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 _populate_driver_result_electronic_energy( self, driver_result: ElectronicStructureDriverResult) -> None: # pylint: disable=import-error from pyquante2 import onee_integrals from pyquante2.ints.integrals import twoe_integrals basis_transform = driver_result.get_property(ElectronicBasisTransform) integrals = onee_integrals(self._bfs, self._mol) hij = integrals.T + integrals.V hijkl = twoe_integrals(self._bfs) one_body_ao = OneBodyElectronicIntegrals(ElectronicBasis.AO, (hij, None)) two_body_ao = TwoBodyElectronicIntegrals( ElectronicBasis.AO, (hijkl.transform(np.identity(self._nmo)), None, None, None), ) one_body_mo = one_body_ao.transform_basis(basis_transform) two_body_mo = two_body_ao.transform_basis(basis_transform) electronic_energy = ElectronicEnergy( [one_body_ao, two_body_ao, one_body_mo, two_body_mo], nuclear_repulsion_energy=self._mol.nuclear_repulsion(), reference_energy=self._calc.energy, ) if hasattr(self._calc, "orbe"): orbs_energy = self._calc.orbe orbs_energy_b = None else: orbs_energy = self._calc.orbea orbs_energy_b = self._calc.orbeb orbital_energies = ((orbs_energy, orbs_energy_b) if orbs_energy_b is not None else orbs_energy) electronic_energy.orbital_energies = np.asarray(orbital_energies) electronic_energy.kinetic = OneBodyElectronicIntegrals( ElectronicBasis.AO, (integrals.T, None)) electronic_energy.overlap = OneBodyElectronicIntegrals( ElectronicBasis.AO, (integrals.S, None)) driver_result.add_property(electronic_energy)
def test_transform_basis(self): """Test transform_basis""" mat_a = np.arange(1, 5).reshape((2, 2)) mat_b = np.arange(-4, 0).reshape((2, 2)) transform = ElectronicBasisTransform(ElectronicBasis.AO, ElectronicBasis.MO, 2 * np.eye(2)) with self.subTest("Pure Alpha"): ints_ao = OneBodyElectronicIntegrals(ElectronicBasis.AO, (mat_a, None)) ints_mo = ints_ao.transform_basis(transform) self.assertTrue(np.allclose(ints_mo._matrices[0], 4 * mat_a)) self.assertIsNone(ints_mo._matrices[1]) with self.subTest("Alpha and Beta"): ints_ao = OneBodyElectronicIntegrals(ElectronicBasis.AO, (mat_a, mat_b)) ints_mo = ints_ao.transform_basis(transform) self.assertTrue(np.allclose(ints_mo._matrices[0], 4 * mat_a)) self.assertTrue(np.allclose(ints_mo._matrices[1], 4 * mat_b)) with self.subTest("Beta custom coeff with only alpha"): transform_beta = ElectronicBasisTransform( ElectronicBasis.AO, ElectronicBasis.MO, 2 * np.eye(2), 3 * np.eye(2) ) ints_ao = OneBodyElectronicIntegrals(ElectronicBasis.AO, (mat_a, None)) ints_mo = ints_ao.transform_basis(transform_beta) self.assertTrue(np.allclose(ints_mo._matrices[0], 4 * mat_a)) self.assertTrue(np.allclose(ints_mo._matrices[1], 9 * mat_a)) with self.subTest("Beta custom coeff"): transform_beta = ElectronicBasisTransform( ElectronicBasis.AO, ElectronicBasis.MO, 2 * np.eye(2), 3 * np.eye(2) ) ints_ao = OneBodyElectronicIntegrals(ElectronicBasis.AO, (mat_a, mat_b)) ints_mo = ints_ao.transform_basis(transform_beta) self.assertTrue(np.allclose(ints_mo._matrices[0], 4 * mat_a)) self.assertTrue(np.allclose(ints_mo._matrices[1], 9 * mat_b)) with self.subTest("Final basis match"): ints_ao = OneBodyElectronicIntegrals(ElectronicBasis.MO, (mat_a, None)) ints_mo = ints_ao.transform_basis(transform) self.assertEqual(ints_ao, ints_mo) with self.subTest("Inital basis mismatch"): with self.assertRaises(QiskitNatureError): ints_ao = OneBodyElectronicIntegrals(ElectronicBasis.SO, mat_a) ints_ao.transform_basis(transform)
def _populate_driver_result_electronic_energy( self, driver_result: ElectronicStructureDriverResult ) -> None: # pylint: disable=import-error from pyscf import gto basis_transform = driver_result.get_property(ElectronicBasisTransform) one_body_ao = OneBodyElectronicIntegrals( ElectronicBasis.AO, (self._calc.get_hcore(), None), ) two_body_ao = TwoBodyElectronicIntegrals( ElectronicBasis.AO, (self._mol.intor("int2e", aosym=1), None, None, None), ) one_body_mo = one_body_ao.transform_basis(basis_transform) two_body_mo = two_body_ao.transform_basis(basis_transform) electronic_energy = ElectronicEnergy( [one_body_ao, two_body_ao, one_body_mo, two_body_mo], nuclear_repulsion_energy=gto.mole.energy_nuc(self._mol), reference_energy=self._calc.e_tot, ) electronic_energy.kinetic = OneBodyElectronicIntegrals( ElectronicBasis.AO, (self._mol.intor_symmetric("int1e_kin"), None), ) electronic_energy.overlap = OneBodyElectronicIntegrals( ElectronicBasis.AO, (self._calc.get_ovlp(), None), ) orbs_energy, orbs_energy_b = self._extract_mo_data("mo_energy") orbital_energies = ( (orbs_energy, orbs_energy_b) if orbs_energy_b is not None else orbs_energy ) electronic_energy.orbital_energies = np.asarray(orbital_energies) driver_result.add_property(electronic_energy)
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