# This code is part of a Qiskit project.
#
# (C) Copyright IBM 2022, 2023.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any modifications or derivative works of this code must retain this
# copyright notice, and modified files need to carry a notice indicating
# that they have been altered from the originals.
"""Translator methods for the QCSchema."""
from __future__ import annotations
import logging
from typing import cast
import numpy as np
from qiskit_nature.units import DistanceUnit
from qiskit_nature.second_q.problems import ElectronicBasis, ElectronicStructureProblem
from qiskit_nature.second_q.hamiltonians import ElectronicEnergy
from qiskit_nature.second_q.operators import ElectronicIntegrals
from qiskit_nature.second_q.operators.symmetric_two_body import (
S1Integrals,
S4Integrals,
S8Integrals,
)
from qiskit_nature.second_q.properties import (
AngularMomentum,
ElectronicDipoleMoment,
Magnetization,
ParticleNumber,
)
from qiskit_nature.second_q.transformers import BasisTransformer
from .molecule_info import MoleculeInfo
from .qcschema import QCSchema
LOGGER = logging.getLogger(__name__)
[ドキュメント]def qcschema_to_problem(
qcschema: QCSchema,
*,
basis: ElectronicBasis = ElectronicBasis.MO,
include_dipole: bool = True,
) -> ElectronicStructureProblem:
"""Builds out an :class:`.ElectronicStructureProblem` from a :class:`.QCSchema` instance.
This method centralizes the construction of an :class:`.ElectronicStructureProblem` from a
:class:`.QCSchema`.
Args:
qcschema: the :class:`.QCSchema` object from which to build the problem.
basis: the :class:`.ElectronicBasis` of the generated problem.
include_dipole: whether or not to include an :class:`.ElectronicDipoleMoment` property
in the generated problem (if the data is available).
Raises:
QiskitNatureError: if either of the required 1- or 2-body electronic integrals are missing.
NotImplementedError: if an unsupported :class:`.ElectronicBasis` is requested.
Returns:
An :class:`.ElectronicStructureProblem` instance.
"""
norb = qcschema.properties.calcinfo_nmo
hamiltonian: ElectronicEnergy = None
dipole_x: ElectronicIntegrals | None = None
dipole_y: ElectronicIntegrals | None = None
dipole_z: ElectronicIntegrals | None = None
overlap: np.ndarray | None = None
if basis == ElectronicBasis.AO:
hamiltonian = _get_ao_hamiltonian(qcschema)
if qcschema.wavefunction.scf_overlap is not None:
nao = hamiltonian.register_length
overlap = _reshape_2(qcschema.wavefunction.scf_overlap, nao, nao)
if include_dipole:
dipole_x = _get_ao_dipole(qcschema, "x")
dipole_y = _get_ao_dipole(qcschema, "y")
dipole_z = _get_ao_dipole(qcschema, "z")
elif basis == ElectronicBasis.MO:
hamiltonian = _get_mo_hamiltonian(qcschema)
if qcschema.wavefunction.scf_overlap is not None:
try:
overlap = get_overlap_ab_from_qcschema(qcschema)
except AttributeError:
if not hamiltonian.electronic_integrals.beta.is_empty() and not np.allclose(
hamiltonian.electronic_integrals.alpha["+-"],
hamiltonian.electronic_integrals.beta["+-"],
):
LOGGER.warning(
"Your MO coefficients appear to differ for the alpha- and beta-spin "
"orbitals but you did not provide any orbital overlap data. This may lead "
"to faulty expectation values of observables which mix alpha- and beta-spin"
" components (for example the AngularMomentum)."
)
if include_dipole:
dipole_x = _get_mo_dipole(qcschema, "x")
dipole_y = _get_mo_dipole(qcschema, "y")
dipole_z = _get_mo_dipole(qcschema, "z")
else:
raise NotImplementedError(f"The basis {basis} is not supported by the translation method.")
