2009-10-30 06:41:53 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>prd command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
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</PRE>
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<UL><LI>N = # of timesteps to run (not including dephasing/quenching)
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<LI>t_event = timestep interval between event checks
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<LI>n_dephase = number of velocity randomizations to perform in each dephase run
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<LI>t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase
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<LI>t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated
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<LI>compute-ID = ID of the compute used for event detection
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<LI>random_seed = random # seed (positive integer)
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>min</I> or <I>temp</I> or <I>vel</I>
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<PRE> <I>min</I> values = etol ftol maxiter maxeval
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etol = stopping tolerance for energy, used in quenching
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ftol = stopping tolerance for force, used in quenching
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maxiter = max iterations of minimize, used in quenching
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maxeval = max number of force/energy evaluations, used in quenching
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<I>temp</I> value = Tdephase
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Tdephase = target temperature for velocity randomization, used in dephasing
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<I>vel</I> values = loop dist
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loop = <I>all</I> or <I>local</I> or <I>geom</I>, used in dephasing
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dist = <I>uniform</I> or <I>gaussian</I>, used in dephasing
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>prd 5000 100 10 10 100 1 54982
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2010-01-29 05:25:54 +08:00
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prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Run a parallel replica dynamics (PRD) simulation using multiple
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replicas of a system. One or more replicas can be used.
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</P>
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<P>PRD is described in <A HREF = "#Voter">this paper</A> by Art Voter. It is a method
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for performing accelerated dynamics that is suitable for
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infrequent-event systems that obey first-order kinetics. A good
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overview of accelerated dynamics methods for such systems in given in
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<A HREF = "#Voter2">this review paper</A> from the same group. To quote from the
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paper: "The dynamical evolution is characterized by vibrational
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excursions within a potential basin, punctuated by occasional
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transitions between basins." The transition probability is
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characterized by p(t) = k*exp(-kt) where k is the rate constant.
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Running multiple replicas gives an effective enhancement in the
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timescale spanned by the multiple simulations, while waiting for an
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event to occur.
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</P>
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<P>Each replica runs on a partition of one or more processors. Processor
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partitions are defined at run-time using the -partition command-line
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switch; see <A HREF = "Section_start.html#start_7">Section_start 6</A> of the
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2011-12-14 04:43:36 +08:00
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manual. Note that if you have MPI installed, you can run a
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multi-replica simulation with more replicas (partitions) than you have
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physical processors, e.g you can run a 10-replica simulation on one or
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two processors. For PRD, this makes little sense, since this offers
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no effective parallel speed-up in searching for infrequent events. See
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<A HREF = "Section_howto.html#howto_5">Section_howto 5</A> of the manual for further
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2011-08-26 00:46:23 +08:00
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discussion.
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</P>
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<P>When a PRD simulation is performed, it is assumed that each replica is
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2009-11-03 01:38:32 +08:00
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running the same model, though LAMMPS does not check for this.
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I.e. the simulation domain, the number of atoms, the interaction
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potentials, etc should be the same for every replica.
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</P>
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<P>A PRD run has several stages, which are repeated each time an "event"
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occurs in one of the replicas, as defined below. The logic for a PRD
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run is as follows:
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</P>
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<PRE>while (time remains):
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dephase for n_dephase*t_dephase steps
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until (event occurs on some replica):
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run dynamics for t_event steps
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quench
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2009-10-31 02:26:17 +08:00
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check for uncorrelated event on any replica
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until (no correlated event occurs):
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run dynamics for t_correlate steps
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quench
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check for correlated event on this replica
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event replica shares state with all replicas
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</PRE>
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<P>Before this loop begins, the state of the system on replica 0 is
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shared with all replicas, so that all replicas begin from the same
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2009-11-03 01:38:32 +08:00
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initial state. The first potential energy basin is identified by
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quenching (an energy minimization, see below) the initial state and
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storing the resulting coordinates for reference.
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</P>
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<P>In the first stage, dephasing is performed by each replica
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independently to eliminate correlations between replicas. This is
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done by choosing a random set of velocities, based on the
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<I>random_seed</I> that is specified, and running <I>t_dephase</I> timesteps of
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dynamics. This is repeated <I>n_dephase</I> times. If the <I>temp</I> keyword
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is not specified, the target temperature for velocity randomization
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2010-02-09 06:34:21 +08:00
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for each replica is the current temperature of that replica.
