Exceptions during v1 processing of NONE FHI-aims calculations

45904 x missing/fhi-aims: 0D4TR7I6R1WBrdPAYgSo1Q/arg/dipeptide/bare/conformer.3410.fhiaims (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1161, 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 453, in get_basis_set
    return settings.to_dict()
  File "/app/nomad/normalizing/method.py", line 506, 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'

1816 x parsers/quantumespresso: z0fcha-sR4iGjrCFbO9wIw/winther/13047.log (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2763, in parse
    date_time = datetime.strptime(date_time.replace(' ', ''), '%H:%M:%S%d%b%Y')
  File "/usr/local/lib/python3.7/_strptime.py", line 588, in _strptime_datetime
    return cls(*args)
ValueError: second must be in 0..59

775 x parsers/castep: oEwd48S_SpmFOYj-nSF-Cw/Ag_2x5/tAB.castep (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1254, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1168, in parse_configurations
    parse_calculation(calculation)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1110, in parse_calculation
    sec_scc = parse_scc(source)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 969, in parse_scc
    parse_eigenvalues(source)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 899, in parse_eigenvalues
    sec_eigenvalues.energies = band_energies
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2310, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 969, in __to_np
    value = value.to(quantity_def.unit).magnitude
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 660, in to
    magnitude = self._convert_magnitude_not_inplace(other, *contexts, **ctx_kwargs)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 609, in _convert_magnitude_not_inplace
    return self._REGISTRY.convert(self._magnitude, self._units, other)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 947, in convert
    return self._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1830, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1433, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 980, in _convert
    raise DimensionalityError(src, dst, src_dim, dst_dim)
pint.errors.DimensionalityError: Cannot convert from 'electron_volt ** 2' ([length] ** 4 * [mass] ** 2 / [time] ** 4) to 'joule' ([length] ** 2 * [mass] / [time] ** 2)

608 x parsers/phonopy: y56SlVIxQdCLL9k8nBeT5Q/clathrates/Si/alpha/222/a10.1656487290/phonon/phonopy-FHI-aims-displacement-01/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1094, in process_phonon
    scc = self._parser_results.run[0].calculation[0]
IndexError: list index out of range

431 x parsers/phonopy: y56SlVIxQdCLL9k8nBeT5Q/clathrates/Si/alpha/222/a10.1656487290/phonon/phonopy-FHI-aims-displacement-01/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 374, in parse
    phonopy_obj = self.phonopy_obj
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 240, in phonopy_obj
    self._build_phonopy_object_fhi_aims()
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 260, in _build_phonopy_object_fhi_aims
    cell_obj = read_aims('geometry.in')
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 60, in read_aims
    if line[0] == 'lattice_vector':
IndexError: list index out of range

321 x parsers/phonopy: kOB1YOl2T9Wq-q4EBcYT0A/nomad_to_upload/SrTiO3/phonopy_SrTiO3_all/3_3_3_supercell/phonopy-FHI-aims-displacement-001/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 374, in parse
    phonopy_obj = self.phonopy_obj
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 240, in phonopy_obj
    self._build_phonopy_object_fhi_aims()
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 260, in _build_phonopy_object_fhi_aims
    cell_obj = read_aims('geometry.in')
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 54, in read_aims
    with open(filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'geometry.in'

229 x parsers/castep: bXAuTn7RTUukCtp0S10r7w/C1x1_Cu1x1_hex_pbe_TS_6Cu_36k/C1x1_Cu1x1_hex_pbe_TS_6Cu_36k.castep (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1254, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1164, in parse_configurations
    parse_calculation(calculation.get('final'))
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1110, in parse_calculation
    sec_scc = parse_scc(source)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 966, in parse_scc
    sec_scc.x_castep_frequency = val.magnitude
UnboundLocalError: local variable 'val' referenced before assignment

221 x parsers/crystal: llZrblH4THCuJvVjEBXBFA/LMP2/Z4b.o (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 654, in parse
    atomic_numbers,
UnboundLocalError: local variable 'atomic_numbers' referenced before assignment

