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undo changes to PRD doc from another branch

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Steve Plimpton 2018-10-11 08:28:10 -06:00
parent 36a1ca7e72
commit d1f260a765
1 changed files with 18 additions and 32 deletions
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doc/src/prd.txt
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@ -48,12 +48,11 @@ replicas of a system. One or more replicas can be used. The total
number of steps {N} to run can be interpreted in one of two ways; see
discussion of the {time} keyword below.
PRD is described in "(Voter1998)"_#Voter1998 by Art Voter. Similar to
global or local hyperdynamics (HD), PRD is a method for performing
accelerated dynamics that is suitable for infrequent-event systems
that obey first-order kinetics. A good overview of accelerated
dynamics methods for such systems in given in this review paper
"(Voter2002)"_#Voter2002prd from Art's group. To quote from the
PRD is described in "this paper"_#Voter1998 by Art Voter. It is a method
for performing accelerated dynamics that is suitable for
infrequent-event systems that obey first-order kinetics. A good
overview of accelerated dynamics methods for such systems in given in
"this review paper"_#Voter2002prd from the same group. To quote from the
paper: "The dynamical evolution is characterized by vibrational
excursions within a potential basin, punctuated by occasional
transitions between basins." The transition probability is
@ -62,27 +61,15 @@ Running multiple replicas gives an effective enhancement in the
timescale spanned by the multiple simulations, while waiting for an
event to occur.
Both PRD and HD produce a time-accurate trajectory that effectively
extends the timescale over which a system can be simulated, but they
do it differently. PRD creates Nr replicas of the system and runs
dynamics on each independently with a normal unbiased potential until
an event occurs in one of the replicas. The time between events is
reduced by a factor of Nr replicas. HD uses a single replica of the
system and accelerates time by biasing the interaction potential in a
manner such that each timestep is effectively longer. For both
methods, per wall-clock second, more physical time elapses and more
events occur. See the "hyper"_hyper.html doc page for more info about
HD.
In PRD, each replica runs on a partition of one or more processors.
Processor partitions are defined at run-time using the "-partition
command-line switch"_Run_options.html. 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 the "Howto replica"_Howto_replica.html doc
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the "-partition command-line
switch"_Run_options.html. 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 the "Howto replica"_Howto_replica.html doc
page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is
@ -91,8 +78,8 @@ I.e. the simulation domain, the number of atoms, the interaction
potentials, etc should be the same for every replica.
A PRD run has several stages, which are repeated each time an "event"
occurs in one of the replicas, as explained below. The logic for a
PRD run is as follows:
occurs in one of the replicas, as defined below. The logic for a PRD
run is as follows:
while (time remains):
dephase for n_dephase*t_dephase steps
@ -142,8 +129,7 @@ Minimization parameters may be set via the
PRD command. The latter are the settings that would be used with the
"minimize"_minimize.html command. Note that typically, you do not
need to perform a highly-converged minimization to detect a transition
event, though you may need to in order to prevent a set of atoms in
the system from relaxing to a saddle point.
event.
The event check is performed by a compute with the specified
{compute-ID}. Currently there is only one compute that works with the
@ -321,7 +307,7 @@ deposit"_fix_deposit.html.
"min_modify"_min_modify.html, "min_style"_min_style.html,
"run_style"_run_style.html, "minimize"_minimize.html,
"velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html,
"tad"_tad.html, "hyper"_hyper.html
"tad"_tad.html
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