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Otherwise, it is the specified <I>Tdephase</I> temperature. The style of
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velocity randomization is controlled using the keyword <I>vel</I> with
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arguments that have the same meaning as their counterparts in the
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<A HREF = "velocity.html">velocity</A> command.
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</P>
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<P>In the second stage, each replica runs dynamics continuously, stopping
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every <I>t_event</I> steps to check if a transition event has occurred.
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This check is performed by quenching the system and comparing the
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resulting atom coordinates to the coordinates from the previous basin.
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The first time through the PRD loop, the "previous basin" is the set
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of quenched coordinates from the initial state of the system.
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</P>
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<P>A quench is an energy minimization and is performed by whichever
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algorithm has been defined by the <A HREF = "min_style.html">min_style</A> command.
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Minimization parameters may be set via the
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<A HREF = "min_modify.html">min_modify</A> command and by the <I>min</I> keyword of the
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PRD command. The latter are the settings that would be used with the
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<A HREF = "minimize.html">minimize</A> command. Note that typically, you do not
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need to perform a highly-converged minimization to detect a transition
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event.
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</P>
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<P>The event check is performed by a compute with the specified
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<I>compute-ID</I>. Currently there is only one compute that works with the
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PRD commmand, which is the <A HREF = "compute_event_displace.html">compute
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event/displace</A> command. Other
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event-checking computes may be added. <A HREF = "compute_event_displace.html">Compute
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event/displace</A> checks whether any atom in
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the compute group has moved further than a specified threshold
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distance. If so, an "event" has occurred.
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</P>
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<P>In the third stage, the replica on which the event occurred (event
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replica) continues to run dynamics to search for correlated events.
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This is done by running dynamics for <I>t_correlate</I> steps, quenching
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every <I>t_event</I> steps, and checking if another event has occurred.
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The first time no correlated event occurs, the final state of the
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event replica is shared with all replicas, the new basin reference
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coordinates are updated with the quenched state, and the outer loop
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begins again. While the replica event is searching for correlated
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events, all the other replicas also run dynamics and event checking
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with the same schedule, but the final states are always overwritten by
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the state of the event replica.
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</P>
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<HR>
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<P>Four kinds of output can be generated during a PRD run: event
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statistics, thermodynamic output by each replica, dump files, and
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restart files.
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</P>
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<P>When running with multiple partitions (each of which is a replica in
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this case), the print-out to the screen and master log.lammps file is
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limited to event statistics. Note that if a PRD run is performed on
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only a single replica then the event statistics will be intermixed
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with the usual thermodynamic output discussed below.
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</P>
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<P>The quantities printed each time an event occurs are the timestep,
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CPU time, clock, event number, a correlation flag,
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the number of coincident events, and the replica number of the chosen event.
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</P>
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<P>The timestep is the usual LAMMPS timestep, except that time does not
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advance during dephasing or quenches, but only during dynamics. Note
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that are two kinds of dynamics in the PRD loop listed above. The
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first is when all replicas are performing independent dynamics. The
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second is when correlated events are being searched for and only one
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replica is running dynamics.
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</P>
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<P>The CPU time is the total processor time since the start of the PRD
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run.
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</P>
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<P>The clock is the same as the timestep except that it advances by M
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steps every timestep during the first kind of dynamics when the M
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replicas are running independently. The clock represents the real
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time that effectively elapses during a PRD simulation of <I>N</I> steps on
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M replicas. If most of the PRD run is spent in the second stage of
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the loop above, searching for infrequent events, then the clock will
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advance nearly N*M steps. Note the clock time between events will be
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drawn from p(t).
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</P>
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<P>The event number is a counter that increments with each event, whether
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it is uncorrelated or correlated.
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</P>
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<P>The correlation flag will be 0 when an uncorrelated event occurs
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during the second stage of the loop listed above, i.e. when all
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replicas are running independently. The correlation flag will be 1
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when a correlated event occurs during the third stage of the loop
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listed above, i.e. when only one replica is running dynamics.
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</P>
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<P>When more than one replica detects an event at the end of the second
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stage, then one of them is chosen at random. The number of coincident
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events is the number of replicas that detected an event. Normally, we
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expect this value to be 1. If it is often greater than 1, then either
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the number of replicas is too large, or <I>t_event</I> is too large.
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</P>
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<P>The replica number is the ID of the replica (from 0 to M-1) that
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found the event.
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</P>
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<HR>
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<P>When running on multiple partitions, LAMMPS produces additional log
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files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
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the PRD command, these contain the thermodynamic output for each
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replica. You will see short runs and minimizations corresponding to
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the dynamics and quench operations of the loop listed above. The
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timestep will be reset aprpopriately depending on whether the
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operation advances time or not.
