quri_parts.chem.mol package#

class quri_parts.chem.mol.ActiveSpace(n_active_ele: int, n_active_orb: int, active_orbs_indices: Sequence[int] | None = None)#

Bases: object

An immutable (frozen) dataclass representing a active space.

n_active_ele: int#: number of active electrons.

n_active_orb: int#: number of active orbitals.

active_orbs_indices: Sequence[int] | None = None#: sequence of spatial orbital indices of the active orbitals.

quri_parts.chem.mol.cas(n_active_ele: int, n_active_orb: int, active_orbs_indices: Sequence[int] | None = None) → ActiveSpace#: Convenient function for constructing the active space.

class quri_parts.chem.mol.ActiveSpaceMolecularOrbitals(mo: MolecularOrbitals, active_space: ActiveSpace)#

Bases: MolecularOrbitals

Represents a data of the active space for the molecule.

Parameters:

mo – MolecularOrbitals for the molecule.
active_space – ActiveSpace for the molecule.

property n_electron: int#: Returns a number of electrons.

property spin: int#: Returns the total spin of the electrons.

property n_active_ele: int#: Returns the number of active electrons.

property n_core_ele: int#: Returns the number of core electrons.

property n_ele_alpha: int#: Return the number of spin up electrons.

property n_ele_beta: int#: Return the number of spin down electrons.

property n_spatial_orb: int#: Returns the number of spatial orbitals.

property n_active_orb: int#: Returns the number of active orbitals.

property n_core_orb: int#: Returns the number of core orbitals.

property n_vir_orb: int#: Returns the number of virtual orbitals.

property mo_coeff: ndarray[Any, dtype[complex128]]#: Returns molecular orbital coefficients.

get_core_and_active_orb() → tuple[Sequence[int], Sequence[int]]#

Returns a set of core and active orbitals.

The output orbitals are represented as the spatial orbital.

orb_type(mo_index: int) → OrbitalType#

Returns a type of the given orbital index.

Parameters:: mo_index – Orbital index.

class quri_parts.chem.mol.AO1eInt(*args, **kwargs)#

Bases: Protocol

Interface protocol for an atomic orbital one-electron integral.

abstract property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

abstract to_mo1int(mo_coeff: ndarray[Any, dtype[complex128]]) → SpinMO1eInt#

This method converts an atomic orbital one-electron integral into the molecular orbital one-electron integral.

Parameters:: mo_coeff – molecular orbital coefficients.

class quri_parts.chem.mol.AO2eInt(*args, **kwargs)#

Bases: Protocol

Interface protocol for an atomic orbital two-electron integral.

abstract property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

abstract to_mo2int(mo_coeff: ndarray[Any, dtype[complex128]]) → SpinMO2eInt#

This method converts an atomic orbital two-electron integral into the molecular orbital two-electron integral.

Parameters:: mo_coeff – molecular orbital coefficients.

class quri_parts.chem.mol.AOeIntSet(*args, **kwargs)#

Bases: Protocol

AOeIntSet holds a constant and the atomic orbital electron integrals.

constant: float#: constant.

ao_1e_int: AO1eInt#: atomic orbital one-electron integral AO1eInt.

ao_2e_int: AO2eInt#: atomic orbital two-electron integral AO2eInt.

to_full_space_mo_int(mo: MolecularOrbitals) → SpinMOeIntSet#: Compute the full space spin mo integral.

to_active_space_mo_int(active_space_mo: ActiveSpaceMolecularOrbitals) → SpinMOeIntSet#: Compute the active space spin mo integral.

class quri_parts.chem.mol.AO1eIntArray(ao1eint_array: ndarray[Any, dtype[complex128]])#

Bases: AO1eInt

property array: ndarray[Any, dtype[complex128]]#: Returns the ao 1-electron integrals in physicist’s notation.

to_spatial_mo1int(mo_coeff: ndarray[Any, dtype[complex128]]) → SpatialMO1eIntArray#: Returns the spatial mo 1-electron integrals in physicist’s notation.

to_mo1int(mo_coeff: ndarray[Any, dtype[complex128]]) → SpinMO1eInt#: Returns the spin mo 1-electron integrals in physicist’s notation.

class quri_parts.chem.mol.AO2eIntArray(ao2eint_array: ndarray[Any, dtype[complex128]])#

Bases: AO2eInt

property array: ndarray[Any, dtype[complex128]]#: Returns the ao 2-electron integrals in physicist’s convention.

to_spatial_mo2int(mo_coeff: ndarray[Any, dtype[complex128]]) → SpatialMO2eIntArray#: Returns the spatial mo 2-electron integrals in physicist’s convention.

to_mo2int(mo_coeff: ndarray[Any, dtype[complex128]]) → SpinMO2eInt#: Returns the spin mo 2-electron integrals in physicist’s convention.

