505 0.20234693 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
111 0.20234693 0.17770387 0.013922966 0.054175505 0.20234693 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764
|
||||
178 0.09975409 0.093814031 0.010577358 0.024247224 0.09975409 0.0071042931 0.0022851195 2.312004 0 -3.0535969 0.31607934 -3.0473923 0.618931 -3.0464926 1 -3.0487777
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (27 Sep 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
|
||||
18
examples/neb/log.28Sep16.neb.hop2.g++.8
Normal file
18
examples/neb/log.28Sep16.neb.hop2.g++.8
Normal file
@ -0,0 +1,18 @@
|
||||
LAMMPS (27 Sep 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
|
||||
100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
|
||||
200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
|
||||
300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941
|
||||
400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943
|
||||
500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943
|
||||
600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944
|
||||
633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
|
||||
733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944
|
||||
833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944
|
||||
933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944
|
||||
996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944
|
||||
14
examples/neb/log.28Sep16.neb.sivac.g++.3
Normal file
14
examples/neb/log.28Sep16.neb.sivac.g++.3
Normal file
@ -0,0 +1,14 @@
|
||||
LAMMPS (27 Sep 2016)
|
||||
Running on 3 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
|
||||
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
|
||||
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
|
||||
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
|
||||
40 0.0421393 0.0037035761 0.01173707 0.0421393 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
|
||||
50 0.025897844 0.0022804241 0.0081056535 0.025897844 0.016908913 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923344 -2212.8272 1 -2213.3373
|
||||
59 0.00962839 0.0012946076 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
59 0.012040803 0.0031505502 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
63 0.009152118 0.0016692472 0.0049645771 0.0081967836 0.009152118 0.51013743 0.51010776 1.7409028 0 -2213.3374 0.50022239 -2212.8272 1 -2213.3373
|
||||
14
examples/neb/log.28Sep16.neb.sivac.g++.6
Normal file
14
examples/neb/log.28Sep16.neb.sivac.g++.6
Normal file
@ -0,0 +1,14 @@
|
||||
LAMMPS (27 Sep 2016)
|
||||
Running on 3 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
|
||||
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
|
||||
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
|
||||
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
|
||||
40 0.042139305 0.0037035764 0.01173707 0.042139305 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
|
||||
50 0.025899631 0.0022805513 0.0081057075 0.025899631 0.016908929 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923345 -2212.8272 1 -2213.3373
|
||||
59 0.0096285044 0.0012946258 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
59 0.012040919 0.0031505771 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
63 0.0091523813 0.0016692845 0.0049647607 0.0081998372 0.0091523813 0.51013743 0.51010775 1.7409028 0 -2213.3374 0.50022236 -2212.8272 1 -2213.3373
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (27 Sep 2016)
|
||||
Running on 3 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
|
||||
@ -6,9 +6,9 @@ Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 P
|
||||
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
|
||||
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
|
||||
40 0.042139318 0.0037035773 0.011737071 0.042139318 0.026104737 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
|
||||
50 0.025904252 0.0022808801 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
|
||||
50 0.025904121 0.0022808707 0.0081058431 0.025904121 0.016908969 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923346 -2212.8272 1 -2213.3373
|
||||
59 0.0096287928 0.0012946716 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
50 0.025904252 0.0044134315 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
|
||||
60 0.011518317 0.0013089596 0.0054472815 0.011518317 0.0091629734 0.51014415 0.51010903 1.7406815 0 -2213.3374 0.50065207 -2212.8272 1 -2213.3373
|
||||
61 0.0089525108 0.0012703829 0.0052524345 0.0088142351 0.0089525108 0.51014321 0.51010962 1.7407173 0 -2213.3374 0.50065779 -2212.8272 1 -2213.3373
|
||||
59 0.01204121 0.0031506449 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373
|
||||
63 0.0091530442 0.0016693787 0.0049652227 0.0082075097 0.0091530442 0.51013743 0.51010775 1.7409027 0 -2213.3374 0.50022228 -2212.8272 1 -2213.3373
|
||||
@ -9,9 +9,9 @@ variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
snap
|
||||
pair_style hybrid/overlay snap &
|
||||
zbl ${zblcutinner} ${zblcutouter}
|
||||
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
|
||||
|
||||
|
||||
1
python/examples/ipython/.gitignore
vendored
Normal file
1
python/examples/ipython/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
*.orig
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@ -18,10 +18,12 @@
|
||||
#include "fix_neb.h"
|
||||
#include "universe.h"
|
||||
#include "update.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "modify.h"
|
||||
#include "compute.h"
|
||||
#include "atom.h"
|
||||
#include "group.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
@ -29,6 +31,8 @@
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
|
||||
@ -41,8 +45,13 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
// nreplica = number of partitions
|
||||
// ireplica = which world I am in universe
|
||||
// nprocs_universe = # of procs in all replicase
|
||||
// procprev,procnext = root proc in adjacent replicas
|
||||
|
||||
me = comm->me;
|
||||
nprocs = comm->nprocs;
|
||||
|
||||
nprocs_universe = universe->nprocs;
|
||||
nreplica = universe->nworlds;
|
||||
ireplica = universe->iworld;
|
||||
|
||||
@ -67,7 +76,17 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
|
||||
// initialize local storage
|
||||
|
||||
maxlocal = 0;
|
||||
ntotal = 0;
|
||||
|
||||
xprev = xnext = tangent = NULL;
|
||||
xsend = xrecv = NULL;
|
||||
tagsend = tagrecv = NULL;
|
||||
xsendall = xrecvall = NULL;
|
||||
tagsendall = tagrecvall = NULL;
|
||||
counts = displacements = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -80,6 +99,19 @@ FixNEB::~FixNEB()
|
||||
memory->destroy(xprev);
|
||||
memory->destroy(xnext);
|
||||
memory->destroy(tangent);
|
||||
|
||||
memory->destroy(xsend);
|
||||
memory->destroy(xrecv);
|
||||
memory->destroy(tagsend);
|
||||
memory->destroy(tagrecv);
|
||||
|
||||
memory->destroy(xsendall);
|
||||
memory->destroy(xrecvall);
|
||||
memory->destroy(tagsendall);
|
||||
memory->destroy(tagrecvall);
|
||||
|
||||
memory->destroy(counts);
|
||||
memory->destroy(displacements);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -104,15 +136,35 @@ void FixNEB::init()
|
||||
|
||||
rclimber = -1;
|
||||
|
||||
// setup xprev and xnext arrays
|
||||
// nebatoms = # of atoms in fix group = atoms with inter-replica forces
|
||||
|
||||
memory->destroy(xprev);
|
||||
memory->destroy(xnext);
|
||||
memory->destroy(tangent);
|
||||
nebatoms = atom->nlocal;
|
||||
memory->create(xprev,nebatoms,3,"neb:xprev");
|
||||
memory->create(xnext,nebatoms,3,"neb:xnext");
|
||||
memory->create(tangent,nebatoms,3,"neb:tangent");
|
||||
bigint count = group->count(igroup);
|
||||
if (count > MAXSMALLINT) error->all(FLERR,"Too many active NEB atoms");
|
||||
nebatoms = count;
|
||||
|
||||
// comm style for inter-replica exchange of coords
|
||||
|
||||
if (nreplica == nprocs_universe &&
|
||||
nebatoms == atom->natoms && atom->sortfreq == 0)
|
||||
cmode = SINGLE_PROC_DIRECT;
|
||||
else if (nreplica == nprocs_universe) cmode = SINGLE_PROC_MAP;
|
||||
else cmode = MULTI_PROC;
|
||||
|
||||
// ntotal = total # of atoms in system, NEB atoms or not
|
||||
|
||||
if (atom->natoms > MAXSMALLINT) error->all(FLERR,"Too many atoms for NEB");
|
||||
ntotal = atom->natoms;
|
||||
|
||||
if (atom->nlocal > maxlocal) reallocate();
|
||||
|
||||
if (MULTI_PROC && counts == NULL) {
|
||||
memory->create(xsendall,ntotal,3,"neb:xsendall");
|
||||
memory->create(xrecvall,ntotal,3,"neb:xrecvall");
|
||||
memory->create(tagsendall,ntotal,"neb:tagsendall");
|
||||
memory->create(tagrecvall,ntotal,"neb:tagrecvall");
|
||||
memory->create(counts,nprocs,"neb:counts");
|
||||
memory->create(displacements,nprocs,"neb:displacements");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -133,40 +185,31 @@ void FixNEB::min_post_force(int vflag)
|
||||
double vprev,vnext,vmax,vmin;
|
||||
double delx,dely,delz;
|
||||
double delta1[3],delta2[3];
|
||||
MPI_Request request;
|
||||
|
||||
// veng = PE of this replica
|
||||
// vprev,vnext = PEs of adjacent replicas
|
||||
