class MolecularDataTest(unittest.TestCase): def setUp(self): self.geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))] self.basis = 'sto-3g' self.multiplicity = 1 self.filename = os.path.join(DATA_DIRECTORY, 'H2_sto-3g_singlet_0.7414') self.molecule = MolecularData(self.geometry, self.basis, self.multiplicity, filename=self.filename) self.molecule.load() def testUnitConversion(self): """Test the unit conversion routines""" unit_angstrom = 1.0 bohr = angstroms_to_bohr(unit_angstrom) self.assertAlmostEqual(bohr, 1.889726) inverse_transform = bohr_to_angstroms(bohr) self.assertAlmostEqual(inverse_transform, 1.0) def test_name_molecule(self): charge = 0 correct_name = str('H2_sto-3g_singlet_0.7414') computed_name = name_molecule(self.geometry, self.basis, self.multiplicity, charge, description="0.7414") self.assertEqual(correct_name, computed_name) self.assertEqual(correct_name, self.molecule.name) # Check (+) charge charge = 1 correct_name = "H2_sto-3g_singlet_1+_0.7414" computed_name = name_molecule(self.geometry, self.basis, self.multiplicity, charge, description="0.7414") self.assertEqual(correct_name, computed_name) # Check > 1 atom type charge = 0 correct_name = "H1-F1_sto-3g_singlet_1.0" test_geometry = [('H', (0, 0, 0)), ('F', (0, 0, 1.0))] computed_name = name_molecule(test_geometry, self.basis, self.multiplicity, charge, description="1.0") self.assertEqual(correct_name, computed_name) # Check errors in naming with self.assertRaises(TypeError): test_molecule = MolecularData(self.geometry, self.basis, self.multiplicity, description=5) correct_name = str('H2_sto-3g_singlet') test_molecule = self.molecule = MolecularData( self.geometry, self.basis, self.multiplicity, data_directory=DATA_DIRECTORY) self.assertSequenceEqual(correct_name, test_molecule.name) def test_invalid_multiplicity(self): geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))] basis = 'sto-3g' multiplicity = -1 with self.assertRaises(MoleculeNameError): MolecularData(geometry, basis, multiplicity) def test_geometry_from_file(self): water_geometry = [('O', (0., 0., 0.)), ('H', (0.757, 0.586, 0.)), ('H', (-.757, 0.586, 0.))] filename = os.path.join(DATA_DIRECTORY, 'geometry_example.txt') test_geometry = geometry_from_file(filename) for atom in range(3): self.assertAlmostEqual(water_geometry[atom][0], test_geometry[atom][0]) for coordinate in range(3): self.assertAlmostEqual(water_geometry[atom][1][coordinate], test_geometry[atom][1][coordinate]) def test_save_load(self): n_atoms = self.molecule.n_atoms orbitals = self.molecule.canonical_orbitals self.assertFalse(orbitals is None) self.molecule.n_atoms += 1 self.assertEqual(self.molecule.n_atoms, n_atoms + 1) self.molecule.load() self.assertEqual(self.molecule.n_atoms, n_atoms) dummy_data = self.molecule.get_from_file("dummy_entry") self.assertTrue(dummy_data is None) def test_dummy_save(self): # Make fake molecule. filename = os.path.join(DATA_DIRECTORY, 'dummy_molecule') geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))] basis = '6-31g*' multiplicity = 7 charge = -1 description = 'openfermion_forever' molecule = MolecularData(geometry, basis, multiplicity, charge, description, filename) # Make some attributes to save. molecule.n_orbitals = 10 molecule.n_qubits = 10 molecule.nuclear_repulsion = -12.3 molecule.hf_energy = 99. molecule.canonical_orbitals = [1, 2, 3, 4] molecule.orbital_energies = [5, 6, 7, 8] molecule.one_body_integrals = [5, 6, 7, 8] molecule.two_body_integrals = [5, 6, 7, 8] molecule.mp2_energy = -12. molecule.cisd_energy = 32. molecule.cisd_one_rdm = numpy.arange(10) molecule.cisd_two_rdm = numpy.arange(10) molecule.fci_energy = 232. molecule.fci_one_rdm = numpy.arange(11) molecule.fci_two_rdm = numpy.arange(11) molecule.ccsd_energy = 88. molecule.ccsd_single_amps = [1, 2, 3] molecule.ccsd_double_amps = [1, 2, 3] molecule.general_calculations['Fake CI'] = 1.2345 molecule.general_calculations['Fake CI 2'] = 5.2345 # Test missing calculation and information exceptions molecule.one_body_integrals = None with self.assertRaises(MissingCalculationError): molecule.get_integrals() molecule.hf_energy = 99. with