def test_bksf_mapping(self):
"""Test bksf mapping
The spectrum of bksf mapping should be half of jordan wigner mapping.
"""
cfg_mgr = ConfigurationManager()
pyscf_cfg = OrderedDict([('atom', 'H .0 .0 0.7414; H .0 .0 .0'), ('unit', 'Angstrom'),
('charge', 0), ('spin', 0), ('basis', 'sto3g')])
section = {}
section['properties'] = pyscf_cfg
driver = cfg_mgr.get_driver_instance('PYSCF')
molecule = driver.run(section)
fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
jw_op = fer_op.mapping('jordan_wigner')
bksf_op = fer_op.mapping('bksf')
jw_op.to_matrix()
bksf_op.to_matrix()
jw_eigs = np.linalg.eigvals(jw_op.matrix.toarray())
bksf_eigs = np.linalg.eigvals(bksf_op.matrix.toarray())
jw_eigs = np.sort(np.around(jw_eigs.real, 6))
bksf_eigs = np.sort(np.around(bksf_eigs.real, 6))
overlapped_spectrum = np.sum(np.isin(jw_eigs, bksf_eigs))
self.assertEqual(overlapped_spectrum, jw_eigs.size // 2)
def test_bksf_mapping(self):
"""Test bksf mapping.
The spectrum of bksf mapping should be half of jordan wigner mapping.
"""
driver = PySCFDriver(atom='H .0 .0 0.7414; H .0 .0 .0',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
jw_op = fer_op.mapping('jordan_wigner')
bksf_op = fer_op.mapping('bksf')
jw_op.to_matrix()
bksf_op.to_matrix()
jw_eigs = np.linalg.eigvals(jw_op.matrix.toarray())
bksf_eigs = np.linalg.eigvals(bksf_op.matrix.toarray())
jw_eigs = np.sort(np.around(jw_eigs.real, 6))
bksf_eigs = np.sort(np.around(bksf_eigs.real, 6))
overlapped_spectrum = np.sum(np.isin(jw_eigs, bksf_eigs))
self.assertEqual(overlapped_spectrum, jw_eigs.size // 2)
def get_qubit_operator(h1, h2=None, qubit_reduction=False, map_type="parity",
threshold=1.e-10):
# half-filling
num_particles = h1.shape[0]/2
fop = FermionicOperator(h1=h1, h2=h2)
qop = fop.mapping(map_type=map_type, threshold=threshold)
if qubit_reduction:
qop = qop.two_qubit_reduced_operator(num_particles)
qop.chop(threshold)
return qop
def test_iqpe(self, distance):
self.algorithm = 'IQPE'
self.log.debug('Testing End-to-End with IQPE on H2 with '
'inter-atomic distance {}.'.format(distance))
try:
driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 {}'.format(distance),
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
self.molecule = driver.run()
qubit_mapping = 'parity'
fer_op = FermionicOperator(h1=self.molecule.one_body_integrals, h2=self.molecule.two_body_integrals)
self.qubit_op = fer_op.mapping(map_type=qubit_mapping, threshold=1e-10).two_qubit_reduced_operator(2)
exact_eigensolver = ExactEigensolver(self.qubit_op, k=1)
results = exact_eigensolver.run()
self.reference_energy = results['energy']
self.log.debug('The exact ground state energy is: {}'.format(results['energy']))
num_particles = self.molecule.num_alpha + self.molecule.num_beta
two_qubit_reduction = True
num_orbitals = self.qubit_op.num_qubits + (2 if two_qubit_reduction else 0)
num_time_slices = 50
num_iterations = 12
state_in = HartreeFock(self.qubit_op.num_qubits, num_orbitals,
num_particles, qubit_mapping, two_qubit_reduction)
iqpe = IQPE(self.qubit_op, state_in, num_time_slices, num_iterations,
paulis_grouping='random', expansion_mode='suzuki', expansion_order=2,
shallow_circuit_concat=True)
backend = qiskit.Aer.get_backend('qasm_simulator')
quantum_instance = QuantumInstance(backend, shots=100, pass_manager=PassManager())
result = iqpe.run(quantum_instance)
self.log.debug('top result str label: {}'.format(result['top_measurement_label']))
self.log.debug('top result in decimal: {}'.format(result['top_measurement_decimal']))
self.log.debug('stretch: {}'.format(result['stretch']))
self.log.debug('translation: {}'.format(result['translation']))
self.log.debug('final energy from QPE: {}'.format(result['energy']))
self.log.debug('reference energy: {}'.format(self.reference_energy))
self.log.debug('ref energy (transformed): {}'.format(
(self.reference_energy + result['translation']) * result['stretch'])
)
self.log.debug('ref binary str label: {}'.format(decimal_to_binary(
(self.reference_energy + result['translation']) * result['stretch'],
max_num_digits=num_iterations + 3,
fractional_part_only=True
)))
np.testing.assert_approx_equal(result['energy'], self.reference_energy, significant=2)
def test_freezing_core(self):
cfg_mgr = ConfigurationManager()
pyscf_cfg = OrderedDict([('atom', 'H .0 .0 -1.160518; Li .0 .0 0.386839'),
('unit', 'Angstrom'), ('charge', 0),
('spin', 0), ('basis', 'sto3g')])
section = {}
section['properties'] = pyscf_cfg
