def test_load_from_dict(self):
json_dict = self.parser.get_sections()
p = InputParser(json_dict)
p.parse()
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_save(self):
save_path = self._get_resource_path('output.txt')
self.parser.save_to_file(save_path)
p = InputParser(save_path)
p.parse()
os.remove(save_path)
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def _run_drive(self, input, save_json_algo_file):
if input is None:
raise QiskitChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser,
save_json_algo_file)
driver_return[1]['input'] = driver_return[2].to_params()
driver_return[1]['input']['name'] = driver_return[2].configuration[
'name']
return driver_return[1]
class TestInputParser(QiskitChemistryTestCase):
"""InputParser tests."""
def setUp(self):
super().setUp()
filepath = self._get_resource_path('test_input_parser.txt')
self.parser = InputParser(filepath)
self.parser.parse()
def test_save(self):
""" save test """
save_path = self._get_resource_path('output.txt')
self.parser.save_to_file(save_path)
parse = InputParser(save_path)
parse.parse()
os.remove(save_path)
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(parse.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_load_from_dict(self):
""" load from dict test """
json_dict = self.parser.get_sections()
parse = InputParser(json_dict)
parse.parse()
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(parse.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_is_modified(self):
""" is modified test """
json_dict = self.parser.get_sections()
parse = InputParser(json_dict)
parse.parse()
parse.set_section_property('optimizer', 'maxfun', 1002)
self.assertTrue(parse.is_modified())
self.assertEqual(parse.get_section_property('optimizer', 'maxfun'),
1002)
def test_validate(self):
""" validate test """
json_dict = self.parser.get_sections()
parse = InputParser(json_dict)
parse.parse()
try:
parse.validate_merge_defaults()
except Exception as ex: # pylint: disable=broad-except
self.fail(str(ex))
with self.assertRaises(AquaError):
parse.set_section_property('backend', 'max_credits', -1)
def test_is_modified(self):
json_dict = self.parser.get_sections()
p = InputParser(json_dict)
p.parse()
p.set_section_property('optimizer', 'maxfun', 1002)
self.assertTrue(p.is_modified())
self.assertEqual(p.get_section_property('optimizer', 'maxfun'), 1002)
def test_validate(self):
json_dict = self.parser.get_sections()
p = InputParser(json_dict)
p.parse()
try:
p.validate_merge_defaults()
except Exception as e:
self.fail(str(e))
p.set_section_property('optimizer', 'dummy', 1002)
self.assertRaises(AquaError, p.validate_merge_defaults)
class TestInputParser(QiskitAquaChemistryTestCase):
"""InputParser tests."""
def setUp(self):
filepath = self._get_resource_path('test_input_parser.txt')
self.parser = InputParser(filepath)
self.parser.parse()
def test_save(self):
save_path = self._get_resource_path('output.txt')
self.parser.save_to_file(save_path)
p = InputParser(save_path)
p.parse()
os.remove(save_path)
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_load_from_dict(self):
json_dict = self.parser.get_sections()
p = InputParser(json_dict)
p.parse()
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_is_modified(self):
json_dict = self.parser.get_sections()
p = InputParser(json_dict)
p.parse()
p.set_section_property('optimizer', 'maxfun', 1002)
self.assertTrue(p.is_modified())
self.assertEqual(p.get_section_property('optimizer', 'maxfun'), 1002)
def test_validate(self):
json_dict = self.parser.get_sections()
p = InputParser(json_dict)
p.parse()
try:
p.validate_merge_defaults()
except Exception as e:
self.fail(str(e))
p.set_section_property('optimizer', 'dummy', 1002)
self.assertRaises(AquaError, p.validate_merge_defaults)
def test_validate(self):
json_dict = self.parser.get_sections()
p = InputParser(json_dict)
p.parse()
try:
p.validate_merge_defaults()
except Exception as e:
self.fail(str(e))
with self.assertRaises(AquaError):
p.set_section_property('backend', 'max_credits', -1)
def run(self, input, output=None, backend=None):
"""
Runs the Aqua Chemistry experiment
Args:
input (dictionary/filename): Input data
output (filename): Output data
backend (BaseBackend): backend object
Returns:
result dictionary
"""
if input is None:
raise QiskitChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser, False)
if driver_return[0] == QiskitChemistry._DRIVER_RUN_TO_HDF5:
logger.info('No further process.')
