Perturbations

Perturbations module contains classes that take steps around a given space. The perturbations have a separate class for each coordinates class, as molecular and atomistic systems require different changes that respect the bonding framework. These instances are passed to the global optimisation instance to drive its step-taking

class topsearch.global_optimisation.perturbations.AtomicPerturbation(max_displacement: float, max_atoms: int)

Description

Simple displacement routine applicable to atomic systems. Applies a 3D displacement vector to selected atoms. Perturbs up to max_atoms atoms with a displacement up to max_displacement

max_displacement

The maximum allowed displacement in a given direction for an atom

Type:: float

max_atoms

The maximum number of atoms that can be perturbed at each call

Type:: int

perturb(coords: AtomicCoordinates) → None: Returns coords perturbed by a displacement to up to max_atoms

class topsearch.global_optimisation.perturbations.MolecularPerturbation(max_displacement: float, max_bonds: int)

Description

Displacement routine applicable to molecular systems. Needs to retain the bonding framework, which it achieves through rotation of bond dihedrals. Selects a random subset of flexible bond dihedrals and rotates through a random angle up to a specified limit

max_displacement

The maximum allowed angle change of a given dihedral

Type:: float

max_bonds

The maximum number of dihedrals that can be perturbed at each call

Type:: int

perturb(coords: MolecularCoordinates) → None: Rotate about randomly selected bonds within a molecular system

class topsearch.global_optimisation.perturbations.StandardPerturbation(max_displacement: float, proportional_distance: bool = False)

Description

Class to perturb a position in Euclidean space for use in global optimisation. For non-atomic systems this is implemented as random displacements

max_displacement

Maximum allowed perturbation size from the given point

Type:: float

proportional_distance

Determines whether max_displacement is an absolute value (if False) or a proportion of the bounds (if True)

Type:: logical

perturb(coords: StandardCoordinates) → None: Displace the given position by randomly up to specified size

set_step_sizes(coords: StandardCoordinates) → NDArray[Any, Any]: Generate an appropriate step size for the given coordinates