def _populate_driver_result_molecule(
self, driver_result: ElectronicStructureDriverResult) -> None:
geometry: List[Tuple[str, List[float]]] = []
for atom in self._mol.atoms:
atuple = atom.atuple()
geometry.append(
(PERIODIC_TABLE[atuple[0]], [a * BOHR for a in atuple[1:]]))
driver_result.molecule = Molecule(geometry,
multiplicity=self._mol.multiplicity,
charge=self._mol.charge)
def _populate_driver_result_molecule(
self, driver_result: ElectronicStructureDriverResult) -> None:
coords = self._mol.atom_coords(unit="Angstrom")
geometry = [(self._mol.atom_pure_symbol(i), list(xyz))
for i, xyz in enumerate(coords)]
driver_result.molecule = Molecule(
geometry,
multiplicity=self._spin + 1,
charge=self._charge,
masses=list(self._mol.atom_mass_list()),
)
def transform(
self, grouped_property: GroupedSecondQuantizedProperty
) -> GroupedElectronicProperty:
"""Reduces the given `GroupedElectronicProperty` to a given active space.
Args:
grouped_property: the `GroupedElectronicProperty` to be transformed.
Returns:
A new `GroupedElectronicProperty` instance.
Raises:
QiskitNatureError: If the provided `GroupedElectronicProperty` does not contain a
`ParticleNumber` or `ElectronicBasisTransform` instance, if more
electrons or orbitals are requested than are available, or if the
number of selected active orbital indices does not match
`num_molecular_orbitals`.
"""
if not isinstance(grouped_property, GroupedElectronicProperty):
raise QiskitNatureError(
"Only `GroupedElectronicProperty` objects can be transformed by this Transformer, "
f"not objects of type, {type(grouped_property)}."
)
particle_number = grouped_property.get_property(ParticleNumber)
if particle_number is None:
raise QiskitNatureError(
"The provided `GroupedElectronicProperty` does not contain a `ParticleNumber` "
"property, which is required by this transformer!"
)
particle_number = cast(ParticleNumber, particle_number)
electronic_basis_transform = grouped_property.get_property(ElectronicBasisTransform)
if electronic_basis_transform is None:
raise QiskitNatureError(
"The provided `GroupedElectronicProperty` does not contain an "
"`ElectronicBasisTransform` property, which is required by this transformer!"
)
electronic_basis_transform = cast(ElectronicBasisTransform, electronic_basis_transform)
# get molecular orbital occupation numbers
occupation_alpha = particle_number.occupation_alpha
occupation_beta = particle_number.occupation_beta
self._mo_occ_total = occupation_alpha + occupation_beta
# determine the active space
self._active_orbs_indices, inactive_orbs_idxs = self._determine_active_space(
grouped_property
)
# get molecular orbital coefficients
coeff_alpha = electronic_basis_transform.coeff_alpha
coeff_beta = electronic_basis_transform.coeff_beta
# initialize size-reducing basis transformation
self._transform_active = ElectronicBasisTransform(
ElectronicBasis.AO,
ElectronicBasis.MO,
coeff_alpha[:, self._active_orbs_indices],
coeff_beta[:, self._active_orbs_indices],
)
# compute inactive density matrix
def _inactive_density(mo_occ, mo_coeff):
return np.dot(
mo_coeff[:, inactive_orbs_idxs] * mo_occ[inactive_orbs_idxs],
np.transpose(mo_coeff[:, inactive_orbs_idxs]),
)
self._density_inactive = OneBodyElectronicIntegrals(
ElectronicBasis.AO,
(
_inactive_density(occupation_alpha, coeff_alpha),
_inactive_density(occupation_beta, coeff_beta),
),
)
# construct new GroupedElectronicProperty
grouped_property_transformed = ElectronicStructureDriverResult()
grouped_property_transformed = self._transform_property(grouped_property) # type: ignore
grouped_property_transformed.molecule = (
grouped_property.molecule # type: ignore[attr-defined]
)
return grouped_property_transformed
def _parse_matrix_file(
fname: str,
useao2e: bool = False) -> ElectronicStructureDriverResult:
"""
get_driver_class is used here because the discovery routine will load all the gaussian
binary dependencies, if not loaded already. It won't work without it.