return {'printable': [driver_return[1]]}
data = run_algorithm(driver_return[1], driver_return[2], True, backend)
if not isinstance(data, dict):
raise QiskitChemistryError(
"Algorithm run result should be a dictionary")
convert_json_to_dict(data)
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Algorithm returned: {}'.format(
pprint.pformat(data, indent=4)))
lines, result = self._format_result(data)
logger.info('Processing complete. Final result available')
result['printable'] = lines
if output is not None:
with open(output, 'w') as f:
for line in lines:
print(line, file=f)
return result
def test_validate(self):
""" validate test """
json_dict = self.parser.get_sections()
parse = InputParser(json_dict)
parse.parse()
try:
parse.validate_merge_defaults()
except Exception as ex: # pylint: disable=broad-except
self.fail(str(ex))
with self.assertRaises(AquaError):
parse.set_section_property('backend', 'max_credits', -1)
def get_operator_section_names(self):
from qiskit.chemistry.parser import InputParser
from qiskit.aqua.parser import JSONSchema
from qiskit.chemistry.core import local_chemistry_operators
problem_name = None
if self._parser is not None:
problem_name = self.get_section_property(JSONSchema.PROBLEM,
JSONSchema.NAME)
if problem_name is None:
problem_name = self.get_property_default_value(
JSONSchema.PROBLEM, JSONSchema.NAME)
if problem_name is None:
return local_chemistry_operators()
operator_names = []
for operator_name in local_chemistry_operators():
problems = InputParser.get_operator_problems(operator_name)
if problem_name in problems:
operator_names.append(operator_name)
return operator_names
class QiskitChemistry:
"""Main Chemistry class."""
def __init__(self):
"""Create an QiskitChemistry object."""
self._parser = None
self._operator = None
self._qiskit_aqua = None
self._hdf5_file = None
self._chemistry_result = None
@property
def qiskit_aqua(self):
"""Returns Qiskit Aqua object."""
return self._qiskit_aqua
@property
def hdf5_file(self):
"""Returns Chemistry hdf5 path with chemistry results, if used."""
return self._hdf5_file
@property
def operator(self):
"""Returns Chemistry Operator."""
return self._operator
@property
def chemistry_result(self):
"""Returns Chemistry result."""
return self._chemistry_result
@property
def parser(self):
"""Returns Chemistry parser."""
return self._parser
def run(self, params, output=None, backend=None):
"""
Runs the Qiskit Chemistry experiment
Args:
params (Union(dictionary, filename)): Chemistry input data
output (filename): Output data
backend (QuantumInstance or BaseBackend): the experimental settings
to be used in place of backend name
Returns:
dict: result dictionary
Raises:
QiskitChemistryError: Missing Input, QiskitAqua object not created,
result should be dictionary
"""
if params is None:
raise QiskitChemistryError("Missing input.")
self.run_driver(params, backend)
if self.hdf5_file:
logger.info('No further process.')
self._chemistry_result = {
'printable': ["HDF5 file saved '{}'".format(self.hdf5_file)]
}
return self.chemistry_result
if self.qiskit_aqua is None:
raise QiskitChemistryError("QiskitAqua object not created.")
