matcalc._neb module

NEB calculations.

class NEBCalc(calculator: Calculator | str, *, optimizer: str | Optimizer = 'BFGS', traj_folder: str | None = None, interval: int = 1, climb: bool = True, fmax: float = 0.1, max_steps: int = 1000, **kwargs: Any)[source]

Bases: PropCalc

NEB calculator.

Initialize the instance of the class.

Parameters:

  • calculator (Calculator | str) – An ASE calculator object used to perform energy and force calculations. If string is provided, the corresponding universal calculator is loaded.

  • optimizer (str | Optimizer, optional) – The optimization algorithm to use. Defaults to “BFGS”.

  • traj_folder (str | None, optional) – The folder to save trajectory information. Defaults to None.

  • interval (int, optional) – The interval for recording trajectory information. Defaults to 1.

  • climb (bool, optional) – Whether to perform climbing image nudged elastic band (CI-NEB). Defaults to True.

  • fmax (float, optional) – The maximum force tolerance for convergence. Defaults to 0.1.

  • max_steps (int, optional) – The maximum number of optimization steps. Defaults to 1000.

  • **kwargs (Any) – Additional keyword arguments.

Returns:

None

_abc_impl = <_abc._abc_data object>[source]
calc(structure: Structure | dict[str, Any]) → dict[str, Any][source]

Calculate the energy barrier using the nudged elastic band method.

Parameters:

structure (-) – A dictionary containing the images with keys ‘image0’, ‘image1’, etc. Must be of type dict.

Returns:

  • “barrier” (float): The energy barrier of the reaction pathway.

  • ”force” (float): The force exerted on the atoms during the NEB calculation.

  • ”mep” (dict): a dictionary containing the images and their respective energies.

Return type:

dict

calc_images(start_struct: Structure, end_struct: Structure, *, n_images: int = 7, interpolate_lattices: bool = False, autosort_tol: float = 0.5) → dict[str, Any][source]

Calculate NEB images between given start and end structures.

Parameters:

  • start_struct (Structure) – Initial structure.

  • end_struct (Structure) – Final structure.

  • n_images (int) – Number of images to calculate (default is 7).

  • interpolate_lattices (bool) – Whether to interpolate lattices between start and end structures (default is False).

  • autosort_tol (float) – Tolerance for autosorting the images (default is 0.5).

Returns:

NEB calculation object containing the interpolated images.

Return type:

NEBCalc