prd command — LAMMPS documentation

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# prd command

## Syntax

    prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...

- N = # of timesteps to run (not including dephasing/quenching)

- t_event = timestep interval between event checks

- n_dephase = number of velocity randomizations to perform in each dephase run

- t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase

- t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated

- compute-ID = ID of the compute used for event detection

- random_seed = random # seed (positive integer)

- zero or more keyword/value pairs may be appended

- keyword = min or temp or vel or time

      min values = etol ftol maxiter maxeval
        etol = stopping tolerance for energy, used in quenching
        ftol = stopping tolerance for force, used in quenching
        maxiter = max iterations of minimize, used in quenching
        maxeval = max number of force/energy evaluations, used in quenching
      temp value = Tdephase
        Tdephase = target temperature for velocity randomization, used in dephasing
      vel values = loop dist
        loop = all or local or geom, used in dephasing
        dist = uniform or gaussian, used in dephasing
      time value = steps or clock
        steps = simulation runs for N timesteps on each replica (default)
        clock = simulation runs for N timesteps across all replicas

## Examples

    prd 5000 100 10 10 100 1 54982
    prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200

## Description

Run a parallel replica dynamics (PRD) simulation using multiple 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) 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 (AMD) for such systems in given in this review paper (Voter2002) 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 characterized by p(t) = k*exp(-kt) where k is the rate constant.”

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 CPU second, more physical time elapses and more events occur. See the hyper 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. 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 doc page 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. 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:

    while (time remains):
      dephase for n_dephase*t_dephase steps
      until (event occurs on some replica):
        run dynamics for t_event steps
        quench
        check for uncorrelated event on any replica
      until (no correlated event occurs):
        run dynamics for t_correlate steps
        quench
        check for correlated event on this replica
      event replica shares state with all replicas

Before this loop begins, the state of the system on replica 0 is shared with all replicas, so that all replicas begin from the same initial state. The first potential energy basin is identified by quenching (an energy minimization, see below) the initial state and storing the resulting coordinates for reference.

In the first stage, dephasing is performed by each replica independently to eliminate correlations between replicas. This is done by choosing a random set of velocities, based on the random_seed that is specified, and running t_dephase timesteps of dynamics. This is repeated n_dephase times. At each of the n_dephase stages, if an event occurs during the t_dephase steps of dynamics for a particular replica, the replica repeats the stage until no event occurs.

If the temp keyword is not specified, the target temperature for velocity randomization for each replica is the current temperature of that replica. Otherwise, it is the specified Tdephase temperature. The style of velocity randomization is controlled using the keyword vel with arguments that have the same meaning as their counterparts in the velocity command.

In the second stage, each replica runs dynamics continuously, stopping every t_event steps to check if a transition event has occurred. This check is performed by quenching the system and comparing the resulting atom coordinates to the coordinates from the previous basin. The first time through the PRD loop, the “previous basin” is the set of quenched coordinates from the initial state of the system.

A quench is an energy minimization and is performed by whichever algorithm has been defined by the min_style command. Minimization parameters may be set via the min_modify command and by the min keyword of the PRD command. The latter are the settings that would be used with the minimize 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.

The event check is performed by a compute with the specified compute-ID. Currently there is only one compute that works with the PRD command, which is the compute event/displace command. Other event-checking computes may be added. Compute event/displace checks whether any atom in the compute group has moved further than a specified threshold distance. If so, an “event” has occurred.

In the third stage, the replica on which the event occurred (event replica) continues to run dynamics to search for correlated events. This is done by running dynamics for t_correlate steps, quenching every t_event steps, and checking if another event has occurred.

The first time no correlated event occurs, the final state of the event replica is shared with all replicas, the new basin reference coordinates are updated with the quenched state, and the outer loop begins again. While the replica event is searching for correlated events, all the other replicas also run dynamics and event checking with the same schedule, but the final states are always overwritten by the state of the event replica.

The outer loop of the pseudocode above continues until N steps of dynamics have been performed. Note that N only includes the dynamics of stages 2 and 3, not the steps taken during dephasing or the minimization iterations of quenching. The specified N is interpreted in one of two ways, depending on the time keyword. If the time value is steps, which is the default, then each replica 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, where M is the number of replicas.

Four kinds of output can be generated during a PRD run: event statistics, thermodynamic output by each replica, dump files, and restart files.

When running with multiple partitions (each of which is a replica in this case), the print-out to the screen and master log.lammps file is limited to event statistics. Note that if a PRD run is performed on only a single replica then the event statistics will be intermixed with the usual thermodynamic output discussed below.

The quantities printed each time an event occurs are the timestep, CPU time, clock, event number, a correlation flag, the number of 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 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 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 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, when only a single replica is checking for a correlated event. Thus “clock” time 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 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.

The correlation flag will be 0 when an uncorrelated event occurs during the second stage of the loop listed above, i.e. when all 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 same event check (every t_event steps) during 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) in which the event occurred.

When running on multiple partitions, LAMMPS produces additional log files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For the PRD command, these contain the thermodynamic output for each replica. You will see short runs and minimizations corresponding to the dynamics and quench operations of the loop listed above. The timestep will be reset appropriately depending on whether the operation advances time or not.

After the PRD command completes, timing statistics for the PRD run are printed in each replica’s log file, giving a breakdown of how much CPU time was spent in each stage (dephasing, dynamics, quenching, etc).

Any dump files defined in the input script, will be written to during a PRD run at timesteps corresponding to both uncorrelated and correlated events. This means the requested dump frequency in the dump command is ignored. There will be one dump file (per dump command) created for all partitions.

The atom coordinates of the dump snapshot are those of the minimum energy configuration resulting from quenching following a transition event. The timesteps written into the dump files correspond to the timestep at which the event occurred and NOT the clock. A dump snapshot corresponding to the initial minimum state used for event detection is written to the dump file at the beginning of each PRD run.

If the restart command is used, a single restart file for all the partitions is generated, which allows a PRD run to be continued by a new input script in the usual manner.

The restart file is generated at the end of the loop listed above. If no correlated events are found, this means it contains a snapshot of the system at time T + t_correlate, where T is the time at which the uncorrelated event occurred. If correlated events were found, then it contains a snapshot of the system at time T + t_correlate, where T is the time of the last correlated event.

The restart frequency specified in the restart command is interpreted differently when performing a PRD run. It does not mean the timestep interval between restart files. Instead it means an event interval for uncorrelated events. Thus a frequency of 1 means write a restart file every time an uncorrelated event occurs. A frequency of 10 means write a restart file every 10th uncorrelated event.

When an input script reads a restart file from a previous PRD run, the new script can be run on a different number of replicas or processors. However, it is assumed that t_correlate in the new PRD command is the same as it was previously. If not, the calculation of the “clock” value for the first event in the new run will be slightly off.

## Restrictions

This command can only be used if LAMMPS was built with the REPLICA package. See the Build package doc page for more info.

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 produce identical results due to changes in the random numbers used for dephasing.

This command cannot be used when any fixes are defined that keep track of elapsed time to perform time-dependent operations. Examples include the “ave” fixes such as fix ave/chunk. Also fix dt/reset and fix deposit.

## Related commands

compute event/displace, min_modify, min_style, run_style, minimize, velocity, temper, neb, tad, hyper

## Default

The option defaults are min = 0.1 0.1 40 50, no temp setting, vel = geom gaussian, and time = steps.

(Voter1998) Voter, Phys Rev B, 57, 13985 (1998).

(Voter2002) Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002).