hamiltonian.nuclear_repulsion_energy = qcschema.properties.nuclear_repulsion_energy
natm = len(qcschema.molecule.symbols)
geo = qcschema.molecule.geometry
molecule = MoleculeInfo(
symbols=qcschema.molecule.symbols,
coords=[(geo[3 * i], geo[3 * i + 1], geo[3 * i + 2]) for i in range(natm)],
multiplicity=qcschema.molecule.molecular_multiplicity or 1,
charge=qcschema.molecule.molecular_charge or 0,
units=DistanceUnit.BOHR,
masses=qcschema.molecule.masses,
)
num_particles = (qcschema.properties.calcinfo_nalpha, qcschema.properties.calcinfo_nbeta)
problem = ElectronicStructureProblem(hamiltonian)
problem.basis = basis
problem.molecule = molecule
problem.num_particles = num_particles
problem.num_spatial_orbitals = norb
problem.reference_energy = qcschema.properties.return_energy
problem.properties.angular_momentum = AngularMomentum(norb, overlap)
problem.properties.magnetization = Magnetization(norb)
problem.properties.particle_number = ParticleNumber(norb)
if qcschema.wavefunction.scf_eigenvalues_a is not None:
problem.orbital_energies = np.asarray(qcschema.wavefunction.scf_eigenvalues_a)
if qcschema.wavefunction.scf_eigenvalues_b is not None:
problem.orbital_energies_b = np.asarray(qcschema.wavefunction.scf_eigenvalues_b)
if include_dipole and dipole_x is not None and dipole_y is not None and dipole_z is not None:
dipole = ElectronicDipoleMoment(dipole_x, dipole_y, dipole_z)
if qcschema.properties.nuclear_dipole_moment is not None:
dipole.nuclear_dipole_moment = qcschema.properties.nuclear_dipole_moment
problem.properties.electronic_dipole_moment = dipole
return problem
def _reshape_2(arr, dim, dim_2=None):
return np.asarray(arr).reshape((dim, dim_2 if dim_2 is not None else dim))
def _reshape_4(arr, dim):
npair = dim * (dim + 1) // 2
if len(arr) == npair * (npair + 1) // 2:
return S8Integrals(np.asarray(arr))
if len(arr) == npair**2:
return S4Integrals(np.asarray(arr).reshape((npair,) * 2))
if len(arr) == dim**4:
return S1Integrals(np.asarray(arr).reshape((dim,) * 4))
return arr
def _get_ao_hamiltonian(qcschema: QCSchema) -> ElectronicEnergy:
nao = int(np.sqrt(len(qcschema.wavefunction.scf_fock_a)))
hcore = _reshape_2(qcschema.wavefunction.scf_fock_a, nao)
hcore_b = None
if qcschema.wavefunction.scf_fock_b is not None:
hcore_b = _reshape_2(qcschema.wavefunction.scf_fock_b, nao)
eri = _reshape_4(qcschema.wavefunction.scf_eri, nao)
hamiltonian = ElectronicEnergy.from_raw_integrals(hcore, eri, hcore_b)
return hamiltonian
def _get_mo_hamiltonian(qcschema: QCSchema) -> ElectronicEnergy:
if qcschema.wavefunction.scf_fock_mo_a is not None:
return _get_mo_hamiltonian_direct(qcschema)
hamiltonian = _get_ao_hamiltonian(qcschema)
transformer = get_ao_to_mo_from_qcschema(qcschema)
return cast(ElectronicEnergy, transformer.transform_hamiltonian(hamiltonian))
def _get_mo_hamiltonian_direct(qcschema: QCSchema) -> ElectronicEnergy:
norb = qcschema.properties.calcinfo_nmo
hij = _reshape_2(qcschema.wavefunction.scf_fock_mo_a, norb)
hijkl = _reshape_4(qcschema.wavefunction.scf_eri_mo_aa, norb)
hij_b = None
hijkl_bb = None
hijkl_ba = None
if qcschema.wavefunction.scf_fock_mo_b is not None:
hij_b = _reshape_2(qcschema.wavefunction.scf_fock_mo_b, norb)
if qcschema.wavefunction.scf_eri_mo_bb is not None:
hijkl_bb = _reshape_4(qcschema.wavefunction.scf_eri_mo_bb, norb)
if qcschema.wavefunction.scf_eri_mo_ba is not None:
hijkl_ba = _reshape_4(qcschema.wavefunction.scf_eri_mo_ba, norb)