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</P>
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<P>After the PRD command completes, timing statistics for the PRD run are
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printed in each replica's log file, giving a breakdown of how much CPU
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time was spent in each stage (dephasing, dynamics, quenching, etc).
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</P>
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<HR>
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<P>Any <A HREF = "dump.html">dump files</A> defined in the input script, will be
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written to during a PRD run at timesteps corresponding to both
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uncorrelated and correlated events. This means the the requested dump
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frequency in the <A HREF = "dump.html">dump</A> command is ignored. There will be
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one dump file (per dump command) created for all partitions.
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</P>
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<P>The atom coordinates of the dump snapshot are those of the minimum
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energy configuration resulting from quenching following a transition
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event. The timesteps written into the dump files correspond to the
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timestep at which the event occurred and NOT the clock. A dump
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snapshot corresponding to the initial minimum state used for event
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detection is written to the dump file at the beginning of each PRD
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run.
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</P>
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<HR>
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<P>If the <A HREF = "restart.html">restart</A> command is used, a single restart file
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for all the partitions is generated, which allows a PRD run to be
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continued by a new input script in the usual manner.
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</P>
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<P>The restart file is generated at the end of the loop listed above. If
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no correlated events are found, this means it contains a snapshot of
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the system at time T + <I>t_correlate</I>, where T is the time at which the
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uncorrelated event occurred. If correlated events were found, then it
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contains a snapshot of the system at time T + <I>t_correlate</I>, where T
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is the time of the last correlated event.
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</P>
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<P>The restart frequency specified in the <A HREF = "restart.html">restart</A> command
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is interpreted differently when performing a PRD run. It does not
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mean the timestep interval between restart files. Instead it means an
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event interval for uncorrelated events. Thus a frequency of 1 means
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write a restart file every time an uncorrelated event occurs. A
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frequency of 10 means write a restart file every 10th uncorrelated
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event.
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</P>
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<P>When an input script reads a restart file from a previous PRD run, the
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new script can be run on a different number of replicas or processors.
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However, it is assumed that <I>t_correlate</I> in the new PRD command is
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the same as it was previously. If not, the calculation of the "clock"
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value for the first event in the new run will be slightly off.
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2009-10-30 06:41:53 +08:00
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</P>
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2009-10-31 02:26:17 +08:00
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<HR>
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2009-10-30 06:41:53 +08:00
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<P><B>Restrictions:</B>
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</P>
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2011-08-27 02:53:00 +08:00
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<P>This command can only be used if LAMMPS was built with the REPLICA
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2011-08-26 00:46:23 +08:00
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package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
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for more info on packages.
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2009-11-03 01:41:54 +08:00
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</P>
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2009-10-31 02:26:17 +08:00
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<P><I>N</I> and <I>t_correlate</I> settings must be integer multiples of
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2009-10-30 06:41:53 +08:00
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<I>t_event</I>.
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</P>
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<P>Runs restarted from restart file written during a PRD run will not
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produce identical results due to changes in the random numbers used
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for dephasing.
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</P>
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<P>This command cannot be used when any fixes are defined that keep track
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of elapsed time to perform time-dependent operations. Examples
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include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
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ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
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2010-05-07 23:11:21 +08:00
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dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
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2009-10-30 06:41:53 +08:00
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_event_displace.html">compute event/displace</A>,
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<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
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<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
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2011-01-05 07:39:13 +08:00
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<A HREF = "velocity.html">velocity</A>, <A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>,
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<A HREF = "tad.html">tad</A>
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2009-10-30 06:41:53 +08:00
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</P>
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<P><B>Default:</B>
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</P>
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2010-02-09 06:34:21 +08:00
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<P>The option defaults are <I>min</I> = 0.1 0.1 40 50, no <I>temp</I> setting, and
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2009-10-30 06:41:53 +08:00
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<I>vel</I> = <I>geom</I> <I>gaussian</I>.
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</P>
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<HR>
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<A NAME = "Voter"></A>
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2009-11-03 23:06:46 +08:00
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<P><B>(Voter)</B> Voter, Phys Rev B, 57, 13985 (1998).
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</P>
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<A NAME = "Voter2"></A>
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<P><B>(Voter2)</B> Voter, Montalenti, Germann, Annual Review of Materials
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2009-10-30 06:41:53 +08:00
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Research 32, 321 (2002).
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</P>
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</HTML>
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