Exceptions in new quantum-espresso parser
Performance and extracted metadata looks good. There are some exceptions though:
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2954, parsers/quantumespresso, y7q5WRH_SGmFwFImtJNLfA:zJDxQxP6VJ5a6YYqMBZcGeWddxQJ
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/quantumespressoparser/quantum_espresso_parser.py", line 2675, in parse
self.parse_configurations(run)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2437, in parse_configurations
parse_configuration(calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2425, in parse_configuration
sec_scc = self.parse_scc(run, calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2194, in parse_scc
sec_scc.energy_reference_fermi = pint.Quantity(fermi_energy, 'eV')
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 952, in __to_np
value = value.to(quantity_def.unit).magnitude
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 661, in to
magnitude = self._convert_magnitude_not_inplace(other, *contexts, **ctx_kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 610, 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 954, in convert
return self._convert(value, src, dst, inplace)
File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1840, in _convert
return super()._convert(value, src, dst, inplace)
File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1442, in _convert
return super()._convert(value, src, dst, inplace)
File "/usr/local/lib/python3.7/site-packages/pint/registry.py", line 1003, in _convert
value = value * factor
TypeError: can't multiply sequence by non-int of type 'float'
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392, parsers/quantumespresso, tNnsUrHkQo2MbG5YRJqz2Q:zLG28sEucTOzMfo8Mxx1mZuo4-7i
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/quantumespressoparser/quantum_espresso_parser.py", line 2673, in parse
self.parse_method(run)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2521, in parse_method
setattr(sec_method, key, val)
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 ['gamma-point', 'specific', 'algorithms', 'are', 'used'] with type <class 'list'> for quantity quantumespressoparser.metainfo.quantum_espresso.section_method.x_qe_gamma_algorithms:Quantity is not of type <class 'bool'>
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328, parsers/quantumespresso, vjHwhnCcSMyn1HwvMRLTBg:r96qDkkLroD8LXmgPcsSeEmptPRG
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/quantumespressoparser/quantum_espresso_parser.py", line 2675, in parse
self.parse_configurations(run)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2452, in parse_configurations
parse_configuration(calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2425, in parse_configuration
sec_scc = self.parse_scc(run, calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2284, in parse_scc
parse_diagonalization(iteration, sec_scf_iteration)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2225, in parse_diagonalization
sec_diagonalization = target.m_create(diagonalization_section)
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 quantumespressoparser.metainfo.quantum_espresso.x_qe_section_bands_diagonalization:Section in nomad.datamodel.metainfo.common_dft.ScfIteration:Section.
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150, parsers/quantumespresso, z0fcha-sR4iGjrCFbO9wIw:iefCGeqAOZYYD5gvba6zIkuJL72y
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/quantumespressoparser/quantum_espresso_parser.py", line 2675, in parse
self.parse_configurations(run)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2437, in parse_configurations
parse_configuration(calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2425, in parse_configuration
sec_scc = self.parse_scc(run, calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2284, in parse_scc
parse_diagonalization(iteration, sec_scf_iteration)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2225, in parse_diagonalization
sec_diagonalization = target.m_create(diagonalization_section)
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 quantumespressoparser.metainfo.quantum_espresso.x_qe_section_bands_diagonalization:Section in nomad.datamodel.metainfo.common_dft.ScfIteration:Section.
