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):
super().setUp()
try:
driver = PySCFDriver(molecule=TestDriver.MOLECULE)
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
self.qmolecule = driver.run()
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))
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
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,
expansion_mode='suzuki',
expansion_order=2, shallow_circuit_concat=True)
backend = qiskit.Aer.get_backend('qasm_simulator')
run_config = RunConfig(shots=100, max_credits=10, memory=False)
quantum_instance = QuantumInstance(backend, run_config, pass_manager=PassManager())
result = qpe.run(quantum_instance)
self.log.debug('eigvals: {}'.format(result['eigvals']))
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)
def get_qubit_op(target_molecule):
geometry, multiplicity, charge = generate_molecule_dict()
driver = PySCFDriver(atom=geometry_convert(target_molecule),
unit=UnitsType.ANGSTROM,
charge=charge[target_molecule],
spin=0,
basis='sto3g')
molecule = driver.run()
repulsion_energy = molecule.nuclear_repulsion_energy
num_particles = molecule.num_alpha + molecule.num_beta
num_spin_orbitals = molecule.num_orbitals * 2
one_RDM = make_one_rdm(target_molecule)
w = calculate_noons(one_RDM)
freeze_list, remove_list = generate_freeze_remove_list(w)
remove_list = [x % molecule.num_orbitals for x in remove_list]
freeze_list = [x % molecule.num_orbitals for x in freeze_list]
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]
ferOp = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
ferOp, energy_shift = ferOp.fermion_mode_freezing(freeze_list)
num_spin_orbitals -= len(freeze_list)
num_particles -= len(freeze_list)
ferOp = ferOp.fermion_mode_elimination(remove_list)
num_spin_orbitals -= len(remove_list)
qubitOp = ferOp.mapping(map_type='bravyi_kitaev', threshold=0.00000001)
qubitOp = Z2Symmetries.two_qubit_reduction(qubitOp, num_particles)
shift = energy_shift + repulsion_energy
return qubitOp, num_particles, num_spin_orbitals, shift
def get_H2_data(dist):
"""
Use the qiskit chemistry package to get the qubit Hamiltonian for LiH
Parameters
----------
dist : float
The nuclear separations
Returns
-------
qubitOp : qiskit.aqua.operators.WeightedPauliOperator
Qiskit representation of the qubit Hamiltonian
shift : float
The ground state of the qubit Hamiltonian needs to be corrected by this amount of
energy to give the real physical energy. This includes the replusive energy between
the nuclei and the energy shift of the frozen orbitals.
"""
driver = PySCFDriver(atom="H .0 .0 .0; H .0 .0 " + str(dist),
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g',
)
molecule = driver.run()
repulsion_energy = molecule.nuclear_repulsion_energy
num_particles = molecule.num_alpha + molecule.num_beta
num_spin_orbitals = molecule.num_orbitals * 2
ferOp = FermionicOperator(h1=molecule.one_body_integrals, h2=molecule.two_body_integrals)
qubitOp = ferOp.mapping(map_type='parity', threshold=1E-8)
qubitOp = Z2Symmetries.two_qubit_reduction(qubitOp,num_particles)
shift = repulsion_energy
return qubitOp, shift
def test_hf_value(self, mapping):
try:
driver = PySCFDriver(atom='Li .0 .0 .0; H .0 .0 1.6',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
qmolecule = driver.run()
core = Hamiltonian(transformation=TransformationType.FULL,
qubit_mapping=mapping,
two_qubit_reduction=False,
freeze_core=False,
orbital_reduction=[])
qubit_op, _ = core.run(qmolecule)
qubit_op = op_converter.to_matrix_operator(qubit_op)
hf = HartreeFock(qubit_op.num_qubits,
core.molecule_info['num_orbitals'],
core.molecule_info['num_particles'], mapping.value,
False)
qc = hf.construct_circuit('vector')
hf_energy = qubit_op.evaluate_with_statevector(
qc)[0].real + core._nuclear_repulsion_energy
self.assertAlmostEqual(qmolecule.hf_energy, hf_energy, places=8)
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 setUp(self):
super().setUp()
self.core_energy = 0.7199
self.num_orbitals = 2
self.num_electrons = 2
self.spin_number = 0
self.wf_symmetry = 1
self.orb_symmetries = [1, 1]
self.mo_onee = [[1.2563, 0.0], [0.0, 0.4719]]
self.mo_eri = [0.6757, 0.0, 0.1809, 0.6646, 0.0, 0.6986]
try:
driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 0.735',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
qmolecule = driver.run()
dump = tempfile.NamedTemporaryFile()
FCIDumpDriver.dump(qmolecule, dump.name)
# pylint: disable=import-outside-toplevel
from pyscf.tools import fcidump as pyscf_fcidump
self.dumped = pyscf_fcidump.read(dump.name)
dump.close()
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed.')