data = self.qiskit_aqua.run()
if not isinstance(data, dict):
raise QiskitChemistryError(
"Algorithm run result should be a dictionary")
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Algorithm returned: %s',
pprint.pformat(data, indent=4))
lines, self._chemistry_result = self.operator.process_algorithm_result(
data)
logger.info('Processing complete. Final result available')
self._chemistry_result['printable'] = lines
if output is not None:
with open(output, 'w') as file:
for line in self.chemistry_result['printable']:
print(line, file=file)
return self.chemistry_result
def run_driver(self, params, backend=None):
"""
Runs the Qiskit Chemistry driver
Args:
params (Union(dictionary, filename)): Chemistry input data
backend (QuantumInstance or BaseBackend): the experimental settings
to be used in place of backend name
Raises:
QiskitChemistryError: Missing Input
"""
if params is None:
raise QiskitChemistryError("Missing input.")
self._operator = None
self._chemistry_result = None
self._qiskit_aqua = None
self._hdf5_file = None
self._parser = InputParser(params)
self._parser.parse()
# before merging defaults attempts to find a provider for the backend in case no
# provider was passed
if backend is None and \
self._parser.get_section_property(JSONSchema.BACKEND, JSONSchema.PROVIDER) is None:
backend_name = self._parser.get_section_property(
JSONSchema.BACKEND, JSONSchema.NAME)
if backend_name is not None:
self._parser.set_section_property(
JSONSchema.BACKEND, JSONSchema.PROVIDER,
get_provider_from_backend(backend_name))
# set provider and name in input file for proper backend schema dictionary build
if isinstance(backend, BaseBackend):
self._parser.backend = backend
self._parser.add_section_properties(
JSONSchema.BACKEND, {
JSONSchema.PROVIDER: get_provider_from_backend(backend),
JSONSchema.NAME: backend.name(),
})
self._parser.validate_merge_defaults()
experiment_name = "-- no &NAME section found --"
if JSONSchema.NAME in self._parser.get_section_names():
name_sect = self._parser.get_section(JSONSchema.NAME)
if name_sect is not None:
experiment_name = str(name_sect)
logger.info('Running chemistry problem from input file: %s',
self._parser.get_filename())
logger.info('Experiment description: %s', experiment_name.rstrip())
driver_name = self._parser.get_section_property(
InputParser.DRIVER, JSONSchema.NAME)
if driver_name is None:
raise QiskitChemistryError(
'Property "{0}" missing in section "{1}"'.format(
JSONSchema.NAME, InputParser.DRIVER))
self._hdf5_file = \
self._parser.get_section_property(InputParser.DRIVER, InputParser.HDF5_OUTPUT)
if driver_name not in local_drivers():
raise QiskitChemistryError(
'Driver "{0}" missing in local drivers'.format(driver_name))
work_path = None
input_file = self._parser.get_filename()
if input_file is not None:
work_path = os.path.dirname(os.path.realpath(input_file))
section = self._parser.get_section(driver_name)
driver = get_driver_class(driver_name).init_from_input(section)
driver.work_path = work_path
molecule = driver.run()
if work_path is not None and \
self._hdf5_file is not None and not os.path.isabs(self._hdf5_file):
self._hdf5_file = os.path.abspath(
os.path.join(work_path, self._hdf5_file))
molecule.log()
if self._hdf5_file is not None:
molecule.save(self._hdf5_file)
logger.info("HDF5 file saved '%s'", self._hdf5_file)
# Run the Hamiltonian to process the QMolecule and get an input for algorithms
clazz = get_chemistry_operator_class(
self._parser.get_section_property(InputParser.OPERATOR,
JSONSchema.NAME))
self._operator = clazz.init_params(
self._parser.get_section_properties(InputParser.OPERATOR))
qubit_op, aux_ops = self.operator.run(molecule)
input_object = EnergyInput(qubit_op, aux_ops)
logger.debug('Core computed substitution variables %s',
self.operator.molecule_info)
result = self._parser.process_substitutions(
self.operator.molecule_info)
logger.debug('Substitutions %s', result)
aqua_params = {}
for section_name, section in self._parser.get_sections().items():
if section_name == JSONSchema.NAME or \
section_name == InputParser.DRIVER or \
section_name == driver_name.lower() or \
section_name == InputParser.OPERATOR or \
not isinstance(section, dict):
continue
aqua_params[section_name] = copy.deepcopy(section)
if JSONSchema.PROBLEM == section_name and \
InputParser.AUTO_SUBSTITUTIONS in aqua_params[section_name]:
del aqua_params[section_name][InputParser.AUTO_SUBSTITUTIONS]
self._qiskit_aqua = QiskitAqua(aqua_params, input_object, backend)
def run_driver(self, params, backend=None):
"""
Runs the Qiskit Chemistry driver
Args:
params (Union(dictionary, filename)): Chemistry input data
backend (QuantumInstance or BaseBackend): the experimental settings
to be used in place of backend name
Raises:
QiskitChemistryError: Missing Input
"""
if params is None:
raise QiskitChemistryError("Missing input.")