// only proc 0 in each replica communicates
|
||||
|
||||
vprev = vnext = veng = pe->compute_scalar();
|
||||
|
||||
if (ireplica < nreplica-1) MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
|
||||
if (ireplica > 0) MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE);
|
||||
if (ireplica < nreplica-1 && me == 0)
|
||||
MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
|
||||
if (ireplica > 0 && me == 0)
|
||||
MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE);
|
||||
|
||||
if (ireplica > 0) MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
|
||||
if (ireplica < nreplica-1)
|
||||
if (ireplica > 0 && me == 0)
|
||||
MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
|
||||
if (ireplica < nreplica-1 && me == 0)
|
||||
MPI_Recv(&vnext,1,MPI_DOUBLE,procnext,0,uworld,MPI_STATUS_IGNORE);
|
||||
|
||||
// xprev,xnext = atom coords of adjacent replicas
|
||||
// assume order of atoms in all replicas is the same
|
||||
// check that number of atoms hasn't changed
|
||||
if (cmode == MULTI_PROC) {
|
||||
MPI_Bcast(&vprev,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&vnext,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal != nebatoms) error->one(FLERR,"Atom count changed in fix neb");
|
||||
// communicate atoms to/from adjacent replicas to fill xprev,xnext
|
||||
|
||||
if (ireplica > 0)
|
||||
MPI_Irecv(xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request);
|
||||
if (ireplica < nreplica-1)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld);
|
||||
if (ireplica > 0) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
|
||||
if (ireplica < nreplica-1)
|
||||
MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
|
||||
if (ireplica > 0)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
|
||||
if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
inter_replica_comm();
|
||||
|
||||
// trigger potential energy computation on next timestep
|
||||
|
||||
@ -175,11 +218,13 @@ void FixNEB::min_post_force(int vflag)
|
||||
// compute norm of GradV for log output
|
||||
|
||||
double **f = atom->f;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double fsq = 0.0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
fsq += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
|
||||
|
||||
MPI_Allreduce(&fsq,&gradvnorm,1,MPI_DOUBLE,MPI_MAX,world);
|
||||
MPI_Allreduce(&fsq,&gradvnorm,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
gradvnorm = sqrt(gradvnorm);
|
||||
|
||||
// first or last replica has no change to forces, just return
|
||||
@ -195,6 +240,9 @@ void FixNEB::min_post_force(int vflag)
|
||||
// depending on relative PEs of 3 replicas
|
||||
// see Henkelman & Jonsson 2000 paper, eqs 8-11
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
|
||||
if (vnext > veng && veng > vprev) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
@ -260,9 +308,15 @@ void FixNEB::min_post_force(int vflag)
|
||||
nlen += delx*delx + dely*dely + delz*delz;
|
||||
}
|
||||
|
||||
tlen = sqrt(tlen);
|
||||
plen = sqrt(plen);
|
||||
nlen = sqrt(nlen);
|
||||
double lenall;
|
||||
MPI_Allreduce(&tlen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
tlen = sqrt(lenall);
|
||||
|
||||
MPI_Allreduce(&plen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
plen = sqrt(lenall);
|
||||
|
||||
MPI_Allreduce(&nlen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
nlen = sqrt(lenall);
|
||||
|
||||
// normalize tangent vector
|
||||
|
||||
@ -295,9 +349,12 @@ void FixNEB::min_post_force(int vflag)
|
||||
f[i][2]*tangent[i][2];
|
||||
}
|
||||
|
||||
double dotall;
|
||||
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double prefactor;
|
||||
if (ireplica == rclimber) prefactor = -2.0*dot;
|
||||
else prefactor = -dot + kspring*(nlen-plen);
|
||||
if (ireplica == rclimber) prefactor = -2.0*dotall;
|
||||
else prefactor = -dotall + kspring*(nlen-plen);
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
@ -306,3 +363,222 @@ void FixNEB::min_post_force(int vflag)
|
||||
f[i][2] += prefactor*tangent[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
send/recv NEB atoms to/from adjacent replicas
|
||||
received atoms matching my local atoms are stored in xprev,xnext
|
||||
replicas 0 and N-1 send but do not receive any atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNEB::inter_replica_comm()
|
||||
{
|
||||
int i,m;
|
||||
MPI_Request request;
|
||||
MPI_Request requests[2];
|
||||
MPI_Status statuses[2];
|
||||
|
||||
// reallocate memory if necessary
|
||||
|
||||
if (atom->nlocal > maxlocal) reallocate();
|
||||
|
||||
double **x = atom->x;
|
||||
tagint *tag = atom->tag;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// -----------------------------------------------------
|
||||
// 3 cases: two for single proc per replica
|
||||
// one for multiple procs per replica
|
||||
// -----------------------------------------------------
|
||||
|
||||
// single proc per replica
|
||||
// all atoms are NEB atoms and no atom sorting is enabled
|
||||
// direct comm of x -> xprev and x -> xnext
|
||||
|
||||
if (cmode == SINGLE_PROC_DIRECT) {
|
||||
if (ireplica > 0)
|
||||
MPI_Irecv(xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request);
|
||||
if (ireplica < nreplica-1)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld);
|
||||
if (ireplica > 0) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
|
||||
if (ireplica < nreplica-1)
|
||||
MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
|
||||
if (ireplica > 0)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
|
||||
if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
// single proc per replica
|
||||
// but only some atoms are NEB atoms or atom sorting is enabled
|
||||
// send atom IDs and coords of only NEB atoms to prev/next proc
|
||||
// recv proc uses atom->map() to match received coords to owned atoms
|
||||
|
||||
if (cmode == SINGLE_PROC_MAP) {
|
||||
m = 0;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
tagsend[m] = tag[i];
|
||||
xsend[m][0] = x[i][0];
|
||||
xsend[m][1] = x[i][1];
|
||||
xsend[m][2] = x[i][2];
|
||||
m++;
|
||||
}
|
||||
|
||||
if (ireplica > 0) {
|
||||
MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]);
|
||||
MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld,&requests[1]);
|
||||
}
|
||||
if (ireplica < nreplica-1) {
|
||||
MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld);
|
||||
MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld);
|
||||
}
|
||||
|
||||
if (ireplica > 0) {
|
||||
MPI_Waitall(2,requests,statuses);
|
||||
for (i = 0; i < nebatoms; i++) {
|
||||
m = atom->map(tagrecv[i]);
|
||||
xprev[m][0] = xrecv[i][0];
|
||||
xprev[m][1] = xrecv[i][1];
|
||||
xprev[m][2] = xrecv[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
if (ireplica < nreplica-1) {
|
||||
MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
|
||||
MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,&requests[1]);
|
||||
}
|
||||
if (ireplica > 0) {
|
||||
MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
|
||||
MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
|
||||
}
|
||||
|
||||
if (ireplica < nreplica-1) {
|
||||
MPI_Waitall(2,requests,statuses);
|
||||
for (i = 0; i < nebatoms; i++) {
|
||||
m = atom->map(tagrecv[i]);
|
||||
xnext[m][0] = xrecv[i][0];
|
||||
xnext[m][1] = xrecv[i][1];
|
||||
xnext[m][2] = xrecv[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
// multiple procs per replica
|
||||
// MPI_Gather all coords and atom IDs to root proc of each replica
|
||||
// send to root of adjacent replicas
|
||||
// bcast within each replica
|
||||
// each proc extracts info for atoms it owns via atom->map()
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
tagsend[m] = tag[i];
|
||||
xsend[m][0] = x[i][0];
|
||||
xsend[m][1] = x[i][1];
|
||||
xsend[m][2] = x[i][2];
|
||||
m++;
|
||||
}
|
||||
|
||||
MPI_Gather(&m,1,MPI_INT,counts,1,MPI_INT,0,world);
|
||||
displacements[0] = 0;
|
||||
for (i = 0; i < nprocs-1; i++)
|
||||
displacements[i+1] = displacements[i] + counts[i];
|
||||
MPI_Gatherv(tagsend,m,MPI_LMP_TAGINT,
|
||||
tagsendall,counts,displacements,MPI_LMP_TAGINT,0,world);
|
||||
for (i = 0; i < nprocs; i++) counts[i] *= 3;
|
||||
for (i = 0; i < nprocs-1; i++)
|
||||
displacements[i+1] = displacements[i] + counts[i];
|
||||
if (xsend)
|
||||
MPI_Gatherv(xsend[0],3*m,MPI_DOUBLE,
|
||||
xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
|
||||
else
|
||||
MPI_Gatherv(NULL,3*m,MPI_DOUBLE,
|
||||
xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
|
||||
|
||||
if (ireplica > 0 && me == 0) {
|
||||
MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]);
|
||||
MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld,
|
||||
&requests[1]);
|
||||
}
|
||||
if (ireplica < nreplica-1 && me == 0) {
|
||||
MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld);
|
||||
MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld);
|
||||
}
|
||||
|
||||
if (ireplica > 0) {
|
||||
if (me == 0) MPI_Waitall(2,requests,statuses);
|
||||
|
||||
MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world);
|
||||
MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
|
||||
|
||||
for (i = 0; i < nebatoms; i++) {
|
||||
m = atom->map(tagrecvall[i]);
|
||||
if (m < 0 || m >= nlocal) continue;
|
||||
xprev[m][0] = xrecvall[i][0];
|
||||
xprev[m][1] = xrecvall[i][1];
|
||||
xprev[m][2] = xrecvall[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
if (ireplica < nreplica-1 && me == 0) {
|
||||
MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
|
||||
MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,
|
||||
&requests[1]);
|
||||
}
|
||||
if (ireplica > 0 && me == 0) {
|
||||
MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
|
||||
MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
|
||||
}
|
||||
|
||||
if (ireplica < nreplica-1) {
|
||||
if (me == 0) MPI_Waitall(2,requests,statuses);
|
||||
|
||||
MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world);
|
||||
MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
|
||||
|
||||
for (i = 0; i < nebatoms; i++) {
|
||||
m = atom->map(tagrecvall[i]);
|
||||
if (m < 0 || m >= nlocal) continue;
|
||||
xnext[m][0] = xrecvall[i][0];
|
||||
xnext[m][1] = xrecvall[i][1];
|
||||
xnext[m][2] = xrecvall[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reallocate xprev,xnext,tangent arrays if necessary
|
||||
reallocate communication arrays if necessary
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNEB::reallocate()
|
||||
{
|
||||
memory->destroy(xprev);
|
||||
memory->destroy(xnext);
|
||||
memory->destroy(tangent);
|
||||
|
||||
if (cmode != SINGLE_PROC_DIRECT) {
|
||||
memory->destroy(xsend);
|
||||
memory->destroy(xrecv);
|
||||
memory->destroy(tagsend);
|
||||
memory->destroy(tagrecv);
|
||||
}
|
||||
|
||||
maxlocal = atom->nmax;
|
||||
|
||||
memory->create(xprev,maxlocal,3,"neb:xprev");
|
||||
memory->create(xnext,maxlocal,3,"neb:xnext");
|
||||
memory->create(tangent,maxlocal,3,"neb:tangent");
|
||||
|
||||
if (cmode != SINGLE_PROC_DIRECT) {
|
||||
memory->create(xsend,maxlocal,3,"neb:xsend");
|
||||
memory->create(xrecv,maxlocal,3,"neb:xrecv");
|
||||
memory->create(tagsend,maxlocal,"neb:tagsend");
|
||||
memory->create(tagrecv,maxlocal,"neb:tagrecv");
|
||||
}
|
||||
}
|
||||
|
||||
@ -38,17 +38,34 @@ class FixNEB : public Fix {
|
||||
void min_post_force(int);
|
||||
|
||||
private:
|
||||
int me,nprocs,nprocs_universe;
|
||||
double kspring;
|
||||
int ireplica,nreplica;
|
||||
int procnext,procprev;
|
||||
int cmode;
|
||||
MPI_Comm uworld;
|
||||
|
||||
char *id_pe;
|
||||
class Compute *pe;
|
||||
|
||||
int nebatoms;
|
||||
double **xprev,**xnext;
|
||||
double **tangent;
|
||||
int nebatoms; // # of active NEB atoms
|
||||
int ntotal; // total # of atoms, NEB or not
|
||||
int maxlocal; // size of xprev,xnext,tangent arrays
|
||||
|
||||
double **xprev,**xnext; // coords of my owned atoms in neighbor replicas
|
||||
double **tangent; // work vector for inter-replica forces
|
||||
|
||||
double **xsend,**xrecv; // coords to send/recv to/from other replica
|
||||
tagint *tagsend,*tagrecv; // ditto for atom IDs
|
||||
|
||||
// info gathered from all procs in my replica
|
||||
double **xsendall,**xrecvall; // coords to send/recv to/from other replica
|
||||
tagint *tagsendall,*tagrecvall; // ditto for atom IDs
|
||||
|
||||
int *counts,*displacements; // used for MPI_Gather
|
||||
|
||||
void inter_replica_comm();
|
||||
void reallocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
@ -137,10 +137,6 @@ void NEB::command(int narg, char **arg)
|
||||
// error checks
|
||||
|
||||
if (nreplica == 1) error->all(FLERR,"Cannot use NEB with a single replica");
|
||||
if (nreplica != universe->nprocs)
|
||||
error->all(FLERR,"Can only use NEB with 1-processor replicas");
|
||||
if (atom->sortfreq > 0)
|
||||
error->all(FLERR,"Cannot use NEB with atom_modify sort enabled");
|
||||
if (atom->map_style == 0)
|
||||
error->all(FLERR,"Cannot use NEB unless atom map exists");
|
||||
|
||||
@ -228,7 +224,7 @@ void NEB::run()
|
||||
|
||||
// perform regular NEB for n1steps or until replicas converge
|
||||
// retrieve PE values from fix NEB and print every nevery iterations
|
||||
// break induced if converged
|
||||
// break out of while loop early if converged
|
||||
// damped dynamic min styles insure all replicas converge together
|
||||
|
||||
timer->init();
|
||||
@ -531,7 +527,7 @@ void NEB::open(char *file)
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
query fix NEB for info on each replica
|
||||
proc 0 prints current NEB status
|
||||
universe proc 0 prints current NEB status
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NEB::print_status()
|
||||
@ -552,6 +548,7 @@ void NEB::print_status()
|
||||
if (output->thermo->normflag) one[0] /= atom->natoms;
|
||||
if (me == 0)
|
||||
MPI_Allgather(one,nall,MPI_DOUBLE,&all[0][0],nall,MPI_DOUBLE,roots);
|
||||
MPI_Bcast(&all[0][0],nall*nreplica,MPI_DOUBLE,0,world);
|
||||
|
||||
rdist[0] = 0.0;
|
||||
for (int i = 1; i < nreplica; i++)
|
||||
|
||||
@ -765,10 +765,10 @@ void PRD::log_event()
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
communicate atom coords and image flags in ireplica to all other replicas
|
||||
one proc per replica:
|
||||
if one proc per replica:
|
||||
direct overwrite via bcast
|
||||
else atoms could be stored in different order or on different procs:
|
||||
collect to root proc of event replica
|
||||
else atoms could be stored in different order on a proc or on different procs:
|
||||
gather to root proc of event replica
|
||||
bcast to roots of other replicas
|
||||
bcast within each replica
|
||||
each proc extracts info for atoms it owns using atom IDs
|
||||
|
||||
407
src/balance.cpp
407
src/balance.cpp
@ -11,6 +11,11 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors, for weighted balancing:
|
||||
Axel Kohlmeyer (Temple U), Iain Bethune (EPCC)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
//#define BALANCE_DEBUG 1
|
||||
|
||||
#include <mpi.h>
|
||||
@ -25,6 +30,16 @@
|
||||
#include "domain.h"
|
||||
#include "force.h"
|
||||
#include "update.h"
|
||||
#include "group.h"
|
||||
#include "modify.h"
|
||||
#include "fix_store.h"
|
||||
#include "imbalance.h"
|
||||
#include "imbalance_group.h"
|
||||
#include "imbalance_time.h"
|
||||
#include "imbalance_neigh.h"
|
||||
#include "imbalance_store.h"
|
||||
#include "imbalance_var.h"
|
||||
#include "timer.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
@ -42,14 +57,16 @@ Balance::Balance(LAMMPS *lmp) : Pointers(lmp)
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Comm_size(world,&nprocs);
|
||||
|
||||
memory->create(proccount,nprocs,"balance:proccount");
|
||||
memory->create(allproccount,nprocs,"balance:allproccount");
|
||||
|
||||
user_xsplit = user_ysplit = user_zsplit = NULL;
|
||||
shift_allocate = 0;
|
||||
proccost = allproccost = NULL;
|
||||
|
||||
rcb = NULL;
|
||||
|
||||
nimbalance = 0;
|
||||
imbalances = NULL;
|
||||
fixstore = NULL;
|
||||
|
||||
fp = NULL;
|
||||
firststep = 1;
|
||||
}
|
||||
@ -58,8 +75,8 @@ Balance::Balance(LAMMPS *lmp) : Pointers(lmp)
|
||||
|
||||
Balance::~Balance()
|
||||
{
|
||||
memory->destroy(proccount);
|
||||
memory->destroy(allproccount);
|
||||
memory->destroy(proccost);
|
||||
memory->destroy(allproccost);
|
||||
|
||||
delete [] user_xsplit;
|
||||
delete [] user_ysplit;
|
||||
@ -67,10 +84,10 @@ Balance::~Balance()
|
||||
|
||||
if (shift_allocate) {
|
||||
delete [] bdim;
|
||||
delete [] count;
|
||||
delete [] onecost;
|
||||
delete [] allcost;
|
||||
delete [] sum;
|
||||
delete [] target;
|
||||
delete [] onecount;
|
||||
delete [] lo;
|
||||
delete [] hi;
|
||||
delete [] losum;
|
||||
@ -79,6 +96,14 @@ Balance::~Balance()
|
||||
|
||||
delete rcb;
|
||||
|
||||
for (int i = 0; i < nimbalance; i++) delete imbalances[i];
|
||||
delete [] imbalances;
|
||||
|
||||
// check nfix in case all fixes have already been deleted
|
||||
|
||||
if (fixstore && modify->nfix) modify->delete_fix(fixstore->id);
|
||||
fixstore = NULL;
|
||||
|
||||
if (fp) fclose(fp);
|
||||
}
|
||||
|
||||
@ -91,9 +116,9 @@ void Balance::command(int narg, char **arg)
|
||||
if (domain->box_exist == 0)
|
||||
error->all(FLERR,"Balance command before simulation box is defined");
|
||||
|
||||
if (comm->me == 0 && screen) fprintf(screen,"Balancing ...\n");
|
||||
if (me == 0 && screen) fprintf(screen,"Balancing ...\n");
|
||||
|
||||
// parse arguments
|
||||
// parse required arguments
|
||||
|
||||
if (narg < 2) error->all(FLERR,"Illegal balance command");
|
||||
|
||||
@ -187,24 +212,7 @@ void Balance::command(int narg, char **arg)
|
||||
} else break;
|
||||
}
|
||||
|
||||
// optional keywords
|
||||
|
||||
outflag = 0;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"out") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
|
||||
if (outflag) error->all(FLERR,"Illegal balance command");
|
||||
outflag = 1;
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[iarg+1],"w");
|
||||
if (fp == NULL) error->one(FLERR,"Cannot open balance output file");
