def do_make_molecule(self, *args, **kwargs) -> MolecularData:
energy = self.compute_energy(method="hf", *args, **kwargs)
wfn = self.logs['hf'].wfn
molecule = MolecularData(**self.parameters.molecular_data_param)
if wfn.nirrep() != 1:
wfn = wfn.c1_deep_copy(wfn.basisset())
molecule.one_body_integrals = self.compute_one_body_integrals(
ref_wfn=wfn)
if "two_body_ordering" not in kwargs:
molecule.two_body_integrals = self.compute_two_body_integrals(
ref_wfn=wfn)
else:
molecule.two_body_integrals = self.compute_two_body_integrals(
ref_wfn=wfn, ordering=kwargs["two_body_ordering"])
molecule.hf_energy = energy
molecule.nuclear_repulsion = wfn.variables(
)['NUCLEAR REPULSION ENERGY']
molecule.canonical_orbitals = numpy.asarray(wfn.Ca())
molecule.overlap_integrals = numpy.asarray(wfn.S())
molecule.n_orbitals = molecule.canonical_orbitals.shape[0]
molecule.n_qubits = 2 * molecule.n_orbitals
molecule.orbital_energies = numpy.asarray(wfn.epsilon_a())
molecule.fock_matrix = numpy.asarray(wfn.Fa())
molecule.save()
return molecule
def test_moleculardata_to_restricted_hamiltonian(self):
"""
Convert an OpenFermion MolecularData object to a
fqe.RestrictedHamiltonian
"""
h1e, h2e, _ = build_lih_data('energy')
# dummy geometry
geometry = [['Li', [0, 0, 0], ['H', [0, 0, 1.4]]]]
charge = 0
multiplicity = 1
molecule = MolecularData(geometry=geometry,
basis='sto-3g',
charge=charge,
multiplicity=multiplicity)
molecule.one_body_integrals = h1e
molecule.two_body_integrals = numpy.einsum('ijlk', -2 * h2e)
molecule.nuclear_repulsion = 0
restricted_ham = openfermion_utils.molecular_data_to_restricted_fqe_op(
molecule=molecule)
h1e_test, h2e_test = restricted_ham.tensors()
self.assertTrue(numpy.allclose(h1e_test, h1e))
self.assertTrue(numpy.allclose(h2e_test, h2e))
def get_ham_from_psi4(
wfn, mints, ndocc=None, nact=None, nuclear_repulsion_energy=0,
):
"""Get a molecular Hamiltonian from a Psi4 calculation.
Args:
wfn (psi4.core.Wavefunction): Psi4 wavefunction object
mints (psi4.core.MintsHelper): Psi4 molecular integrals helper
ndocc (int): number of doubly occupied molecular orbitals to
include in the saved Hamiltonian.
nact (int): number of active molecular orbitals to include in the
saved Hamiltonian.
nuclear_repulsion_energy (float): The ion-ion interaction energy.
Returns:
hamiltonian (openfermion.ops.InteractionOperator): the electronic
Hamiltonian.
"""
assert wfn.same_a_b_orbs(), (
"Extraction of Hamiltonian from wavefunction"
+ "with different alpha and beta orbitals not yet supported :("
)
orbitals = wfn.Ca().to_array(dense=True)
if nact is None and ndocc is None:
trf_mat = orbitals
ndocc = 0
nact = orbitals.shape[1]
print(
f"Active space selection options were reset to: ndocc = {ndocc} and nact = {nact}"
)
elif nact is not None and ndocc is None:
assert nact <= orbitals.shape[1]
ndocc = 0
trf_mat = orbitals[:, :nact]
print(
f"Active space selection options were reset to: ndocc = {ndocc} and nact = {nact}"
)
elif ndocc is not None and nact is None:
assert ndocc <= orbitals.shape[1]
nact = orbitals.shape[1] - ndocc
trf_mat = orbitals
print(
f"Active space selection options were reset to: ndocc = {ndocc} and nact = {nact}"
)
else:
assert orbitals.shape[1] >= nact + ndocc
trf_mat = orbitals[:, : nact + ndocc]
# Note: code refactored to use Psi4 integral-transformation routines
# no more storing the whole two-electron integral tensor when only an
# active space is needed
one_body_integrals = general_basis_change(
np.asarray(mints.ao_kinetic()), orbitals, (1, 0)
)
one_body_integrals += general_basis_change(
np.asarray(mints.ao_potential()), orbitals, (1, 0)
)
# Build the transformation matrices, i.e. the orbitals for which
# we want the integrals, as Psi4.core.Matrix objects
trf_mat = psi4.core.Matrix.from_array(trf_mat)
two_body_integrals = np.asarray(mints.mo_eri(trf_mat, trf_mat, trf_mat, trf_mat))
n_orbitals = trf_mat.shape[1]
two_body_integrals.reshape((n_orbitals, n_orbitals, n_orbitals, n_orbitals))
two_body_integrals = np.einsum("psqr", two_body_integrals)
# Truncate
one_body_integrals[np.absolute(one_body_integrals) < EQ_TOLERANCE] = 0.0
two_body_integrals[np.absolute(two_body_integrals) < EQ_TOLERANCE] = 0.0
occupied_indices = range(ndocc)
active_indices = range(ndocc, ndocc + nact)
# In order to keep the MolecularData class happy, we need a 'valid' molecule
molecular_data = MolecularData(
geometry=[("H", (0, 0, 0))], basis="", multiplicity=2
)
molecular_data.one_body_integrals = one_body_integrals
molecular_data.two_body_integrals = two_body_integrals
molecular_data.nuclear_repulsion = nuclear_repulsion_energy
hamiltonian = molecular_data.get_molecular_hamiltonian(
occupied_indices, active_indices
)
return hamiltonian
def get_ham_from_psi4(wfn,
mints,
n_active_extract=None,
freeze_core_extract=False,
orbs=None,
nuclear_repulsion_energy=0):
"""Get a molecular Hamiltonian from a Psi4 calculation.
