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doc/src/balance.txt
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@ -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 +58,41 @@ 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 weight to each processor, which typically
means a different number of particles per processor. Details on the
various weighting options 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 +105,9 @@ 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 +135,7 @@ 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 +161,11 @@ 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 +173,8 @@ 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 +257,7 @@ 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 +289,129 @@ 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 +477,7 @@ 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

99
doc/src/fix_balance.txt
View File

@ -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 +61,31 @@ 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 weight to each processor, which typically means a
different number of atoms per 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. The 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 +98,9 @@ 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 +151,8 @@ 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 +173,9 @@ 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 +256,7 @@ 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 +281,10 @@ 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 +352,8 @@ 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 +367,11 @@ 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

16
doc/src/neb.txt
View File

@ -48,14 +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.
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: The current NEB implementation in LAMMPS only allows there to be
one processor per replica.

56
doc/src/prd.txt
View File

@ -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