Exceptions during v1 processing of FHI-aims calculations
- [x] 437823 x
[**parsers/fhi-aims**: *zgWhyFkzSfy78LBmnd25HQ/ArgCu_0018_r1/ArgCu_0018_r1.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/zgWhyFkzSfy78LBmnd25HQ/UdgTk30mQpOGM9AU4N7aupvEOa20),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/zgWhyFkzSfy78LBmnd25HQ/UdgTk30mQpOGM9AU4N7aupvEOa20/raw)
```
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
```
- [x] 58114 x
[**parsers/fhi-aims**: *tq_nhWthSeGb2sxnEBNiIQ/relaxation_test/aims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/tq_nhWthSeGb2sxnEBNiIQ/oFxGU8ucFQnQKhLN4VHyz3Mi1nWt),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/tq_nhWthSeGb2sxnEBNiIQ/oFxGU8ucFQnQKhLN4VHyz3Mi1nWt/raw)
```
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 227, in normalize_run
self.geometry_optimization(results.method, results.properties)
File "/app/nomad/normalizing/results.py", line 425, in geometry_optimization
structure_optimized = self.nomad_system_to_structure(StructureOptimized, system_ref)
File "/app/nomad/normalizing/results.py", line 739, in nomad_system_to_structure
struct.atomic_density = len(system.atoms.labels) / cell_volume
TypeError: object of type 'NoneType' has no len()
```
- [ ] 1616 x
[**parsers/fhi-aims**: *vZFlWi73QF2OmB6W5PKTfQ/AminoAcids/hisH/Dipeptide/Mg/conf_0063/FHIaims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/vZFlWi73QF2OmB6W5PKTfQ/40FLSn0yPxQz3Ob1Svuxw_4tR2mv),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/vZFlWi73QF2OmB6W5PKTfQ/40FLSn0yPxQz3Ob1Svuxw_4tR2mv/raw)
```
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 953, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 704, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 766, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'AminoAcids/hisH/Dipeptide/Mg/conf_0063/FHIaims.out'
```
- [x] 1053 x
[**parsers/fhi-aims**: *y56SlVIxQdCLL9k8nBeT5Q/clathrates/Si/bench/func/Si45/i/Z0/rpbe/tmp.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/y56SlVIxQdCLL9k8nBeT5Q/ujoNX6joT_Z-YMl6eonNxNg8Vk6q),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/y56SlVIxQdCLL9k8nBeT5Q/ujoNX6joT_Z-YMl6eonNxNg8Vk6q/raw)
```
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 106, in method
functional_long_name = self.functional_long_name()
File "/app/nomad/normalizing/method.py", line 377, in functional_long_name
xc_functional = MethodNormalizer.functional_long_name_from_method(self.repr_method, self.run.method)
File "/app/nomad/normalizing/method.py", line 409, in functional_long_name_from_method
for component in sec_xc_functionals[functional]:
TypeError: 'NoneType' object is not subscriptable
```
- [x] 721 x
[**parsers/fhi-aims**: *oOhSAezVSB6SNOgVKoH08A/mnt/lxfs2/scratch/villaseca/Fe_MgO/Fe-MgO_Cluster_Calculations/DoubleZ/S_0/HF/aims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/oOhSAezVSB6SNOgVKoH08A/wmNoj_8OZXp_nfqn_Hm7TjXIxmdm),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/oOhSAezVSB6SNOgVKoH08A/wmNoj_8OZXp_nfqn_Hm7TjXIxmdm/raw)
```
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 1003, in parse_section
sec_atoms.positions = structure.get('positions') * ureg.angstrom
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 187, in __mul__
return self._REGISTRY.Quantity(1, self._units) * other
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1249, in __mul__
return self._mul_div(other, operator.mul)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 115, in wrapped
return f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 95, in wrapped
result = f(self, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1215, in _mul_div
magnitude = magnitude_op(self._magnitude, other_magnitude)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('int64'), dtype('<U32')) -> None
```
- [x] 635 x
