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 _update_driver_input_schemas(self):
driver_name = self.get_section_property(InputParser.DRIVER,
JSONSchema.NAME)
if driver_name is not None:
driver_name = driver_name.strip().lower()
mgr = ConfigurationManager()
configs = mgr.configurations
for (name, config) in configs.items():
name = name.lower()
if driver_name is not None and driver_name == name:
input_schema = copy.deepcopy(
config['input_schema']) if 'input_schema' in config else {
'type': 'object'
}
if '$schema' in input_schema:
del input_schema['$schema']
if 'id' in input_schema:
del input_schema['id']
self._json_schema.schema['properties'][
driver_name] = input_schema
else:
if name in self._json_schema.schema['properties']:
del self._json_schema.schema['properties'][name]
def _update_driver_sections(self):
driver_name = self.get_section_property(InputParser.DRIVER,
JSONSchema.NAME)
if driver_name is not None:
driver_name = driver_name.strip().lower()
mgr = ConfigurationManager()
configs = mgr.configurations
for (name, config) in configs.items():
name = name.lower()
if driver_name is not None and driver_name == name:
continue
if name in self._sections:
del self._sections[name]
if driver_name is not None and driver_name not in self._sections:
self.set_section(driver_name)
value = self.get_section_default_properties(driver_name)
if isinstance(value, dict):
for property_name, property_value in value.items():
self.set_section_property(driver_name, property_name,
property_value)
else:
if value is None:
types = self.get_section_types(driver_name)
if 'null' not in types:
if 'string' in types:
value = ''
elif 'object' in types:
value = {}
elif 'array' in types:
value = []
self.set_section_data(driver_name, value)
def __init__(self,view):
self._view = view
self._model = Model()
self._filemenu = None
self._title = tk.StringVar()
self._sectionsView = None
self._emptyView = None
self._sectionView_title = tk.StringVar()
self._propertiesView = None
self._textView = None
self._outputView = None
self._progress = None
self._button_text = None
self._start_button = None
self._save_algo_json = tk.IntVar()
self._save_algo_json.set(0)
self._thread_queue = queue.Queue()
self._thread = None
self._command = Controller._START
self._driver_names = []
config_mgr = ConfigurationManager()
for name in config_mgr.module_names:
try:
config_mgr.get_driver_instance(name)
self._driver_names.append(name)
except:
pass
self._process_stop = False
self._validate_integer_command = self._view.register(Controller._validate_integer)
self._validate_float_command = self._view.register(Controller._validate_float)
self._available_backends = []
self._backendsthread = None
self.get_available_backends()
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('bravyi_kitaev_sf')
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):
cfg_mgr = ConfigurationManager()
hdf5_cfg = OrderedDict([
('hdf5_input', self._get_resource_path('test_driver_hdf5.hdf5'))
])
section = {'properties': hdf5_cfg}
driver = cfg_mgr.get_driver_instance('HDF5')
self.qmolecule = driver.run(section)
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
driver = cfg_mgr.get_driver_instance('PYSCF')
molecule = driver.run(section)
self.fer_op = FermionicOperator(h1=molecule._one_body_integrals,
h2=molecule._two_body_integrals)
def procesar_molecula(configuracionmolecula, distancia=None):
"""Esta función analiza que tipo de procesado necesita una molécula para pedir su construcción"""
gestorconfiguracion = ConfigurationManager()
if configuracionmolecula["driver"] == "PYSCF":
molecula = __procesar_molecula_pyscf(configuracionmolecula, distancia)
else:
driver = gestorconfiguracion.get_driver_instance(
configuracionmolecula["driver"])
molecula = driver.run(configuracionmolecula["configuracion"])
return molecula
def setUp(self):
cfg_mgr = ConfigurationManager()
pyscf_cfg = OrderedDict([('atom', 'H .0 .0 .0; H .0 .0 0.735'),
('unit', 'Angstrom'), ('charge', 0),
('spin', 0), ('basis', 'sto3g')])
section = {'properties': pyscf_cfg}
try:
