Minima properties

Module contains the functions for analysing the properties of individual minima. All methods loop through and find minima that meet, or fail, specified criteria

topsearch.analysis.minima_properties.get_all_bounds_minima(ktn: KineticTransitionNetwork, coords: StandardCoordinates) → list

Find any minima that are at the bounds in all dimensions

topsearch.analysis.minima_properties.get_bounds_minima(ktn: KineticTransitionNetwork, coords: StandardCoordinates) → list

Find any minima that are at the bounds in any dimension

topsearch.analysis.minima_properties.get_distance_from_minimum(ktn: KineticTransitionNetwork, similarity: StandardSimilarity, coords: StandardCoordinates, node: int) → NDArray[Any, Any]

Compute the distance of all nodes from specified minimum node1

topsearch.analysis.minima_properties.get_distance_matrix(ktn: KineticTransitionNetwork, similarity: StandardSimilarity, coords: StandardCoordinates) → NDArray[Any, Any]

Compute a distance matrix for all minima in the network

topsearch.analysis.minima_properties.get_invalid_minima(ktn: KineticTransitionNetwork, potential: Potential, coords: StandardCoordinates) → list[int]

Find any minima in the network G that do not meet the gradient or eigenspectrum criteria

topsearch.analysis.minima_properties.get_minima_above_cutoff(ktn: KineticTransitionNetwork, cutoff: float) → list

Find all minima with an energy above cutoff

topsearch.analysis.minima_properties.get_minima_energies(ktn: KineticTransitionNetwork) → NDArray[Any, Any]

Return the energies of all the minima

topsearch.analysis.minima_properties.get_ordered_minima(ktn: KineticTransitionNetwork) → NDArray[Any, Any]

Return the ordered list of indices with increasing energy

topsearch.analysis.minima_properties.get_similar_minima(ktn: KineticTransitionNetwork, proximity_measure: float, comparison_points: NDArray[Any, Any]) → list

Locate any minima within proximity_measure of the comparison_points