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130, parsers/quantumespresso, M1YLE4ehThC7G6KliyJF3g:uavkg0_NG66e_YT9VdVTTS6wHP2Y
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/quantumespressoparser/quantum_espresso_parser.py", line 2675, in parse
self.parse_configurations(run)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2437, in parse_configurations
parse_configuration(calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2424, in parse_configuration
sec_system = self.parse_system(run, calculation)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2403, in parse_system
setattr(sec_system, 'x_qe_%s_g_vectors' % grid_type, int(grid[0]))
ValueError: invalid literal for int() with base 10: '1922.6652'
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102, parsers/quantumespresso, t1Yy3492Sr6wXMHG_5FuzA:zfDoHhKmj5VZaIUFSYDonbFSKY8v
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/quantumespressoparser/quantum_espresso_parser.py", line 2673, in parse
self.parse_method(run)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2596, in parse_method
sec_method_atom_kind.x_qe_pp_l_idx = val[0]
IndexError: too many indices for array: array is 0-dimensional, but 1 were indexed
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43, in normalizer, rECCI6B-TlSZp9By4r00YA:wQYQsqB8K8ViSXtzrIVAuVxGGlHE
Traceback (most recent call last):
File "/app/nomad/normalizing/optimade.py", line 219, in normalize_system
self.add_optimade_data(system.m_parent_index)
File "/app/nomad/normalizing/optimade.py", line 189, in add_optimade_data
optimade.lattice_vectors = get_value(section_system.lattice_vectors, numpy=True, unit=ureg.m)
File "/app/nomad/normalizing/optimade.py", line 151, in get_value
value = value * unit
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 188, in __mul__
return self._REGISTRY.Quantity(1, self._units) * other
TypeError: unsupported operand type(s) for *: 'Quantity' and 'NoneType'
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17, in normalizer, U_zHhUjsQA6B3PkqEIAlpA:ggTUQIwnihLa1QWwu68UlorIZkNS
Traceback (most recent call last):
File "/app/nomad/normalizing/optimade.py", line 219, in normalize_system
self.add_optimade_data(system.m_parent_index)
File "/app/nomad/normalizing/optimade.py", line 199, in add_optimade_data
element_label = match.group(1)
AttributeError: 'NoneType' object has no attribute 'group'
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5, in normalizer, zLYwk2xRSOmClxPiL28N5A:undefined
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 433, in wrapper
func(self, *args, **kwargs)
File "/app/nomad/processing/data.py", line 1410, in cleanup
self._cleanup_after_re_processing()
File "/app/nomad/processing/data.py", line 1391, in _cleanup_after_re_processing
staging_upload_files.pack(self.user_metadata(), skip_raw=True)
File "/app/nomad/files.py", line 713, in pack
super().pack(entries, target_dir=self.public_upload_files, skip_raw=True)
File "/app/nomad/files.py", line 447, in pack
assert not self.is_frozen, "Cannot pack an upload that is packed, or packing."
AssertionError: Cannot pack an upload that is packed, or packing.
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4, parsers/elastic, -aHbuecNQ8yYRAkTEXZCHg:Ws7222TLkRakAa-OQMARpz9HGrUU
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/elasticparser/elastic_parser.py", line 640, in parse
self.parse_strain()
File "/usr/local/lib/python3.7/site-packages/elasticparser/elastic_parser.py", line 513, in parse_strain
stress_i = np.transpose(np.array(stress[diagram_type]), axes=(2, 0, 1))
File "<__array_function__ internals>", line 6, in transpose
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 658, in transpose
return _wrapfunc(a, 'transpose', axes)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 58, in _wrapfunc
return bound(*args, **kwds)
ValueError: axes don't match array
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4, parsers/quantumespresso, t1Yy3492Sr6wXMHG_5FuzA:nkFuKwTHES_V-CWcjgxqv5HWV6iy
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/quantumespressoparser/quantum_espresso_parser.py", line 2673, in parse
self.parse_method(run)
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 2469, in parse_method
xc_section_method, xc_functionals = run.get_xc_functional()
File "/usr/local/lib/python3.7/site-packages/quantumespressoparser/quantum_espresso_parser.py", line 1415, in get_xc_functional
xc_terms = get_data(_libxc_shortcut[xc_functional]['xc_terms'])
KeyError: 'PBE0 ( 6 4 8 4 0 0)'
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3, in normalizer, DLpXm6AbTc64oVO8luYgag:SHh1xr_l58eCk-JphIicR28nv6Yn
Traceback (most recent call last):
File "/app/nomad/normalizing/optimade.py", line 219, in normalize_system
self.add_optimade_data(system.m_parent_index)
File "/app/nomad/normalizing/optimade.py", line 162, in add_optimade_data
atoms = normalized_atom_labels(nomad_species)
File "/app/nomad/normalizing/system.py", line 52, in normalized_atom_labels
for match in [re.search(atom_label_re, atom_label) for atom_label in atom_labels]]
TypeError: 'NoneType' object is not iterable
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1, in normalizer, DLpXm6AbTc64oVO8luYgag:WGJMimitFtkUhbq3YF7b_sVrnQGw
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 259, 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]))