Parallel Replica Dynamics (PRD)

Parallel replica dynamics (PRD) is a type of simulation used for performing accelerated dynamics on a system where events are infrequent.

Starting with an initial configuration, it creates multiple copies across several processors and randomizes their velocities. While each copy is simulated in parallel, the PRD periodically checks for jump "events." If one is found, an NEB simulation is performed to find the minimum energy path of this jump. Then, all simulations sync to the endpoint of that jump, and the process is repeated.

The advantage of this method is that it can run multiple searches for statistically significant "events" simultaneously.

It is accessible in the "LAMMPS - PRD" tab of the simulation generator dialog:

PRD tab of the simulation builder dialog

For more information on parallel replica dynamics, see here, or Voter, Phys Rev B, 57, 13985 (1998).

Requirements

In order to build a PRD simulation, a structure with a non-zero bounding box must already be set up in the viewer:

Bounding box example

Optionally, any atom marked as a vacancy (including starting vacancies) will be deleted at runtime.

General Options

The first set of options involve basic information about the simulation and structure:

Screenshot of the general options area in the dialog

Field Description
Working Directory Location to generate the files to
Secondary Name Name of simulation. This will decide the name of the output directory
Structure Name Name of structure. Used in deciding file names of simulation outputs
Mass Table Atomic masses to use in the simulation. Defaults to the masses defined in the atom styles table
Bounding Box Bounding box of the structure. Defaults to the bounding box already defined for the structure

Potentials Options

The next set of options controls the potential coefficients and potential style used in the simulation.

Screenshot of the potentials options area in the dialog

Field Description
Pair Coefficients Coefficients used in the pair potentials
Potential Style Style to use for the potential

In order for a simulation to be considered valid, you must have enough potentials for all elements:

Potential coefficient table with all required pair potentials Potential coefficient table with that's missing some required pair potentials

For convenience, both potential coefficients and styles can be saved and loaded. More information on saving/loading potential coefficients can be found here. Additionally, more information on saving/loading/creating potential styles can be found here.

Slurm Options

The next set of options controls some variables used by slurm.

Screenshot of the slurm options area in the dialog

Field Description
Memory Amount of memory, in megabytes, to allocate per job

LAMMPS Options

The next set of options are those specific to LAMMPS:

Screenshot of the LAMMPS options area in the dialog

Field Description
LAMMPS Version LAMMPS module name for slurm to load
KSpace Solver Name of long-range force solver for LAMMPS to use. For more information on kspace styles, see here
KSpace Accuracy Accuracy of kspace solver
Timestep Timestep used in simulations. Measured in picoseconds by default
Unit System Unit system used by LAMMPS. For more information on LAMMPS unit systems, see here. Note: unit systems besides metal have not been tested, use at your own risk!

PRD Options

The final set of options configures the PRD process. For a more complete explanation of how these parameters effect the simulation, it is recommended you see here.

Screenshot of the full PRD options area in the dialog

The following settings are used in the PRD's quenching stage:

Field Description
Energy Tolerance Stopping tolerance for energy in the PRD's minimizer
Force Tolerance Stopping tolerance for force in the PRD's minimizer
Max. Steps Maximum number of steps to run the quenching stage for
Max. Force Calls Maximum number of times to evaluate the forces during the quenching stage before terminating

The remaining options control how the PRD detects and handles jump events:

Field Description
Event Distance Distance an atom must move for a jump event to be detected
Temperature Temperature, in kelvin, to run the simulation at
Event Region A jump event must occur within the specified region in order to be detected
Number of Timesteps Number of timesteps to run the PRD for
T-Event Timestep interval between checking for events
N-Dephase Number of velocity randomizations performed during each dephasing stage
T-Dephase Number of timesteps to run molecular dynamics during the dephasing stage
T-Correlate Number of timesteps within which two events are considered correlated