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More problems in new parsers

@ladinesa These are aims/exciting/abinit errors in the last reprocess run.

TypeError: float() argument must be a string or a number, not 'list'

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

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1535, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1236, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1202, in parse_section
    parse_scf(scf_iteration)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1051, in parse_scf
    sec_eigenvalues.eigenvalues_values = eigenvalues[1]
  File "/app/nomad/metainfo/metainfo.py", line 879, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2141, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 986, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 950, in __to_np
    value = value.astype(quantity_def.type)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1654, in _numpy_method_wrap
    value = func(*args, **kwargs)
ValueError: setting an array element with a sequence.
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2163, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2106, in parse_configurations
    sec_scc = parse_configuration(structure_optimization)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2068, in parse_configuration
    sec_system = self.parse_system(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1987, in parse_system
    for n in range(len(atoms)):
TypeError: object of type 'numpy.float64' has no len()
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2163, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2106, in parse_configurations
    sec_scc = parse_configuration(structure_optimization)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2068, in parse_configuration
    sec_system = self.parse_system(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1988, in parse_system
    atom_labels.extend([species[n].split('.')[0]] * len(atoms[n]))
TypeError: object of type 'numpy.float64' has no len()
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 985, in parse
    self.parse_var()
  File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 943, in parse_var
    if val[i] is None:
IndexError: list index out of range
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2163, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2081, in parse_configurations
    sec_scc = parse_configuration(self.info_parser.get('groundstate'))
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2068, in parse_configuration
    sec_system = self.parse_system(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2023, in parse_system
    setattr(sec_system, name, val)
  File "/app/nomad/metainfo/metainfo.py", line 879, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2141, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 986, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 964, in __to_np
    value = quantity_def.type.type(value)
ValueError: invalid literal for int() with base 10: '********'
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1535, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1236, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1220, in parse_section
    parse_gw(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1089, in parse_gw
    sec_calc_to_calc_refs = sec_run.m_create(CalculationToCalculationRefs)
  File "/app/nomad/metainfo/metainfo.py", line 1129, in m_create
    raise TypeError('There is no sub section to hold a %s in %s.' % (section_def, self.m_def))
TypeError: There is no sub section to hold a nomad.datamodel.metainfo.common_dft.CalculationToCalculationRefs:Section in nomad.datamodel.metainfo.common_dft.Run:Section.
TypeError: float() argument must be a string or a number, not 'list'