except ImportError:
self.skipTest('PYSCF driver does not appear to be installed.')
def lih(dist=1.5):
mol = PySCFDriver(atom=
'H 0.0 0.0 0.0;'\
'Li 0.0 0.0 {}'.format(dist), unit=UnitsType.ANGSTROM, charge=0,
spin=0, basis='sto-3g')
mol = mol.run()
freeze_list = [0]
remove_list = [-3, -2]
repulsion_energy = mol.nuclear_repulsion_energy
num_particles = mol.num_alpha + mol.num_beta
num_spin_orbitals = mol.num_orbitals * 2
remove_list = [x % mol.num_orbitals for x in remove_list]
freeze_list = [x % mol.num_orbitals for x in freeze_list]
remove_list = [x - len(freeze_list) for x in remove_list]
remove_list += [
x + mol.num_orbitals - len(freeze_list) for x in remove_list
]
freeze_list += [x + mol.num_orbitals for x in freeze_list]
ferOp = FermionicOperator(h1=mol.one_body_integrals,
h2=mol.two_body_integrals)
ferOp, energy_shift = ferOp.fermion_mode_freezing(freeze_list)
num_spin_orbitals -= len(freeze_list)
num_particles -= len(freeze_list)
ferOp = ferOp.fermion_mode_elimination(remove_list)
num_spin_orbitals -= len(remove_list)
qubitOp = ferOp.mapping(map_type='parity', threshold=0.00000001)
qubitOp = Z2Symmetries.two_qubit_reduction(qubitOp, num_particles)
shift = energy_shift + repulsion_energy
cHam = op_converter.to_matrix_operator(qubitOp)
cHam = cHam.dense_matrix + shift * numpy.identity(16)
return cHam
def get_qubit_op(dist):
#atom="Li .0 .0 .0; H .0 .0 " + str(dist)
#atom="Be .0 .0 .0; H .0 .0 -" + str(dist) + "; H .0 .0 " + str(dist)
driver = PySCFDriver("Li .0 .0 .0; H .0 .0 " + str(dist),
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
freeze_list = [0]
remove_list = [-3, -2]
repulsion_energy = molecule.nuclear_repulsion_energy
num_particles = molecule.num_alpha + molecule.num_beta
num_spin_orbitals = molecule.num_orbitals * 2
remove_list = [x % molecule.num_orbitals for x in remove_list]
freeze_list = [x % molecule.num_orbitals for x in freeze_list]
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]
ferOp = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
ferOp, energy_shift = ferOp.fermion_mode_freezing(freeze_list)
num_spin_orbitals -= len(freeze_list)
num_particles -= len(freeze_list)
ferOp = ferOp.fermion_mode_elimination(remove_list)
num_spin_orbitals -= len(remove_list)
qubitOp = ferOp.mapping(map_type='parity', threshold=0.00000001)
qubitOp = Z2Symmetries.two_qubit_reduction(qubitOp, num_particles)
shift = energy_shift + repulsion_energy
return qubitOp, num_particles, num_spin_orbitals, shift
def test_particle_hole(self, atom, charge=0, spin=0, basis='sto3g', hf_method=HFMethodType.RHF):
""" particle hole test """
try:
driver = PySCFDriver(atom=atom,
unit=UnitsType.ANGSTROM,
charge=charge,
spin=spin,
basis=basis,
hf_method=hf_method)
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
config = '{}, charge={}, spin={}, basis={}, {}'.format(atom, charge,
spin, basis,
hf_method.value)
molecule = driver.run()
fer_op = FermionicOperator(h1=molecule.one_body_integrals, h2=molecule.two_body_integrals)
ph_fer_op, ph_shift = fer_op.particle_hole_transformation([molecule.num_alpha,
molecule.num_beta])
# ph_shift should be the electronic part of the hartree fock energy
self.assertAlmostEqual(-ph_shift,
molecule.hf_energy-molecule.nuclear_repulsion_energy, msg=config)
# Energy in original fer_op should same as ph transformed one added with ph_shift
jw_op = fer_op.mapping('jordan_wigner')
result = ExactEigensolver(jw_op).run()
ph_jw_op = ph_fer_op.mapping('jordan_wigner')
ph_result = ExactEigensolver(ph_jw_op).run()
self.assertAlmostEqual(result['energy'], ph_result['energy']-ph_shift, msg=config)
def setUp(self):
"""Setup."""
