Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/gaussianparser/gaussian_parser.py", line 1116, in parse
self.parse_configurations(n)
File "/usr/local/lib/python3.7/site-packages/gaussianparser/gaussian_parser.py", line 926, in parse_configurations
sec_scc = self.parse_scc(calculation)
File "/usr/local/lib/python3.7/site-packages/gaussianparser/gaussian_parser.py", line 823, in parse_scc
reduced_masses = np.hstack(reduced_masses) * ureg.amu
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 291, in __array_ufunc__
**kwargs,
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1655, in __array_ufunc__
return numpy_wrap("ufunc", ufunc, inputs, kwargs, types)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 921, in numpy_wrap
return handled[name](*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 303, in implementation
result_magnitude = func(*stripped_args, **stripped_kwargs)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U7'), dtype('int64')) -> None
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1058, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/results.py", line 103, in normalize
self.normalize_run(logger=self.logger)
File "/app/nomad/normalizing/results.py", line 226, in normalize_run
results.method = MethodNormalizer(self.entry_archive, repr_system, results.material, logger).method()
File "/app/nomad/normalizing/method.py", line 105, in method
settings_basis_set = get_basis_set(self.entry_archive, self.repr_method, self.repr_system, self.logger)
File "/app/nomad/normalizing/method.py", line 455, in get_basis_set
return settings.to_dict()
File "/app/nomad/normalizing/method.py", line 508, in to_dict
aims_bs = self._repr_method.x_fhi_aims_section_controlIn_basis_set
AttributeError: 'NoneType' object has no attribute 'x_fhi_aims_section_controlIn_basis_set'
Traceback (most recent call last):
File "/app/nomad/normalizing/results.py", line 658, in structures_1d
raise ValueError("could not detect the periodic dimensions in a 1D system")
ValueError: could not detect the periodic dimensions in a 1D system
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1065, in normalizing
parser.after_normalization(self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 490, in after_normalization
first_referenced_calculation = archive.run[0].calculation[0].calculations_ref[0]
IndexError: list index out of range
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1541, in parse
self.parse_configurations_quickstep()
File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1224, in parse_configurations_quickstep
parse_calculations([single_point])
File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1213, in parse_calculations
sec_system = self.parse_system(atomic_coord)
File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1100, in parse_system
lattice_vectors = self.get_lattice_vectors(trajectory._frame)
File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 943, in get_lattice_vectors
lattice_vectors = lattice_vectors[:3] * units
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 187, in __mul__
return self._REGISTRY.Quantity(1, self._units) * other
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1249, in __mul__
return self._mul_div(other, operator.mul)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 115, in wrapped
return f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 95, in wrapped
result = f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1215, in _mul_div
magnitude = magnitude_op(self._magnitude, other_magnitude)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('int64'), dtype('<U6')) -> None
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1422, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1125, in parse_configurations
parse_bandstructure()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 744, in parse_bandstructure
nbands = np.shape(eigs)[-1] if n == 0 else nbands
UnboundLocalError: local variable 'nbands' referenced before assignment
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1058, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/workflow.py", line 470, in normalize
workflow_type = self._resolve_workflow_type(sec_run)
File "/app/nomad/normalizing/workflow.py", line 423, in _resolve_workflow_type
program_name = run.program.name
AttributeError: 'NoneType' object has no attribute 'name'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_f3cd14c9411e416bbe4cf59501567017.json'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1475, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1415, in parse_configurations
forces, stress = self.parser.get_forces_stress(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1024, in get_forces_stress
array=True).get('v', None)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 823, in _get_key_values
result[base_name] = np.array(value, dtype=self._dtypes.get(dtype, float))
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (83,) + inhomogeneous part.