|
||||
}
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal balance command");
|
||||
}
|
||||
|
||||
// error check
|
||||
// error checks
|
||||
|
||||
if (style == XYZ) {
|
||||
if (zflag != NONE && dimension == 2)
|
||||
@ -240,10 +248,18 @@ void Balance::command(int narg, char **arg)
|
||||
if (style == BISECTION && comm->style == 0)
|
||||
error->all(FLERR,"Balance rcb cannot be used with comm_style brick");
|
||||
|
||||
// insure atoms are in current box & update box via shrink-wrap
|
||||
// process remaining optional args
|
||||
|
||||
options(iarg,narg,arg);
|
||||
if (wtflag) weight_storage(NULL);
|
||||
|
||||
// insure particles are in current box & update box via shrink-wrap
|
||||
// init entire system since comm->setup is done
|
||||
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
|
||||
|
||||
MPI_Barrier(world);
|
||||
double start_time = MPI_Wtime();
|
||||
|
||||
lmp->init();
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
@ -255,8 +271,10 @@ void Balance::command(int narg, char **arg)
|
||||
|
||||
// imbinit = initial imbalance
|
||||
|
||||
int maxinit;
|
||||
double imbinit = imbalance_nlocal(maxinit);
|
||||
double maxinit;
|
||||
init_imbalance();
|
||||
set_weights();
|
||||
double imbinit = imbalance_factor(maxinit);
|
||||
|
||||
// no load-balance if imbalance doesn't exceed threshhold
|
||||
// unless switching from tiled to non tiled layout, then force rebalance
|
||||
@ -267,11 +285,11 @@ void Balance::command(int narg, char **arg)
|
||||
// debug output of initial state
|
||||
|
||||
#ifdef BALANCE_DEBUG
|
||||
if (outflag) dumpout(update->ntimestep,fp);
|
||||
if (outflag) dumpout(update->ntimestep);
|
||||
#endif
|
||||
|
||||
int niter = 0;
|
||||
|
||||
|
||||
// perform load-balance
|
||||
// style XYZ = explicit setting of cutting planes of logical 3d grid
|
||||
|
||||
@ -331,20 +349,22 @@ void Balance::command(int narg, char **arg)
|
||||
if (domain->triclinic) domain->set_lamda_box();
|
||||
domain->set_local_box();
|
||||
|
||||
// move atoms to new processors via irregular()
|
||||
// move particles to new processors via irregular()
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
Irregular *irregular = new Irregular(lmp);
|
||||
if (wtflag) fixstore->disable = 0;
|
||||
if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc);
|
||||
else irregular->migrate_atoms(1);
|
||||
if (wtflag) fixstore->disable = 1;
|
||||
delete irregular;
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
||||
// output of final result
|
||||
|
||||
if (outflag) dumpout(update->ntimestep,fp);
|
||||
if (outflag) dumpout(update->ntimestep);
|
||||
|
||||
// check if any atoms were lost
|
||||
// check if any particles were lost
|
||||
|
||||
bigint natoms;
|
||||
bigint nblocal = atom->nlocal;
|
||||
@ -356,22 +376,30 @@ void Balance::command(int narg, char **arg)
|
||||
error->all(FLERR,str);
|
||||
}
|
||||
|
||||
// imbfinal = final imbalance based on final nlocal
|
||||
// imbfinal = final imbalance
|
||||
|
||||
int maxfinal;
|
||||
double imbfinal = imbalance_nlocal(maxfinal);
|
||||
double maxfinal;
|
||||
double imbfinal = imbalance_factor(maxfinal);
|
||||
|
||||
// stats output
|
||||
|
||||
double stop_time = MPI_Wtime();
|
||||
|
||||
if (me == 0) {
|
||||
if (screen) {
|
||||
fprintf(screen," rebalancing time: %g seconds\n",stop_time-start_time);
|
||||
fprintf(screen," iteration count = %d\n",niter);
|
||||
fprintf(screen," initial/final max atoms/proc = %d %d\n",
|
||||
for (int i = 0; i < nimbalance; ++i) imbalances[i]->info(screen);
|
||||
fprintf(screen," initial/final max load/proc = %g %g\n",
|
||||
maxinit,maxfinal);
|
||||
fprintf(screen," initial/final imbalance factor = %g %g\n",
|
||||
imbinit,imbfinal);
|
||||
}
|
||||
if (logfile) {
|
||||
fprintf(logfile," rebalancing time: %g seconds\n",stop_time-start_time);
|
||||
fprintf(logfile," iteration count = %d\n",niter);
|
||||
fprintf(logfile," initial/final max atoms/proc = %d %d\n",
|
||||
for (int i = 0; i < nimbalance; ++i) imbalances[i]->info(logfile);
|
||||
fprintf(logfile," initial/final max load/proc = %g %g\n",
|
||||
maxinit,maxfinal);
|
||||
fprintf(logfile," initial/final imbalance factor = %g %g\n",
|
||||
imbinit,imbfinal);
|
||||
@ -413,61 +441,162 @@ void Balance::command(int narg, char **arg)
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
calculate imbalance based on nlocal
|
||||
return max = max atom per proc
|
||||
return imbalance factor = max atom per proc / ave atom per proc
|
||||
process optional command args for Balance and FixBalance
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double Balance::imbalance_nlocal(int &max)
|
||||
void Balance::options(int iarg, int narg, char **arg)
|
||||
{
|
||||
MPI_Allreduce(&atom->nlocal,&max,1,MPI_INT,MPI_MAX,world);
|
||||
double imbalance = 1.0;
|
||||
if (max) imbalance = max / (1.0 * atom->natoms / nprocs);
|
||||
return imbalance;
|
||||
// count max number of weight settings
|
||||
|
||||
nimbalance = 0;
|
||||
for (int i = iarg; i < narg; i++)
|
||||
if (strcmp(arg[i],"weight") == 0) nimbalance++;
|
||||
if (nimbalance) imbalances = new Imbalance*[nimbalance];
|
||||
nimbalance = 0;
|
||||
|
||||
wtflag = 0;
|
||||
varflag = 0;
|
||||
outflag = 0;
|
||||
int outarg = 0;
|
||||
fp = NULL;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"weight") == 0) {
|
||||
wtflag = 1;
|
||||
Imbalance *imb;
|
||||
int nopt = 0;
|
||||
if (strcmp(arg[iarg+1],"group") == 0) {
|
||||
imb = new ImbalanceGroup(lmp);
|
||||
nopt = imb->options(narg-iarg,arg+iarg+2);
|
||||
imbalances[nimbalance++] = imb;
|
||||
} else if (strcmp(arg[iarg+1],"time") == 0) {
|
||||
imb = new ImbalanceTime(lmp);
|
||||
nopt = imb->options(narg-iarg,arg+iarg+2);
|
||||
imbalances[nimbalance++] = imb;
|
||||
} else if (strcmp(arg[iarg+1],"neigh") == 0) {
|
||||
imb = new ImbalanceNeigh(lmp);
|
||||
nopt = imb->options(narg-iarg,arg+iarg+2);
|
||||
imbalances[nimbalance++] = imb;
|
||||
} else if (strcmp(arg[iarg+1],"var") == 0) {
|
||||
varflag = 1;
|
||||
imb = new ImbalanceVar(lmp);
|
||||
nopt = imb->options(narg-iarg,arg+iarg+2);
|
||||
imbalances[nimbalance++] = imb;
|
||||
} else if (strcmp(arg[iarg+1],"store") == 0) {
|
||||
imb = new ImbalanceStore(lmp);
|
||||
nopt = imb->options(narg-iarg,arg+iarg+2);
|
||||
imbalances[nimbalance++] = imb;
|
||||
} else {
|
||||
error->all(FLERR,"Unknown (fix) balance weight method");
|
||||
}
|
||||
iarg += 2+nopt;
|
||||
|
||||
} else if (strcmp(arg[iarg],"out") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal (fix) balance command");
|
||||
outflag = 1;
|
||||
outarg = iarg+1;
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal (fix) balance command");
|
||||
}
|
||||
|
||||
// output file
|
||||
|
||||
if (outflag && comm->me == 0) {
|
||||
fp = fopen(arg[outarg],"w");
|
||||
if (fp == NULL) error->one(FLERR,"Cannot open (fix) balance output file");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
calculate imbalance based on processor splits in 3 dims
|
||||
atoms must be in lamda coords (0-1) before called
|
||||
map atoms to 3d grid of procs
|
||||
return max = max atom per proc
|
||||
return imbalance factor = max atom per proc / ave atom per proc
|
||||
allocate per-particle weight storage via FixStore
|
||||
use prefix to distinguish Balance vs FixBalance storage
|
||||
fix could already be allocated if fix balance is re-specified
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double Balance::imbalance_splits(int &max)
|
||||
void Balance::weight_storage(char *prefix)
|
||||
{
|
||||
double *xsplit = comm->xsplit;
|
||||
double *ysplit = comm->ysplit;
|
||||
double *zsplit = comm->zsplit;
|
||||
char *fixargs[6];
|
||||
|
||||
int nx = comm->procgrid[0];
|
||||
int ny = comm->procgrid[1];
|
||||
int nz = comm->procgrid[2];
|
||||
if (prefix) {
|
||||
int n = strlen(prefix) + 32;
|
||||
fixargs[0] = new char[n];
|
||||
strcpy(fixargs[0],prefix);
|
||||
strcat(fixargs[0],"IMBALANCE_WEIGHTS");
|
||||
} else fixargs[0] = (char *) "IMBALANCE_WEIGHTS";
|
||||
|
||||
for (int i = 0; i < nprocs; i++) proccount[i] = 0;
|
||||
fixargs[1] = (char *) "all";
|
||||
fixargs[2] = (char *) "STORE";
|
||||
fixargs[3] = (char *) "peratom";
|
||||
fixargs[4] = (char *) "0";
|
||||
fixargs[5] = (char *) "1";
|
||||
|
||||
int ifix = modify->find_fix(fixargs[0]);
|
||||
if (ifix < 1) {
|
||||
modify->add_fix(6,fixargs);
|
||||
fixstore = (FixStore *) modify->fix[modify->nfix-1];
|
||||
} else fixstore = (FixStore *) modify->fix[ifix];
|
||||
|
||||
fixstore->disable = 1;
|
||||
|
||||
if (prefix) delete [] fixargs[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
invoke init() for each Imbalance class
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Balance::init_imbalance()
|
||||
{
|
||||
if (!wtflag) return;
|
||||
for (int n = 0; n < nimbalance; n++) imbalances[n]->init();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set weight for each particle
|
||||
via list of Nimbalance classes
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Balance::set_weights()