215 x parsers/cp2k: vzUBuy7xQNOoCWmzNeinDA/mos2_multi/MoS2_type2H_clustertypen5-n7_pristine_Hn1_cnstrcluster_ver3_MJ20170509/h_n6_cut1_s100/H21/gopt_freezecluster_mos2h.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 188, in trajectory
    atoms_list = [atoms for atoms in aseio.iread(self.mainfile, format=self.format)]
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 188, in <listcomp>
    atoms_list = [atoms for atoms in aseio.iread(self.mainfile, format=self.format)]
  File "/usr/local/lib/python3.7/site-packages/ase/io/formats.py", line 629, in iread
    **kwargs):
  File "/usr/local/lib/python3.7/site-packages/ase/parallel.py", line 264, in new_generator
    for result in generator(*args, **kwargs):
  File "/usr/local/lib/python3.7/site-packages/ase/io/formats.py", line 663, in _iread
    for dct in io.read(fd, *args, **kwargs):
  File "/usr/local/lib/python3.7/site-packages/ase/io/extxyz.py", line 584, in read_xyz
    fileobj.seek(0)
AttributeError: 'NoneType' object has no attribute 'seek'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1527, in parse
    self.parse_configurations_quickstep()
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1220, in parse_configurations_quickstep
    parse_calculations(optimization_steps)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1202, in parse_calculations
    sec_system = self.parse_system(atomic_coord)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1079, in parse_system
    trajectory = self.get_trajectory(frame)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 860, in get_trajectory
    if self.traj_parser.trajectory is not None:
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 196, in trajectory
    result = [traj.positions for traj in self._xyz_parser.get('trajectory')]
TypeError: 'NoneType' object is not iterable

185 x parsers/turbomole: hHwrZ0vbRGOkJR6KzRtA9A/7803-62-5/ridft_014.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/turbomoleparser/turbomole_parser.py", line 1179, in parse
    start = datetime.strptime(time[0][0], '%Y-%m-%d %H:%M:%S.%f') - datetime.utcfromtimestamp(0)
IndexError: list index out of range

163 x parsers/phonopy: kOB1YOl2T9Wq-q4EBcYT0A/nomad_to_upload/SrTiO3/phonopy_SrTiO3_all/3_3_3_supercell/phonopy-FHI-aims-displacement-001/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1409, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1100, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1087, in parse_section
    parse_vdW(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 970, in parse_vdW
    if sec.atom_type_name == atom['atom']:
  File "/app/nomad/metainfo/metainfo.py", line 906, in __getattr__
    raise AttributeError(name)
AttributeError: atom_type_name

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/nomad/processing/base.py", line 565, in proc_task
    rv = func(self, *process_args, **process_kwargs)
  File "/app/nomad/processing/data.py", line 960, in process_calc
    self.parsing()
  File "/app/nomad/processing/data.py", line 1064, in parsing
    raise ProcessFailure('parser failed with exception', exc_info=e, error=str(e), **context)
nomad.processing.base.ProcessFailure: parser failed with exception

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1094, in process_phonon
    scc = self._parser_results.run[0].calculation[0]
IndexError: list index out of range

107 x parsers/orca: _b-hD5zFS0a7EY1KGjbEAw/m4-m6_TD-DFT.out (v1), raw files (v0)

TypeError: only size-1 arrays can be converted to Python scalars

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 893, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 842, in parse_configurations
    parse_configuration(self.out_parser.get('single_point'))
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 838, in parse_configuration
    sec_scc = self.parse_scc(section)
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 822, in parse_scc
    spectrum[5:7]) * ureg.elementary_charge * ureg.bohr
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2310, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 967, in __to_np
    value = value.astype(quantity_def.type)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1671, in _numpy_method_wrap
    value = func(*args, **kwargs)
ValueError: setting an array element with a sequence.

90 x parsers/quantumespresso: tIhxbzE5TTuiIBOFLfc8nQ/logs/jrboes/34115.log (v1), raw files (v0)

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

75 x parsers/nwchem: gTAWbfgMRDiQlT0qE3oc4A/Counterions/hso4_4/hso4426.log (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 547, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 475, in parse_configurations
    parse_calculation(iteration)
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 467, in parse_calculation
    sec_method = self.parse_method(source)
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 430, in parse_method
    sec_scf.n_max_iteration = val
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2310, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 981, in __to_np
    value = quantity_def.type.type(value)
ValueError: invalid literal for int() with base 10: ''