[**parsers/fhi-aims**: *z8c4kB4xSISGKIjhYNE3nQ/DopingTEST/1e19/output* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/z8c4kB4xSISGKIjhYNE3nQ/ZIhnS230n42IUsXf1HvPzPCvr8N8),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/z8c4kB4xSISGKIjhYNE3nQ/ZIhnS230n42IUsXf1HvPzPCvr8N8/raw)
```
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 1074, in parse_section
parse_dos(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 842, in parse_dos
sec_dos_values = sec_dos.m_create(DosValues, sec_def)
AttributeError: 'NoneType' object has no attribute 'm_create'
```
- [x] 71 x
[**parsers/fhi-aims**: *UjTSEq0fRQeEsVNZEBCXJA/binaries_unrelaxed_expanded_5pc/pw-lda/tight/tier2/atomic_zora/8/67_Ho/output.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/UjTSEq0fRQeEsVNZEBCXJA/t9SJiQfHNeJlcFtllOWNTD3dn47A),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/UjTSEq0fRQeEsVNZEBCXJA/t9SJiQfHNeJlcFtllOWNTD3dn47A/raw)
```
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/band_structure.py", line 68, in normalize
energy_lowest
File "/app/nomad/normalizing/band_structure.py", line 192, in add_band_gap
energies = np.concatenate(energies, axis=2)
File "<__array_function__ internals>", line 6, in concatenate
ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 348 and the array at index 9 has size 196
```
- [x] 19 x
[**parsers/fhi-aims**: *XuQgFPI0SAixWW5R1Khzqw/letsgo/NaI/aimsNaI4.32720219692.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/XuQgFPI0SAixWW5R1Khzqw/rK2YszgQz8BsSQTQ9BZ5kT7JSMZg),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/XuQgFPI0SAixWW5R1Khzqw/rK2YszgQz8BsSQTQ9BZ5kT7JSMZg/raw)
```
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 1103, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1067, in parse_section
parse_scf(scf_iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 903, in parse_scf
eigenvalues = get_eigenvalues(iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 870, in get_eigenvalues
return kpts, occs_eigs[1] * ureg.hartree, occs_eigs[0]
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 291, in __array_ufunc__
**kwargs,
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1655, in __array_ufunc__
return numpy_wrap("ufunc", ufunc, inputs, kwargs, types)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 921, in numpy_wrap
return handled[name](*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 303, in implementation
result_magnitude = func(*stripped_args, **stripped_kwargs)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U9'), dtype('int64')) -> None
```
- [x] 17 x
[**parsers/fhi-aims**: *nXIM-kNGSNOOBFY7swQlPA/rocksaltzincblende/zincblende/aimszincblendeBeSe5.084.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/nXIM-kNGSNOOBFY7swQlPA/u2HiLEFDSoTWH68C-RUinKSuTnqt),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/nXIM-kNGSNOOBFY7swQlPA/u2HiLEFDSoTWH68C-RUinKSuTnqt/raw)
```
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 1067, in parse_section
parse_scf(scf_iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 903, in parse_scf
eigenvalues = get_eigenvalues(iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 870, in get_eigenvalues
return kpts, occs_eigs[1] * ureg.hartree, occs_eigs[0]
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 291, in __array_ufunc__
**kwargs,
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1655, in __array_ufunc__
return numpy_wrap("ufunc", ufunc, inputs, kwargs, types)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 921, in numpy_wrap
return handled[name](*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 303, in implementation
result_magnitude = func(*stripped_args, **stripped_kwargs)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U32'), dtype('int64')) -> None
```
- [x] 14 x
[**parsers/fhi-aims**: *ozK5RJx9QB-sE9ZLPy7vzw/mnt/lxfs2/scratch/villaseca/Fe_MgO/Transfers_hydra/Fe-MgO_Periodic/alpha_0.6/4xa/aims_final.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/ozK5RJx9QB-sE9ZLPy7vzw/bC7CeU9XaGKDsAc3EjAOS3l-0z1t),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/ozK5RJx9QB-sE9ZLPy7vzw/bC7CeU9XaGKDsAc3EjAOS3l-0z1t/raw)