self.assertRaises(ValueError): molecule.get_active_space_integrals([], []) molecule.fci_energy = None with self.assertRaises(MissingCalculationError): molecule.get_molecular_rdm(use_fci=True) molecule.fci_energy = 232. molecule.cisd_energy = None with self.assertRaises(MissingCalculationError): molecule.get_molecular_rdm(use_fci=False) molecule.cisd_energy = 232. # Save molecule. molecule.save() try: # Change attributes and load. molecule.ccsd_energy = -2.232 # Load molecule. new_molecule = MolecularData(filename=filename) molecule.general_calculations = {} molecule.load() self.assertEqual(molecule.general_calculations['Fake CI'], 1.2345) # Tests re-load functionality molecule.save() # Check CCSD energy. self.assertAlmostEqual(new_molecule.ccsd_energy, molecule.ccsd_energy) self.assertAlmostEqual(molecule.ccsd_energy, 88.) finally: os.remove(filename + '.hdf5') def test_file_loads(self): """Test different filename specs""" data_directory = os.path.join(DATA_DIRECTORY) molecule = MolecularData(self.geometry, self.basis, self.multiplicity, filename=self.filename) test_hf_energy = molecule.hf_energy molecule = MolecularData(self.geometry, self.basis, self.multiplicity, filename=self.filename + ".hdf5", data_directory=data_directory) self.assertAlmostEqual(test_hf_energy, molecule.hf_energy) molecule = MolecularData(filename=self.filename + ".hdf5") integrals = molecule.one_body_integrals self.assertTrue(integrals is not None) with self.assertRaises(ValueError): MolecularData() def test_active_space(self): """Test simple active space truncation features""" # Start w/ no truncation core_const, one_body_integrals, two_body_integrals = ( self.molecule.get_active_space_integrals(active_indices=[0, 1])) self.assertAlmostEqual(core_const, 0.0) self.assertAlmostEqual( scipy.linalg.norm(one_body_integrals - self.molecule.one_body_integrals), 0.0) self.assertAlmostEqual( scipy.linalg.norm(two_body_integrals - self.molecule.two_body_integrals), 0.0) def test_energies(self): self.assertAlmostEqual(self.molecule.hf_energy, -1.1167, places=4) self.assertAlmostEqual(self.molecule.mp2_energy, -1.1299, places=4) self.assertAlmostEqual(self.molecule.cisd_energy, -1.1373, places=4) self.assertAlmostEqual(self.molecule.ccsd_energy, -1.1373, places=4) self.assertAlmostEqual(self.molecule.ccsd_energy, -1.1373, places=4) def test_rdm_and_rotation(self): # Compute total energy from RDM. molecular_hamiltonian = self.molecule.get_molecular_hamiltonian() molecular_rdm = self.molecule.get_molecular_rdm() total_energy = molecular_rdm.expectation(molecular_hamiltonian) self.assertAlmostEqual(total_energy, self.molecule.cisd_energy) # Build random rotation with correction dimension. num_spatial_orbitals = self.molecule.n_orbitals rotation_generator = numpy.random.randn(num_spatial_orbitals, num_spatial_orbitals) rotation_matrix = scipy.linalg.expm(rotation_generator - rotation_generator.T) # Compute total energy from RDM under some basis set rotation. molecular_rdm.rotate_basis(rotation_matrix) molecular_hamiltonian.rotate_basis(rotation_matrix) total_energy = molecular_rdm.expectation(molecular_hamiltonian) self.assertAlmostEqual(total_energy, self.molecule.cisd_energy) def test_get_up_down_electrons(self): largest_atom = 10 # Test first row correct_alpha = [0, 1, 1, 2, 2, 3, 4, 5, 5, 5, 5] correct_beta = [0, 0, 1, 1, 2, 2, 2, 2, 3, 4, 5] for n_electrons in range(1, largest_atom + 1): # Make molecule. basis = 'sto-3g' atom_name = periodic_table[n_electrons] molecule = make_atom(atom_name, basis) # Test. self.assertAlmostEqual(molecule.get_n_alpha_electrons(), correct_alpha[n_electrons]) self.assertAlmostEqual(molecule.get_n_beta_electrons(), correct_beta[n_electrons]) def test_abstract_molecule(self): """Test an abstract molecule like jellium for saving and loading""" jellium_interaction = get_interaction_operator( jellium_model(Grid(2, 2, 1.0))) jellium_molecule = get_molecular_data(jellium_interaction, geometry="Jellium", basis="PlaneWave22", multiplicity=1, n_electrons=4) jellium_filename = jellium_molecule.filename jellium_molecule.save() jellium_molecule.load() correct_name = "Jellium_PlaneWave22_singlet" self.assertEqual(jellium_molecule.name, correct_name) os.remove("{}.hdf5".format(jellium_filename)) def