qrunch.chemistry.molecule.molecular_configuration

Module with the definition of a molecular configuration.

Classes

MolecularConfiguration

Describes a molecular configuration of a molecule.
class MolecularConfiguration

Bases: object

Describes a molecular configuration of a molecule.

__init__(molecule: Molecule, basis_set: BasisSet | dict[Atom, BasisSet], charge: int = 0, spin_difference: int = 0, embedded_atoms: Sequence[int] | None = None, solvent: Solvent | None = None, aux_basis_set: BasisSet | dict[Atom, BasisSet] | None = None) → None

Initialize a molecular configuration.

Parameters:

  • molecule (Molecule) – Molecule to specify configuration for.

  • basis_set (BasisSet | dict[Atom, BasisSet]) – Basis set to use for the atoms types in the molecule. Either a single basis set to use for all atoms, or a dictionary specifying specific basis sets for each chemical element in the molecule.

  • charge (int) – Overall charge of the molecule.

  • spin_difference (int) – Difference between the number of spin up and spin down electrons (default: 0).

  • embedded_atoms (Sequence[int] | None) – Optional field describing which atoms are embedded.

  • solvent (Solvent | None) – Solvent for the molecular configuration to be embedded in.

  • aux_basis_set (BasisSet | dict[Atom, BasisSet] | None) – Auxiliary basis set, used for density fitting, to use for the atoms types in the molecule. Either a single basis set to use for all atoms, or a dictionary specifying specific basis sets for each chemical element in the molecule.

Return type:

None

atom_to_atomic_orbital_indices_map() → dict[int, tuple[int, int]]

Return a map from the atom index to the start and end atomic orbital index.

Return type:

dict[int, tuple[int, int]]

property aux_basis_set: dict[Atom, BasisSet] | None

Auxiliary Basis set for the configuration.

property basis_set: dict[Atom, BasisSet]

Basis set for the configuration.

property charge: int

Charge of the configuration.

core_hamiltonian() → ndarray[Any, dtype[float64]]

Return core hamiltonian in atomic basis.

Return type:

ndarray[Any, dtype[float64]]

embedded_atoms_string() → str

Provide a human-readable string representation for the embedded atoms.

Return type:

str

property molecule: Molecule

Molecule for the configuration.

nuclear_repulsion_energy() → float

Calculate the nuclear repulsion energy of the atoms in the molecule.

Return type:

float

number_of_alpha_electrons() → int

Calculate number of alpha electrons.

Return type:

int

number_of_atomic_orbitals() → int

Return the number of atomic orbitals.

Return type:

int

number_of_beta_electrons() → int

Calculate number of beta electrons.

Return type:

int

number_of_electrons() → int

Calculate the total number of electrons on the molecule.

Return type:

int

number_of_spatial_orbitals() → int

Calculate the number of spatial orbitals.

Return type:

int

overlap_matrix() → ndarray[Any, dtype[float64]]

Return the atomic orbital overlap matrix.

Return type:

ndarray[Any, dtype[float64]]

property pyscf_molecule: Mole

Get the PySCF molecule.

property spin_difference: int

Spin of the configuration.

update_spin_and_charge(new_spin_difference: int, new_charge: int) → None

Update both spin_difference and charge at the same time.

If both spin_difference and charge are changed separately, the intermediate molecule might fail validation. To avoid this, this method can be used instead.

Parameters:

  • new_spin_difference (int) – new spin_difference to be set on the molecule.

  • new_charge (int) – new charge to be set on the molecule.

Return type:

None