driver = cfg_mgr.get_driver_instance('PYSCF')
molecule = driver.run(section)
fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
fer_op, energy_shift = fer_op.fermion_mode_freezing([0, 6])
gt = -7.8187092970493755
diff = abs(energy_shift - gt)
self.assertLess(diff, 1e-6)
cfg_mgr = ConfigurationManager()
pyscf_cfg = OrderedDict([('atom', 'H .0 .0 .0; Na .0 .0 1.888'), ('unit', 'Angstrom'),
('charge', 0), ('spin', 0), ('basis', 'sto3g')])
section = {}
section['properties'] = pyscf_cfg
driver = cfg_mgr.get_driver_instance('PYSCF')
molecule = driver.run(section)
fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
fer_op, energy_shift = fer_op.fermion_mode_freezing([0, 1, 2, 3, 4, 10, 11, 12, 13, 14])
gt = -162.58414559586748
diff = abs(energy_shift - gt)
self.assertLess(diff, 1e-6)
def test_freezing_core(self):
driver = PySCFDriver(atom='H .0 .0 -1.160518; Li .0 .0 0.386839',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
fer_op, energy_shift = fer_op.fermion_mode_freezing([0, 6])
gt = -7.8187092970493755
diff = abs(energy_shift - gt)
self.assertLess(diff, 1e-6)
driver = PySCFDriver(atom='H .0 .0 .0; Na .0 .0 1.888',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
fer_op, energy_shift = fer_op.fermion_mode_freezing(
[0, 1, 2, 3, 4, 10, 11, 12, 13, 14])
gt = -162.58414559586748
diff = abs(energy_shift - gt)
self.assertLess(diff, 1e-6)
def setUp(self):
try:
driver = PySCFDriver(atom='Li .0 .0 .0; H .0 .0 1.595',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
molecule = driver.run()
self.fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
def setUp(self):
cfg_mgr = ConfigurationManager()
pyscf_cfg = OrderedDict([('atom', 'Li .0 .0 .0; H .0 .0 1.595'), ('unit', 'Angstrom'),
('charge', 0), ('spin', 0), ('basis', 'sto3g')])
section = {}
section['properties'] = pyscf_cfg
try:
driver = cfg_mgr.get_driver_instance('PYSCF')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
molecule = driver.run(section)
self.fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
# convert all negative idx to positive
remove_list = [x % molecule.num_orbitals for x in remove_list]
freeze_list = [x % molecule.num_orbitals for x in freeze_list]
# update the idx in remove_list of the idx after frozen, since the idx of orbitals are changed after freezing
remove_list = [x - len(freeze_list) for x in remove_list]
remove_list += [
x + molecule.num_orbitals - len(freeze_list) for x in remove_list
]
freeze_list += [x + molecule.num_orbitals for x in freeze_list]
# prepare fermionic hamiltonian with orbital freezing and eliminating, and then map to qubit hamiltonian
# and if PARITY mapping is selected, reduction qubits
energy_shift = 0.0
qubit_reduction = True if map_type == 'parity' else False
ferOp = FermionicOperator(h1=h1, h2=h2)
# if len(freeze_list) > 0:
# ferOp, energy_shift = ferOp.fermion_mode_freezing(freeze_list)
# num_spin_orbitals -= len(freeze_list)
# num_particles -= len(freeze_list)
# if len(remove_list) > 0:
# ferOp = ferOp.fermion_mode_elimination(remove_list)
# num_spin_orbitals -= len(remove_list)
qubitOp = ferOp.mapping(map_type=map_type, threshold=0.00000001)
qubitOp = qubitOp.two_qubit_reduced_operator(
num_particles) if qubit_reduction else qubitOp
qubitOp.chop(10**-10)
print(qubitOp.print_operators())
print(qubitOp)
]
qubit_mappings = {
'JW': 'jordan_wigner'
# 'P':'parity'
# 'BK':'bravyi_kitaev'
}
for basis in bases:
for qm_name, qubit_mapping in qubit_mappings.items():
for var_form_name, var_form_class in var_forms.items():
for mol_name, molecule_str in molecules.items():
driver = PySCFDriver(molecule_str, basis=basis)
mol = driver.run()
n_qubits = mol.one_body_integrals.shape[0]
n_electrons = mol.num_alpha + mol.num_beta - mol.molecular_charge
ferOp = FermionicOperator(h1=mol.one_body_integrals,
h2=mol.two_body_integrals)
qubitOp = ferOp.mapping(map_type=qubit_mapping, threshold=1e-8)
qubitOp.chop(1e-10)
initial_hf = HartreeFock(num_qubits=n_qubits,
num_orbitals=n_qubits,
qubit_mapping=qubit_mapping,
two_qubit_reduction=False,
num_particles=n_electrons)
var_form = UCCSD(num_qubits=n_qubits,
num_orbitals=n_qubits,
num_particles=n_electrons,
depth=1,
initial_state=initial_hf,
qubit_mapping=qubit_mapping)
number_amplitudes = len(var_form._single_excitations) + len(
var_form._double_excitations)
def test_qpe(self, distance):
self.algorithm = 'QPE'
self.log.debug(
'Testing End-to-End with QPE on H2 with inter-atomic distance {}.'.
