qiskit.chemistry.drivers.Molecule

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

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.

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

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

__init__(geometry[, multiplicity, charge, …])	type geometry List[Tuple[str, List[float]]]
absolute_angle(angle, geometry, atom_trio)	type angle float
absolute_bending(bend, geometry, atom_trio)	type bend float
absolute_distance(distance, geometry, atom_pair)	type distance float
absolute_stretching(perturbation, geometry, …)	type perturbation float
relative_bending(bend, geometry, atom_trio)	type bend float
relative_stretching(perturbation, geometry, …)	type perturbation float

Attributes

charge	Get charge
geometry	Get geometry accounting for any perturbations
masses	Get masses
multiplicity	Get multiplicity
perturbations	Get perturbations
units	The geometry coordinate units

classmethod absolute_angle(angle, geometry, atom_trio)

Parameters

• angle (float) – The magnitude of the perturbation in radians. Positive bend is always in the direction toward Atom3. the direction of increasing the starting angle.**

• geometry (List[Tuple[str, List[float]]]) – The initial geometry to perturb.

• atom_trio (Tuple[int, int, int]) – A tuple with three integers, indexing which atoms from the starting geometry should be bent apart. Atom1 is bent *away* from Atom3 by an angle whose vertex is Atom2 and equal to **angle, while Atom2 and Atom3 remain stationary.**

Return type

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

Returns

end geometry

classmethod absolute_bending(bend, geometry, atom_trio)

Parameters

• bend (float) – The magnitude of the perturbation in radians. Positive bend is always in the direction toward Atom3. the direction of increasing the starting angle.**

• geometry (List[Tuple[str, List[float]]]) – The initial geometry to perturb.

• atom_trio (Tuple[int, int, int]) – A tuple with three integers, indexing which atoms from the starting geometry should be bent apart. Atom1 is bent *away* from Atom3 by an angle whose vertex is Atom2 and equal to the initial angle **plus bend, while Atom2 and Atom3 remain stationary.**

Return type

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

Returns

end geometry

classmethod absolute_distance(distance, geometry, atom_pair)

Parameters

• distance (float) – The (new) distance between the two atoms.

• geometry (List[Tuple[str, List[float]]]) – The initial geometry to perturb.

• atom_pair (Tuple[int, int]) – A tuple with two integers, indexing which atoms from the starting geometry should be moved apart. Atom1 is moved away (at the given distance) from Atom2, while Atom2 remains stationary.

Return type

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

Returns

end geometry

classmethod absolute_stretching(perturbation, geometry, atom_pair)

Parameters

• perturbation (float) – The magnitude of the stretch. (New distance = stretch + old distance)

• geometry (List[Tuple[str, List[float]]]) – The initial geometry to perturb.

• atom_pair (Tuple[int, int]) – A tuple with two integers, indexing which atoms from the starting geometry should be stretched apart. Atom1 is stretched away from Atom2, while Atom2 remains stationary.

Return type

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

Returns

end geometry

property charge

Get charge

Return type

int

property geometry

Get geometry accounting for any perturbations

Return type

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

property masses

Get masses

Return type

Optional[List[float]]

property multiplicity

Get multiplicity

Return type

int

property perturbations

Get perturbations

Return type

Optional[List[float]]

classmethod relative_bending(bend, geometry, atom_trio)

Parameters

• bend (float) – The magnitude of the perturbation in radians. Positive bend is always in the direction toward Atom3. the direction of increasing the starting angle.**

• geometry (List[Tuple[str, List[float]]]) – The initial geometry to perturb.

• atom_trio (Tuple[int, int, int]) – A tuple with three integers, indexing which atoms from the starting geometry should be bent apart. Atom1 is bent *away* from Atom3 by an angle whose vertex is Atom2 and equal to the initial angle **times bend, while Atom2 and Atom3 remain stationary.**

Return type

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

Returns

end geometry

classmethod relative_stretching(perturbation, geometry, atom_pair)

Parameters

• perturbation (float) – The magnitude of the stretch. (New distance = stretch * old distance)

• geometry (List[Tuple[str, List[float]]]) – The initial geometry to perturb.

• atom_pair (Tuple[int, int]) – A tuple with two integers, indexing which atoms from the starting geometry should be stretched apart. Atom1 is stretched away from Atom2, while Atom2 remains stationary.

Return type

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

Returns

end geometry

property units

The geometry coordinate units