59 x parsers/octopus: WhBQEOjBQweOqGOeAEt_Gw/output.00212/out.txt (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 185, in classify
    system.wrap()
  File "/usr/local/lib/python3.7/site-packages/ase/atoms.py", line 1890, in wrap
    self.positions[:] = self.get_positions(wrap=True, **wrap_kw)
  File "/usr/local/lib/python3.7/site-packages/ase/atoms.py", line 678, in get_positions
    return wrap_positions(self.positions, self.cell, **wrap_kw)
  File "/usr/local/lib/python3.7/site-packages/ase/geometry/geometry.py", line 77, in wrap_positions
    assert np.asarray(cell)[np.asarray(pbc)].any(axis=1).all(), (cell, pbc)
AssertionError: (Cell([0.0, 0.0, 0.0]), array([ True,  True,  True]))

40 x parsers/cp2k: xo1qblJBQz2CqyohkNcLvA/test_upload_30gb/aucu_multi/AuCu_clustertype13atomic_pristine_Hn1_cnstr_ver3_MJ20170509/hau8cu5_id13_1_420/pes_h_cluster.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1484, in parse
    compilation_host=self.settings['cp2k']['program_compilation_host'])
  File "/app/nomad/metainfo/metainfo.py", line 774, in __init__
    self.m_update(**other_kwargs)
  File "/app/nomad/metainfo/metainfo.py", line 1200, in m_update
    self.m_set(prop, value)
  File "/app/nomad/metainfo/metainfo.py", line 1008, in m_set
    value = self.__set_normalize(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 955, in __set_normalize
    (value, type(value), quantity_def, quantity_def.type))
TypeError: The value ['CP2K version 4.1', 'CP2K version 4.1'] with type <class 'list'> for quantity nomad.datamodel.metainfo.simulation.run.Program.version:Quantity is not of type <class 'str'>

39 x parsers/cp2k: qu3u9rtUSZOqssEKhsS_gg/aucu_single/AuCu_typealloy_clustertypeau40cu40_pristine_Hn1_cnstr_ver2_MJ20170404/au40cu40h_2401_2500/pes_h_au40cu40.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 188, in trajectory
    atoms_list = [atoms for atoms in aseio.iread(self.mainfile, format=self.format)]
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 188, in <listcomp>
    atoms_list = [atoms for atoms in aseio.iread(self.mainfile, format=self.format)]
  File "/usr/local/lib/python3.7/site-packages/ase/io/formats.py", line 629, in iread
    **kwargs):
  File "/usr/local/lib/python3.7/site-packages/ase/parallel.py", line 264, in new_generator
    for result in generator(*args, **kwargs):
  File "/usr/local/lib/python3.7/site-packages/ase/io/formats.py", line 663, in _iread
    for dct in io.read(fd, *args, **kwargs):
  File "/usr/local/lib/python3.7/site-packages/ase/io/extxyz.py", line 584, in read_xyz
    fileobj.seek(0)
AttributeError: 'NoneType' object has no attribute 'seek'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1527, in parse
    self.parse_configurations_quickstep()
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1226, in parse_configurations_quickstep
    parse_calculations(md_steps)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1202, in parse_calculations
    sec_system = self.parse_system(atomic_coord)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1079, in parse_system
    trajectory = self.get_trajectory(frame)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 860, in get_trajectory
    if self.traj_parser.trajectory is not None:
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 196, in trajectory
    result = [traj.positions for traj in self._xyz_parser.get('trajectory')]
TypeError: 'NoneType' object is not iterable

38 x parsers/wien2k: mc_oLJTPS3mVzCrN5I9q9w/0.5/64k_8Rk_mBJkol/64k_8Rk_mBJkol.scf0 (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/wien2kparser/wien2k_parser.py", line 796, in parse
    self.parse_scc()
  File "/usr/local/lib/python3.7/site-packages/wien2kparser/wien2k_parser.py", line 628, in parse_scc
    sec_scc.energy = Energy(total=EnergyEntry(value=sec_scf.energy.total.value))
AttributeError: 'NoneType' object has no attribute 'value'

36 x parsers/exciting: PNXMAlWfQUCHTZ9Q4DR0gw/CF-BN/h-BN/rectangle/G0W0/q7x12x1/nempty1000/INFO.OUT (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2309, in parse
    self.parse_gw()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1871, in parse_gw
    self.parse_file(f, sec_scc)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1463, in parse_file
    parser_function(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1416, in _parse_band_out
    sec_k_band_segment.value = band_energies + energy_fermi
TypeError: can only concatenate list (not "Quantity") to list

32 x parsers/cp2k: fnheOhs7Q3W3GCf710gQQQ/layers/coverage-dependent/rank2/simulated-annealing/full/equilibrate1500/equilibrate.out-wrong-copy (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1497, in parse
    sec_endinformation.x_cp2k_end_id = val[1]
TypeError: 'int' object is not subscriptable