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1058, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/dos.py", line 69, in normalize
self.add_energy_references(dos, energy_fermi, energy_highest, energy_lowest, dos_values_normalized)
File "/app/nomad/normalizing/dos.py", line 172, in add_energy_references
fermi_idx = (np.abs(dos.energies - eref)).argmin()
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1089, in __sub__
return self._add_sub(other, operator.sub)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 115, in wrapped
return f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1005, in _add_sub
magnitude = op(self._magnitude, other._magnitude)
ValueError: operands could not be broadcast together with shapes (602,) (2,)
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1058, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/results.py", line 103, in normalize
self.normalize_run(logger=self.logger)
File "/app/nomad/normalizing/results.py", line 224, in normalize_run
logger
File "/app/nomad/normalizing/material.py", line 62, in material
symbols, reduced_counts = atomutils.get_hill_decomposition(self.repr_system.atoms.labels, reduced=True)
File "/app/nomad/atomutils.py", line 416, in get_hill_decomposition
greatest_common_divisor = reduce(math.gcd, counts)
TypeError: reduce() of empty sequence with no initial value
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 651, in parse
atomic_numbers = labels_positions[:, 2]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1475, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1437, in parse_configurations
parse_dos(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1393, in parse_dos
dos, fields = self.parser.get_partial_dos(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 612, in get_partial_dos
n_atoms = self.atom_info['n_atoms']
KeyError: 'n_atoms'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/app/nomad/parsing/parser.py", line 121, in parse
raise Exception('Failed on purpose.')
Exception: Failed on purpose.
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 1267, in mark_as_worker_lost
human_status(exitcode), job._job),
billiard.exceptions.WorkerLostError: Worker exited prematurely: signal 9 (SIGKILL) Job: 189162.
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1110, in write_archive
write_partial_archive_to_mongo(archive)
File "/app/nomad/archive/partial.py", line 128, in write_partial_archive_to_mongo
mongo_collection.replace_one(dict(_id=mongo_id), partial_archive_dict, upsert=True)
File "/usr/local/lib/python3.7/site-packages/pymongo/collection.py", line 947, in replace_one
collation=collation, hint=hint, session=session),
File "/usr/local/lib/python3.7/site-packages/pymongo/collection.py", line 870, in _update_retryable
_update, session)
File "/usr/local/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1498, in _retryable_write
return self._retry_with_session(retryable, func, s, None)
File "/usr/local/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1384, in _retry_with_session
return self._retry_internal(retryable, func, session, bulk)
File "/usr/local/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1416, in _retry_internal
return func(session, sock_info, retryable)
File "/usr/local/lib/python3.7/site-packages/pymongo/collection.py", line 866, in _update
retryable_write=retryable_write)
File "/usr/local/lib/python3.7/site-packages/pymongo/collection.py", line 836, in _update
retryable_write=retryable_write).copy()
File "/usr/local/lib/python3.7/site-packages/pymongo/pool.py", line 699, in command
self._raise_connection_failure(error)
File "/usr/local/lib/python3.7/site-packages/pymongo/pool.py", line 694, in command
exhaust_allowed=exhaust_allowed)
File "/usr/local/lib/python3.7/site-packages/pymongo/network.py", line 136, in command
name, size, max_bson_size + message._COMMAND_OVERHEAD)
File "/usr/local/lib/python3.7/site-packages/pymongo/message.py", line 1092, in _raise_document_too_large
raise DocumentTooLarge("%r command document too large" % (operation,))
pymongo.errors.DocumentTooLarge: 'update' command document too large
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1475, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1429, in parse_configurations
sec_system = parse_system(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1268, in parse_system
structure = self.parser.get_structure(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 992, in get_structure
f'{structure}/varray[@name="positions"]/v', array=True).get('v', None)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 823, in _get_key_values
result[base_name] = np.array(value, dtype=self._dtypes.get(dtype, float))
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (132,) + inhomogeneous part.