format(distance))
cfg_mgr = ConfigurationManager()
pyscf_cfg = OrderedDict([('atom',
'H .0 .0 .0; H .0 .0 {}'.format(distance)),
('unit', 'Angstrom'), ('charge', 0),
('spin', 0), ('basis', 'sto3g')])
section = {}
section['properties'] = pyscf_cfg
try:
driver = cfg_mgr.get_driver_instance('PYSCF')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
self.molecule = driver.run(section)
qubit_mapping = 'parity'
fer_op = FermionicOperator(h1=self.molecule.one_body_integrals,
h2=self.molecule.two_body_integrals)
self.qubit_op = fer_op.mapping(
map_type=qubit_mapping,
threshold=1e-10).two_qubit_reduced_operator(2)
exact_eigensolver = ExactEigensolver(self.qubit_op, k=1)
results = exact_eigensolver.run()
self.reference_energy = results['energy']
self.log.debug('The exact ground state energy is: {}'.format(
results['energy']))
num_particles = self.molecule.num_alpha + self.molecule.num_beta
two_qubit_reduction = True
num_orbitals = self.qubit_op.num_qubits + \
(2 if two_qubit_reduction else 0)
num_time_slices = 50
n_ancillae = 9
state_in = HartreeFock(self.qubit_op.num_qubits, num_orbitals,
num_particles, qubit_mapping,
two_qubit_reduction)
iqft = Standard(n_ancillae)
qpe = QPE(self.qubit_op,
state_in,
iqft,
num_time_slices,
n_ancillae,
paulis_grouping='random',
expansion_mode='suzuki',
expansion_order=2,
shallow_circuit_concat=True)
backend = get_aer_backend('qasm_simulator')
quantum_instance = QuantumInstance(backend,
shots=100,
pass_manager=PassManager())
result = qpe.run(quantum_instance)
self.log.debug('measurement results: {}'.format(
result['measurements']))
self.log.debug('top result str label: {}'.format(
result['top_measurement_label']))
self.log.debug('top result in decimal: {}'.format(
result['top_measurement_decimal']))
self.log.debug('stretch: {}'.format(
result['stretch']))
self.log.debug('translation: {}'.format(
result['translation']))
self.log.debug('final energy from QPE: {}'.format(result['energy']))
self.log.debug('reference energy: {}'.format(
self.reference_energy))
self.log.debug('ref energy (transformed): {}'.format(
(self.reference_energy + result['translation']) *
result['stretch']))
self.log.debug('ref binary str label: {}'.format(
decimal_to_binary((self.reference_energy + result['translation']) *
result['stretch'],
max_num_digits=n_ancillae + 3,
fractional_part_only=True)))
np.testing.assert_approx_equal(result['energy'],
self.reference_energy,
significant=2)
from qiskit_chemistry import FermionicOperator
from qiskit_chemistry.drivers import PySCFDriver, UnitsType
from pyscf import mp, fci
# Use PySCF, a classical computational chemistry software package, to compute the one-body and two-body integrals in
# molecular-orbital basis, necessary to form the Fermionic operator
driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 0.735; H .0 .0 1.2',
unit=UnitsType.ANGSTROM,
spin=1,
basis='sto3g')
molecule = driver.run()
num_particles = molecule.num_alpha + molecule.num_beta
num_spin_orbitals = molecule.num_orbitals * 2
# Build the qubit operator, which is the input to the VQE algorithm in Aqua
ferOp = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
map_type = 'PARITY'
qubitOp = ferOp.mapping(map_type)
qubitOp = qubitOp.two_qubit_reduced_operator(num_particles)
num_qubits = qubitOp.num_qubits
# set the backend for the quantum computation
from qiskit import Aer
backend = Aer.get_backend('statevector_simulator')
# setup a classical optimizer for VQE
from qiskit_aqua.components.optimizers import L_BFGS_B
optimizer = L_BFGS_B()
# setup the initial state for the variational form
from qiskit_chemistry.aqua_extensions.components.initial_states import HartreeFock