31 x parsers/quantumespresso: t1Yy3492Sr6wXMHG_5FuzA/nomad_upload/benchmark.out.v5.3.0.inp=plugin-pw2casino_1.in.1452257026 (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2746, in parse
    self.parse_configurations(run)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2472, in parse_configurations
    parse_configuration(calculation)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2460, in parse_configuration
    sec_scc = self.parse_scc(run, calculation)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2228, in parse_scc
    sec_energy.highest_occupied = [homo] * 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('<U6')) -> None

30 x parsers/vasp: vBGEQacNQq6MZgmwFTs1rg/oqmd/perovskite/O/U_Pb/fine_relax/stdout.txt.gz (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1161, 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'

22 x parsers/quantumespresso: tahRaqSlQoiiCjnjspQWVw/logs/jrboes/61657.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.

18 x parsers/vasp: wS4nTynCRVinVLoXPp283w/oqmd/icsd/240377/relaxation/1_convergence/vasprun.xml.gz (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1470, in parse
    self.parse_method()
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1169, in parse_method
    atomtypes = self.parser.atom_info.get('atomtypes', {})
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 967, in atom_info
    array_info[fields[i]].append(rcs[n * len(fields) + i])
IndexError: list index out of range

16 x parsers/crystal: gddy5rHgRceN2sZZ6yTnrA/contrib3/STOFeVocomplex/remote1to1/ionic/ionic_test.cryst.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 577, in parse
    f25_filepath1 = out["f25_filepath1"]
  File "/app/nomad/parsing/file_parser/file_parser.py", line 148, in __getitem__
    return self.get(key)
  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 533, in parse
    self._parse_quantity(quantity)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 452, in _parse_quantity
    quantity.re_pattern.search(self.file_mmap)]
  File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 229, in soft_timeout_sighandler
    raise SoftTimeLimitExceeded()
billiard.exceptions.SoftTimeLimitExceeded: SoftTimeLimitExceeded()

14 x parsers/broken: XKOfN3R9QoKOsOmOAiuYHQ/mnt/lxfs2/scratch/xunhuazhao/upload/upload-MgO_CaO_SrO_BaO/water_MgO/2d_H2O_MgO/6H2O_3_2_MgO/surf/others/hse06_k231/aims.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/app/nomad/parsing/parser.py", line 104, in parse
    raise Exception('Failed on purpose.')
Exception: Failed on purpose.

12 x parsers/phonopy: UOm6k1H7SM6B60sSt9m1ow/bulk_references/C/C_graphene/140617_graphene_QHA/140619_TS_phonopy/phonopy_TS_vdW/lattice_2.473/phonopy-FHI-aims-displacement-01/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1409, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1100, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1087, in parse_section
    parse_vdW(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 970, in parse_vdW
    if sec.atom_type_name == atom['atom']:
  File "/app/nomad/metainfo/metainfo.py", line 906, in __getattr__
    raise AttributeError(name)
AttributeError: atom_type_name

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/nomad/processing/base.py", line 565, in proc_task
    rv = func(self, *process_args, **process_kwargs)
  File "/app/nomad/processing/data.py", line 960, in process_calc
    self.parsing()
  File "/app/nomad/processing/data.py", line 1064, in parsing
    raise ProcessFailure('parser failed with exception', exc_info=e, error=str(e), **context)
nomad.processing.base.ProcessFailure: parser failed with exception

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1108, in process_phonon
    ref_method = ref_archive.results.method
AttributeError: 'NoneType' object has no attribute 'method'

12 x parsers/wien2k: X78d1GK-QJGbpM9y0sgY2w/SiTiO2-am-WIENrelax/0.1875/7x7x7k_7.5Rk_mBJkol/7x7x7k_7.5Rk_mBJkol.scf (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/wien2kparser/wien2k_parser.py", line 796, in parse
    self.parse_scc()
  File "/usr/local/lib/python3.7/site-packages/wien2kparser/wien2k_parser.py", line 664, in parse_scc
    sec_dos_values.atom_label = labels[species]
IndexError: list index out of range

11 x parsers/crystal: oauTCma3Sd6SF8T0gHWNNQ/TiS2_PBE0D3_ZD_fc3_00276.o (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 765, in parse
    atomic_number = label_to_atomic_number(bs["species"][1])
  File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 1075, in label_to_atomic_number
    atomic_number = ase.data.atomic_numbers[symbol]
KeyError: 'Working'