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1422, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1116, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1016, in parse_section
sec_atoms.positions = structure.get('positions') * ureg.angstrom
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 187, in __mul__
return self._REGISTRY.Quantity(1, self._units) * other
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1249, in __mul__
return self._mul_div(other, operator.mul)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 115, in wrapped
return f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 95, in wrapped
result = f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1215, in _mul_div
magnitude = magnitude_op(self._magnitude, other_magnitude)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('int64'), dtype('<U32')) -> None
Traceback (most recent call last):
File "/app/nomad/normalizing/results.py", line 583, in structures_2d
raise ValueError("could not detect the periodic dimensions in a 2D system")
ValueError: could not detect the periodic dimensions in a 2D system
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1422, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1113, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1016, in parse_section
sec_atoms.positions = structure.get('positions') * ureg.angstrom
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 187, in __mul__
return self._REGISTRY.Quantity(1, self._units) * other
TypeError: unsupported operand type(s) for *: 'Quantity' and 'NoneType'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1475, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1412, in parse_configurations
parse_energy(n, n_scf)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1304, in parse_energy
val = val * ureg.eV
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 187, in __mul__
return self._REGISTRY.Quantity(1, self._units) * other
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1249, in __mul__
return self._mul_div(other, operator.mul)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 115, in wrapped
return f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 95, in wrapped
result = f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1215, in _mul_div
magnitude = magnitude_op(self._magnitude, other_magnitude)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('int64'), dtype('<U32')) -> None
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 256, in system_type_analysis
cls = classifier.classify(atoms)
File "/usr/local/lib/python3.7/site-packages/matid/classification/classifier.py", line 242, in classify
global_min_dist = dist_matrix_mod.min()
File "/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py", line 44, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation minimum which has no identity
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1058, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/results.py", line 103, in normalize
self.normalize_run(logger=self.logger)
File "/app/nomad/normalizing/results.py", line 214, in normalize_run
properties, conv_atoms, wyckoff_sets, spg_number = self.properties(repr_system, repr_symmetry)
File "/app/nomad/normalizing/results.py", line 459, in properties
conv_atoms, prim_atoms, wyckoff_sets, spg_number = self.structures_2d(original_atoms)
File "/app/nomad/normalizing/results.py", line 632, in structures_2d
return conv_atoms, prim_atoms, wyckoff_sets, spg_number
UnboundLocalError: local variable 'conv_atoms' referenced before assignment
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/octopusparser/octopus_parser.py", line 935, in parse
self.parse_scc()
File "/usr/local/lib/python3.7/site-packages/octopusparser/octopus_parser.py", line 704, in parse_scc
cell = sec_run.system[-1].lattice_vectors
File "/app/nomad/metainfo/metainfo.py", line 1031, in __getattr__
raise AttributeError(name)
AttributeError: lattice_vectors
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'Ag1Co1O2_ICSD_246157/aflowlib.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1420, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1248, in parse_method
self.parse_topology()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1366, in parse_topology
parse_atom_type(specie)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1318, in parse_atom_type
sec_atom_species.x_fhi_aims_controlInOut_species_cut_pot_scale = val[0][2]
File "/app/nomad/metainfo/metainfo.py", line 1021, in __setattr__
return super().__setattr__(name, value)
File "/app/nomad/metainfo/metainfo.py", line 2501, in __set__
obj.m_set(self, value)
File "/app/nomad/metainfo/metainfo.py", line 1128, in m_set
value = self.__to_np(quantity_def, value)
File "/app/nomad/metainfo/metainfo.py", line 1106, in __to_np
value = quantity_def.type.type(value)
ValueError: could not convert string to float: 'Task'
Traceback (most recent call last):
File "/app/nomad/metainfo/metainfo.py", line 2558, in __get__
return obj.__dict__[self._name]
KeyError: 'derived'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 954, in process_calc
self.archiving()
File "/app/nomad/processing/data.py", line 1103, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1137, in write_archive
return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
File "/app/nomad/metainfo/metainfo.py", line 1591, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1591, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1585, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1585, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1591, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1591, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1585, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1585, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1591, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1591, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1589, in items
yield name, sub_section.m_to_dict(**kwargs)
File "/app/nomad/metainfo/metainfo.py", line 1591, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1591, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1589, in items
yield name, sub_section.m_to_dict(**kwargs)
File "/app/nomad/metainfo/metainfo.py", line 1591, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1591, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1566, in items
is_set = self.m_is_set(quantity)
File "/app/nomad/metainfo/metainfo.py", line 1160, in m_is_set
if quantity_def.derived is not None:
File "/app/nomad/metainfo/metainfo.py", line 2560, in __get__
return self._default
File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 229, in soft_timeout_sighandler
raise SoftTimeLimitExceeded()
billiard.exceptions.SoftTimeLimitExceeded: SoftTimeLimitExceeded()
