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')