|
||||
{
|
||||
if (!wtflag) return;
|
||||
weight = fixstore->vstore;
|
||||
|
||||
double **x = atom->x;
|
||||
int nlocal = atom->nlocal;
|
||||
int ix,iy,iz;
|
||||
for (int i = 0; i < nlocal; i++) weight[i] = 1.0;
|
||||
for (int n = 0; n < nimbalance; n++) imbalances[n]->compute(weight);
|
||||
}
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
ix = binary(x[i][0],nx,xsplit);
|
||||
iy = binary(x[i][1],ny,ysplit);
|
||||
iz = binary(x[i][2],nz,zsplit);
|
||||
proccount[iz*nx*ny + iy*nx + ix]++;
|
||||
}
|
||||
/* ----------------------------------------------------------------------
|
||||
calculate imbalance factor based on particle count or particle weights
|
||||
return max = max load per proc
|
||||
return imbalance = max load per proc / ave load per proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double Balance::imbalance_factor(double &maxcost)
|
||||
{
|
||||
double mycost,totalcost;
|
||||
|
||||
if (wtflag) {
|
||||
weight = fixstore->vstore;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
mycost = 0.0;
|
||||
for (int i = 0; i < nlocal; i++) mycost += weight[i];
|
||||
|
||||
} else mycost = atom->nlocal;
|
||||
|
||||
MPI_Allreduce(&mycost,&maxcost,1,MPI_DOUBLE,MPI_MAX,world);
|
||||
MPI_Allreduce(&mycost,&totalcost,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
MPI_Allreduce(proccount,allproccount,nprocs,MPI_INT,MPI_SUM,world);
|
||||
max = 0;
|
||||
for (int i = 0; i < nprocs; i++) max = MAX(max,allproccount[i]);
|
||||
double imbalance = 1.0;
|
||||
if (max) imbalance = max / (1.0 * atom->natoms / nprocs);
|
||||
if (maxcost > 0.0) imbalance = maxcost / (totalcost/nprocs);
|
||||
return imbalance;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform balancing via RCB class
|
||||
sortflag = flag for sorting order of received messages by proc ID
|
||||
return list of procs to send my atoms to
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int *Balance::bisection(int sortflag)
|
||||
@ -512,8 +641,11 @@ int *Balance::bisection(int sortflag)
|
||||
// invoke RCB
|
||||
// then invert() to create list of proc assignements for my atoms
|
||||
|
||||
//rcb->compute(dim,atom->nlocal,atom->x,NULL,boxlo,boxhi);
|
||||
rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
|
||||
if (wtflag) {
|
||||
weight = fixstore->vstore;
|
||||
rcb->compute(dim,atom->nlocal,atom->x,weight,shrinklo,shrinkhi);
|
||||
} else rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
|
||||
|
||||
rcb->invert(sortflag);
|
||||
|
||||
// reset RCB lo/hi bounding box to full simulation box as needed
|
||||
@ -530,9 +662,9 @@ int *Balance::bisection(int sortflag)
|
||||
|
||||
// store RCB cut, dim, lo/hi box in CommTiled
|
||||
// cut and lo/hi need to be in fractional form so can
|
||||
// OK if changes by epsilon from what RCB used since particles
|
||||
// OK if changes by epsilon from what RCB used since atoms
|
||||
// will subsequently migrate to new owning procs by exchange() anyway
|
||||
// ditto for particles exactly on lo/hi RCB box boundaries due to ties
|
||||
// ditto for atoms exactly on lo/hi RCB box boundaries due to ties
|
||||
|
||||
comm->rcbnew = 1;
|
||||
|
||||
@ -570,6 +702,9 @@ void Balance::shift_setup_static(char *str)
|
||||
{
|
||||
shift_allocate = 1;
|
||||
|
||||
memory->create(proccost,nprocs,"balance:proccost");
|
||||
memory->create(allproccost,nprocs,"balance:allproccost");
|
||||
|
||||
ndim = strlen(str);
|
||||
bdim = new int[ndim];
|
||||
|
||||
@ -582,14 +717,14 @@ void Balance::shift_setup_static(char *str)
|
||||
int max = MAX(comm->procgrid[0],comm->procgrid[1]);
|
||||
max = MAX(max,comm->procgrid[2]);
|
||||
|
||||
count = new bigint[max];
|
||||
onecount = new bigint[max];
|
||||
sum = new bigint[max+1];
|
||||
target = new bigint[max+1];
|
||||
onecost = new double[max];
|
||||
allcost = new double[max];
|
||||
sum = new double[max+1];
|
||||
target = new double[max+1];
|
||||
lo = new double[max+1];
|
||||
hi = new double[max+1];
|
||||
losum = new bigint[max+1];
|
||||
hisum = new bigint[max+1];
|
||||
losum = new double[max+1];
|
||||
hisum = new double[max+1];
|
||||
|
||||
// if current layout is TILED, set initial uniform splits in Comm
|
||||
// this gives starting point to subsequent shift balancing
|
||||
@ -632,6 +767,7 @@ void Balance::shift_setup(char *str, int nitermax_in, double thresh_in)
|
||||
int Balance::shift()
|
||||
{
|
||||
int i,j,k,m,np,max;
|
||||
double mycost,totalcost;
|
||||
double *split;
|
||||
|
||||
// no balancing if no atoms
|
||||
@ -661,24 +797,32 @@ int Balance::shift()
|
||||
else if (bdim[idim] == Z) split = comm->zsplit;
|
||||
else continue;
|
||||
|
||||
// intial count and sum
|
||||
// initial count and sum
|
||||
|
||||
np = procgrid[bdim[idim]];
|
||||
tally(bdim[idim],np,split);
|
||||
|
||||
// target[i] = desired sum at split I
|
||||
|
||||
for (i = 0; i < np; i++)
|
||||
target[i] = static_cast<int> (1.0*natoms/np * i + 0.5);
|
||||
target[np] = natoms;
|
||||
if (wtflag) {
|
||||
weight = fixstore->vstore;
|
||||
int nlocal = atom->nlocal;
|
||||
mycost = 0.0;
|
||||
for (i = 0; i < nlocal; i++) mycost += weight[i];
|
||||
} else mycost = atom->nlocal;
|
||||
|
||||
MPI_Allreduce(&mycost,&totalcost,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
for (i = 0; i < np; i++) target[i] = totalcost/np * i;
|
||||
target[np] = totalcost;
|
||||
|
||||
// lo[i] = closest split <= split[i] with a sum <= target
|
||||
// hi[i] = closest split >= split[i] with a sum >= target
|
||||
|
||||
lo[0] = hi[0] = 0.0;
|
||||
lo[np] = hi[np] = 1.0;
|
||||
losum[0] = hisum[0] = 0;
|
||||
losum[np] = hisum[np] = natoms;
|
||||
losum[0] = hisum[0] = 0.0;
|
||||
losum[np] = hisum[np] = totalcost;
|
||||
|
||||
for (i = 1; i < np; i++) {
|
||||
for (j = i; j >= 0; j--)
|
||||
@ -710,7 +854,7 @@ int Balance::shift()
|
||||
|
||||
#ifdef BALANCE_DEBUG
|
||||
if (me == 0) debug_shift_output(idim,m+1,np,split);
|
||||
if (outflag) dumpout(update->ntimestep,fp);
|
||||
if (outflag) dumpout(update->ntimestep);
|
||||
#endif
|
||||
|
||||
// stop if no change in splits, b/c all targets are met exactly
|
||||
@ -792,28 +936,36 @@ int Balance::shift()
|
||||
N = # of slices
|
||||
split = N+1 cuts between N slices
|
||||
return updated count = particles per slice
|
||||
retrun updated sum = cummulative count below each of N+1 splits
|
||||
return updated sum = cummulative count below each of N+1 splits
|
||||
use binary search to find which slice each atom is in
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Balance::tally(int dim, int n, double *split)
|
||||
{
|
||||
for (int i = 0; i < n; i++) onecount[i] = 0;
|
||||
for (int i = 0; i < n; i++) onecost[i] = 0.0;
|
||||
|
||||
double **x = atom->x;
|
||||
int nlocal = atom->nlocal;
|
||||
int index;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
index = binary(x[i][dim],n,split);
|
||||
onecount[index]++;
|
||||
if (wtflag) {
|
||||
weight = fixstore->vstore;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
index = binary(x[i][dim],n,split);
|
||||
onecost[index] += weight[i];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
index = binary(x[i][dim],n,split);
|
||||
onecost[index] += 1.0;
|
||||
}
|
||||
}
|
||||
|
||||
MPI_Allreduce(onecount,count,n,MPI_LMP_BIGINT,MPI_SUM,world);
|
||||
MPI_Allreduce(onecost,allcost,n,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
sum[0] = 0;
|
||||
sum[0] = 0.0;
|
||||
for (int i = 1; i < n+1; i++)
|
||||
sum[i] = sum[i-1] + count[i-1];
|
||||
sum[i] = sum[i-1] + allcost[i-1];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -875,6 +1027,63 @@ int Balance::adjust(int n, double *split)
|
||||
return change;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
calculate imbalance based on processor splits in 3 dims
|
||||
atoms must be in lamda coords (0-1) before called
|
||||
map particles to 3d grid of procs
|
||||
return maxcost = max load per proc
|
||||
return imbalance factor = max load per proc / ave load per proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double Balance::imbalance_splits(int &maxcost)
|
||||
{
|
||||
double *xsplit = comm->xsplit;
|
||||
double *ysplit = comm->ysplit;
|
||||
double *zsplit = comm->zsplit;
|
||||
|
||||
int nx = comm->procgrid[0];
|
||||
int ny = comm->procgrid[1];
|
||||
int nz = comm->procgrid[2];
|
||||
|
||||
for (int i = 0; i < nprocs; i++) proccost[i] = 0.0;
|
||||
|
||||
double **x = atom->x;
|
||||
int nlocal = atom->nlocal;
|
||||
int ix,iy,iz;
|
||||
|
||||
if (wtflag) {
|
||||
weight = fixstore->vstore;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
ix = binary(x[i][0],nx,xsplit);
|
||||
iy = binary(x[i][1],ny,ysplit);
|
||||
iz = binary(x[i][2],nz,zsplit);
|
||||
proccost[iz*nx*ny + iy*nx + ix] += weight[i];
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
ix = binary(x[i][0],nx,xsplit);
|
||||
iy = binary(x[i][1],ny,ysplit);
|
||||
iz = binary(x[i][2],nz,zsplit);
|
||||
proccost[iz*nx*ny + iy*nx + ix] += 1.0;
|
||||
}
|
||||
}
|
||||
|
||||