self._operator = None
self._chemistry_result = None
self._qiskit_aqua = None
self._hdf5_file = None
self._parser = InputParser(params)
self._parser.parse()
# before merging defaults attempts to find a provider for the backend in case no
# provider was passed
if backend is None and \
self._parser.get_section_property(JSONSchema.BACKEND, JSONSchema.PROVIDER) is None:
backend_name = self._parser.get_section_property(
JSONSchema.BACKEND, JSONSchema.NAME)
if backend_name is not None:
self._parser.set_section_property(
JSONSchema.BACKEND, JSONSchema.PROVIDER,
get_provider_from_backend(backend_name))
# set provider and name in input file for proper backend schema dictionary build
if isinstance(backend, BaseBackend):
self._parser.backend = backend
self._parser.add_section_properties(
JSONSchema.BACKEND, {
JSONSchema.PROVIDER: get_provider_from_backend(backend),
JSONSchema.NAME: backend.name(),
})
self._parser.validate_merge_defaults()
experiment_name = "-- no &NAME section found --"
if JSONSchema.NAME in self._parser.get_section_names():
name_sect = self._parser.get_section(JSONSchema.NAME)
if name_sect is not None:
experiment_name = str(name_sect)
logger.info('Running chemistry problem from input file: %s',
self._parser.get_filename())
logger.info('Experiment description: %s', experiment_name.rstrip())
driver_name = self._parser.get_section_property(
InputParser.DRIVER, JSONSchema.NAME)
if driver_name is None:
raise QiskitChemistryError(
'Property "{0}" missing in section "{1}"'.format(
JSONSchema.NAME, InputParser.DRIVER))
self._hdf5_file = \
self._parser.get_section_property(InputParser.DRIVER, InputParser.HDF5_OUTPUT)
if driver_name not in local_drivers():
raise QiskitChemistryError(
'Driver "{0}" missing in local drivers'.format(driver_name))
work_path = None
input_file = self._parser.get_filename()
if input_file is not None:
work_path = os.path.dirname(os.path.realpath(input_file))
section = self._parser.get_section(driver_name)
driver = get_driver_class(driver_name).init_from_input(section)
driver.work_path = work_path
molecule = driver.run()
if work_path is not None and \
self._hdf5_file is not None and not os.path.isabs(self._hdf5_file):
self._hdf5_file = os.path.abspath(
os.path.join(work_path, self._hdf5_file))
molecule.log()
if self._hdf5_file is not None:
molecule.save(self._hdf5_file)
logger.info("HDF5 file saved '%s'", self._hdf5_file)
# Run the Hamiltonian to process the QMolecule and get an input for algorithms
clazz = get_chemistry_operator_class(
self._parser.get_section_property(InputParser.OPERATOR,
JSONSchema.NAME))
self._operator = clazz.init_params(
self._parser.get_section_properties(InputParser.OPERATOR))
qubit_op, aux_ops = self.operator.run(molecule)
input_object = EnergyInput(qubit_op, aux_ops)
logger.debug('Core computed substitution variables %s',
self.operator.molecule_info)
result = self._parser.process_substitutions(
self.operator.molecule_info)
logger.debug('Substitutions %s', result)
aqua_params = {}
for section_name, section in self._parser.get_sections().items():
if section_name == JSONSchema.NAME or \
section_name == InputParser.DRIVER or \
section_name == driver_name.lower() or \
section_name == InputParser.OPERATOR or \
not isinstance(section, dict):
continue
aqua_params[section_name] = copy.deepcopy(section)
if JSONSchema.PROBLEM == section_name and \
InputParser.AUTO_SUBSTITUTIONS in aqua_params[section_name]:
del aqua_params[section_name][InputParser.AUTO_SUBSTITUTIONS]
self._qiskit_aqua = QiskitAqua(aqua_params, input_object, backend)
def setUp(self):
filepath = self._get_resource_path('test_input_parser.txt')
self.parser = InputParser(filepath)
self.parser.parse()
class QiskitChemistry(object):
"""Main entry point."""
