def test_from_hdf5(self):
"""Test from_hdf5."""
with tempfile.TemporaryFile() as tmp_file:
with h5py.File(tmp_file, "w") as file:
self.prop.to_hdf5(file)
with h5py.File(tmp_file, "r") as file:
read_prop = ElectronicDipoleMoment.from_hdf5(
file["ElectronicDipoleMoment"])
self.assertEqual(self.prop, read_prop)
def test_electronic_dipole_moment(self) -> None:
"""Tests the ElectronicDipoleMoment property."""
container = ElectronicPropertiesContainer()
with self.subTest("initially None"):
self.assertIsNone(container.electronic_dipole_moment)
with self.subTest("wrong setting type"):
with self.assertRaises(TypeError):
container.electronic_dipole_moment = OccupiedModals() # type: ignore[assignment]
with self.subTest("successful setting"):
container.electronic_dipole_moment = ElectronicDipoleMoment()
self.assertIn(ElectronicDipoleMoment, container)
with self.subTest("removal via None setting"):
container.electronic_dipole_moment = None
self.assertNotIn(ElectronicDipoleMoment, container)
def test_occupied_modals(self) -> None:
"""Tests the OccupiedModals property."""
container = VibrationalPropertiesContainer()
with self.subTest("initially None"):
self.assertIsNone(container.occupied_modals)
with self.subTest("wrong setting type"):
with self.assertRaises(TypeError):
container.occupied_modals = ElectronicDipoleMoment(
) # type: ignore[assignment]
with self.subTest("successful setting"):
container.occupied_modals = OccupiedModals()
self.assertIn(OccupiedModals, container)
with self.subTest("removal via None setting"):
container.occupied_modals = None
self.assertNotIn(OccupiedModals, container)
def _populate_driver_result_electronic_dipole_moment(
self, driver_result: ElectronicStructureDriverResult
) -> None:
basis_transform = driver_result.get_property(ElectronicBasisTransform)
self._mol.set_common_orig((0, 0, 0))
ao_dip = self._mol.intor_symmetric("int1e_r", comp=3)
d_m = self._calc.make_rdm1(self._calc.mo_coeff, self._calc.mo_occ)
if not (isinstance(d_m, np.ndarray) and d_m.ndim == 2):
d_m = d_m[0] + d_m[1]
elec_dip = np.negative(np.einsum("xij,ji->x", ao_dip, d_m).real)
elec_dip = np.round(elec_dip, decimals=8)
nucl_dip = np.einsum("i,ix->x", self._mol.atom_charges(), self._mol.atom_coords())
nucl_dip = np.round(nucl_dip, decimals=8)
logger.info("HF Electronic dipole moment: %s", elec_dip)
logger.info("Nuclear dipole moment: %s", nucl_dip)
logger.info("Total dipole moment: %s", nucl_dip + elec_dip)
x_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO, (ao_dip[0], None))
y_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO, (ao_dip[1], None))
z_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO, (ao_dip[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)])
driver_result.add_property(
ElectronicDipoleMoment(
[x_dipole, y_dipole, z_dipole],
nuclear_dipole_moment=nucl_dip,
reverse_dipole_sign=True,
)
)
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
def test_tuple_num_electrons_with_manual_orbitals(self):
"""Regression test against https://github.com/Qiskit/qiskit-nature/issues/434."""
driver = HDF5Driver(hdf5_input=self.get_resource_path(
"H2_631g.hdf5", "second_q/transformers"))
driver_result = driver.run()
trafo = ActiveSpaceTransformer(
num_electrons=(1, 1),
num_molecular_orbitals=2,
active_orbitals=[0, 1],
)
driver_result_reduced = trafo.transform(driver_result)
expected = ElectronicStructureDriverResult()
expected.add_property(
ElectronicEnergy(
[
OneBodyElectronicIntegrals(
ElectronicBasis.MO,
(np.asarray([[-1.24943841, 0.0], [0.0, -0.547816138]
]), None),
),
TwoBodyElectronicIntegrals(
ElectronicBasis.MO,
(
np.asarray([
[
[[0.652098466, 0.0], [0.0, 0.433536565]],
[[0.0, 0.0794483182], [0.0794483182, 0.0]],
],
[
[[0.0, 0.0794483182], [0.0794483182, 0.0]],
[[0.433536565, 0.0], [0.0, 0.385524695]],
],
]),
None,
None,
None,
),
),
],
energy_shift={"ActiveSpaceTransformer": 0.0},
))
expected.add_property(
ElectronicDipoleMoment([
DipoleMoment(
"x",
[
OneBodyElectronicIntegrals(ElectronicBasis.MO,
(np.zeros((2, 2)), None))
],
shift={"ActiveSpaceTransformer": 0.0},
),
DipoleMoment(
"y",
[
OneBodyElectronicIntegrals(ElectronicBasis.MO,
(np.zeros((2, 2)), None))
],
shift={"ActiveSpaceTransformer": 0.0},
),
DipoleMoment(
"z",
[
OneBodyElectronicIntegrals(
ElectronicBasis.MO,
(
np.asarray([[0.69447435, -1.01418298],
[-1.01418298, 0.69447435]]),
None,
),
)
],
shift={"ActiveSpaceTransformer": 0.0},
),
]))
self.assertDriverResult(driver_result_reduced, expected)
def test_arbitrary_active_orbitals(self):
"""Test manual selection of active orbital indices."""