"""
try:
# add gauopen to sys.path so that binaries can be loaded
gauopen_directory = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "gauopen")
if gauopen_directory not in sys.path:
sys.path.insert(0, gauopen_directory)
# pylint: disable=import-outside-toplevel
from .gauopen.QCMatEl import MatEl
except ImportError as mnfe:
msg = ((
"qcmatrixio extension not found. "
"See Gaussian driver readme to build qcmatrixio.F using f2py")
if mnfe.name == "qcmatrixio" else str(mnfe))
logger.info(msg)
raise QiskitNatureError(msg) from mnfe
mel = MatEl(file=fname)
logger.debug("MatrixElement file:\n%s", mel)
driver_result = ElectronicStructureDriverResult()
# molecule
coords = np.reshape(mel.c, (len(mel.ian), 3))
geometry: list[tuple[str, list[float]]] = []
for atom, xyz in zip(mel.ian, coords):
geometry.append((PERIODIC_TABLE[atom], BOHR * xyz))
driver_result.molecule = Molecule(
geometry,
multiplicity=mel.multip,
charge=mel.icharg,
)
# driver metadata
driver_result.add_property(DriverMetadata("GAUSSIAN", mel.gversion,
""))
# basis transform
moc = GaussianDriver._get_matrix(mel, "ALPHA MO COEFFICIENTS")
moc_b = GaussianDriver._get_matrix(mel, "BETA MO COEFFICIENTS")
if np.array_equal(moc, moc_b):
logger.debug(
"ALPHA and BETA MO COEFFS identical, keeping only ALPHA")
moc_b = None
nmo = moc.shape[0]
basis_transform = ElectronicBasisTransform(ElectronicBasis.AO,
ElectronicBasis.MO, moc,
moc_b)
driver_result.add_property(basis_transform)
# particle number
num_alpha = (mel.ne + mel.multip - 1) // 2
num_beta = (mel.ne - mel.multip + 1) // 2
driver_result.add_property(
ParticleNumber(num_spin_orbitals=nmo * 2,
num_particles=(num_alpha, num_beta)))
# electronic energy
hcore = GaussianDriver._get_matrix(mel, "CORE HAMILTONIAN ALPHA")
logger.debug("CORE HAMILTONIAN ALPHA %s", hcore.shape)
hcore_b = GaussianDriver._get_matrix(mel, "CORE HAMILTONIAN BETA")
if np.array_equal(hcore, hcore_b):
# From Gaussian interfacing documentation: "The two core Hamiltonians are identical
# unless a Fermi contact perturbation has been applied."
logger.debug(
"CORE HAMILTONIAN ALPHA and BETA identical, keeping only ALPHA"
)
hcore_b = None
logger.debug(
"CORE HAMILTONIAN BETA %s",
"- Not present" if hcore_b is None else hcore_b.shape,
)
one_body_ao = OneBodyElectronicIntegrals(ElectronicBasis.AO,
(hcore, hcore_b))
one_body_mo = one_body_ao.transform_basis(basis_transform)
eri = GaussianDriver._get_matrix(mel, "REGULAR 2E INTEGRALS")
logger.debug("REGULAR 2E INTEGRALS %s", eri.shape)
if moc_b is None and mel.matlist.get("BB MO 2E INTEGRALS") is not None:
