Molecule

class Molecule(geometry, multiplicity=1, charge=0, degrees_of_freedom=None, masses=None)

Bases: object

Driver-independent Molecule definition.

This module implements an interface for a driver-independent, i.e. generic molecule definition. It defines the composing atoms (with properties like masses), and allows for changing the molecular geometry through given degrees of freedom (e.g. bond-stretching, angle-bending, etc.). The geometry as provided in the constructor can be affected, through setting perturbations, and it is this perturbed geometry that is supplied by the geometry getter. Setting perturbations to None will cause the original geometry to be returned, and there is a getter to get this value directly if its needed.

Parameters

• geometry (List[Tuple[str, List[float]]]) – A list of atoms defining a given molecule where each item in the list is an atom name together with a list of 3 floats representing the x,y and z Cartesian coordinates of the atom’s position in units of Angstrom.

• multiplicity (int) – Multiplicity (2S+1) of the molecule

• charge (int) – Charge on the molecule

• degrees_of_freedom (Optional[List[Callable]]) – List of functions taking a perturbation value and geometry and returns a perturbed geometry. Helper functions for typical perturbations are provided and can be used by the form itertools.partial(Molecule.stretching_potential,{‘atom_pair’: (1, 2)) to specify the desired degree of freedom.

• masses (Optional[List[float]]) – Mass of each atom the molecule may optionally be provided.

Raises

ValueError – Length of masses must match length of geometries.

Methods

absolute_angle	type angle float
absolute_bending	type bend float
absolute_distance	type distance float
absolute_stretching	type perturbation float
relative_bending	type bend float
relative_stretching	type perturbation float

Attributes

charge

Get charge

Return type

int

geometry

Get geometry accounting for any perturbations

Return type

List[Tuple[str, List[float]]]

masses

Get masses

Return type

Optional[List[float]]

multiplicity

Get multiplicity

Return type

int

perturbations

Get perturbations

Return type

Optional[List[float]]

units

The geometry coordinate units