Args:
wfn (psi4.core.Wavefunction): Psi4 wavefunction object
mints (psi4.core.MintsHelper): Psi4 molecular integrals helper
n_active_extract (int): number of molecular orbitals to include in the
saved Hamiltonian. If None, includes all orbitals, else you must provide
active orbitals in orbs.
freeze_core_extract (bool): whether to freeze core orbitals as doubly
occupied in the saved Hamiltonian.
orbs (psi4.core.Matrix): Psi4 orbitals for active space transformations. Must
include all occupied (also core in all cases).
nuclear_repulsion_energy (float): The ion-ion interaction energy.
Returns:
hamiltonian (openfermion.ops.InteractionOperator): the electronic
Hamiltonian. Note that the ion-ion electrostatic energy is not
included.
"""
assert wfn.same_a_b_orbs(), "Extraction of Hamiltonian from wavefunction" + \
"with different alpha and beta orbitals not yet supported :("
# Note: code refactored to use Psi4 integral-transformation routines
# no more storing the whole two-electron integral tensor when only an
# active space is needed
orbitals = wfn.Ca().to_array(dense=True)
one_body_integrals = general_basis_change(np.asarray(mints.ao_kinetic()),
orbitals, (1, 0))
one_body_integrals += general_basis_change(
np.asarray(mints.ao_potential()), orbitals, (1, 0))
# Build the transformation matrices, i.e. the orbitals for which
# we want the integrals, as Psi4.core.Matrix objects
n_core_extract = 0
if freeze_core_extract:
n_core_extract = wfn.nfrzc()
if n_active_extract is None:
trf_mat = wfn.Ca()
n_active_extract = wfn.nmo() - n_core_extract
else:
# If orbs is given, it allows us to perform the two-electron integrals
# transformation only in the space of active orbitals. Otherwise, we
# transform all orbitals and filter them out in the get_ham_from_integrals
# function
if orbs is None:
trf_mat = wfn.Ca()
else:
assert (orbs.to_array(dense=True).shape[1] == n_active_extract +
n_core_extract)
trf_mat = orbs
two_body_integrals = np.asarray(
mints.mo_eri(trf_mat, trf_mat, trf_mat, trf_mat))
n_orbitals = trf_mat.shape[1]
two_body_integrals.reshape(
(n_orbitals, n_orbitals, n_orbitals, n_orbitals))
two_body_integrals = np.einsum('psqr', two_body_integrals)
# Truncate
one_body_integrals[np.absolute(one_body_integrals) < EQ_TOLERANCE] = 0.
two_body_integrals[np.absolute(two_body_integrals) < EQ_TOLERANCE] = 0.
if n_active_extract is None and not freeze_core_extract:
occupied_indices = None
active_indices = None
else:
# Indices of occupied molecular orbitals
occupied_indices = range(n_core_extract)
# Indices of active molecular orbitals
active_indices = range(n_core_extract,
n_core_extract + n_active_extract)
# In order to keep the MolecularData class happy, we need a 'valid' molecule
molecular_data = MolecularData(geometry=[('H', (0, 0, 0))],
basis='',
multiplicity=2)
molecular_data.one_body_integrals = one_body_integrals
molecular_data.two_body_integrals = two_body_integrals
molecular_data.nuclear_repulsion = nuclear_repulsion_energy
hamiltonian = molecular_data.get_molecular_hamiltonian(
occupied_indices, active_indices)
return (hamiltonian)