super().setUp()
try:
atom = 'H .0 .0 .7414; H .0 .0 .0'
pyscf_driver = PySCFDriver(atom=atom,
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
self.molecule = pyscf_driver.run()
warnings.filterwarnings('ignore', category=DeprecationWarning)
core = Hamiltonian(transformation=TransformationType.FULL,
qubit_mapping=QubitMappingType.PARITY,
two_qubit_reduction=True,
freeze_core=False,
orbital_reduction=[])
warnings.filterwarnings('always', category=DeprecationWarning)
qubit_op, _ = core.run(self.molecule)
exact_eigensolver = NumPyEigensolver(qubit_op,
k=2**qubit_op.num_qubits)
result = exact_eigensolver.run()
self.reference = result.eigenvalues.real
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
def setUp(self):
super().setUp()
# np.random.seed(50)
self.seed = 50
aqua_globals.random_seed = self.seed
try:
driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 0.735',
unit=UnitsType.ANGSTROM,
basis='sto3g')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
return
molecule = driver.run()
self.num_particles = molecule.num_alpha + molecule.num_beta
self.num_spin_orbitals = molecule.num_orbitals * 2
fer_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
map_type = 'PARITY'
qubit_op = fer_op.mapping(map_type)
self.qubit_op = Z2Symmetries.two_qubit_reduction(
to_weighted_pauli_operator(qubit_op), self.num_particles)
self.num_qubits = self.qubit_op.num_qubits
self.init_state = HartreeFock(self.num_spin_orbitals,
self.num_particles)
self.var_form_base = None
def test_qpe(self, distance):
""" qpe test """
self.log.debug('Testing End-to-End with QPE on '
'H2 with inter-atomic distance %s.', 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')
molecule = driver.run()
qubit_mapping = 'parity'
fer_op = FermionicOperator(
h1=molecule.one_body_integrals, h2=molecule.two_body_integrals)
qubit_op = fer_op.mapping(map_type=qubit_mapping, threshold=1e-10)
qubit_op = Z2Symmetries.two_qubit_reduction(qubit_op, 2)
exact_eigensolver = ExactEigensolver(qubit_op, k=1)
results = exact_eigensolver.run()
reference_energy = results['energy']
self.log.debug('The exact ground state energy is: %s', results['energy'])
num_particles = molecule.num_alpha + molecule.num_beta
two_qubit_reduction = True
num_orbitals = qubit_op.num_qubits + \
(2 if two_qubit_reduction else 0)
num_time_slices = 1
n_ancillae = 6
state_in = HartreeFock(qubit_op.num_qubits, num_orbitals,
num_particles, qubit_mapping, two_qubit_reduction)
iqft = Standard(n_ancillae)
qpe = QPE(qubit_op, state_in, iqft, num_time_slices, n_ancillae,
expansion_mode='suzuki',
expansion_order=2, shallow_circuit_concat=True)
backend = qiskit.BasicAer.get_backend('qasm_simulator')
quantum_instance = QuantumInstance(backend, shots=100)
result = qpe.run(quantum_instance)
self.log.debug('eigvals: %s', result['eigvals'])
self.log.debug('top result str label: %s', result['top_measurement_label'])
self.log.debug('top result in decimal: %s', result['top_measurement_decimal'])
self.log.debug('stretch: %s', result['stretch'])
self.log.debug('translation: %s', result['translation'])
self.log.debug('final energy from QPE: %s', result['energy'])
self.log.debug('reference energy: %s', reference_energy)
self.log.debug('ref energy (transformed): %s',
(reference_energy + result['translation']) * result['stretch'])
self.log.debug('ref binary str label: %s',
decimal_to_binary(
(reference_energy + result['translation']) * result['stretch'],