// one proc's particles may map to many partitions, so must Allreduce
|
||||
|
||||
MPI_Allreduce(proccost,allproccost,nprocs,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
maxcost = 0.0;
|
||||
double totalcost = 0.0;
|
||||
for (int i = 0; i < nprocs; i++) {
|
||||
maxcost = MAX(maxcost,allproccost[i]);
|
||||
totalcost += allproccost[i];
|
||||
}
|
||||
|
||||
double imbalance = 1.0;
|
||||
if (maxcost > 0.0) imbalance = maxcost / (totalcost/nprocs);
|
||||
return imbalance;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
binary search for where value falls in N-length vec
|
||||
note that vec actually has N+1 values, but ignore last one
|
||||
@ -917,7 +1126,7 @@ int Balance::binary(double value, int n, double *vec)
|
||||
NOTE: only implemented for orthogonal boxes, not triclinic
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Balance::dumpout(bigint tstep, FILE *fp)
|
||||
void Balance::dumpout(bigint tstep)
|
||||
{
|
||||
int dimension = domain->dimension;
|
||||
int triclinic = domain->triclinic;
|
||||
|
||||
@ -28,15 +28,23 @@ namespace LAMMPS_NS {
|
||||
class Balance : protected Pointers {
|
||||
public:
|
||||
class RCB *rcb;
|
||||
class FixStore *fixstore; // per-atom weights stored in FixStore
|
||||
int wtflag; // 1 if particle weighting is used
|
||||
int varflag; // 1 if weight style var(iable) is used
|
||||
int outflag; // 1 for output of balance results to file
|
||||
|
||||
Balance(class LAMMPS *);
|
||||
~Balance();
|
||||
void command(int, char **);
|
||||
void options(int, int, char **);
|
||||
void weight_storage(char *);
|
||||
void init_imbalance();
|
||||
void set_weights();
|
||||
double imbalance_factor(double &);
|
||||
void shift_setup(char *, int, double);
|
||||
int shift();
|
||||
int *bisection(int sortflag = 0);
|
||||
double imbalance_nlocal(int &);
|
||||
void dumpout(bigint, FILE *);
|
||||
void dumpout(bigint);
|
||||
|
||||
private:
|
||||
int me,nprocs;
|
||||
@ -53,20 +61,23 @@ class Balance : protected Pointers {
|
||||
int shift_allocate; // 1 if SHIFT vectors have been allocated
|
||||
int ndim; // length of balance string bstr
|
||||
int *bdim; // XYZ for each character in bstr
|
||||
bigint *count; // counts for slices in one dim
|
||||
bigint *onecount; // work vector of counts in one dim
|
||||
bigint *sum; // cummulative count for slices in one dim
|
||||
bigint *target; // target sum for slices in one dim
|
||||
double *onecost; // work vector of counts in one dim
|
||||
double *allcost; // counts for slices in one dim
|
||||
double *sum; // cummulative count for slices in one dim
|
||||
double *target; // target sum for slices in one dim
|
||||
double *lo,*hi; // lo/hi split coords that bound each target
|
||||
bigint *losum,*hisum; // cummulative counts at lo/hi coords
|
||||
double *losum,*hisum; // cummulative counts at lo/hi coords
|
||||
int rho; // 0 for geometric recursion
|
||||
// 1 for density weighted recursion
|
||||
|
||||
int *proccount; // particle count per processor
|
||||
int *allproccount;
|
||||
double *proccost; // particle cost per processor
|
||||
double *allproccost; // proccost summed across procs
|
||||
|
||||
int outflag; // for output of balance results to file
|
||||
FILE *fp;
|
||||
int nimbalance; // number of user-specified weight styles
|
||||
class Imbalance **imbalances; // list of Imb classes, one per weight style
|
||||
double *weight; // ptr to FixStore weight vector
|
||||
|
||||
FILE *fp; // balance output file
|
||||
int firststep;
|
||||
|
||||
double imbalance_splits(int &);
|
||||
|
||||
@ -23,6 +23,8 @@
|
||||
#include "irregular.h"
|
||||
#include "force.h"
|
||||
#include "kspace.h"
|
||||
#include "modify.h"
|
||||
#include "fix_store.h"
|
||||
#include "rcb.h"
|
||||
#include "error.h"
|
||||
|
||||
@ -35,7 +37,7 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg), fp(NULL)
|
||||
Fix(lmp, narg, arg), balance(NULL), irregular(NULL)
|
||||
{
|
||||
if (narg < 6) error->all(FLERR,"Illegal fix balance command");
|
||||
|
||||
@ -47,7 +49,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
extvector = 0;
|
||||
global_freq = 1;
|
||||
|
||||
// parse arguments
|
||||
// parse required arguments
|
||||
|
||||
int dimension = domain->dimension;
|
||||
|
||||
@ -62,7 +64,8 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
int iarg = 5;
|
||||
if (lbstyle == SHIFT) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix balance command");
|
||||
if (strlen(arg[iarg+1]) > 3) error->all(FLERR,"Illegal fix balance command");
|
||||
if (strlen(arg[iarg+1]) > 3)
|
||||
error->all(FLERR,"Illegal fix balance command");
|
||||
strcpy(bstr,arg[iarg+1]);
|
||||
nitermax = force->inumeric(FLERR,arg[iarg+2]);
|
||||
if (nitermax <= 0) error->all(FLERR,"Illegal fix balance command");
|
||||
@ -73,22 +76,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg++;
|
||||
}
|
||||
|
||||
// optional args
|
||||
|
||||
outflag = 0;
|
||||
int outarg = 0;
|
||||
fp = NULL;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"out") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix balance command");
|
||||
outflag = 1;
|
||||
outarg = iarg+1;
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal fix balance command");
|
||||
}
|
||||
|
||||
// error check
|
||||
// error checks
|
||||
|
||||
if (lbstyle == SHIFT) {
|
||||
int blen = strlen(bstr);
|
||||
@ -108,37 +96,35 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
// create instance of Balance class
|
||||
// if SHIFT, initialize it with params
|
||||
// process remaining optional args via Balance
|
||||
|
||||
balance = new Balance(lmp);
|
||||
if (lbstyle == SHIFT) balance->shift_setup(bstr,nitermax,thresh);
|
||||
balance->options(iarg,narg,arg);
|
||||
wtflag = balance->wtflag;
|
||||
|
||||
if (balance->varflag && nevery == 0)
|
||||
error->all(FLERR,"Fix balance nevery = 0 cannot be used with weight var");
|
||||
|
||||
// create instance of Irregular class
|
||||
|
||||
irregular = new Irregular(lmp);
|
||||
|
||||
// output file
|
||||
|
||||
if (outflag && comm->me == 0) {
|
||||
fp = fopen(arg[outarg],"w");
|
||||
if (fp == NULL) error->one(FLERR,"Cannot open fix balance output file");
|
||||
}
|
||||
|
||||
// only force reneighboring if nevery > 0
|
||||
|
||||
if (nevery) force_reneighbor = 1;
|
||||
|
||||
// compute initial outputs
|
||||
|
||||
imbfinal = imbprev = balance->imbalance_nlocal(maxperproc);
|
||||
itercount = 0;
|
||||
pending = 0;
|
||||
imbfinal = imbprev = maxloadperproc = 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixBalance::~FixBalance()
|
||||
{
|
||||
if (fp) fclose(fp);
|
||||
delete balance;
|
||||
delete irregular;
|
||||
}
|
||||
@ -155,10 +141,19 @@ int FixBalance::setmask()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixBalance::post_constructor()
|
||||
{
|
||||
if (wtflag) balance->weight_storage(id);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixBalance::init()
|
||||
{
|
||||
if (force->kspace) kspace_flag = 1;
|
||||
else kspace_flag = 0;
|
||||
|
||||
balance->init_imbalance();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -188,10 +183,11 @@ void FixBalance::setup_pre_exchange()
|
||||
|
||||
// perform a rebalance if threshhold exceeded
|
||||
|
||||
imbnow = balance->imbalance_nlocal(maxperproc);
|
||||
balance->set_weights();
|
||||
imbnow = balance->imbalance_factor(maxloadperproc);
|
||||
if (imbnow > thresh) rebalance();
|
||||
|
||||
// next_reneighbor = next time to force reneighboring
|
||||
// next timestep to rebalance
|
||||
|
||||
if (nevery) next_reneighbor = (update->ntimestep/nevery)*nevery + nevery;
|
||||
}
|
||||
@ -214,15 +210,15 @@ void FixBalance::pre_exchange()
|
||||
domain->reset_box();
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
||||
// return if imbalance < threshhold
|
||||
// perform a rebalance if threshhold exceeded
|
||||
// if weight variable is used, wrap weight setting in clear/add compute
|
||||
|
||||
imbnow = balance->imbalance_nlocal(maxperproc);
|
||||
if (imbnow <= thresh) {
|
||||
if (nevery) next_reneighbor = (update->ntimestep/nevery)*nevery + nevery;
|
||||
return;
|
||||
}
|
||||
if (balance->varflag) modify->clearstep_compute();
|
||||
balance->set_weights();
|
||||
if (balance->varflag) modify->addstep_compute(update->ntimestep + nevery);
|
||||
|
||||
rebalance();
|
||||
imbnow = balance->imbalance_factor(maxloadperproc);
|
||||
if (imbnow > thresh) rebalance();
|
||||
|
||||
// next timestep to rebalance
|
||||
|
||||
@ -237,7 +233,7 @@ void FixBalance::pre_exchange()
|
||||
void FixBalance::pre_neighbor()
|
||||
{
|
||||
if (!pending) return;
|
||||
imbfinal = balance->imbalance_nlocal(maxperproc);
|
||||
imbfinal = balance->imbalance_factor(maxloadperproc);
|
||||
pending = 0;
|
||||
}
|
||||
|
||||
@ -262,7 +258,7 @@ void FixBalance::rebalance()
|
||||
|
||||
// output of new decomposition
|
||||
|
||||
if (outflag) balance->dumpout(update->ntimestep,fp);
|
||||
if (balance->outflag) balance->dumpout(update->ntimestep);
|
||||
|
||||
// reset proc sub-domains
|
||||