9 x parsers/asap: JMvB4xYfTs2dvHW7NrpMHg/fhi/Pd_calculations/Surface_Pd/old/WL.traj (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/asapparser/asap_parser.py", line 165, in parse
    if self.traj_parser.traj is None:
  File "/usr/local/lib/python3.7/site-packages/asapparser/asap_parser.py", line 48, in traj
    if hasattr(self._file_handler.backend, 'calculator'):
  File "/usr/local/lib/python3.7/site-packages/ase/io/ulm.py", line 534, in __getattr__
    value = self._data[attr]
KeyError: 'calculator'

9 x parsers/vasp: shkXg_DnSzuTMGAwJubS8g/oqmd/binaries/B_h/Lu_Rb/static/vasprun.xml (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/normalizing/dos.py", line 87, in normalize
    n_atoms=number_of_atoms
  File "/usr/local/lib/python3.7/site-packages/nomad_dos_fingerprints/DOSfingerprint.py", line 22, in calculate
    raw_energies, raw_dos = self._integrate_to_bins(energy, dos)
  File "/usr/local/lib/python3.7/site-packages/nomad_dos_fingerprints/DOSfingerprint.py", line 59, in _integrate_to_bins
    xstart = round(int(xs[0] / (self.stepsize * 1.)) * self.stepsize, 8)  # define the limits that fit with the predefined stepsize
ValueError: cannot convert float NaN to integer

9 x parsers/vasp: 5dNStveWRkmPdodW1Rdf1g/RhCu_AlkaneC1Activation_Final/Figures_01a_S1_S2/ActivationEnergies/RhAg_CH4/OUTCAR (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1472, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1434, in parse_configurations
    parse_dos(n)
  File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1390, 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'

9 x parsers/onetep: Ohw7JTzLTpC83Y7dMv3ICg/benz_dim/benzene_dimer_vdw.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1161, 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

8 x parsers/nwchem: cpeb9vqgTfmbDh_kKuumyw/NO3/no3_12wa_cpmd_dft_only/no312waonly.log (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 547, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 486, in parse_configurations
    parse_calculation(self.out_parser.get('single_point'))
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 467, in parse_calculation
    sec_method = self.parse_method(source)
  File "/usr/local/lib/python3.7/site-packages/nwchemparser/nwchem_parser.py", line 430, in parse_method
    sec_scf.n_max_iteration = val
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2310, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 981, in __to_np
    value = quantity_def.type.type(value)
ValueError: invalid literal for int() with base 10: ''

8 x parsers/castep: _vXNyPwgTVmvudw8wGjChA/C3x6_Cu2x7_sedc_21/C3x6_Cu2x7_sedc_21.castep (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1254, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1160, in parse_configurations
    parse_calculation(iteration.get('iteration')[-1])
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1110, in parse_calculation
    sec_scc = parse_scc(source)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 969, in parse_scc
    parse_eigenvalues(source)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 899, in parse_eigenvalues
    sec_eigenvalues.energies = band_energies
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2310, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 969, in __to_np
    value = value.to(quantity_def.unit).magnitude
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 660, in to
    magnitude = self._convert_magnitude_not_inplace(other, *contexts, **ctx_kwargs)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 609, in _convert_magnitude_not_inplace
    return self._REGISTRY.convert(self._magnitude, self._units, other)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 947, in convert
    return self._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1830, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1433, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 980, in _convert
    raise DimensionalityError(src, dst, src_dim, dst_dim)
pint.errors.DimensionalityError: Cannot convert from 'electron_volt ** 2' ([length] ** 4 * [mass] ** 2 / [time] ** 4) to 'joule' ([length] ** 2 * [mass] / [time] ** 2)

7 x parsers/phonopy: CGqhyN8SQFWuSjkxTIW3lg/3A-anthracene/phonopy.yaml (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1100, in process_phonon
    relative_ref = scc.calculations_path[0]
IndexError: list index out of range