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1420, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1280, in parse_method
xc_parameters.setdefault('$\\omega$ in m^-1', hse_omega.to('1/m').magnitude)
AttributeError: 'float' object has no attribute 'to'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'fe_test/reference_d.log'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 954, in process_calc
self.archiving()
File "/app/nomad/processing/data.py", line 1103, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1137, in write_archive
return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
File "/app/nomad/files.py", line 760, in write_archive
raise e
File "/app/nomad/files.py", line 754, in write_archive
write_archive(archive_file_object.os_path, 1, data=[(calc_id, data)])
File "/app/nomad/archive/storage.py", line 506, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive/storage.py", line 169, in __exit__
raise exc_val
File "/app/nomad/archive/storage.py", line 506, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive/storage.py", line 204, in add
packed = self._toc_packer.pack(data)
File "/app/nomad/archive/storage.py", line 69, in pack
result = super().pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 848, in pack
self._pack(obj)
File "/app/nomad/archive/storage.py", line 85, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive/storage.py", line 108, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive/storage.py", line 85, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive/storage.py", line 108, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive/storage.py", line 82, in _pack
pack_result = self._buffer.write(packb(obj))
File "/app/nomad/archive/storage.py", line 35, in packb
return __packer.pack(o)
File "msgpack/_packer.pyx", line 284, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 290, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 287, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 281, in msgpack._packer.Packer._pack
TypeError: can't serialize 1
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1420, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1206, in parse_method
parse_basis_set(species)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1171, in parse_basis_set
val[0], dtype=float))
ValueError: could not convert string to float: '#'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'mp-149/mp-149_materials.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'fe_test/md2.log'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'fe_test/dhdl.xvg'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_6_LRBE/OUTCAR.static.xz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_5_ZEROSTATE/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 197, in normalize_system
atoms.set_positions(1e10 * atom_positions.magnitude)
File "/usr/local/lib/python3.7/site-packages/ase/atoms.py", line 662, in set_positions
self.set_array('positions', newpositions, shape=(3,))
File "/usr/local/lib/python3.7/site-packages/ase/atoms.py", line 475, in set_array
(name, a.shape, b.shape))
ValueError: Array "positions" has wrong shape (0,) != (0, 3).
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 298, in symmetry_analysis
space_group_number = symm.get_space_group_number()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 114, in get_space_group_number
dataset = self.get_symmetry_dataset()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 566, in get_symmetry_dataset
'Spglib error when finding symmetry dataset.')
matid.exceptions.CellNormalizationError: Spglib error when finding symmetry dataset.
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_e1dc1b8ea14e488494b69ab5e383562f.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1058, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/results.py", line 103, in normalize
self.normalize_run(logger=self.logger)
File "/app/nomad/normalizing/results.py", line 227, in normalize_run
self.geometry_optimization(results.method, results.properties)
File "/app/nomad/normalizing/results.py", line 425, in geometry_optimization
structure_optimized = self.nomad_system_to_structure(StructureOptimized, system_ref)
File "/app/nomad/normalizing/results.py", line 739, in nomad_system_to_structure
struct.atomic_density = len(system.atoms.labels) / cell_volume
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_ac1e9d59eb5a45c38edeb2c1f74b3542.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1422, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1119, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1080, in parse_section
parse_scf(scf_iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 891, in parse_scf
sec_scf.x_fhi_aims_scf_date_start = date_time[0]
File "/app/nomad/metainfo/metainfo.py", line 1018, in __setattr__
if all_aliases is not None and name in self.m_def.all_aliases:
File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 229, in soft_timeout_sighandler
raise SoftTimeLimitExceeded()
billiard.exceptions.SoftTimeLimitExceeded: SoftTimeLimitExceeded()
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 256, in system_type_analysis
cls = classifier.classify(atoms)
File "/usr/local/lib/python3.7/site-packages/matid/classification/classifier.py", line 318, in classify
dist_matrix_radii_pbc
File "/usr/local/lib/python3.7/site-packages/matid/classification/classifier.py", line 463, in cross_validate_region
dist_matrix_radii_pbc,
File "/usr/local/lib/python3.7/site-packages/matid/classification/periodicfinder.py", line 134, in get_region
bond_threshold
File "/usr/local/lib/python3.7/site-packages/matid/classification/periodicfinder.py", line 487, in _find_proto_cell
best_adjacency_lists_sub,
File "/usr/local/lib/python3.7/site-packages/matid/classification/periodicfinder.py", line 699, in _find_proto_cell_3d
-1e-8,
File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 980, in get_positions_within_basis
vec_new_rel = change_basis(vec_new_cart - origin, basis)
File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 891, in change_basis
new_basis_inverse = np.linalg.inv(basis.T)
File "<__array_function__ internals>", line 6, in inv
File "/usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 545, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
File "/usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_ccdc26c4f32546c5a00ad03a093b73dc.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 862, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 769, in parse_method
if not interaction[0] or not interaction[1]:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'fe_test/reference_s.log'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 954, in process_calc
self.archiving()
File "/app/nomad/processing/data.py", line 1103, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1137, in write_archive
