def run(self) -> ElectronicStructureDriverResult: """Returns an ElectronicStructureDriverResult instance out of a FCIDump file.""" fcidump_data = parse(self._fcidump_input) hij = fcidump_data.get("hij", None) hij_b = fcidump_data.get("hij_b", None) hijkl = fcidump_data.get("hijkl", None) hijkl_ba = fcidump_data.get("hijkl_ba", None) hijkl_bb = fcidump_data.get("hijkl_bb", None) multiplicity = fcidump_data.get("MS2", 0) + 1 num_beta = (fcidump_data.get("NELEC") - (multiplicity - 1)) // 2 num_alpha = fcidump_data.get("NELEC") - num_beta particle_number = ParticleNumber( num_spin_orbitals=fcidump_data.get("NORB") * 2, num_particles=(num_alpha, num_beta), ) electronic_energy = ElectronicEnergy( [ OneBodyElectronicIntegrals(ElectronicBasis.MO, (hij, hij_b)), TwoBodyElectronicIntegrals(ElectronicBasis.MO, (hijkl, hijkl_ba, hijkl_bb, None)), ], nuclear_repulsion_energy=fcidump_data.get("ecore", None), ) driver_result = ElectronicStructureDriverResult() driver_result.add_property(electronic_energy) driver_result.add_property(particle_number) return driver_result
def _construct_driver_result(self) -> ElectronicStructureDriverResult: driver_result = ElectronicStructureDriverResult() self._populate_driver_result_molecule(driver_result) self._populate_driver_result_metadata(driver_result) self._populate_driver_result_basis_transform(driver_result) self._populate_driver_result_particle_number(driver_result) self._populate_driver_result_electronic_energy(driver_result) # 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(self._nmo * 2)) driver_result.add_property(Magnetization(self._nmo * 2)) return driver_result
def _construct_driver_result(self) -> ElectronicStructureDriverResult: # NOTE: under Python 3.6, pylint appears to be unable to properly identify this case of # nested abstract classes (cf. https://github.com/Qiskit/qiskit-nature/runs/3245395353). # However, since the tests pass I am adding an exception for this specific case. # pylint: disable=abstract-class-instantiated driver_result = ElectronicStructureDriverResult() self._populate_driver_result_molecule(driver_result) self._populate_driver_result_metadata(driver_result) self._populate_driver_result_basis_transform(driver_result) self._populate_driver_result_particle_number(driver_result) self._populate_driver_result_electronic_energy(driver_result) self._populate_driver_result_electronic_dipole_moment(driver_result) # TODO: once https://github.com/Qiskit/qiskit-terra/issues/6772 is resolved, we no longer # _have_ to add these properties. However, until then the interpret method relies on indices # of the aux_operators which are incorrect if these properties are not added. driver_result.add_property(AngularMomentum(self._mol.nao * 2)) driver_result.add_property(Magnetization(self._mol.nao * 2)) return driver_result
def run(self) -> ElectronicStructureDriverResult: """Returns an ElectronicStructureDriverResult instance out of a FCIDump file.""" fcidump_data = parse(self._fcidump_input) hij = fcidump_data.get("hij", None) hij_b = fcidump_data.get("hij_b", None) hijkl = fcidump_data.get("hijkl", None) hijkl_ba = fcidump_data.get("hijkl_ba", None) hijkl_bb = fcidump_data.get("hijkl_bb", None) multiplicity = fcidump_data.get("MS2", 0) + 1 num_beta = (fcidump_data.get("NELEC") - (multiplicity - 1)) // 2 num_alpha = fcidump_data.get("NELEC") - num_beta particle_number = ParticleNumber( num_spin_orbitals=fcidump_data.get("NORB") * 2, num_particles=(num_alpha, num_beta), ) electronic_energy = ElectronicEnergy( [ OneBodyElectronicIntegrals(ElectronicBasis.MO, (hij, hij_b)), TwoBodyElectronicIntegrals(ElectronicBasis.MO, (hijkl, hijkl_ba, hijkl_bb, None)), ], nuclear_repulsion_energy=fcidump_data.get("ecore", None), ) # NOTE: under Python 3.6, pylint appears to be unable to properly identify this case of # nested abstract classes (cf. https://github.com/Qiskit/qiskit-nature/runs/3245395353). # However, since the tests pass I am adding an exception for this specific case. # pylint: disable=abstract-class-instantiated driver_result = ElectronicStructureDriverResult() driver_result.add_property(electronic_energy) driver_result.add_property(particle_number) 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", "transformers/second_quantization/electronic")) 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", "transformers/second_quantization/electronic")) 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 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