7 x parsers/orca: SB9YIQf8SviLiIsBoDMP_g/windmill/soc-tddft/windmill_bi/mot1bi.out-copy (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 893, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 842, in parse_configurations
    parse_configuration(self.out_parser.get('single_point'))
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 838, in parse_configuration
    sec_scc = self.parse_scc(section)
  File "/usr/local/lib/python3.7/site-packages/orcaparser/orca_parser.py", line 760, in parse_scc
    sec_scf_iteration.energy = Energy(total=EnergyEntry(value=energy))
  File "/app/nomad/metainfo/metainfo.py", line 774, in __init__
    self.m_update(**other_kwargs)
  File "/app/nomad/metainfo/metainfo.py", line 1200, in m_update
    self.m_set(prop, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 969, in __to_np
    value = value.to(quantity_def.unit).magnitude
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 660, in to
    magnitude = self._convert_magnitude_not_inplace(other, *contexts, **ctx_kwargs)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 609, in _convert_magnitude_not_inplace
    return self._REGISTRY.convert(self._magnitude, self._units, other)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 947, in convert
    return self._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1830, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1433, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 996, in _convert
    value = value * factor
TypeError: can't multiply sequence by non-int of type 'float'

7 x parsers/vaspoutcar: j9qDBjUkQtKY5Ak_i_H7MQ/oqmd/icsd/23887/standard/OUTCAR (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: 429403.

6 x parsers/crystal: Zgm159M-QGaBHimkBL-_aA/contrib2/thesis_outputs/y4h4_sho_9s_NOTR.cryst.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 787, in parse
    section_scf.energy.total = EnergyEntry(value=energies[0])
TypeError: 'NoneType' object is not subscriptable

6 x parsers/elastic: sEZHv9NZQT-Jv0l-C1r8EA/beta_Ga2O3_Elastic_Constants_10.0GPa/Elastic_complete/INFO_ElaStic (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/elasticparser/elastic_parser.py", line 661, in parse
    self.parse_elastic_constant()
  File "/usr/local/lib/python3.7/site-packages/elasticparser/elastic_parser.py", line 562, in parse_elastic_constant
    sec_elastic.elastic_constants_notation_matrix_second_order = matrices['voigt']
KeyError: 'voigt'

6 x parsers/abinit: dkZ_BRDqSA2DeGsH3ItFyw/conv_ecut/Si.out0005 (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 1028, in parse
    self.parse_dataset(n)
  File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 876, in parse_dataset
    sec_method = self.parse_method(n_dataset)
  File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 781, in parse_method
    sec_electronic.n_spin_channels = int(self.out_parser.get_input_var('nsppol', nd, 1))
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

5 x parsers/cp2k: hLOmO-NSQ-ayMP6nMTmbyw/NOMAD_dataset/cp2k/PBE/CP2K-AE/BULK/7x7x7/s7-pbe-01.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/normalizing/system.py", line 210, in normalize_system
    atoms.set_cell(1e10 * lattice_vectors.magnitude)
  File "/usr/local/lib/python3.7/site-packages/ase/atoms.py", line 355, in set_cell
    cell = Cell.new(cell)
  File "/usr/local/lib/python3.7/site-packages/ase/cell.py", line 105, in new
    raise ValueError('Cell must be length 3 sequence, length 6 '
ValueError: Cell must be length 3 sequence, length 6 sequence or 3x3 matrix!

5 x parsers/phonopy: CGqhyN8SQFWuSjkxTIW3lg/4A-tetracene/phonopy.yaml (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1205, 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

5 x parsers/cp2k: HNiiLJx-RKKmt1a7SHf_Lw/lowscalingGW_PH/CP2K/GW100/30_C5H6/cp2k.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1527, in parse
    self.parse_configurations_quickstep()
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1213, in parse_configurations_quickstep
    parse_calculations([single_point])
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1202, in parse_calculations
    sec_system = self.parse_system(atomic_coord)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1089, in parse_system
    lattice_vectors = self.get_lattice_vectors(trajectory._frame)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 932, in get_lattice_vectors
    lattice_vectors = lattice_vectors * 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

5 x parsers/exciting: ML2qGfRqSnmxDLvPKkrLMQ/LiH-pbc/145/INFO.OUT (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2307, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2215, 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 2205, in parse_configuration
    sec_system = self.parse_system(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2158, in parse_system
    setattr(sec_system, name, val)
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2310, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 981, in __to_np
    value = quantity_def.type.type(value)
ValueError: invalid literal for int() with base 10: '********'