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

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1535, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1236, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1176, in parse_section
    sec_eigenvalues.eigenvalues_values = eigenvalues[1]
  File "/app/nomad/metainfo/metainfo.py", line 879, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2141, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 986, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 950, in __to_np
    value = value.astype(quantity_def.type)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1654, in _numpy_method_wrap
    value = func(*args, **kwargs)
ValueError: setting an array element with a sequence.
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2165, in parse
    self.parse_gw()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1721, in parse_gw
    self.parse_file(f, sec_method)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1341, in parse_file
    parser_function(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1674, in _parse_input_gw
    'gw/selfenergy/npol', 0)
  File "/app/nomad/metainfo/metainfo.py", line 879, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2251, in __set__
    (value, type(value), self, self.type))
TypeError: The value 2 with type <class 'numpy.int64'> for quantity nomad.datamodel.metainfo.common_dft.Method.gw_self_energy_c_number_of_poles:Quantity is not of type <class 'int'>
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1533, in parse
    self.parse_method()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1266, in parse_method
    species = self.control_parser.get('species')
  File "/app/nomad/parsing/file_parser/file_parser.py", line 81, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
    self.parse(self._key, **self._kwargs)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 513, in parse
    self._parse_quantities(quantities_findall)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 370, 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()
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1514, in parse
    value = self.out_parser.get(key)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 81, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
    self.parse(self._key, **self._kwargs)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 521, in parse
    self._parse_quantity(quantity)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 460, in _parse_quantity
    value.append(sub_parser.parse())
  File "/app/nomad/parsing/file_parser/text_parser.py", line 513, in parse
    self._parse_quantities(quantities_findall)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 393, in _parse_quantities
    values.append(' '.join([m.decode() for m in non_empty_match]))
  File "/app/nomad/parsing/file_parser/text_parser.py", line 393, in <listcomp>
    values.append(' '.join([m.decode() for m in non_empty_match]))
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 2665: invalid start byte
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2163, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2081, in parse_configurations
    sec_scc = parse_configuration(self.info_parser.get('groundstate'))
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2068, in parse_configuration
    sec_system = self.parse_system(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1981, in parse_system
    lattice_vectors *= self.input_xml_parser.get('structure/crystal/scale', 1.0)
numpy.core._exceptions.UFuncTypeError: Cannot cast ufunc 'multiply' output from dtype('float64') to dtype('int64') with casting rule 'same_kind'
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2163, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2088, in parse_configurations
    self.parse_file(f, sec_scc)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1341, in parse_file
    parser_function(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1106, in _parse_dos
    if self.dos_parser.get('totaldos', None) is None:
  File "/app/nomad/parsing/file_parser/file_parser.py", line 81, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
    self.parse(self._key, **self._kwargs)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 505, in parse
    if not self.total_dos:
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 471, in total_dos
    self._total_dos = self.root.findall('./%s/%s' % (self._totaldos_key, self._diagram_key))
  File "/app/nomad/parsing/file_parser/xml_parser.py", line 52, in root
    self._file_handler = ElementTree.parse(self.mainfile).getroot()
  File "/usr/local/lib/python3.7/xml/etree/ElementTree.py", line 1197, in parse
    tree.parse(source, parser)
  File "/usr/local/lib/python3.7/xml/etree/ElementTree.py", line 598, in parse
    self._root = parser._parse_whole(source)
  File "<string>", line None
xml.etree.ElementTree.ParseError: no element found: line 111468, column 0
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2167, in parse
    self.parse_xs()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1653, in parse_xs
    if xstype.lower() == 'bse':
AttributeError: 'NoneType' object has no attribute 'lower'
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2163, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2088, in parse_configurations
    self.parse_file(f, sec_scc)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1341, in parse_file
    parser_function(section)
  File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1162, in _parse_eigenvalues
    if self.eigval_parser.get('eigenvalues_occupancies', None) is None:
  File "/app/nomad/parsing/file_parser/file_parser.py", line 81, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
    self.parse(self._key, **self._kwargs)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 498, in parse
    if self.file_mmap is None:
  File "/app/nomad/parsing/file_parser/text_parser.py", line 343, in file_mmap
    offset=self._file_offset)
ValueError: cannot mmap an empty file
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1514, in parse
    value = self.out_parser.get(key)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 81, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
    self.parse(self._key, **self._kwargs)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 513, in parse
    self._parse_quantities(quantities_findall)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 393, in _parse_quantities
    values.append(' '.join([m.decode() for m in non_empty_match]))
  File "/app/nomad/parsing/file_parser/text_parser.py", line 393, in <listcomp>
    values.append(' '.join([m.decode() for m in non_empty_match]))
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 542: invalid start byte
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1533, in parse
    self.parse_method()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1330, in parse_method
    parse_basis_set(species)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1295, in parse_basis_set
    val[0], dtype=float))
ValueError: could not convert string to float: '#'
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1535, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1242, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1202, in parse_section
    parse_scf(scf_iteration)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1012, in parse_scf
    sec_scf = sec_scc.m_create(ScfIteration)
  File "/app/nomad/metainfo/metainfo.py", line 1144, in m_create
    sub_section = section_cls(**kwargs)
  File "/app/nomad/metainfo/metainfo.py", line 726, in __init__
    self.m_def = cls.m_def
  File "/app/nomad/metainfo/metainfo.py", line 879, in __setattr__
    return super().__setattr__(name, value)
  File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 229, in soft_timeout_sighandler
    raise SoftTimeLimitExceeded()
billiard.exceptions.SoftTimeLimitExceeded: SoftTimeLimitExceeded()
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1514, in parse
    value = self.out_parser.get(key)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 81, in get
    val = self.results.get(key, None)
  File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
    self.parse(self._key, **self._kwargs)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 521, in parse
    self._parse_quantity(quantity)
  File "/app/nomad/parsing/file_parser/text_parser.py", line 446, in _parse_quantity
    for res in quantity.re_pattern.finditer(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()
TypeError: float() argument must be a string or a number, not 'list'

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

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1535, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1239, in parse_configurations
    parse_section(section)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1202, in parse_section
    parse_scf(scf_iteration)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1051, in parse_scf
    sec_eigenvalues.eigenvalues_values = eigenvalues[1]
  File "/app/nomad/metainfo/metainfo.py", line 879, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2141, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 986, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 950, in __to_np
    value = value.astype(quantity_def.type)
  File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1654, in _numpy_method_wrap
    value = func(*args, **kwargs)
ValueError: setting an array element with a sequence.
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1533, in parse
    self.parse_method()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1401, in parse_method
    xc_parameters.setdefault('$\\omega$ in m^-1', hse_omega.to('1/m').magnitude)
AttributeError: 'float' object has no attribute 'to'
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1533, in parse
    self.parse_method()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1370, in parse_method
    self.parse_topology()
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1482, in parse_topology
    parse_atom_type(specie)
  File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1434, in parse_atom_type
    sec_atom_species.x_fhi_aims_controlInOut_species_cut_pot_scale = val[0][2]
  File "/app/nomad/metainfo/metainfo.py", line 879, in __setattr__
    return super().__setattr__(name, value)
  File "/app/nomad/metainfo/metainfo.py", line 2141, in __set__
    obj.m_set(self, value)
  File "/app/nomad/metainfo/metainfo.py", line 986, in m_set
    value = self.__to_np(quantity_def, value)
  File "/app/nomad/metainfo/metainfo.py", line 964, in __to_np
    value = quantity_def.type.type(value)
ValueError: could not convert string to float: 'Task'
Edited by Markus Scheidgen