test_load_molecular_hamiltonian(self): bond_length = 1.45 geometry = [('Li', (0., 0., 0.)), ('H', (0., 0., bond_length))] lih_hamiltonian = load_molecular_hamiltonian(geometry, 'sto-3g', 1, format(bond_length), 2, 2) self.assertEqual(count_qubits(lih_hamiltonian), 4) lih_hamiltonian = load_molecular_hamiltonian(geometry, 'sto-3g', 1, format(bond_length), 2, 3) self.assertEqual(count_qubits(lih_hamiltonian), 6) lih_hamiltonian = load_molecular_hamiltonian(geometry, 'sto-3g', 1, format(bond_length), None, None) self.assertEqual(count_qubits(lih_hamiltonian), 12) def test_jk_matr(self): h2mol = self.molecule j = h2mol.get_j() k = h2mol.get_k() pyscf_j = [[0.67448877, 0.6634681], [0.6634681, 0.69739377]] pyscf_k = [[0.67448877, 0.18128881], [0.18128881, 0.69739377]] for p in range(j.shape[0]): for q in range(j.shape[1]): self.assertAlmostEqual(j[p][q], pyscf_j[p][q]) self.assertAlmostEqual(k[p][q], pyscf_k[p][q]) ndocc = h2mol.n_electrons // 2 E1bdy = 2 * h2mol.one_body_integrals[:ndocc, :ndocc] E2bdy = (2 * j[:ndocc, :ndocc]) - k[:ndocc, :ndocc] E_test = h2mol.nuclear_repulsion + E1bdy + E2bdy self.assertAlmostEqual(E_test, h2mol.hf_energy) def test_antisymint(self): h2mol = self.molecule antisymm_spin_orb_tei = h2mol.get_antisym() nocc = h2mol.n_electrons mol_H = h2mol.get_molecular_hamiltonian() E1bdy = np.sum(np.diag(mol_H.one_body_tensor[:nocc, :nocc])) E2bdy = 1/2.*np.einsum('ijij',\ antisymm_spin_orb_tei[:nocc,:nocc,:nocc,:nocc]) E_test = h2mol.nuclear_repulsion + E1bdy + E2bdy self.assertAlmostEqual(E_test, h2mol.hf_energy) def test_missing_calcs_for_integrals(self): geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.8764))] basis = 'sto-3g' multiplicity = 1 molecule = MolecularData(geometry, basis, multiplicity) with self.assertRaises(MissingCalculationError): molecule.get_j() with self.assertRaises(MissingCalculationError): molecule.get_k() with self.assertRaises(MissingCalculationError): molecule.get_antisym()
def test_dummy_save(self): # Make fake molecule. filename = os.path.join(DATA_DIRECTORY, 'dummy_molecule') geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))] basis = '6-31g*' multiplicity = 7 charge = -1 description = 'openfermion_forever' molecule = MolecularData(geometry, basis, multiplicity, charge, description, filename) # Make some attributes to save. molecule.n_orbitals = 10 molecule.n_qubits = 10 molecule.nuclear_repulsion = -12.3 molecule.hf_energy = 99. molecule.canonical_orbitals = [1, 2, 3, 4] molecule.orbital_energies = [5, 6, 7, 8] molecule.one_body_integrals = [5, 6, 7, 8] molecule.two_body_integrals = [5, 6, 7, 8] molecule.mp2_energy = -12. molecule.cisd_energy = 32. molecule.cisd_one_rdm = numpy.arange(10) molecule.cisd_two_rdm = numpy.arange(10) molecule.fci_energy = 232. molecule.fci_one_rdm = numpy.arange(11) molecule.fci_two_rdm = numpy.arange(11) molecule.ccsd_energy = 88. molecule.ccsd_single_amps = [1, 2, 3] molecule.ccsd_double_amps = [1, 2, 3] molecule.general_calculations['Fake CI'] = 1.2345 molecule.general_calculations['Fake CI 2'] = 5.2345 # Test missing calculation and information exceptions molecule.one_body_integrals = None with self.assertRaises(MissingCalculationError): molecule.get_integrals() molecule.hf_energy = 99. with self.assertRaises(ValueError): molecule.get_active_space_integrals([], []) molecule.fci_energy = None with self.assertRaises(MissingCalculationError): molecule.get_molecular_rdm(use_fci=True) molecule.fci_energy = 232. molecule.cisd_energy = None with self.assertRaises(MissingCalculationError): molecule.get_molecular_rdm(use_fci=False) molecule.cisd_energy = 232. # Save molecule. molecule.save() try: # Change attributes and load. molecule.ccsd_energy = -2.232 # Load molecule. new_molecule = MolecularData(filename=filename) molecule.general_calculations = {} molecule.load() self.assertEqual(molecule.general_calculations['Fake CI'], 1.2345) # Tests re-load functionality molecule.save() # Check CCSD energy. self.assertAlmostEqual(new_molecule.ccsd_energy, molecule.ccsd_energy) self.assertAlmostEqual(molecule.ccsd_energy, 88.) finally: os.remove(filename + '.hdf5')