max_num_digits=n_ancillae + 3, fractional_part_only=True))
np.testing.assert_approx_equal(result['energy'], reference_energy, significant=2)
def createPlot(exactGroundStateEnergy=-1.14,
numberOfIterations=1000,
bondLength=0.735,
initialParameters=None,
numberOfParameters=16,
shotsPerPoint=1000,
registerSize=12,
map_type='jordan_wigner'):
if initialParameters is None:
initialParameters = np.random.rand(numberOfParameters)
global qubitOp
global qr_size
global shots
global values
global plottingTime
plottingTime = True
shots = shotsPerPoint
qr_size = registerSize
optimizer = COBYLA(maxiter=numberOfIterations)
iterations = []
values = []
for i in range(numberOfIterations):
iterations.append(i + 1)
#Build molecule with PySCF
driver = PySCFDriver(atom="H .0 .0 .0; H .0 .0 " + str(bondLength),
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
repulsion_energy = molecule.nuclear_repulsion_energy
num_spin_orbitals = molecule.num_orbitals * 2
num_particles = molecule.num_alpha + molecule.num_beta
#Map fermionic operator to qubit operator and start optimization
ferOp = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
qubitOp = ferOp.mapping(map_type=map_type, threshold=0.00000001)
sol_opt = optimizer.optimize(numberOfParameters,
energy_opt,
gradient_function=None,
variable_bounds=None,
initial_point=initialParameters)
#Adjust values to obtain Energy Error
for i in range(len(values)):
values[i] = values[i] + repulsion_energy - exactGroundStateEnergy
#Saving and Plotting Data
filename = 'Energy Error - Iterations'
with open(filename, 'wb') as f:
pickle.dump([iterations, values], f)
plt.plot(iterations, values)
plt.ylabel('Energy Error')
plt.xlabel('Iterations')
plt.show()
def setUp(self):
try:
driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 0.735',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
self.qmolecule = driver.run()
def test_h4(self):
""" Test for H4 chain """
atom = 'H 0 0 0; H 0 0 1; H 0 0 2; H 0 0 3'
driver = PySCFDriver(atom=atom,
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
self.assertAlmostEqual(molecule.hf_energy, -2.09854593699776, places=5)
def test_readme_sample(self):
""" readme sample test """
# pylint: disable=import-outside-toplevel
# --- Exact copy of sample code ----------------------------------------
from qiskit.chemistry import FermionicOperator
from qiskit.chemistry.drivers import PySCFDriver, UnitsType
from qiskit.aqua.operators import Z2Symmetries
# 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',
unit=UnitsType.ANGSTROM,
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
ferm_op = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
map_type = 'PARITY'
qubit_op = ferm_op.mapping(map_type)
qubit_op = Z2Symmetries.two_qubit_reduction(qubit_op, num_particles)
num_qubits = qubit_op.num_qubits
# 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.components.initial_states import HartreeFock
init_state = HartreeFock(num_qubits, num_spin_orbitals, num_particles)
# setup the variational form for VQE
from qiskit.aqua.components.variational_forms import RYRZ
var_form = RYRZ(num_qubits, initial_state=init_state)
# setup and run VQE
from qiskit.aqua.algorithms import VQE
algorithm = VQE(qubit_op, var_form, optimizer)
# set the backend for the quantum computation
from qiskit import Aer
backend = Aer.get_backend('statevector_simulator')
result = algorithm.run(backend)
print(result['energy'])
