qrunch.chemistry.molecule.molecular_configuration

Module with the definition of a molecular configuration.

Module Attributes

DEFAULT_BASIS

Sentinel key used in a basis set dictionary to specify the default basis set for atoms not explicitly listed.

Classes

MolecularConfiguration

Describes a molecular configuration of a molecule.

DEFAULT_BASIS = <qrunch.chemistry.molecule.molecular_configuration._DefaultBasisKey object>

Sentinel key used in a basis set dictionary to specify the default basis set for atoms not explicitly listed.

Example:

# Use cc-pvdz for all atoms, but 321g specifically for Carbon
config = MolecularConfiguration(
    molecule=my_molecule,
    basis_set={
        DEFAULT_BASIS: BasisSet.CCPVDZ,
        Atom("C"): BasisSet.POPLE_321G,
    },
)

class MolecularConfiguration

Bases: object

Describes a molecular configuration of a molecule.

Initialize a molecular configuration.

Parameters:

molecule (Molecule) – Molecule to specify configuration for.
basis_set (BasisSet | dict[Atom, BasisSet] | dict[Atom | _DefaultBasisKey, BasisSet]) –
Basis set to use for the atoms types in the molecule. Can be specified as:
- A single BasisSet to use for all atoms.
- A dictionary mapping Atom to BasisSet for element-specific basis sets. Use DEFAULT_BASIS as a key to specify a default basis set for any atoms not explicitly listed in the dictionary.
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] | dict[Atom | _DefaultBasisKey, BasisSet] | None) – Auxiliary basis set, used for density fitting, to use for the atoms types in the molecule. Can be specified in the same way as basis_set.

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[tuple[int, ...], dtype[float64]]

Return core hamiltonian in atomic basis.

Return type:: ndarray[tuple[int, …], 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[tuple[int, ...], dtype[float64]]

Return the atomic orbital overlap matrix.

Return type:: ndarray[tuple[int, …], 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