class quri_parts.chem.mol.AOeIntArraySet(constant: float, ao_1e_int: quri_parts.chem.mol.non_relativistic_models.AO1eIntArray, ao_2e_int: quri_parts.chem.mol.non_relativistic_models.AO2eIntArray)#

Bases: AOeIntSet

constant: float#: constant.

ao_1e_int: AO1eIntArray#: atomic orbital one-electron integral AO1eInt.

ao_2e_int: AO2eIntArray#: atomic orbital two-electron integral AO2eInt.

to_full_space_mo_int(mo: MolecularOrbitals) → SpinMOeIntSet#: Computes the full space spin mo integrals.

to_full_space_spatial_mo_int(mo: MolecularOrbitals) → SpatialMOeIntSet#: Computes the full space spatial mo integrals.

to_active_space_mo_int(active_space_mo: ActiveSpaceMolecularOrbitals) → SpinMOeIntSet#

Computes the active space spin mo integrals.

Note: Does not provide speed advantage compared to PySCFAOeIntSet as it takes additional time to convert ao_eint to mo_eint. Performance penalty grows when the full space mo integral is large.

to_active_space_spatial_mo_int(active_space_mo: ActiveSpaceMolecularOrbitals) → SpatialMOeIntSet#

Computes the active space spatial mo integrals.

Note: Does not provide speed advantage compared to PySCFAOeIntSet as it takes additional time to convert ao_eint to mo_eint. Performance penalty grows when the full space mo integral is large.

class quri_parts.chem.mol.MolecularOrbitals(*args, **kwargs)#

Bases: Protocol

Interface protocol for a data of the molecule.

abstract property n_electron: int#: Returns the number of electrons.

abstract property spin: int#: Returns the total spin of the electrons.

Note

We follow the quantum chemistry convention where:

\[N_{\alpha} - N_{\beta} = 2S\]

and spin = 2S.

abstract property n_spatial_orb: int#: Returns the number of spatial orbitals.

abstract property mo_coeff: ndarray[Any, dtype[complex128]]#: Returns molecular orbital coefficients.

class quri_parts.chem.mol.SpatialMO1eInt(*args, **kwargs)#

Bases: Protocol

Interface protocol for a molecular orbital one-electron integral.

abstract property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpatialMO1eIntArray(array: ndarray[Any, dtype[complex128]])#

Bases: SpatialMO1eInt

A class of a molecular orbital one-electron integral.

This interface has an integral as numpy ndarray.

property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpatialMO2eInt(*args, **kwargs)#

Bases: Protocol

Interface protocol for a molecular orbital two-electron integral.

abstract property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpatialMO2eIntArray(array: ndarray[Any, dtype[complex128]])#

Bases: SpatialMO2eInt

A class of a molecular orbital two-electron integral.

This interface has an integral as numpy ndarray.

property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpatialMOeIntSet(const: float, mo_1e_int: SpatialMO1eInt, mo_2e_int: SpatialMO2eInt)#

Bases: NamedTuple

SpatialMOeIntSet holds a constant and a set of molecular orbital electron integral.

const: float#: constant.

mo_1e_int: SpatialMO1eInt#: molecular orbital one-electron integral.

mo_2e_int: SpatialMO2eInt#: molecular orbital two-electron integral.

class quri_parts.chem.mol.SpinMO1eInt(*args, **kwargs)#

Bases: Protocol

Interface protocol for a molecular spin orbital one-electron integral.

abstract property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpinMO2eInt(*args, **kwargs)#

Bases: Protocol

Interface protocol for a molecular spin orbital two-electron integral.

abstract property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpinMO1eIntArray(array: ndarray[Any, dtype[complex128]])#

Bases: SpinMO1eInt

Stores the array of the 1-electron integrals.

property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpinMO2eIntArray(array: ndarray[Any, dtype[complex128]])#

Bases: SpinMO2eInt

Stores the array of the 2-electron integrals.

property array: ndarray[Any, dtype[complex128]]#: Returns integral as numpy ndarray.

class quri_parts.chem.mol.SpinMOeIntSet(const: float, mo_1e_int: SpinMO1eInt, mo_2e_int: SpinMO2eInt)#

Bases: NamedTuple

SpinMOeIntSet holds a constant and a set of molecular orbital electron integral.

const: float#: constant.

mo_1e_int: SpinMO1eInt#: spin molecular orbital one-electron integral.

mo_2e_int: SpinMO2eInt#: spin molecular orbital two-electron integral.

quri_parts.chem.mol.convert_to_spin_orbital_indices(occupied_indices: Sequence[int], active_indices: Sequence[int]) → tuple[Sequence[int], Sequence[int]]#

Convert each spatial occupied orbital indices and active orbitals indices into the spin occupied orbital indices and active spin indices.