return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
File "/app/nomad/files.py", line 760, in write_archive
raise e
File "/app/nomad/files.py", line 754, in write_archive
write_archive(archive_file_object.os_path, 1, data=[(calc_id, data)])
File "/app/nomad/archive/storage.py", line 506, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive/storage.py", line 169, in __exit__
raise exc_val
File "/app/nomad/archive/storage.py", line 506, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive/storage.py", line 204, in add
packed = self._toc_packer.pack(data)
File "/app/nomad/archive/storage.py", line 69, in pack
result = super().pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 848, in pack
self._pack(obj)
File "/app/nomad/archive/storage.py", line 85, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive/storage.py", line 108, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive/storage.py", line 85, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive/storage.py", line 108, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive/storage.py", line 82, in _pack
pack_result = self._buffer.write(packb(obj))
File "/app/nomad/archive/storage.py", line 35, in packb
return __packer.pack(o)
File "msgpack/_packer.pyx", line 284, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 290, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 287, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 281, in msgpack._packer.Packer._pack
TypeError: can't serialize 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1005, in on_fail
self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1137, in write_archive
return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
File "/app/nomad/files.py", line 760, in write_archive
raise e
File "/app/nomad/files.py", line 754, in write_archive
write_archive(archive_file_object.os_path, 1, data=[(calc_id, data)])
File "/app/nomad/archive/storage.py", line 506, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive/storage.py", line 169, in __exit__
raise exc_val
File "/app/nomad/archive/storage.py", line 506, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive/storage.py", line 204, in add
packed = self._toc_packer.pack(data)
File "/app/nomad/archive/storage.py", line 69, in pack
result = super().pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 848, in pack
self._pack(obj)
File "/app/nomad/archive/storage.py", line 85, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive/storage.py", line 108, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive/storage.py", line 85, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive/storage.py", line 108, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive/storage.py", line 82, in _pack
pack_result = self._buffer.write(packb(obj))
File "/app/nomad/archive/storage.py", line 35, in packb
return __packer.pack(o)
File "msgpack/_packer.pyx", line 284, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 290, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 287, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 281, in msgpack._packer.Packer._pack
TypeError: can't serialize 1
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1422, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1116, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1080, in parse_section
parse_scf(scf_iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 916, in parse_scf
eigenvalues = get_eigenvalues(iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 881, in get_eigenvalues
np.reshape(occs_eigs, (len(kpts), n_spin, n_eigs, 2)), axes=(3, 1, 0, 2))
File "<__array_function__ internals>", line 6, in reshape
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 298, in reshape
return _wrapfunc(a, 'reshape', newshape, order=order)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 54, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 43, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: cannot reshape array of size 126 into shape (2,1,31,2)
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_f3cd14c9411e416bbe4cf59501567017.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/openkimparser/openkim_parser.py", line 81, in parse
sec_run.program = Program(name='OpenKIM', version=entry.get('meta.runner.short-id'))
AttributeError: 'str' object has no attribute 'get'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/wien2kparser/wien2k_parser.py", line 801, in parse
self.parse_scc()
File "/usr/local/lib/python3.7/site-packages/wien2kparser/wien2k_parser.py", line 638, in parse_scc
sec_scc.energy.fermi = sec_scf.energy.fermi
AttributeError: 'NoneType' object has no attribute 'fermi'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'fe_test/md.log'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_6_LRBE/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_b878ff7e0a254c03ab839b395bd3dde0.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1543, in parse
self.parse_workflow()
File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1405, in parse_workflow
geometry_change = sec_geometry_opt_step.x_cp2k_optimization_step_size_convergence_limit
UnboundLocalError: local variable 'sec_geometry_opt_step' referenced before assignment
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1422, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1113, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1087, in parse_section
parse_dos(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 822, in parse_dos
energies = data[0] * ureg.eV
IndexError: index 0 is out of bounds for axis 0 with size 0
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_4_A125D0M/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_3_A125D0P/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_8a072ed8e7814bff86419f2f3c1a8a76.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_3_A108D0P/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_4_A108D0M/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'MgO/ARUN.APL_1_A0D0P/aflow.in'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'fe_test/mdrun.out'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1033, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2301, in parse
self.parse_xs()
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1754, in parse_xs
if xstype.lower() == 'bse':
AttributeError: 'NoneType' object has no attribute 'lower'
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 808, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 945, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 706, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 768, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'archive_21a4f99721d8418cb11d7d2dce5b8293.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 981, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
