jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

changes to prd command doc page

This commit is contained in:
Steve Plimpton 2018-10-11 08:29:25 -06:00
parent 265c11dca9
commit 56598fcd0b
1 changed files with 32 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

50
doc/src/prd.txt
View File

@ -48,11 +48,12 @@ 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 number of steps {N} to run can be interpreted in one of two ways; see
discussion of the {time} keyword below. discussion of the {time} keyword below.
PRD is described in "this paper"_#Voter1998 by Art Voter. It is a method PRD is described in "(Voter1998)"_#Voter1998 by Art Voter. Similar to
for performing accelerated dynamics that is suitable for global or local hyperdynamics (HD), PRD is a method for performing
infrequent-event systems that obey first-order kinetics. A good accelerated dynamics that is suitable for infrequent-event systems
overview of accelerated dynamics methods for such systems in given in that obey first-order kinetics. A good overview of accelerated
"this review paper"_#Voter2002prd from the same group. To quote from the 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 paper: "The dynamical evolution is characterized by vibrational
excursions within a potential basin, punctuated by occasional excursions within a potential basin, punctuated by occasional
transitions between basins." The transition probability is transitions between basins." The transition probability is
@ -61,15 +62,27 @@ Running multiple replicas gives an effective enhancement in the
timescale spanned by the multiple simulations, while waiting for an timescale spanned by the multiple simulations, while waiting for an
event to occur. event to occur.
Each replica runs on a partition of one or more processors. Processor Both PRD and HD produce a time-accurate trajectory that effectively
partitions are defined at run-time using the "-partition command-line extends the timescale over which a system can be simulated, but they
switch"_Run_options.html. Note that if you have MPI installed, you do it differently. PRD creates Nr replicas of the system and runs
can run a multi-replica simulation with more replicas (partitions) dynamics on each independently with a normal unbiased potential until
than you have physical processors, e.g you can run a 10-replica an event occurs in one of the replicas. The time between events is
simulation on one or two processors. However for PRD, this makes reduced by a factor of Nr replicas. HD uses a single replica of the
little sense, since running a replica on virtual instead of physical system and accelerates time by biasing the interaction potential in a
processors,offers no effective parallel speed-up in searching for manner such that each timestep is effectively longer. For both
infrequent events. See the "Howto replica"_Howto_replica.html doc 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. page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is When a PRD simulation is performed, it is assumed that each replica is
@ -78,8 +91,8 @@ I.e. the simulation domain, the number of atoms, the interaction
potentials, etc should be the same for every replica. potentials, etc should be the same for every replica.
A PRD run has several stages, which are repeated each time an "event" 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 occurs in one of the replicas, as explained below. The logic for a
run is as follows: PRD run is as follows:
while (time remains): while (time remains):
dephase for n_dephase*t_dephase steps dephase for n_dephase*t_dephase steps
@ -129,7 +142,8 @@ Minimization parameters may be set via the
PRD command. The latter are the settings that would be used with the PRD command. The latter are the settings that would be used with the
"minimize"_minimize.html command. Note that typically, you do not "minimize"_minimize.html command. Note that typically, you do not
need to perform a highly-converged minimization to detect a transition 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 The event check is performed by a compute with the specified
{compute-ID}. Currently there is only one compute that works with the {compute-ID}. Currently there is only one compute that works with the
@ -307,7 +321,7 @@ deposit"_fix_deposit.html.
"min_modify"_min_modify.html, "min_style"_min_style.html, "min_modify"_min_modify.html, "min_style"_min_style.html,
"run_style"_run_style.html, "minimize"_minimize.html, "run_style"_run_style.html, "minimize"_minimize.html,
"velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html, "velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html,
"tad"_tad.html "tad"_tad.html, "hyper"_hyper.html
[Default:] [Default:]