Parameters:

occupied_indices – A Sequence of spatial occupied orbital indices.
active_indices – A Sequence of spatial active orbital indices.

quri_parts.chem.mol.get_active_space_spin_integrals_from_ao_eint(active_space_mo: ActiveSpaceMolecularOrbitals, electron_ao_ints: AOeIntArraySet) → SpinMOeIntSet#: Compute the active space spin electron integrals from ao electron integrals.

quri_parts.chem.mol.get_active_space_spatial_integrals_from_ao_eint(active_space_mo: ActiveSpaceMolecularOrbitals, electron_ao_ints: AOeIntArraySet) → SpatialMOeIntSet#: Compute the active space spatial electron integrals from ao electron integrals.

quri_parts.chem.mol.get_active_space_spin_integrals_from_mo_eint(active_space_mo: ActiveSpaceMolecularOrbitals, electron_mo_ints: SpatialMOeIntSet) → SpinMOeIntSet#: Compute the active space spin electron integrals from mo electron integrals.

quri_parts.chem.mol.get_active_space_spatial_integrals_from_mo_eint(active_space_mo: ActiveSpaceMolecularOrbitals, electron_mo_ints: SpatialMOeIntSet) → SpatialMOeIntSet#

Compute the active space effective core energy and all the spin space electron integrals in the physicist’s convention.

Note: This function yields the active space electron integral faster than pyscf_get_active_space_integrals function in the quri_parts.pyscf package, as it stores the mo electron integrals on memory for computations.

quri_parts.chem.mol.get_core_and_active_orbital_indices(n_active_ele: int, n_active_orb: int, n_electrons: int, active_orbs_indices: Sequence[int] | None = None) → tuple[Sequence[int], Sequence[int]]#

Returns sequences of spatial occupied orbital indices and active orbitals indices obtained from the number of active electrons, number of active orbitals, and number of total electrons.

Parameters:

n_active_ele – number of active electrons.
n_active_orb – number of active orbitals.
n_electrons – total number of electrons.
active_orbs_indices – sequence of spatial orbital indices of the active orbitals.

quri_parts.chem.mol.get_effective_active_space_core_energy(core_energy: float, mo_1e_int: ndarray[Any, dtype[complex128]], mo_2e_int: ndarray[Any, dtype[complex128]], core_spatial_orb_idx: Sequence[int]) → float#

Compute the effective active space core energy for a given active space configuration.

Parameters:

core_energy – The full space core erengy.
mo_1e_int – The full space spatial mo 1-electron integral.
mo_2e_int – The full space spatial mo 2-electron integral.
core_spatial_orb_idx – The core spatial orbital indices.

quri_parts.chem.mol.get_effective_active_space_1e_integrals(mo_1e_int: ndarray[Any, dtype[complex128]], mo_2e_int: ndarray[Any, dtype[complex128]], core_spatial_orb_idx: Sequence[int], active_spatial_orb_idx: Sequence[int]) → ndarray[Any, dtype[complex128]]#

Compute the effective active space 1-electron spatial integral for a given active space configuration.

Parameters:

mo_1e_int – The orginal space spatial mo 1-electron integral.
mo_2e_int – The orginal space spatial mo 2-electron integral.
core_spatial_orb_idx – The core spatial orbital indices.

quri_parts.chem.mol.get_effective_active_space_2e_integrals(mo_2e_int: ndarray[Any, dtype[complex128]], active_spatial_orb_idx: Sequence[int]) → ndarray[Any, dtype[complex128]]#

Compute the effective active space 2-electron spatial integral for a given active space configuration.

Parameters:

mo_1e_int – The orginal space spatial mo 1-electron integral.
mo_2e_int – The orginal space spatial mo 2-electron integral.
core_spatial_orb_idx – The core spatial orbital indices.

quri_parts.chem.mol.spatial_mo_eint_set_to_spin_mo_eint_set(spatial_mo_eint_set: SpatialMOeIntSet) → SpinMOeIntSet#: Compute the spin space mo_eint_set from spatial mo_eint_set.

quri_parts.chem.mol.to_spin_orbital_integrals(n_spin_orb: int, spatial_1e_integrals: ndarray[Any, dtype[complex128]], spatial_2e_integrals: ndarray[Any, dtype[complex128]]) → tuple[ndarray[Any, dtype[complex128]], ndarray[Any, dtype[complex128]]]#: Convert spatial orbital electron integrals to spin orbital electron integrals.

quri_parts.chem.mol.spatial_mo_1e_int_to_spin_mo_1e_int(n_spin_orb: int, spatial_1e_integrals: ndarray[Any, dtype[complex128]]) → ndarray[Any, dtype[complex128]]#: Convert spatial mo 1e electron integrals to spin mo 1e electron integrals.

quri_parts.chem.mol.spatial_mo_2e_int_to_spin_mo_2e_int(n_spin_orb: int, spatial_2e_integrals: ndarray[Any, dtype[complex128]]) → ndarray[Any, dtype[complex128]]#: Convert spatial mo 2e electron integrals to spin mo 2e electron integrals.

quri_parts.chem.mol package#

Submodules#