def make_h3_2_5() -> Tuple[RestrictedHartreeFockObjective, of.MolecularData,
np.ndarray, np.ndarray, np.ndarray]:
# load the molecule from moelcular data
h3_2_5_path = os.path.join(
hfvqe.__path__[0],
'molecular_data/hydrogen_chains/h_3_p_sto-3g/bond_distance_2.5')
molfile = os.path.join(h3_2_5_path,
'H3_plus_sto-3g_singlet_linear_r-2.5.hdf5')
molecule = of.MolecularData(filename=molfile)
molecule.load()
S = np.load(os.path.join(h3_2_5_path, 'overlap.npy'))
Hcore = np.load(os.path.join(h3_2_5_path, 'h_core.npy'))
TEI = np.load(os.path.join(h3_2_5_path, 'tei.npy'))
_, X = sp.linalg.eigh(Hcore, S)
obi = of.general_basis_change(Hcore, X, (1, 0))
tbi = np.einsum('psqr', of.general_basis_change(TEI, X, (1, 0, 1, 0)))
molecular_hamiltonian = generate_hamiltonian(obi, tbi,
molecule.nuclear_repulsion)
rhf_objective = RestrictedHartreeFockObjective(molecular_hamiltonian,
molecule.n_electrons)
scipy_result = rhf_minimization(rhf_objective)
return rhf_objective, molecule, scipy_result.x, obi, tbi
def make_h3_2_5(molecular_data_directory=None) \
-> Tuple[RestrictedHartreeFockObjective, of.MolecularData,
np.ndarray, np.ndarray, np.ndarray]:
if molecular_data_directory is None:
molecular_data_directory = _MOLECULAR_DATA_DIRECTORY
h3_2_5_path = f'{molecular_data_directory}/hydrogen_chains/h_3_p_sto-3g/bond_distance_2.5'
molfile = f'{h3_2_5_path}/H3_plus_sto-3g_singlet_linear_r-2.5.hdf5'
molecule = of.MolecularData(filename=molfile)
molecule.load()
S = np.load(os.path.join(h3_2_5_path, 'overlap.npy'))
Hcore = np.load(os.path.join(h3_2_5_path, 'h_core.npy'))
TEI = np.load(os.path.join(h3_2_5_path, 'tei.npy'))
_, X = sp.linalg.eigh(Hcore, S)
obi = of.general_basis_change(Hcore, X, (1, 0))
tbi = np.einsum('psqr', of.general_basis_change(TEI, X, (1, 0, 1, 0)))
molecular_hamiltonian = generate_hamiltonian(obi, tbi,
molecule.nuclear_repulsion)
rhf_objective = RestrictedHartreeFockObjective(molecular_hamiltonian,
molecule.n_electrons)
scipy_result = rhf_minimization(rhf_objective)
return rhf_objective, molecule, scipy_result.x, obi, tbi
def make_rhf_objective(molecule: of.MolecularData):
S, Hcore, TEI = get_ao_integrals(molecule)
_, X = sp.linalg.eigh(Hcore, S)
obi = of.general_basis_change(Hcore, X, (1, 0))
tbi = np.einsum('psqr', of.general_basis_change(TEI, X, (1, 0, 1, 0)))
molecular_hamiltonian = generate_hamiltonian(obi, tbi,
molecule.nuclear_repulsion)
rhf_objective = RestrictedHartreeFockObjective(molecular_hamiltonian,
molecule.n_electrons)
return rhf_objective, S, Hcore, TEI, obi, tbi
def make_rhf_objective(molecule):
# coverage: ignore
S, Hcore, TEI = get_ao_integrals(molecule)
_, X = scipy.linalg.eigh(Hcore, S)
molecular_hamiltonian = generate_hamiltonian(
general_basis_change(Hcore, X, (1, 0)),
numpy.einsum('psqr', general_basis_change(TEI, X, (1, 0, 1, 0)),
molecule.nuclear_repulsion))
rhf_objective = RestrictedHartreeFockObjective(molecular_hamiltonian,
molecule.n_electrons)
return rhf_objective, S, Hcore, TEI
def energy_from_opdm(opdm, constant, one_body_tensor, two_body_tensor):
"""Evaluate the energy of an opdm assuming the 2-RDM is opdm ^ opdm.
Args:
opdm: single spin-component of the full spin-orbital opdm.
constant: constant shift to the Hamiltonian. Commonly this is the
nuclear repulsion energy.
one_body_tensor: spatial one-body integrals
two_body_tensor: spatial two-body integrals
"""
spin_opdm = np.kron(opdm, np.eye(2))
spin_tpdm = 2 * wedge(spin_opdm, spin_opdm, (1, 1), (1, 1))
molecular_hamiltonian = generate_hamiltonian(
constant=constant,
one_body_integrals=one_body_tensor,
two_body_integrals=two_body_tensor)
rdms = InteractionRDM(spin_opdm, spin_tpdm)
return rdms.expectation(molecular_hamiltonian).real