```
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 1103, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1074, in parse_section
parse_dos(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 842, in parse_dos
sec_dos_values = sec_dos.m_create(DosValues, sec_def)
AttributeError: 'NoneType' object has no attribute 'm_create'
```
- [x] 8 x
[**parsers/fhi-aims**: *u9DydQxjQXu1xTJjXVAUtQ/scr_relaxation_dataset/.P42nmc/GeS2/pbe/sym_trm_2012/aims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/u9DydQxjQXu1xTJjXVAUtQ/zARxDEwqP1dOf0n-ukRn3zmcJ1n6),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/u9DydQxjQXu1xTJjXVAUtQ/zARxDEwqP1dOf0n-ukRn3zmcJ1n6/raw)
```
Traceback (most recent call last):
File "/app/nomad/normalizing/results.py", line 583, in structures_2d
raise ValueError("could not detect the periodic dimensions in a 2D system")
ValueError: could not detect the periodic dimensions in a 2D system
```
- [x] 8 x
[**parsers/fhi-aims**: *u9DydQxjQXu1xTJjXVAUtQ/scr_relaxation_dataset/.P42nmc/GeS2/pbe/sym_trm_2012/aims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/u9DydQxjQXu1xTJjXVAUtQ/zARxDEwqP1dOf0n-ukRn3zmcJ1n6),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/u9DydQxjQXu1xTJjXVAUtQ/zARxDEwqP1dOf0n-ukRn3zmcJ1n6/raw)
```
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 214, in normalize_run
properties, conv_atoms, wyckoff_sets, spg_number = self.properties(repr_system, repr_symmetry)
File "/app/nomad/normalizing/results.py", line 459, in properties
conv_atoms, prim_atoms, wyckoff_sets, spg_number = self.structures_2d(original_atoms)
File "/app/nomad/normalizing/results.py", line 632, in structures_2d
return conv_atoms, prim_atoms, wyckoff_sets, spg_number
UnboundLocalError: local variable 'conv_atoms' referenced before assignment
```
- [x] 6 x
[**parsers/fhi-aims**: *hSVvPAypRVmhmJB6Nuhnbw/58_Ce/cebulk/real-space/fcc/fm/k_04/tier1/pbe0/restart_2.1/1.9/Ce.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/hSVvPAypRVmhmJB6Nuhnbw/mvHiZVAj7ye7XlXM_TixQmry83hf),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/hSVvPAypRVmhmJB6Nuhnbw/mvHiZVAj7ye7XlXM_TixQmry83hf/raw)
```
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 1067, in parse_section
parse_scf(scf_iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 903, in parse_scf
eigenvalues = get_eigenvalues(iteration)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 868, in get_eigenvalues
np.reshape(occs_eigs, (len(kpts), n_spin, n_eigs, 2)), axes=(3, 1, 0, 2))
File "<__array_function__ internals>", line 6, in reshape
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 298, in reshape
return _wrapfunc(a, 'reshape', newshape, order=order)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 54, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 43, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: cannot reshape array of size 278 into shape (1,2,69,2)
```
- [x] 5 x
[**parsers/fhi-aims**: *XuQgFPI0SAixWW5R1Khzqw/letsgo/KCl/aimsKCl4.17398155871.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/XuQgFPI0SAixWW5R1Khzqw/TLqcF15T3FAuV5Z6HabEZC_rBWDi),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/XuQgFPI0SAixWW5R1Khzqw/TLqcF15T3FAuV5Z6HabEZC_rBWDi/raw)
```
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 1103, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1035, in parse_section
eigenvalues = get_eigenvalues(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 870, in get_eigenvalues
return kpts, occs_eigs[1] * ureg.hartree, occs_eigs[0]
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 291, in __array_ufunc__
**kwargs,
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1655, in __array_ufunc__
