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
classmethod Molecule.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
absolute_bending
classmethod Molecule.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
absolute_distance
classmethod Molecule.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
absolute_stretching
classmethod Molecule.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
relative_bending
classmethod Molecule.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
relative_stretching
classmethod Molecule.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
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