# ----------------------------------------------------------------------
self.assertAlmostEqual(result['energy'], -1.8572750301938803, places=6)
def test_h3(self):
""" Test for H3 chain, see also issue 1148 """
atom = 'H 0 0 0; H 0 0 1; H 0 0 2'
driver = PySCFDriver(atom=atom,
unit=UnitsType.ANGSTROM,
charge=0,
spin=1,
basis='sto3g')
molecule = driver.run()
self.assertAlmostEqual(molecule.hf_energy,
-1.523996200246108,
places=5)
def test_zmatrix(self):
""" Check z-matrix input """
atom = 'H; H 1 1.0'
driver = PySCFDriver(atom=atom,
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
self.assertAlmostEqual(molecule.hf_energy,
-1.0661086493179366,
places=5)
def setUp(self):
super().setUp()
try:
driver = PySCFDriver(atom='Li .0 .0 .0; H .0 .0 1.6',
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
self.qmolecule = driver.run()
self.mp2info = MP2Info(self.qmolecule)
def test_list_atom(self):
""" Check input with list of strings """
atom = ['H 0 0 0', 'H 0 0 1']
driver = PySCFDriver(atom=atom,
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
self.assertAlmostEqual(molecule.hf_energy,
-1.0661086493179366,
places=5)
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 get_LiH_qubit_op(dist):
"""
Use the qiskit chemistry package to get the qubit Hamiltonian for LiH
Parameters
----------
dist : float
The nuclear separations
Returns
-------
qubitOp : qiskit.aqua.operators.WeightedPauliOperator
Qiskit representation of the qubit Hamiltonian
shift : float
The ground state of the qubit Hamiltonian needs to be corrected by this amount of
energy to give the real physical energy. This includes the replusive energy between
the nuclei and the energy shift of the frozen orbitals.
"""
driver = PySCFDriver(
atom="Li .0 .0 .0; H .0 .0 " + str(dist),
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g',
)
molecule = driver.run()
freeze_list = [0]
remove_list = [-3, -2]
repulsion_energy = molecule.nuclear_repulsion_energy
num_particles = molecule.num_alpha + molecule.num_beta
num_spin_orbitals = molecule.num_orbitals * 2
remove_list = [x % molecule.num_orbitals for x in remove_list]
freeze_list = [x % molecule.num_orbitals for x in freeze_list]
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]
ferOp = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
ferOp, energy_shift = ferOp.fermion_mode_freezing(freeze_list)
num_spin_orbitals -= len(freeze_list)
num_particles -= len(freeze_list)
ferOp = ferOp.fermion_mode_elimination(remove_list)
num_spin_orbitals -= len(remove_list)
qubitOp = ferOp.mapping(map_type='parity', threshold=1E-8)
#qubitOp = qubitOp.two_qubit_reduced_operator(num_particles)
qubitOp = Z2Symmetries.two_qubit_reduction(qubitOp, num_particles)
shift = repulsion_energy + energy_shift
return qubitOp, shift
def test_logging_emit(self):
""" logging emit test """
with self.assertLogs(QiskitLogDomains.DOMAIN_CHEMISTRY.value,
level='INFO') as log:
try:
driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 0.735',
unit=UnitsType.ANGSTROM,
basis='sto3g')
except QiskitChemistryError:
self.skipTest('PYSCF driver does not appear to be installed')
return
_ = driver.run()
self.assertIn('PySCF', log.output[0])
def get_uccsd_circuit(molecule, theta_vector=None, use_basis_gates=False):
"""Produce the full UCCSD circuit.
Args:
molecule :: string - must be a key of MOLECULE_TO_INFO
theta_vector :: array - arguments for the vqe ansatz. If None, will generate random angles.
use_basis_gates :: bool - Mike and Ike gates if False, Basis gates if True.