driver = cfg_mgr.get_driver_instance('PYSCF')
except ModuleNotFoundError:
self.skipTest('PYSCF driver does not appear to be installed')
self.qmolecule = driver.run(section)
def driver_names(self):
from qiskit_aqua_chemistry.drivers import ConfigurationManager
if self._driver_names is None:
self._driver_names = []
config_mgr = ConfigurationManager()
for name in config_mgr.module_names:
try:
config_mgr.get_driver_instance(name)
self._driver_names.append(name)
except:
pass
return self._driver_names
def setUp(self):
cfg_mgr = ConfigurationManager()
gaussian_cfg = """
# rhf/sto-3g scf(conventional) geom=nocrowd
h2 molecule
0 1
H 0.0 0.0 0.0
H 0.0 0.0 0.735
"""
section = {'data': gaussian_cfg}
try:
driver = cfg_mgr.get_driver_instance('GAUSSIAN')
except AquaChemistryError:
self.skipTest('GAUSSIAN driver does not appear to be installed')
self.qmolecule = driver.run(section)
def setUp(self):
cfg_mgr = ConfigurationManager()
hdf5_cfg = OrderedDict([
('hdf5_input', self._get_resource_path('test_driver_hdf5.hdf5'))
])
section = {'properties': hdf5_cfg}
driver = cfg_mgr.get_driver_instance('HDF5')
self.qmolecule = driver.run(section)
core = Hamiltonian(transformation='full',
qubit_mapping='parity',
two_qubit_reduction=True,
freeze_core=False,
orbital_reduction=[],
max_workers=4)
self.algo_input = core.run(self.qmolecule)
self.reference_energy = -1.857275027031588
def setUp(self):
cfg_mgr = ConfigurationManager()
psi4_cfg = """
molecule h2 {
0 1
H 0.0 0.0 0.0
H 0.0 0.0 0.735
}
set {
basis sto-3g
scf_type pk
}
"""
section = {'data': psi4_cfg}
try:
driver = cfg_mgr.get_driver_instance('PSI4')
except AquaChemistryError:
self.skipTest('PSI4 driver does not appear to be installed')
self.qmolecule = driver.run(section)
def apply(self, preferences):
changed = False
packages = self._preferences.get_packages(
Preferences.PACKAGE_TYPE_DRIVERS, [])
if packages != preferences.get_packages(
Preferences.PACKAGE_TYPE_DRIVERS, []):
preferences.set_packages(Preferences.PACKAGE_TYPE_DRIVERS,
packages)
changed = True
packages = self._preferences.get_packages(
Preferences.PACKAGE_TYPE_CHEMISTRY, [])
if packages != preferences.get_packages(
Preferences.PACKAGE_TYPE_CHEMISTRY, []):
preferences.set_packages(Preferences.PACKAGE_TYPE_CHEMISTRY,
packages)
changed = True
if changed:
preferences.save()
refresh_operators()
configuration_mgr = ConfigurationManager()
configuration_mgr.refresh_drivers()
def __init__(self):
"""Create an AquaChemistry object."""
self._configuration_mgr = ConfigurationManager()
self._parser = None
self._core = None
def __init__(self):
"""Create Model object."""
self._configuration_mgr = ConfigurationManager()
self._parser = InputParser()
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 ModuleNotFoundError:
self.skipTest('PYSCF driver does not appear to be installed')
self.molecule = driver.run(section)
ferOp = FermionicOperator(h1=self.molecule._one_body_integrals,
h2=self.molecule._two_body_integrals)
self.qubitOp = ferOp.mapping(
map_type='PARITY', threshold=1e-10).two_qubit_reduced_operator(2)
exact_eigensolver = get_algorithm_instance('ExactEigensolver')
exact_eigensolver.init_args(self.qubitOp, 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.qubitOp.num_qubits + (2 if two_qubit_reduction else
0)
qubit_mapping = 'parity'
num_time_slices = 50
n_ancillae = 9
qpe = get_algorithm_instance('QPE')
qpe.setup_quantum_backend(backend='local_qasm_simulator',
shots=100,
skip_transpiler=True)
state_in = get_initial_state_instance('HartreeFock')
state_in.init_args(self.qubitOp.num_qubits, num_orbitals,
qubit_mapping, two_qubit_reduction, num_particles)
iqft = get_iqft_instance('STANDARD')
iqft.init_args(n_ancillae)
qpe.init_args(self.qubitOp,
state_in,
iqft,
num_time_slices,
n_ancillae,
paulis_grouping='random',
expansion_mode='suzuki',
expansion_order=2)
result = qpe.run()
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)
def _load_driver_names():
if InputParser._DRIVER_NAMES is None:
mgr = ConfigurationManager()
InputParser._DRIVER_NAMES = [
name.lower() for name in mgr.module_names
]