4 x parsers/crystal: HY6fjvpoS_6hxmlI8BZJaw/inp-out_cry14_nomad/test_cases/test19.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 658, in parse
    pos_type=pos_type,
  File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 1022, in to_system
    cart_pos = atomutils.to_cartesian(scaled_pos, lattice_vectors)
  File "/app/nomad/atomutils.py", line 170, in to_cartesian
    cartesian_positions = np.dot(positions, complete_cell(cell))
  File "/app/nomad/atomutils.py", line 185, in complete_cell
    return ase.geometry.complete_cell(cell)
  File "/usr/local/lib/python3.7/site-packages/ase/geometry/cell.py", line 209, in complete_cell
    missing = np.nonzero(~cell.any(axis=1))[0]
  File "/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py", line 57, in _any
    return umr_any(a, axis, dtype, out, keepdims)
numpy.AxisError: axis 1 is out of bounds for array of dimension 0

3 x parsers/octopus: fn7aPJsRTVS0mQejQmKz-Q/share/log (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/octopusparser/octopus_parser.py", line 933, in parse
    self.parse_system()
  File "/usr/local/lib/python3.7/site-packages/octopusparser/octopus_parser.py", line 810, in parse_system
    sec_atoms.positions = coordinates * self._units_mapping.get(units.lower())
AttributeError: 'Unit' object has no attribute 'lower'

3 x parsers/phonopy: UOm6k1H7SM6B60sSt9m1ow/bulk_references/C/C_graphene/140617_graphene_QHA/140619_MBD_phonopy/140619_MBD_phonopy.old/phonopy_MBD_vdW/lattice_2.469/phonopy-FHI-aims-displacement-01/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 374, in parse
    phonopy_obj = self.phonopy_obj
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 240, in phonopy_obj
    self._build_phonopy_object_fhi_aims()
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 291, in _build_phonopy_object_fhi_aims
    phonopy_obj.produce_force_constants()
  File "/usr/local/lib/python3.7/site-packages/phonopy/api_phonopy.py", line 967, in produce_force_constants
    decimals=self._force_constants_decimals)
  File "/usr/local/lib/python3.7/site-packages/phonopy/api_phonopy.py", line 3132, in _run_force_constants_from_forces
    decimals=decimals)
  File "/usr/local/lib/python3.7/site-packages/phonopy/harmonic/force_constants.py", line 98, in get_fc2
    atom_list=atom_list)
  File "/usr/local/lib/python3.7/site-packages/phonopy/harmonic/force_constants.py", line 728, in _get_force_constants_disps
    atom_list=atom_list)
  File "/usr/local/lib/python3.7/site-packages/phonopy/harmonic/force_constants.py", line 314, in solve_force_constants
    symprec)
  File "/usr/local/lib/python3.7/site-packages/phonopy/harmonic/force_constants.py", line 673, in _solve_force_constants_svd
    _get_rotated_forces(forces[rot_map_syms[:, i]],
IndexError: index 0 is out of bounds for axis 0 with size 0

3 x parsers/quantumespresso: t1Yy3492Sr6wXMHG_5FuzA/nomad_upload/benchmark.out.r11920.inp=uspp-hyb-g.in.1451158822 (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2744, in parse
    self.parse_method(run)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2585, in parse_method
    setattr(sec_method, key, val)
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2420, in __set__
    (value, type(value), self, self.type))
TypeError: The value ['Real', 'space', 'treatment', 'of', 'Q(r)'] with type <class 'list'> for quantity quantumespressoparser.metainfo.quantum_espresso.Method.x_qe_core_charge_realspace:Quantity is not of type <class 'bool'>

3 x parsers/phonopy: UOm6k1H7SM6B60sSt9m1ow/bulk_references/C/C_graphene/140617_graphene_QHA/140619_TS_phonopy/140619_TS_phonopy.old/Etot/lattice_2.475/phonopy-FHI-aims-displacement-01/control.in (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 378, in parse
    unit_cell = self.phonopy_obj.unitcell.get_cell()
AttributeError: 'NoneType' object has no attribute 'unitcell'

2 x parsers/vaspoutcar: nHo8kktjSviBVsqMt0BLuw/oqmd/icsd/16713/deep_relax/3_ionic_convergence_zpotrf/OUTCAR (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 212, in classify
    return_factors=True
  File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 676, in get_displacement_tensor
    D, D_len, factors = find_mic(flattened_disp, cell, pbc, max_distance)
  File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 750, in find_mic
    tvecs = np.dot(tvec_factors, cell)
  File "<__array_function__ internals>", line 6, in dot
ValueError: On entry to DGEMM parameter number 4 had an illegal value