// check and warn if any proc's subbox is smaller than neigh skin
|
||||
@ -277,8 +273,10 @@ void FixBalance::rebalance()
|
||||
// else allow caller's comm->exchange() to do it
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
if (wtflag) balance->fixstore->disable = 0;
|
||||
if (lbstyle == BISECTION) irregular->migrate_atoms(0,1,sendproc);
|
||||
else if (irregular->migrate_check()) irregular->migrate_atoms();
|
||||
if (wtflag) balance->fixstore->disable = 1;
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
||||
// invoke KSpace setup_grid() to adjust to new proc sub-domains
|
||||
@ -306,7 +304,7 @@ double FixBalance::compute_scalar()
|
||||
|
||||
double FixBalance::compute_vector(int i)
|
||||
{
|
||||
if (i == 0) return (double) maxperproc;
|
||||
if (i == 0) return maxloadperproc;
|
||||
if (i == 1) return (double) itercount;
|
||||
return imbprev;
|
||||
}
|
||||
|
||||
@ -30,6 +30,7 @@ class FixBalance : public Fix {
|
||||
FixBalance(class LAMMPS *, int, char **);
|
||||
~FixBalance();
|
||||
int setmask();
|
||||
void post_constructor();
|
||||
void init();
|
||||
void setup(int);
|
||||
void setup_pre_exchange();
|
||||
@ -40,15 +41,15 @@ class FixBalance : public Fix {
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int nevery,lbstyle,nitermax,outflag;
|
||||
int nevery,lbstyle,nitermax;
|
||||
double thresh,stopthresh;
|
||||
char bstr[4];
|
||||
FILE *fp;
|
||||
int wtflag; // 1 for weighted balancing
|
||||
|
||||
double imbnow; // current imbalance factor
|
||||
double imbprev; // imbalance factor before last rebalancing
|
||||
double imbfinal; // imbalance factor after last rebalancing
|
||||
int maxperproc; // max atoms on any processor
|
||||
double maxloadperproc; // max load on any processor
|
||||
int itercount; // iteration count of last call to Balance
|
||||
int kspace_flag; // 1 if KSpace solver defined
|
||||
int pending;
|
||||
|
||||
20
src/imbalance.cpp
Normal file
20
src/imbalance.cpp
Normal file
@ -0,0 +1,20 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "imbalance.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Imbalance::Imbalance(LAMMPS *lmp) : Pointers(lmp) {}
|
||||
45
src/imbalance.h
Normal file
45
src/imbalance.h
Normal file
@ -0,0 +1,45 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_IMBALANCE_H
|
||||
#define LMP_IMBALANCE_H
|
||||
|
||||
#include <stdio.h>
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class Imbalance : protected Pointers {
|
||||
public:
|
||||
Imbalance(class LAMMPS *);
|
||||
virtual ~Imbalance() {};
|
||||
|
||||
// parse options. return number of arguments consumed (required)
|
||||
virtual int options(int narg, char **arg) = 0;
|
||||
// reinitialize internal data (needed for fix balance) (optional)
|
||||
virtual void init() {};
|
||||
// compute and apply weight factors to local atom array (required)
|
||||
virtual void compute(double *weights) = 0;
|
||||
// print information about the state of this imbalance compute (required)
|
||||
virtual void info(FILE *fp) = 0;
|
||||
|
||||
// disallow default and copy constructor, assignment operator
|
||||
// private:
|
||||
//Imbalance() {};
|
||||
//Imbalance(const Imbalance &) {};
|
||||
//Imbalance &operator=(const Imbalance &) {return *this;};
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
89
src/imbalance_group.cpp
Normal file
89
src/imbalance_group.cpp
Normal file
@ -0,0 +1,89 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "imbalance_group.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "group.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceGroup::ImbalanceGroup(LAMMPS *lmp) : Imbalance(lmp), id(0), factor(0)
|
||||
{}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceGroup::~ImbalanceGroup()
|
||||
{
|
||||
delete [] id;
|
||||
delete [] factor;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
int ImbalanceGroup::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 3) error->all(FLERR,"Illegal balance weight command");
|
||||
|
||||
num = force->inumeric(FLERR,arg[0]);
|
||||
if (num < 1) error->all(FLERR,"Illegal balance weight command");
|
||||
if (2*num+1 > narg) error->all(FLERR,"Illegal balance weight command");
|
||||
|
||||
id = new int[num];
|
||||
factor = new double[num];
|
||||
for (int i = 0; i < num; ++i) {
|
||||
id[i] = group->find(arg[2*i+1]);
|
||||
if (id[i] < 0)
|
||||
error->all(FLERR,"Unknown group in balance weight command");
|
||||
factor[i] = force->numeric(FLERR,arg[2*i+2]);
|
||||
}
|
||||
return 2*num+1;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceGroup::compute(double *weight)
|
||||
{
|
||||
const int * const mask = atom->mask;
|
||||
const int * const bitmask = group->bitmask;
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
if (num == 0) return;
|
||||
|
||||
for (int i = 0; i < nlocal; ++i) {
|
||||
const int imask = mask[i];
|
||||
double iweight = weight[i];
|
||||
for (int j = 0; j < num; ++j) {
|
||||
if (imask & bitmask[id[j]])
|
||||
iweight *= factor[j];
|
||||
}
|
||||
weight[i] = iweight;
|
||||
}
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceGroup::info(FILE *fp)
|
||||
{
|
||||
if (num > 0) {
|
||||
const char * const * const names = group->names;
|
||||
|
||||
fprintf(fp," group weights:");
|
||||
for (int i = 0; i < num; ++i)
|
||||
fprintf(fp," %s=%g",names[id[i]],factor[i]);
|
||||
fputs("\n",fp);
|
||||
}
|
||||
}
|
||||
41
src/imbalance_group.h
Normal file
41
src/imbalance_group.h
Normal file
@ -0,0 +1,41 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_IMBALANCE_GROUP_H
|
||||
#define LMP_IMBALANCE_GROUP_H
|
||||
|
||||
#include "imbalance.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ImbalanceGroup : public Imbalance {
|
||||
public:
|
||||
ImbalanceGroup(class LAMMPS *);
|
||||
virtual ~ImbalanceGroup();
|
||||
|
||||
// parse options, return number of arguments consumed
|
||||
virtual int options(int, char **);
|
||||
// compute and apply weight factors to local atom array
|
||||
virtual void compute(double *);
|
||||
// print information about the state of this imbalance compute
|
||||
virtual void info(FILE *);
|
||||
|
||||
private:
|
||||
int num; // number of groups with weights
|
||||
int *id; // numerical IDs of groups
|
||||
double *factor; // group weight factors
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
102
src/imbalance_neigh.cpp
Normal file
102
src/imbalance_neigh.cpp
Normal file
@ -0,0 +1,102 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
#include "imbalance_neigh.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_request.h"
|
||||
#include "neigh_list.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceNeigh::ImbalanceNeigh(LAMMPS *lmp) : Imbalance(lmp)
|
||||
{
|
||||
did_warn = 0;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
int ImbalanceNeigh::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1) error->all(FLERR,"Illegal balance weight command");
|
||||
factor = force->numeric(FLERR,arg[0]);
|
||||
if (factor < 0.0) error->all(FLERR,"Illegal balance weight command");
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceNeigh::compute(double *weight)
|
||||
{
|
||||
int req;
|
||||
|
||||
if (factor == 0.0) return;
|
||||
|
||||
// find suitable neighbor list
|
||||
// we can only make use of certain (conventional) neighbor lists
|
||||
|
||||
for (req = 0; req < neighbor->old_nrequest; ++req) {
|
||||
if ((neighbor->old_requests[req]->half ||
|
||||
neighbor->old_requests[req]->gran ||
|
||||
neighbor->old_requests[req]->respaouter ||
|
||||
neighbor->old_requests[req]->half_from_full) &&
|
||||
neighbor->old_requests[req]->skip == 0 &&
|
||||
neighbor->lists[req] && neighbor->lists[req]->numneigh) break;
|
||||
}
|
||||
|
||||
if (req >= neighbor->old_nrequest || neighbor->ago < 0) {
|
||||
if (comm->me == 0 && !did_warn)
|
||||
error->warning(FLERR,"No suitable neighbor list found. "
|
||||
"Neighbor weighted balancing skipped");
|
||||
did_warn = 1;
|
||||
return;
|
||||
}
|
||||
|
||||
NeighList *list = neighbor->lists[req];
|
||||
bigint neighsum = 0;
|
||||
|
||||
const int inum = list->inum;
|
||||
const int * const ilist = list->ilist;
|
||||
const int * const numneigh = list->numneigh;
|
||||
|
||||
// first pass: get local number of neighbors
|
||||
|
||||
for (int i = 0; i < inum; ++i) neighsum += numneigh[ilist[i]];
|
||||
|
||||
double allatoms = static_cast <double>(atom->natoms);
|
||||
if (allatoms == 0.0) allatoms = 1.0;
|
||||
double allavg;
|
||||
double myavg = static_cast<double>(neighsum)/allatoms;
|
||||
MPI_Allreduce(&myavg,&allavg,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// second pass: compute and apply weights
|
||||
|
||||
double scale = 1.0/allavg;
|
||||
for (int ii = 0; ii < inum; ++ii) {
|
||||
const int i = ilist[ii];
|
||||
weight[i] *= (1.0-factor) + factor*scale*numneigh[i];
|
||||
}
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceNeigh::info(FILE *fp)
|
||||
{
|
||||
fprintf(fp," neigh weight factor: %g\n",factor);
|
||||
}
|
||||
41
src/imbalance_neigh.h
Normal file
41
src/imbalance_neigh.h
