Even more v1 parser errors

• 175278 x parsers/gaussian: Sv0sxBCMTH-thjqog0duBQ/cccbdb_data/m/m5b1/h2.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1035, 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('<U6'), dtype('int64')) -> None

• 45383 x missing/fhi-aims: 0D4TR7I6R1WBrdPAYgSo1Q/cys/dipeptide/Sr/conformer.0040.fhiaims (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1060, in normalizing
    normalizer(self._parser_results).normalize(logger=logger)
  File "/app/nomad/normalizing/results.py", line 102, in normalize
    self.normalize_run(logger=self.logger)
  File "/app/nomad/normalizing/results.py", line 225, 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'

• 31481 x parsers/vaspoutcar: SobHx8fSRuC0eC3fZuRPLA/oqmd/binaries/B4/Te_W/fine_relax/OUTCAR (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1060, in normalizing
    normalizer(self._parser_results).normalize(logger=logger)
  File "/app/nomad/normalizing/results.py", line 102, in normalize
    self.normalize_run(logger=self.logger)
  File "/app/nomad/normalizing/results.py", line 223, in normalize_run
    logger
  File "/app/nomad/normalizing/material.py", line 77, in material
    material.material_name = self.material_name(symbols, reduced_counts)
  File "/app/nomad/normalizing/material.py", line 221, in material_name
    atomicnumbers = [ase.data.atomic_numbers[i] for i in symbols]
  File "/app/nomad/normalizing/material.py", line 221, in <listcomp>
    atomicnumbers = [ase.data.atomic_numbers[i] for i in symbols]
KeyError: 'W_pv'

• 235 x parsers/vaspoutcar: PPfOfWzuS3WA_oE0h7gzww/iodido-bi/opt/OUTCAR (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1060, in normalizing
    normalizer(self._parser_results).normalize(logger=logger)
  File "/app/nomad/normalizing/results.py", line 102, in normalize
    self.normalize_run(logger=self.logger)
  File "/app/nomad/normalizing/results.py", line 223, 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

• 227 x parsers/phonopy: H_pr_6edS_-whLFmUB5PTA/RXfQgXVYU_cFtvPJ_qCGBXErctSYB/data/withBa/phonon/Ba8Ge43/phonopy-FHI-aims-displacement-0001/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1067, 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

• 119 x parsers/vaspoutcar: ROc3S3MuRsyMxvN1LTRF1Q/oqmd/icsd/105588/standard/OUTCAR (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1060, in normalizing
    normalizer(self._parser_results).normalize(logger=logger)
  File "/app/nomad/normalizing/results.py", line 102, in normalize
    self.normalize_run(logger=self.logger)
  File "/app/nomad/normalizing/results.py", line 223, in normalize_run
    logger
  File "/app/nomad/normalizing/material.py", line 77, in material
    material.material_name = self.material_name(symbols, reduced_counts)
  File "/app/nomad/normalizing/material.py", line 217, in material_name
    number = ase.data.atomic_numbers[symbols[0]]
KeyError: 'Pb_d'

• 11 x parsers/vasp: SwfLaVzkQ86arFftaA6hHA/nomad_upload_thread_5/block_2013-10-16-17-01-33-682490/launcher_2013-10-16-17-01-40-138446/vasprun.xml.relax2.gz (v1), raw files (v0)

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: 1119091.

• 10 x parsers/quantumespresso: OxkMeUgRTq2FYAJYC6yinA/mamunm/48362.log (v1), raw files (v0)

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.

• 8 x parsers/broken: Fsse-mIwSoCiKKPIJG2xUQ/on_Clean/HighCoverage/Down/One_Eight/Tier1.5/vdW/monolayer/output (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1035, 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.

• 5 x parsers/octopus: F_8FvE1WSMCfl5-GN-gWFA/octopus/impulse/out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1106, 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

• 2 x parsers/vasp: DmJl502EQWyq1HgWuH8Z_Q/nomad_upload_thread_8/block_2019-12-20-03-50-09-463422/launcher_2019-12-20-06-02-41-462689/vasprun.xml.gz (v1), raw files (v0)

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 586, in _find_proto_cell
    offset = proto_cell.get_positions()[seed_group_index]
IndexError: index 1 is out of bounds for axis 0 with size 1

• 2 x parsers/exciting: S_VGYLsmTaOctilGKGvicA/nickel-moke/INFO.OUT (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1035, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2297, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2205, in parse_configurations
    sec_scc = parse_configuration(self.info_parser.get(module))
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2195, in parse_configuration
    sec_system = self.parse_system(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2159, in parse_system
    sec_atoms_group.x_exciting_atom_position_format = positions_format
  File "/app/nomad/metainfo/metainfo.py", line 1021, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2627, in __set__
    (value, type(value), self, self.type))
TypeError: The value ['lattice),', 'magnetic', 'fields', '(Cartesian'] with type <class 'list'> for quantity excitingparser.metainfo.exciting.x_exciting_section_atoms_group.x_exciting_atom_position_format:Quantity is not of type <class 'str'>

• 2 x parsers/charmm: 5pACEJKERFa_kNrSiAoIVA/charmm/test/examples/nose1/nose1.out (v1), raw files (v0)