KEY_HDF5_OUTPUT = 'hdf5_output'
_DRIVER_RUN_TO_HDF5 = 1
_DRIVER_RUN_TO_ALGO_INPUT = 2
def __init__(self):
"""Create an QiskitChemistry object."""
self._parser = None
self._core = None
def run(self, input, output=None, backend=None):
"""
Runs the Aqua Chemistry experiment
Args:
input (dictionary/filename): Input data
output (filename): Output data
backend (BaseBackend): backend object
Returns:
result dictionary
"""
if input is None:
raise QiskitChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser, False)
if driver_return[0] == QiskitChemistry._DRIVER_RUN_TO_HDF5:
logger.info('No further process.')
return {'printable': [driver_return[1]]}
data = run_algorithm(driver_return[1], driver_return[2], True, backend)
if not isinstance(data, dict):
raise QiskitChemistryError(
"Algorithm run result should be a dictionary")
convert_json_to_dict(data)
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Algorithm returned: {}'.format(
pprint.pformat(data, indent=4)))
lines, result = self._format_result(data)
logger.info('Processing complete. Final result available')
result['printable'] = lines
if output is not None:
with open(output, 'w') as f:
for line in lines:
print(line, file=f)
return result
def save_input(self, input_file):
"""
Save the input of a run to a file.
Params:
input_file (string): file path
"""
if self._parser is None:
raise QiskitChemistryError("Missing input information.")
self._parser.save_to_file(input_file)
def run_drive_to_jsonfile(self, input, jsonfile):
if jsonfile is None:
raise QiskitChemistryError("Missing json file")
data = self._run_drive(input, True)
if data is None:
logger.info('No data to save. No further process.')
return
with open(jsonfile, 'w') as fp:
json.dump(data, fp, sort_keys=True, indent=4)
print("Algorithm input file saved: '{}'".format(jsonfile))
def run_algorithm_from_jsonfile(self, jsonfile, output=None, backend=None):
"""
Runs the Aqua Chemistry experiment from json file
Args:
jsonfile (filename): Input data
output (filename): Output data
backend (BaseBackend): backend object
Returns:
result dictionary
"""
with open(jsonfile) as json_file:
return self.run_algorithm_from_json(json.load(json_file), output,
backend)
def run_algorithm_from_json(self, params, output=None, backend=None):
"""
Runs the Aqua Chemistry experiment from json dictionary
Args:
params (dictionary): Input data
output (filename): Output data
backend (BaseBackend): backend object
Returns:
result dictionary
"""
ret = run_algorithm(params, None, True, backend)
if not isinstance(ret, dict):
raise QiskitChemistryError(
"Algorithm run result should be a dictionary")
convert_json_to_dict(ret)
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Algorithm returned: {}'.format(
pprint.pformat(ret, indent=4)))
print('Output:')
if isinstance(ret, dict):
for k, v in ret.items():
print("'{}': {}".format(k, v))
else:
print(ret)
return ret
def _format_result(self, data):
lines, result = self._core.process_algorithm_result(data)
return lines, result
def run_drive(self, input):
return self._run_drive(input, False)
def _run_drive(self, input, save_json_algo_file):
if input is None:
raise QiskitChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser,
save_json_algo_file)
driver_return[1]['input'] = driver_return[2].to_params()
driver_return[1]['input']['name'] = driver_return[2].configuration[
'name']