Normal file
@ -0,0 +1,41 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_IMBALANCE_NEIGH_H
|
||||
#define LMP_IMBALANCE_NEIGH_H
|
||||
|
||||
#include "imbalance.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ImbalanceNeigh : public Imbalance {
|
||||
public:
|
||||
ImbalanceNeigh(class LAMMPS *);
|
||||
virtual ~ImbalanceNeigh() {}
|
||||
|
||||
public:
|
||||
// parse options, return number of arguments consumed
|
||||
virtual int options(int, char **);
|
||||
// compute and apply weight factors to local atom array
|
||||
virtual void compute(double *);
|
||||
// print information about the state of this imbalance compute
|
||||
virtual void info(FILE *);
|
||||
|
||||
private:
|
||||
double factor; // weight factor for neighbor imbalance
|
||||
int did_warn; // 1 if warned about no suitable neighbor list
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
69
src/imbalance_store.cpp
Normal file
69
src/imbalance_store.cpp
Normal file
@ -0,0 +1,69 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <string.h>
|
||||
#include "imbalance_store.h"
|
||||
#include "atom.h"
|
||||
#include "input.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceStore::ImbalanceStore(LAMMPS *lmp) : Imbalance(lmp), name(0) {}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceStore::~ImbalanceStore()
|
||||
{
|
||||
delete [] name;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
int ImbalanceStore::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1) error->all(FLERR,"Illegal balance weight command");
|
||||
|
||||
int len = strlen(arg[0]) + 1;
|
||||
name = new char[len];
|
||||
memcpy(name,arg[0],len);
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceStore::compute(double *weight)
|
||||
{
|
||||
int dflag = 0;
|
||||
int idx = atom->find_custom(name,dflag);
|
||||
|
||||
// property does not exist
|
||||
|
||||
if (idx < 0 || dflag != 1) return;
|
||||
|
||||
double *prop = atom->dvector[idx];
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; ++i)
|
||||
prop[i] = weight[i];
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceStore::info(FILE *fp)
|
||||
{
|
||||
fprintf(fp," storing weight in atom property d_%s\n",name);
|
||||
}
|
||||
40
src/imbalance_store.h
Normal file
40
src/imbalance_store.h
Normal file
@ -0,0 +1,40 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_IMBALANCE_STORE_H
|
||||
#define LMP_IMBALANCE_STORE_H
|
||||
|
||||
#include "imbalance.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ImbalanceStore : public Imbalance {
|
||||
public:
|
||||
ImbalanceStore(class LAMMPS *);
|
||||
virtual ~ImbalanceStore();
|
||||
|
||||
public:
|
||||
// parse options, return number of arguments consumed
|
||||
virtual int options(int, char **);
|
||||
// compute per-atom imbalance and apply to weight array
|
||||
virtual void compute(double *);
|
||||
// print information about the state of this imbalance compute (required)
|
||||
virtual void info(FILE *);
|
||||
|
||||
private:
|
||||
char *name; // property name
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
86
src/imbalance_time.cpp
Normal file
86
src/imbalance_time.cpp
Normal file
@ -0,0 +1,86 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
#include "imbalance_time.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "timer.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceTime::ImbalanceTime(LAMMPS *lmp) : Imbalance(lmp) {}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
int ImbalanceTime::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1) error->all(FLERR,"Illegal balance weight command");
|
||||
factor = force->numeric(FLERR,arg[0]);
|
||||
if (factor < 0.0) error->all(FLERR,"Illegal balance weight command");
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reset last, needed for fix balance caller
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceTime::init()
|
||||
{
|
||||
last = 0.0;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceTime::compute(double *weight)
|
||||
{
|
||||
const int nlocal = atom->nlocal;
|
||||
const bigint natoms = atom->natoms;
|
||||
|
||||
if (factor == 0.0) return;
|
||||
|
||||
// compute the cost function of based on relevant timers
|
||||
|
||||
if (timer->has_normal()) {
|
||||
double cost = -last;
|
||||
cost += timer->get_wall(Timer::PAIR);
|
||||
cost += timer->get_wall(Timer::NEIGH);
|
||||
cost += timer->get_wall(Timer::BOND);
|
||||
cost += timer->get_wall(Timer::KSPACE);
|
||||
|
||||
double allcost;
|
||||
MPI_Allreduce(&cost,&allcost,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
if ((allcost > 0.0) && (nlocal > 0)) {
|
||||
const double avgcost = allcost/natoms;
|
||||
const double localcost = cost/nlocal;
|
||||
const double scale = (1.0-factor) + factor*localcost/avgcost;
|
||||
for (int i = 0; i < nlocal; ++i) weight[i] *= scale;
|
||||
}
|
||||
|
||||
// record time up to this point
|
||||
|
||||
last += cost;
|
||||
}
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceTime::info(FILE *fp)
|
||||
{
|
||||
fprintf(fp," time weight factor: %g\n",factor);
|
||||
}
|
||||
43
src/imbalance_time.h
Normal file
43
src/imbalance_time.h
Normal file
@ -0,0 +1,43 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_IMBALANCE_TIME_H
|
||||
#define LMP_IMBALANCE_TIME_H
|
||||
|
||||
#include "imbalance.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ImbalanceTime : public Imbalance {
|
||||
public:
|
||||
ImbalanceTime(class LAMMPS *);
|
||||
virtual ~ImbalanceTime() {}
|
||||
|
||||
public:
|
||||
// parse options, return number of arguments consumed
|
||||
virtual int options(int, char **);
|
||||
// reinitialize internal data
|
||||
virtual void init();
|
||||
// compute and apply weight factors to local atom array
|
||||
virtual void compute(double *);
|
||||
// print information about the state of this imbalance compute
|
||||
virtual void info(FILE *);
|
||||
|
||||
private:
|
||||
double factor; // weight factor for time imbalance
|
||||
double last; // combined wall time from last call
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
88
src/imbalance_var.cpp
Normal file
88
src/imbalance_var.cpp
Normal file
@ -0,0 +1,88 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <string.h>
|
||||
#include "imbalance_var.h"
|
||||
#include "atom.h"
|
||||
#include "group.h"
|
||||
#include "input.h"
|
||||
#include "variable.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
// DEBUG
|
||||
#include "update.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceVar::ImbalanceVar(LAMMPS *lmp) : Imbalance(lmp), name(0) {}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
ImbalanceVar::~ImbalanceVar()
|
||||
{
|
||||
delete [] name;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
int ImbalanceVar::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1) error->all(FLERR,"Illegal balance weight command");
|
||||
|
||||
int len = strlen(arg[0]) + 1;
|
||||
name = new char[len];
|
||||
memcpy(name,arg[0],len);
|
||||
init();
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceVar::init()
|
||||
{
|
||||
id = input->variable->find(name);
|
||||
if (id < 0) {
|
||||
error->all(FLERR,"Variable name for balance weight does not exist");
|
||||
} else {
|
||||
if (input->variable->atomstyle(id) == 0)
|
||||
error->all(FLERR,"Variable for balance weight has invalid style");
|
||||
}
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceVar::compute(double *weight)
|
||||
{
|
||||
const int all = group->find("all");
|
||||
if (all < 0) return;
|
||||
|
||||
double *values;
|
||||
const int nlocal = atom->nlocal;
|
||||
memory->create(values,nlocal,"imbalance:values");
|
||||
|
||||
input->variable->compute_atom(id,all,values,1,0);
|
||||
for (int i = 0; i < nlocal; ++i) weight[i] *= values[i];
|
||||
|
||||
memory->destroy(values);
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------- */
|
||||
|
||||
void ImbalanceVar::info(FILE *fp)
|
||||
{
|
||||
fprintf(fp," weight variable: %s\n",name);
|
||||
}
|
||||
43
src/imbalance_var.h
Normal file
43
src/imbalance_var.h
Normal file
@ -0,0 +1,43 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_IMBALANCE_VAR_H
|
||||
#define LMP_IMBALANCE_VAR_H
|
||||
|
||||
#include "imbalance.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ImbalanceVar : public Imbalance {
|
||||
public:
|
||||
ImbalanceVar(class LAMMPS *);
|
||||
virtual ~ImbalanceVar();
|
||||
|
||||
public:
|
||||
// parse options. return number of arguments consumed.
|
||||
virtual int options(int, char **);
|
||||
// re-initialize internal data, e.g. variable ID
|
||||
virtual void init();
|
||||
// compute per-atom imbalance and apply to weight array
|
||||
virtual void compute(double *);
|
||||
// print information about the state of this imbalance compute (required)
|
||||
virtual void info(FILE *);
|
||||
|
||||
private:
|
||||
char *name; // variable name
|
||||
int id; // variable index
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "26 Sep 2016"
|
||||
#define LAMMPS_VERSION "28 Sep 2016"
|
||||
|
||||
Reference in New Issue
Block a user