# It seems that when using ROHF, where alpha and beta coeffs are
# the same, that integrals
# for BB and BA are included in the output, as well as just AA
# that would have been expected
# Using these fails to give the right answer (is ok for UHF).
# So in this case we revert to
# using 2 electron ints in atomic basis from the output and
# converting them ourselves.
useao2e = True
logger.info(
"Identical A and B coeffs but BB ints are present - using regular 2E ints instead"
)
two_body_ao = TwoBodyElectronicIntegrals(ElectronicBasis.AO,
(eri, None, None, None))
two_body_mo: TwoBodyElectronicIntegrals
if useao2e:
# eri are 2-body in AO. We can convert to MO via the ElectronicBasisTransform but using
# ints in MO already, as in the else here, is better
two_body_mo = two_body_ao.transform_basis(basis_transform)
else:
# These are in MO basis but by default will be reduced in size by frozen core default so
# to use them we need to add Window=Full above when we augment the config
mohijkl = GaussianDriver._get_matrix(mel, "AA MO 2E INTEGRALS")
logger.debug("AA MO 2E INTEGRALS %s", mohijkl.shape)
mohijkl_bb = GaussianDriver._get_matrix(mel, "BB MO 2E INTEGRALS")
logger.debug(
"BB MO 2E INTEGRALS %s",
"- Not present" if mohijkl_bb is None else mohijkl_bb.shape,
)
mohijkl_ba = GaussianDriver._get_matrix(mel, "BA MO 2E INTEGRALS")
logger.debug(
"BA MO 2E INTEGRALS %s",
"- Not present" if mohijkl_ba is None else mohijkl_ba.shape,
)
two_body_mo = TwoBodyElectronicIntegrals(
ElectronicBasis.MO, (mohijkl, mohijkl_ba, mohijkl_bb, None))
electronic_energy = ElectronicEnergy(
[one_body_ao, two_body_ao, one_body_mo, two_body_mo],
nuclear_repulsion_energy=mel.scalar("ENUCREP"),
reference_energy=mel.scalar("ETOTAL"),
)
kinetic = GaussianDriver._get_matrix(mel, "KINETIC ENERGY")
logger.debug("KINETIC ENERGY %s", kinetic.shape)
electronic_energy.kinetic = OneBodyElectronicIntegrals(
ElectronicBasis.AO, (kinetic, None))
overlap = GaussianDriver._get_matrix(mel, "OVERLAP")
logger.debug("OVERLAP %s", overlap.shape)
electronic_energy.overlap = OneBodyElectronicIntegrals(
ElectronicBasis.AO, (overlap, None))
orbs_energy = GaussianDriver._get_matrix(mel, "ALPHA ORBITAL ENERGIES")
logger.debug("ORBITAL ENERGIES %s", overlap.shape)
orbs_energy_b = GaussianDriver._get_matrix(mel,
"BETA ORBITAL ENERGIES")
logger.debug("BETA ORBITAL ENERGIES %s", overlap.shape)
orbital_energies = (
orbs_energy, orbs_energy_b) if moc_b is not None else orbs_energy
electronic_energy.orbital_energies = np.asarray(orbital_energies)
driver_result.add_property(electronic_energy)
# dipole moment
dipints = GaussianDriver._get_matrix(mel, "DIPOLE INTEGRALS")
dipints = np.einsum("ijk->kji", dipints)
x_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO,
(dipints[0], None))
y_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO,
(dipints[1], None))
z_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO,
(dipints[2], None))
x_dipole = DipoleMoment(
"x", [x_dip_ints,
x_dip_ints.transform_basis(basis_transform)])
y_dipole = DipoleMoment(
"y", [y_dip_ints,
y_dip_ints.transform_basis(basis_transform)])
z_dipole = DipoleMoment(
"z", [z_dip_ints,
z_dip_ints.transform_basis(basis_transform)])
nucl_dip = np.einsum("i,ix->x", mel.ian, coords)
nucl_dip = np.round(nucl_dip, decimals=8)
driver_result.add_property(
ElectronicDipoleMoment(
[x_dipole, y_dipole, z_dipole],
nuclear_dipole_moment=nucl_dip,
reverse_dipole_sign=True,
))
# extra properties
# TODO: once https://github.com/Qiskit/qiskit-nature/issues/312 is fixed we can stop adding
# these properties by default.
# if not settings.dict_aux_operators:
driver_result.add_property(AngularMomentum(nmo * 2))
driver_result.add_property(Magnetization(nmo * 2))
return driver_result