Bias Functions

class erbs.bias.potential.ERBS(base_calc: Calculator, dim_reduction_factory: DimReduction, energy_fn_factory: OPESExploreFactory, feature_fn: callable | None = None, model_dir: Path | list[Path] | None = None, n_basis=5, r_max=6.0, dr_threshold=0.5, interval=10000, update_iterations=inf, **kwargs)

calculate(atoms=None, properties=['energy'], system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms'])

Do the calculation.

properties: list of str

List of what needs to be calculated. Can be any combination of ‘energy’, ‘forces’, ‘stress’, ‘dipole’, ‘charges’, ‘magmom’ and ‘magmoms’.

system_changes: list of str

List of what has changed since last calculation. Can be any combination of these six: ‘positions’, ‘numbers’, ‘cell’, ‘pbc’, ‘initial_charges’ and ‘initial_magmoms’.

Subclasses need to implement this, but can ignore properties and system_changes if they want. Calculated properties should be inserted into results dictionary like shown in this dummy example:

self.results = {'energy': 0.0,
                'forces': np.zeros((len(atoms), 3)),
                'stress': np.zeros(6),
                'dipole': np.zeros(3),
                'charges': np.zeros(len(atoms)),
                'magmom': 0.0,
                'magmoms': np.zeros(len(atoms))}

The subclass implementation should first call this implementation to set the atoms attribute and create any missing directories.

implemented_properties: List[str] = ['energy', 'forces', 'stress']

Properties calculator can handle (energy, forces, …)

class erbs.bias.state.BiasState(std: float, compression_threshold: float, g: jax.Array | None = None, height: jax.Array | None = None, cov: jax.Array | None = None, normalisation: jax.Array | None = None)

replace(**updates)

Returns a new object replacing the specified fields with new values.