driver = HDF5Driver(hdf5_input=self.get_resource_path(
"H2_631g.hdf5", "second_q/transformers"))
driver_result = driver.run()
trafo = ActiveSpaceTransformer(num_electrons=2,
num_molecular_orbitals=2,
active_orbitals=[0, 2])
driver_result_reduced = trafo.transform(driver_result)
expected = ElectronicStructureDriverResult()
expected.add_property(
ElectronicEnergy(
[
OneBodyElectronicIntegrals(
ElectronicBasis.MO,
(
np.asarray([[-1.24943841, -0.16790838],
[-0.16790838, -0.18307469]]),
None,
),
),
TwoBodyElectronicIntegrals(
ElectronicBasis.MO,
(
np.asarray([
[
[[0.65209847, 0.16790822],
[0.16790822, 0.53250905]],
[[0.16790822, 0.10962908],
[0.10962908, 0.11981429]],
],
[
[[0.16790822, 0.10962908],
[0.10962908, 0.11981429]],
[[0.53250905, 0.11981429],
[0.11981429, 0.46345617]],
],
]),
None,
None,
None,
),
),
],
energy_shift={"ActiveSpaceTransformer": 0.0},
))
expected.add_property(
ElectronicDipoleMoment([
DipoleMoment(
"x",
[
OneBodyElectronicIntegrals(ElectronicBasis.MO,
(np.zeros((2, 2)), None))
],
shift={"ActiveSpaceTransformer": 0.0},
),
DipoleMoment(
"y",
[
OneBodyElectronicIntegrals(ElectronicBasis.MO,
(np.zeros((2, 2)), None))
],
shift={"ActiveSpaceTransformer": 0.0},
),
DipoleMoment(
"z",
[
OneBodyElectronicIntegrals(
ElectronicBasis.MO,
(np.asarray([[0.69447435, 0.0], [0.0, 0.69447435]
]), None),
)
],
shift={"ActiveSpaceTransformer": 0.0},
),
]))
self.assertDriverResult(driver_result_reduced, expected)
def test_minimal_active_space(self):
"""Test a minimal active space manually."""
driver = HDF5Driver(hdf5_input=self.get_resource_path(
"H2_631g.hdf5", "second_q/transformers"))
driver_result = driver.run()
trafo = ActiveSpaceTransformer(num_electrons=2,
num_molecular_orbitals=2)
driver_result_reduced = trafo.transform(driver_result)
expected = ElectronicStructureDriverResult()
expected.add_property(
ElectronicEnergy(
[
OneBodyElectronicIntegrals(
ElectronicBasis.MO,
(np.asarray([[-1.24943841, 0.0], [0.0, -0.547816138]
]), None),
),
TwoBodyElectronicIntegrals(
ElectronicBasis.MO,
(
np.asarray([
[
[[0.652098466, 0.0], [0.0, 0.433536565]],
[[0.0, 0.0794483182], [0.0794483182, 0.0]],
],
[
[[0.0, 0.0794483182], [0.0794483182, 0.0]],
[[0.433536565, 0.0], [0.0, 0.385524695]],
],
]),
None,
None,
None,
),
),
],
energy_shift={"ActiveSpaceTransformer": 0.0},
))
expected.add_property(
ElectronicDipoleMoment([
DipoleMoment(
"x",
[
OneBodyElectronicIntegrals(ElectronicBasis.MO,
(np.zeros((2, 2)), None))
],
shift={"ActiveSpaceTransformer": 0.0},
),
DipoleMoment(
"y",
[
OneBodyElectronicIntegrals(ElectronicBasis.MO,
(np.zeros((2, 2)), None))
],
shift={"ActiveSpaceTransformer": 0.0},
),
DipoleMoment(
"z",
[
OneBodyElectronicIntegrals(
ElectronicBasis.MO,
(
np.asarray([[0.69447435, -1.01418298],
[-1.01418298, 0.69447435]]),
None,
),
)
],
shift={"ActiveSpaceTransformer": 0.0},
),
]))
self.assertDriverResult(driver_result_reduced, expected)
def test_custom_property(self) -> None:
"""Tests support for custom property objects."""
container = VibrationalPropertiesContainer()
container.add(ElectronicDipoleMoment())
self.assertIn(ElectronicDipoleMoment, container)