2 x parsers/elastic: -aHbuecNQ8yYRAkTEXZCHg/NOMAD-espresso-stress/al/INFO_ElaStic (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/elasticparser/elastic_parser.py", line 660, in parse
    self.parse_strain()
  File "/usr/local/lib/python3.7/site-packages/elasticparser/elastic_parser.py", line 546, in parse_strain
    for fit_order in stress_fit[diagram_type][si][0].keys():
IndexError: list index out of range

2 x parsers/castep: CTTru-A7REe4XWGaV-l3cA/GS_2x5/no-DISP/tAB.castep (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1254, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1152, in parse_configurations
    parse_calculation(iteration)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 1110, in parse_calculation
    sec_scc = parse_scc(source)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 969, in parse_scc
    parse_eigenvalues(source)
  File "/usr/local/lib/python3.7/site-packages/castepparser/castep_parser.py", line 899, in parse_eigenvalues
    sec_eigenvalues.energies = band_energies
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2310, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 1003, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 969, in __to_np
    value = value.to(quantity_def.unit).magnitude
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 660, in to
    magnitude = self._convert_magnitude_not_inplace(other, *contexts, **ctx_kwargs)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 609, in _convert_magnitude_not_inplace
    return self._REGISTRY.convert(self._magnitude, self._units, other)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 947, in convert
    return self._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1830, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1433, in _convert
    return super()._convert(value, src, dst, inplace)
  File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 980, in _convert
    raise DimensionalityError(src, dst, src_dim, dst_dim)
pint.errors.DimensionalityError: Cannot convert from 'electron_volt ** 2' ([length] ** 4 * [mass] ** 2 / [time] ** 4) to 'joule' ([length] ** 2 * [mass] / [time] ** 2)

2 x parsers/quantumespresso: y49TZQfZSJCrTGQMrOO7_Q/out/ti2co2 - h/ti2coh2_3_2oh.log (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2746, in parse
    self.parse_configurations(run)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2472, in parse_configurations
    parse_configuration(calculation)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2460, in parse_configuration
    sec_scc = self.parse_scc(run, calculation)
  File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2199, in parse_scc
    reciprocal_cell = sec_run.system[-1].x_qe_reciprocal_cell.to('1/m').magnitude
IndexError: list index out of range

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

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 863, in parse
    self.parse_system()
  File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 735, in parse_system
    atom_labels = self.traj_parser.get_atom_labels(i)
  File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 258, in get_atom_labels
    atom_labels = [self._chemical_symbols[atype] for atype in atoms_type]
  File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 258, in <listcomp>
    atom_labels = [self._chemical_symbols[atype] for atype in atoms_type]
KeyError: 6

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/cp2k: NOCnL8mERjW3YxKnxqq3Fg/3EBA-MONOMER-STUDY/CALCITE/OPT.out (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1526, in parse
    self.parse_method_quickstep()
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1289, in parse_method_quickstep
    setattr(sec_vdw, 'x_cp2k_vdw_%s' % key, val)
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2420, in __set__
    (value, type(value), self, self.type))
TypeError: The value 15.12 with type <class 'float'> for quantity cp2kparser.metainfo.cp2k_general.x_cp2k_section_vdw_settings.x_cp2k_vdw_cutoff_radius:Quantity is not of type <class 'str'>

2 x parsers/exciting: sB1iGmp5Sq2U4CH2y47HRQ/Molecule/INFO.OUT (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2307, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2215, 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 2205, in parse_configuration
    sec_system = self.parse_system(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2119, in parse_system
    lattice_vectors *= self.input_xml_parser.get('structure/crystal/scale', 1.0)
numpy.core._exceptions._UFuncOutputCastingError: Cannot cast ufunc 'multiply' output from dtype('float64') to dtype('int64') with casting rule 'same_kind'

2 x parsers/exciting: bBwLURrsQzyT-avIDAsNhA/silicon-gw/INFO.OUT (v1), raw files (v0)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1061, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2309, in parse
    self.parse_gw()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1834, in parse_gw
    self.parse_file(f, sec_method)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1463, in parse_file
    parser_function(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1791, in _parse_input_gw
    'gw/selfenergy/npol', 0)
  File "/app/nomad/metainfo/metainfo.py", line 896, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2420, in __set__
    (value, type(value), self, self.type))
TypeError: The value 2 with type <class 'numpy.int64'> for quantity nomad.datamodel.metainfo.simulation.method.GW.self_energy_c_number_of_poles:Quantity is not of type <class 'int'>

Edited Dec 15, 2021 by Alvin Noe Ladines