changes to prd command doc page

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 "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

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

paper: "The dynamical evolution is characterized by vibrational

excursions within a potential basin, punctuated by occasional

transitions between basins."  The transition probability is

timescale spanned by the multiple simulations, while waiting for an

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"_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

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

page for further discussion.

When a PRD simulation is performed, it is assumed that each replica is

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 defined below.  The logic for a PRD

run is as follows:

occurs in one of the replicas, as explained below.  The logic for a

PRD run is as follows:

while (time remains):

  dephase for n_dephase*t_dephase steps

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.

event, though you may need to in order to prevent a set of atoms in

the system from relaxing to a saddle point.

The event check is performed by a compute with the specified

{compute-ID}.  Currently there is only one compute that works with the

"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

"tad"_tad.html, "hyper"_hyper.html

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