Reaction_coord

class mlptrain.sampling.reaction_coord.AverageDistance(*args)

Bases: ReactionCoordinate, _Distances

Average distance between each pair of atoms specified

__init__(*args)

Average of a set of distances e.g.

# Average of a single distance between atoms 0 and 1 dists = AverageDistance((0, 1))

# or multiple distances (0-1 and 1-2) dists = AverageDistance((0, 1), (1, 2))

property n_pairs: int

Number of pairs of atoms in this set

class mlptrain.sampling.reaction_coord.DifferenceDistance(*args)

Bases: ReactionCoordinate, _Distances

Difference in distance between two pairs of specified atoms

__init__(*args)

Difference of a pair of distances e.g.

# Δr = r_1 - r_2, where r_i is the distance between atoms j and k dists = DifferenceDistance((0, 1), (0, 2))

Must comprise two pairs of atoms

class mlptrain.sampling.reaction_coord.DummyCoordinate

Bases: ReactionCoordinate

class mlptrain.sampling.reaction_coord.ReactionCoordinate

Bases: Function, ABC

__call__(arg: Atoms | Configuration | ConfigurationSet) → float | ndarray

Value of this reaction coordinate

grad(atoms: Atoms)

Gradient of this reaction coordinate for a set of ase atoms