return driver_return[1]
def _run_driver_from_parser(self, p, save_json_algo_file):
if p is None:
raise QiskitChemistryError("Missing parser")
# before merging defaults attempts to find a provider for the backend in case no
# provider was passed
if p.get_section_property(JSONSchema.BACKEND,
JSONSchema.PROVIDER) is None:
backend_name = p.get_section_property(JSONSchema.BACKEND,
JSONSchema.NAME)
if backend_name is not None:
p.set_section_property(JSONSchema.BACKEND, JSONSchema.PROVIDER,
get_provider_from_backend(backend_name))
p.validate_merge_defaults()
# logger.debug('ALgorithm Input Schema: {}'.format(json.dumps(p..get_sections(), sort_keys=True, indent=4)))
experiment_name = "-- no &NAME section found --"
if JSONSchema.NAME in p.get_section_names():
name_sect = p.get_section(JSONSchema.NAME)
if name_sect is not None:
experiment_name = str(name_sect)
logger.info('Running chemistry problem from input file: {}'.format(
p.get_filename()))
logger.info('Experiment description: {}'.format(
experiment_name.rstrip()))
driver_name = p.get_section_property(InputParser.DRIVER,
JSONSchema.NAME)
if driver_name is None:
raise QiskitChemistryError(
'Property "{0}" missing in section "{1}"'.format(
JSONSchema.NAME, InputParser.DRIVER))
hdf5_file = p.get_section_property(InputParser.DRIVER,
QiskitChemistry.KEY_HDF5_OUTPUT)
if driver_name not in local_drivers():
raise QiskitChemistryError(
'Driver "{0}" missing in local drivers'.format(driver_name))
work_path = None
input_file = p.get_filename()
if input_file is not None:
work_path = os.path.dirname(os.path.realpath(input_file))
section = p.get_section(driver_name)
driver = get_driver_class(driver_name).init_from_input(section)
driver.work_path = work_path
molecule = driver.run()
if work_path is not None and hdf5_file is not None and not os.path.isabs(
hdf5_file):
hdf5_file = os.path.abspath(os.path.join(work_path, hdf5_file))
molecule.log()
if hdf5_file is not None:
molecule._origin_driver_name = driver_name
molecule._origin_driver_config = section if isinstance(
section, str) else json.dumps(
section, sort_keys=True, indent=4)
molecule.save(hdf5_file)
text = "HDF5 file saved '{}'".format(hdf5_file)
logger.info(text)
if not save_json_algo_file:
logger.info('Run ended with hdf5 file saved.')
return QiskitChemistry._DRIVER_RUN_TO_HDF5, text
# Run the Hamiltonian to process the QMolecule and get an input for algorithms
cls = get_chemistry_operator_class(
p.get_section_property(InputParser.OPERATOR, JSONSchema.NAME))
self._core = cls.init_params(
p.get_section_properties(InputParser.OPERATOR))
input_object = self._core.run(molecule)
logger.debug('Core computed substitution variables {}'.format(
self._core.molecule_info))
result = p.process_substitutions(self._core.molecule_info)
logger.debug('Substitutions {}'.format(result))
params = {}
for section_name, section in p.get_sections().items():
if section_name == JSONSchema.NAME or \
section_name == InputParser.DRIVER or \
section_name == driver_name.lower() or \
section_name == InputParser.OPERATOR or \
not isinstance(section, dict):
continue
params[section_name] = copy.deepcopy(section)
if JSONSchema.PROBLEM == section_name and InputParser.AUTO_SUBSTITUTIONS in params[
section_name]:
del params[section_name][InputParser.AUTO_SUBSTITUTIONS]
return QiskitChemistry._DRIVER_RUN_TO_ALGO_INPUT, params, input_object