Returns:
circuit :: qiskit.QuantumCircuit - the UCCSD circuit parameterized
by theta_vector, unoptimized
"""
molecule_info = MOLECULE_TO_INFO[molecule]
driver = PySCFDriver(atom=molecule_info.atomic_string, basis='sto3g')
qmolecule = driver.run()
hamiltonian = Hamiltonian(
qubit_mapping=QubitMappingType.PARITY,
two_qubit_reduction=True,
freeze_core=True,
orbital_reduction=molecule_info.orbital_reduction)
energy_input = hamiltonian.run(qmolecule)
qubit_op = energy_input.qubit_op
num_spin_orbitals = hamiltonian.molecule_info['num_orbitals']
num_particles = hamiltonian.molecule_info['num_particles']
map_type = hamiltonian._qubit_mapping
qubit_reduction = hamiltonian.molecule_info['two_qubit_reduction']
HF_state = HartreeFock(qubit_op.num_qubits, num_spin_orbitals,
num_particles, map_type, qubit_reduction)
var_form = UCCSD(qubit_op.num_qubits,
depth=1,
num_orbitals=num_spin_orbitals,
num_particles=num_particles,
active_occupied=molecule_info.active_occupied,
active_unoccupied=molecule_info.active_unoccupied,
initial_state=HF_state,
qubit_mapping=map_type,
two_qubit_reduction=qubit_reduction,
num_time_slices=1)
if theta_vector is None:
theta_vector = [
np.random.rand() * 2 * np.pi
for _ in range(var_form._num_parameters)
]
circuit = var_form.construct_circuit(theta_vector,
use_basis_gates=use_basis_gates)
return circuit
def get_qubit_op(dist):
driver = PySCFDriver(atom="H .0 .0 .0; H .0 .0 " + str(dist),
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
nuc_energy = molecule.nuclear_repulsion_energy
num_particles = molecule.num_alpha + molecule.num_beta
num_spin_orbitals = molecule.num_orbitals * 2
ferOp = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
qubitOp = ferOp.mapping(map_type='parity', threshold=0.00000001)
qubitOp = Z2Symmetries.two_qubit_reduction(qubitOp, num_particles)
return qubitOp, num_particles, num_spin_orbitals, nuc_energy
def JW_H(systemData={'driver_string': 'Li 0.0 0.0 0.0; H 0.0 0.0 1.548', 'basis': 'sto3g'}):
driver = PySCFDriver( atom=systemData["atomstring"],
basis=systemData["basis"] )
mol = driver.run()
OB = mol.one_body_integrals
TB = mol.two_body_integrals
FerOp = FermionicOperator(OB, TB)
mapping = FerOp.mapping('jordan_wigner')
weights = [w[0] for w in mapping.paulis]
operators = [w[1].to_label() for w in mapping.paulis]
return nk.operator.PauliStrings(operators, weights)
def test_mp2_h2(self):
""" Just one double excitation expected - see issue 1151 """
driver = PySCFDriver(atom="H 0 0 0; H 0 0 0.7",
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
mp2info = MP2Info(molecule)
terms = mp2info.mp2_terms()
self.assertEqual(1, len(terms.keys()))
np.testing.assert_array_almost_equal(
[-0.06834019757197064, -0.012232934733533095],
terms['0_1_2_3'],
decimal=6)
def createPlot1(bondLengthMin=0.5,
bondLengthMax=1.5,
numberOfPoints=10,
initialParameters=None,
numberOfParameters=16,
shotsPerPoint=1000,
registerSize=12,
map_type='jordan_wigner'):
if initialParameters is None:
initialParameters = np.random.rand(numberOfParameters)
global qubitOp
global qr_size
global shots
shots = shotsPerPoint
qr_size = registerSize
optimizer = COBYLA(maxiter=20)
bondLengths = []
values = []
delta = (bondLengthMax - bondLengthMin) / numberOfPoints
for i in range(numberOfPoints):
bondLengths.append(bondLengthMin + i * delta)
for bondLength in bondLengths:
driver = PySCFDriver(atom="H .0 .0 .0; H .0 .0 " + str(bondLength),
unit=UnitsType.ANGSTROM,
charge=0,
spin=0,
basis='sto3g')
molecule = driver.run()
repulsion_energy = molecule.nuclear_repulsion_energy
num_spin_orbitals = molecule.num_orbitals * 2
num_particles = molecule.num_alpha + molecule.num_beta
ferOp = FermionicOperator(h1=molecule.one_body_integrals,
h2=molecule.two_body_integrals)
qubitOp = ferOp.mapping(map_type=map_type, threshold=0.00000001)
sol_opt = optimizer.optimize(numberOfParameters,
energy_opt,
gradient_function=None,
variable_bounds=None,
initial_point=initialParameters)
values.append(sol_opt[1] + repulsion_energy)
filename = 'Energy - BondLengths'
with open(filename, 'wb') as f:
pickle.dump([bondLengths, values], f)
plt.plot(bondLengths, values)
plt.ylabel('Ground State Energy')
plt.xlabel('Bond Length')
plt.show()