def run(self) -> GroupedSecondQuantizedProperty:
"""
Returns:
GroupedSecondQuantizedProperty re-constructed from the HDF5 file.
Raises:
LookupError: file not found.
QiskitNatureError: Legacy HDF5 format.
QiskitNatureError: if the HDF5 file did not contain a GroupedSecondQuantizedProperty.
"""
hdf5_file = self._get_path()
with h5py.File(hdf5_file, "r") as file:
if "origin_driver" in file.keys():
raise QiskitNatureError(
"Your HDF5 file contains a not supported legacy QMolecule object!"
)
driver_result = load_from_hdf5(str(hdf5_file))
if not isinstance(driver_result, GroupedSecondQuantizedProperty):
raise QiskitNatureError(
f"Expected a GroupedSecondQuantizedProperty but found a {type(driver_result)} "
"object instead.")
return driver_result
def test_save_to_hdf5(self):
"""Test save_to_hdf5."""
driver_result = load_from_hdf5(
self.get_resource_path(
"electronic_structure_driver_result.hdf5",
"second_q/properties/resources",
))
with self.subTest("Normal behavior"):
with TemporaryDirectory() as tmp_dir:
tmp_file = Path(tmp_dir) / "tmp.hdf5"
save_to_hdf5(driver_result, tmp_file)
self.assertTrue(tmp_file.exists())
with self.subTest("FileExistsError"):
with NamedTemporaryFile() as tmp_file:
with self.assertRaises(FileExistsError):
save_to_hdf5(driver_result, tmp_file.name)
with self.subTest("replace=True"):
with TemporaryDirectory() as tmp_dir:
tmp_file = Path(tmp_dir) / "tmp.hdf5"
tmp_file.touch()
self.assertTrue(tmp_file.exists())
save_to_hdf5(driver_result, tmp_file, replace=True)
def test_vibrational_energy(self):
"""Test the VibrationalEnergy."""
result = GaussianLogResult(self.logfile)
vib_energy = result.get_vibrational_energy()
expected = load_from_hdf5(
self.get_resource_path(
"test_driver_gaussian_log_vibrational_energy.hdf5",
"drivers/second_quantization/gaussiand",
))
self.addTypeEqualityFunc(VibrationalIntegrals,
self.compare_vibrational_integral)
self.addTypeEqualityFunc(VibrationalEnergy,
self.compare_vibrational_energy)
self.assertEqual(vib_energy, expected)
def run(self) -> GroupedSecondQuantizedProperty:
"""
Returns:
GroupedSecondQuantizedProperty re-constructed from the HDF5 file.
Raises:
LookupError: file not found.
QiskitNatureError: if the HDF5 file did not contain a GroupedSecondQuantizedProperty.
"""
hdf5_file = self._get_path()
legacy_hdf5_file = False
with h5py.File(hdf5_file, "r") as file:
if "origin_driver" in file.keys():
legacy_hdf5_file = True
warn_deprecated(
"0.4.0",
DeprecatedType.METHOD,
"HDF5Driver.run with legacy HDF5 file",
additional_msg=
(". Your HDF5 file contains the legacy QMolecule object! You should consider "
"converting it to the new property framework. See also HDF5Driver.convert"
),
)
if legacy_hdf5_file:
warnings.filterwarnings("ignore", category=DeprecationWarning)
try:
molecule = QMolecule(hdf5_file)
molecule.load()
return ElectronicStructureDriverResult.from_legacy_driver_result(
molecule)
finally:
warnings.filterwarnings("default", category=DeprecationWarning)
driver_result = load_from_hdf5(str(hdf5_file))
if not isinstance(driver_result, GroupedSecondQuantizedProperty):
raise QiskitNatureError(
f"Expected a GroupedSecondQuantizedProperty but found a {type(driver_result)} "
"object instead.")
return driver_result
def test_load_from_hdf5(self):
"""Test load_from_hdf5."""
