Nudged Elastic Band (NEB)

The nudged elastic band (NEB) method is a computational technique used to study the transition states between different states of a system. It finds the minimum energy pathway by optimizing a chain of intermediate configurations, resembling a stretched elastic band, connecting the initial and final states. More information on the NEB method is available here.

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

NEB tab of the simulation builder dialog

Requirements

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

Bounding box example

Besides that, a starting vacancy must be defined. Additional vacancies are optional.

Finally, migration paths must be defined for the NEB to know what paths to calculate.

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

NEB Options

The final set of options configures the NEB process:

Screenshot of the NEB options area in the dialog

To achieve a high throughput, the simulator runs many NEB simulations in parallel using slurm's job scheduler. Essentially, simulations are divided up into "divisions," within which several simulations are run in series. Then, each division is scheduled as a separate job using slurm.

Field Description
Paths Per Division Number of paths to place in each division
Division Count Total number of divisions to create

The remaining options directly configure the NEB process:

Field Description
NEB Timeout Maximum time, in seconds, to run an individual NEB before terminating. Useful for preventing non-converging simulations from hogging compute time
Minimizer Style Minimizer style to use in the NEB's minimization process
Number of Replicas Number of intermediate configurations (including the start and end). Note: increasing this will drastically increase the memory requirements
NEB Spring Constant Spring constant used in the "elastic band"
NEB Energy Tolerance Stopping tolerance for energy in the NEB's minimization process
NEB Force Tolerance Stopping tolerance for force in the NEB's minimization process
Max. Initial Iterations Maximum number of iterations to run the initial NEB process that find the minimum-energy path
Max. Barrier-Climbing Iterations After the minimum energy path is found, maximum number of iterations to run the NEB that finds the peak of the energy barrier