if qcschema.wavefunction.scf_eri_mo_ab is not None and hijkl_ba is None:
hijkl_ba = np.transpose(_reshape_4(qcschema.wavefunction.scf_eri_mo_ab, norb))
hamiltonian = ElectronicEnergy.from_raw_integrals(hij, hijkl, hij_b, hijkl_bb, hijkl_ba)
return hamiltonian
def _get_ao_dipole(qcschema, axis) -> ElectronicIntegrals | None:
name = f"scf_dipole_{axis}"
integrals = getattr(qcschema.wavefunction, name, None)
if integrals is None:
return None
nao = int(np.sqrt(len(integrals)))
ints = _reshape_2(integrals, nao)
return ElectronicIntegrals.from_raw_integrals(ints)
def _get_mo_dipole(qcschema, axis) -> ElectronicIntegrals | None:
name_a = f"scf_dipole_mo_{axis}_a"
if getattr(qcschema.wavefunction, name_a, None) is not None:
return _get_mo_dipole_direct(qcschema, axis)
dipole = _get_ao_dipole(qcschema, axis)
transformer = get_ao_to_mo_from_qcschema(qcschema)
return transformer.transform_electronic_integrals(dipole)
def _get_mo_dipole_direct(qcschema, axis) -> ElectronicIntegrals | None:
norb = qcschema.properties.calcinfo_nmo
name_a = f"scf_dipole_mo_{axis}_a"
integrals_a = getattr(qcschema.wavefunction, name_a, None)
if integrals_a is None:
return None
ints_a = _reshape_2(integrals_a, norb)
name_b = f"scf_dipole_mo_{axis}_b"
integrals_b = getattr(qcschema.wavefunction, name_b, None)
ints_b = None
if integrals_b is not None:
ints_b = _reshape_2(integrals_b, norb)
return ElectronicIntegrals.from_raw_integrals(ints_a, h1_b=ints_b)
[ドキュメント]def get_ao_to_mo_from_qcschema(qcschema: QCSchema) -> BasisTransformer:
"""Builds out a :class:`.BasisTransformer` from a :class:`.QCSchema` instance.
This utility extracts the AO-to-MO conversion coefficients, contained in a :class:`.QCSchema`
object.
Args:
qcschema: the :class:`.QCSchema` object from which to build the problem.
Returns:
A :class:`.BasisTransformer` instance.
"""
nmo = qcschema.properties.calcinfo_nmo
nao = len(qcschema.wavefunction.scf_orbitals_a) // nmo
coeff_a = _reshape_2(qcschema.wavefunction.scf_orbitals_a, nao, nmo)
coeff_b = None
if qcschema.wavefunction.scf_orbitals_b is not None:
coeff_b = _reshape_2(qcschema.wavefunction.scf_orbitals_b, nao, nmo)
transformer = BasisTransformer(
ElectronicBasis.AO,
ElectronicBasis.MO,
ElectronicIntegrals.from_raw_integrals(coeff_a, h1_b=coeff_b),
)
return transformer
[ドキュメント]def get_overlap_ab_from_qcschema(qcschema: QCSchema) -> np.ndarray | None:
"""Builds the alpha-beta spin orbital overlap matrix from a :class:`.QCSchema` instance.
Args:
qcschema: the :class:`.QCSchema` object from which to build the problem.
Raises:
AttributeError: when the overlap or MO coefficients are missing.
Returns:
The overlap matrix as a 2-dimensional numpy array or `None` if the overlap is equal to the
identity matrix.
"""
if qcschema.wavefunction.scf_orbitals_a is None or qcschema.wavefunction.scf_overlap is None:
raise AttributeError
nmo = qcschema.properties.calcinfo_nmo
nao = len(qcschema.wavefunction.scf_orbitals_a) // nmo
coeff_a = _reshape_2(qcschema.wavefunction.scf_orbitals_a, nao, nmo)
coeff_b = None
if qcschema.wavefunction.scf_orbitals_b is not None:
coeff_b = _reshape_2(qcschema.wavefunction.scf_orbitals_b, nao, nmo)
if coeff_b is None:
# when coeff_b is None, that means it is equal to coeff_a, which in turn means that the
# overlap is equal to the identity
return None
overlap = _reshape_2(qcschema.wavefunction.scf_overlap, nao, nao)
return coeff_a.T @ overlap @ coeff_b