with self.subTest("Normal behavior"):
driver_result = load_from_hdf5(
self.get_resource_path(
"electronic_structure_driver_result.hdf5",
"second_q/properties/resources",
))
self.assertTrue(
isinstance(driver_result, ElectronicStructureDriverResult))
with self.subTest("multiple groups"):
with self.assertRaisesRegex(QiskitNatureError,
"more than one HDF5Storable"):
_ = load_from_hdf5(
self.get_resource_path(
"test_hdf5_error_multiple_groups.hdf5", "resources"))
with self.subTest("missing class"):
with self.assertRaisesRegex(QiskitNatureError,
"faulty object without a '__class__'"):
_ = load_from_hdf5(
self.get_resource_path(
"test_hdf5_error_missing_class.hdf5", "resources"))
with self.subTest("non native"):
with self.assertRaisesRegex(QiskitNatureError,
"non-native object"):
_ = load_from_hdf5(
self.get_resource_path("test_hdf5_error_non_native.hdf5",
"resources"))
with self.subTest("import failure"):
with self.assertRaisesRegex(QiskitNatureError,
"import failure of .+ from .+"):
_ = load_from_hdf5(
self.get_resource_path(
"test_hdf5_error_import_failure.hdf5", "resources"))
with self.subTest("non protocol"):
with self.assertRaisesRegex(
QiskitNatureError,
"object of type .+ which is not an HDF5Storable"):
_ = load_from_hdf5(
self.get_resource_path("test_hdf5_error_non_protocol.hdf5",
"resources"))
def test_save_to_hdf5(self):
"""Test save_to_hdf5."""
driver_result = load_from_hdf5(
self.get_resource_path(
"electronic_structure_driver_result.hdf5",
"properties/second_quantization/electronic/resources",
))
with self.subTest("Normal behavior"):
# pylint: disable=consider-using-with
tmp_file = tempfile.NamedTemporaryFile(delete=False,
suffix=".hdf5")
tmp_file.close()
os.unlink(tmp_file.name)
save_to_hdf5(driver_result, tmp_file.name)
try:
self.assertTrue(os.path.exists(tmp_file.name))
finally:
os.unlink(tmp_file.name)
with self.subTest("FileExistsError"):
with tempfile.NamedTemporaryFile() as tmp_file:
with self.assertRaises(FileExistsError):
save_to_hdf5(driver_result, tmp_file.name)
with self.subTest("replace=True"):
# pylint: disable=consider-using-with
tmp_file = tempfile.NamedTemporaryFile(delete=False,
suffix=".hdf5")
# we need to use delete=False here because on Windows it is not possible to open an
# existing file a second time:
# https://docs.python.org/3.9/library/tempfile.html#tempfile.NamedTemporaryFile
tmp_file.close()
try:
save_to_hdf5(driver_result, tmp_file.name, replace=True)
finally:
os.unlink(tmp_file.name)
def run(self) -> ElectronicStructureDriverResult:
cfg = self._config
psi4d_directory = Path(__file__).resolve().parent
template_file = psi4d_directory.joinpath("_template.txt")
qiskit_nature_directory = psi4d_directory.parent.parent
input_text = [cfg]
input_text += ["import sys"]
syspath = ("['" + qiskit_nature_directory.as_posix() + "','" +
"','".join(Path(p).as_posix() for p in sys.path) + "']")
input_text += ["sys.path = " + syspath + " + sys.path"]
with open(template_file, "r", encoding="utf8") as file:
input_text += [line.strip("\n") for line in file.readlines()]
file_fd, hdf5_file = tempfile.mkstemp(suffix=".hdf5")
os.close(file_fd)
input_text += [
f'save_to_hdf5(_q_driver_result, "{Path(hdf5_file).as_posix()}", replace=True)'
]
file_fd, input_file = tempfile.mkstemp(suffix=".inp")
os.close(file_fd)
with open(input_file, "w", encoding="utf8") as stream:
stream.write("\n".join(input_text))
file_fd, output_file = tempfile.mkstemp(suffix=".out")
os.close(file_fd)
try:
PSI4Driver._run_psi4(input_file, output_file)
if logger.isEnabledFor(logging.DEBUG):
with open(output_file, "r", encoding="utf8") as file:
logger.debug("PSI4 output file:\n%s", file.read())
finally:
run_directory = os.getcwd()
for local_file in os.listdir(run_directory):
if local_file.endswith(".clean"):
os.remove(run_directory + "/" + local_file)
try:
os.remove("timer.dat")
except Exception: # pylint: disable=broad-except
pass
try:
os.remove(input_file)
except Exception: # pylint: disable=broad-except
pass
try:
os.remove(output_file)
except Exception: # pylint: disable=broad-except
pass
driver_result = cast(ElectronicStructureDriverResult,
load_from_hdf5(hdf5_file))
try:
os.remove(hdf5_file)
except Exception: # pylint: disable=broad-except
pass
# TODO: once https://github.com/Qiskit/qiskit-nature/issues/312 is fixed we can stop adding
# these properties by default.
# if not settings.dict_aux_operators:
num_spin_orbitals = driver_result.get_property(
"ParticleNumber").num_spin_orbitals
driver_result.add_property(AngularMomentum(num_spin_orbitals))
driver_result.add_property(Magnetization(num_spin_orbitals))
# inject Psi4 config (because it is not available at runtime inside the template)
driver_metadata = driver_result.get_property("DriverMetadata")
driver_metadata.config = cfg
return driver_result