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

• 2 x parsers/fhi-aims: HHcFe6e-SPi5pLarKXpFmg/Au25-38-40_MD_DiegoSobrinho/Au25/600_OK/molecular_dynamics_Au.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1035, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1440, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1135, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1096, in parse_section
    parse_scf(scf_iteration)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 932, in parse_scf
    eigenvalues = get_eigenvalues(iteration)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 880, in get_eigenvalues
    kpts = data.get('kpoints', [np.zeros(3)] * n_spin)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 127, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 61, in results
    self.parse(self._key, **self._kwargs)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 509, in parse
    self._parse_quantities(quantities_findall)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 416, in _parse_quantities
    matches = re.findall(re_findall, self.file_mmap)
  File "/usr/local/lib/python3.7/re.py", line 225, in findall
    return _compile(pattern, flags).findall(string)
  File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 229, in soft_timeout_sighandler
    raise SoftTimeLimitExceeded()
billiard.exceptions.SoftTimeLimitExceeded: SoftTimeLimitExceeded()

• 1 x parsers/lammps: 5pACEJKERFa_kNrSiAoIVA/lammps/test/examples/1_methyl_naphthalene/log.1_methyl_naphthalene (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/base.py", line 790, in proc_task
    rv = unwrapped_func(proc, *args, **kwargs)
  File "/app/nomad/processing/data.py", line 956, in process_calc
    self.archiving()
  File "/app/nomad/processing/data.py", line 1099, in archiving
    archive_size = self.write_archive(self._parser_results)
  File "/app/nomad/processing/data.py", line 1133, in write_archive
    return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
  File "/app/nomad/files.py", line 762, in write_archive
    raise e
  File "/app/nomad/files.py", line 756, 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 1007, in on_fail
    self.write_archive(self._parser_results)
  File "/app/nomad/processing/data.py", line 1133, in write_archive
    return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
  File "/app/nomad/files.py", line 762, in write_archive
    raise e
  File "/app/nomad/files.py", line 756, 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

• 1 x parsers/fhi-aims: RfpFzoO2T4mTVhblG3gTbg/tm10_2OH_2O/dft-data-1/(4, -2, 3, 3, 7, 31, 0, 14)/aims.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1035, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1408, in parse
    name='FHI-aims', version=self.out_parser.get('version', ''),
  File "/app/nomad/parsing/file_parser/file_parser.py", line 127, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 61, in results
    self.parse(self._key, **self._kwargs)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 517, in parse
    self._parse_quantity(quantity)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 470, in _parse_quantity
    value.append(sub_parser.parse())
  File "/app/nomad/parsing/file_parser/text_parser.py", line 517, in parse
    self._parse_quantity(quantity)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 470, in _parse_quantity
    value.append(sub_parser.parse())
  File "/app/nomad/parsing/file_parser/text_parser.py", line 509, in parse
    self._parse_quantities(quantities_findall)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 439, in _parse_quantities
    values.append(' '.join([m.decode() for m in non_empty_match]))
  File "/app/nomad/parsing/file_parser/text_parser.py", line 439, in <listcomp>
    values.append(' '.join([m.decode() for m in non_empty_match]))
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb8 in position 402: invalid start byte

• 1 x parsers/cp2k: FbK6ZA7rTfOiLapwU3gILw/aucu_single/AuCu_typealloy_clustertypeau40cu40_pristine_Hn1_cnstr_ver2_MJ20170404/au40cu40h_2801_2900/pes_h_au40cu40.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1035, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1542, in parse
    self.parse_configurations_quickstep()
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1237, in parse_configurations_quickstep
    parse_calculations(md_steps)
  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 1090, in parse_system
    trajectory = self.get_trajectory(frame)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 872, in get_trajectory
    result = self.traj_parser.trajectory[0]
IndexError: list index out of range

• 1 x parsers/nwchem: 5vBgcHWMSAOyHuAlCDy_hw/Vanadium_FINAL/Vanadium_Complexes/G_Final/V3_2I/freq.log (v1), raw files (v0)

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).

• 1 x parsers/quantumespresso: 9yS2m8IzRsOdeTOhaEeKzg/mamunm/8767.log (v1), raw files (v0)

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

• 1 x parsers/lammps: 5pACEJKERFa_kNrSiAoIVA/lammps/test/examples/1_methyl_naphthalene/log.1_methyl_naphthalene (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/base.py", line 790, in proc_task
    rv = unwrapped_func(proc, *args, **kwargs)
  File "/app/nomad/processing/data.py", line 956, in process_calc
    self.archiving()
  File "/app/nomad/processing/data.py", line 1099, in archiving
    archive_size = self.write_archive(self._parser_results)
  File "/app/nomad/processing/data.py", line 1133, in write_archive
    return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
  File "/app/nomad/files.py", line 762, in write_archive
    raise e
  File "/app/nomad/files.py", line 756, 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

• 8 x parsers/vaspoutcar: TKaxZCOERLCOl7mC_y9yCg/poly(benzoisoindole)/model-system/M7a/OUTCAR (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1035, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1495, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1456, in parse_configurations
    parse_dos(n)
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1412, 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 625, in get_partial_dos
    n_atoms = self.atom_info['n_atoms']
KeyError: 'n_atoms'