return numpy_wrap("ufunc", ufunc, inputs, kwargs, types)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 921, in numpy_wrap
return handled[name](*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 303, in implementation
result_magnitude = func(*stripped_args, **stripped_kwargs)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U32'), dtype('int64')) -> None
```
- [x] 4 x
[**parsers/fhi-aims**: *SC-EGrH7R-6wLrgSHkOOcA/binaries_unrelaxed/pbe/light/tier1/zora/2/71_Lu/output.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/SC-EGrH7R-6wLrgSHkOOcA/oM6dV06EC6nBLjpn7-FVrTrRzNmB),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/SC-EGrH7R-6wLrgSHkOOcA/oM6dV06EC6nBLjpn7-FVrTrRzNmB/raw)
```
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/band_structure.py", line 68, in normalize
energy_lowest
File "/app/nomad/normalizing/band_structure.py", line 187, in add_band_gap
seg_energies = np.swapaxes(seg_energies, 1, 2)
File "<__array_function__ internals>", line 6, in swapaxes
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 594, in swapaxes
return _wrapfunc(a, 'swapaxes', axis1, axis2)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
return bound(*args, **kwds)
numpy.AxisError: axis2: axis 2 is out of bounds for array of dimension 2
```
- [x] 3 x
[**parsers/fhi-aims**: *iF5Y7WouTRGd68KfVHJzbA/good_surface/CuCl/aims2.04.07407407407.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/iF5Y7WouTRGd68KfVHJzbA/sLs-zL0MD9BVnFVtzt9TwaFc1F0D),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/iF5Y7WouTRGd68KfVHJzbA/sLs-zL0MD9BVnFVtzt9TwaFc1F0D/raw)
```
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 1035, in parse_section
eigenvalues = get_eigenvalues(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 870, in get_eigenvalues
return kpts, occs_eigs[1] * ureg.hartree, occs_eigs[0]
File "/usr/local/lib/python3.7/site-packages/pint/unit.py", line 291, in __array_ufunc__
**kwargs,
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1655, in __array_ufunc__
return numpy_wrap("ufunc", ufunc, inputs, kwargs, types)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 921, in numpy_wrap
return handled[name](*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/pint/numpy_func.py", line 303, in implementation
result_magnitude = func(*stripped_args, **stripped_kwargs)
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U32'), dtype('int64')) -> None
```
- [x] 2 x
[**parsers/fhi-aims**: *hb5jvpgBSACVtVLJOmFhCw/Ga_P_F/Projections/AB/Planar/z.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/hb5jvpgBSACVtVLJOmFhCw/MM83sgu3kQH6TT5fVH3RC74BW2yV),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/hb5jvpgBSACVtVLJOmFhCw/MM83sgu3kQH6TT5fVH3RC74BW2yV/raw)
```
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 1035, in parse_section
eigenvalues = get_eigenvalues(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 861, in get_eigenvalues
kpts = np.reshape(kpts, (len(kpts) // n_spin, n_spin, 3))
File "<__array_function__ internals>", line 6, in reshape
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 298, in reshape
return _wrapfunc(a, 'reshape', newshape, order=order)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 54, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 43, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: cannot reshape array of size 3 into shape (0,2,3)
```
- [ ] 1 x
[**parsers/fhi-aims**: *NJxp4QcKQRSfKpve6zm8zw/AminoAcids/arg/Dipeptide/bare/conf_0403/FHIaims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/NJxp4QcKQRSfKpve6zm8zw/Zf213os89VES2XJRPjwJI1Efa8-5),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/NJxp4QcKQRSfKpve6zm8zw/Zf213os89VES2XJRPjwJI1Efa8-5/raw)
```
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 953, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 704, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 766, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'AminoAcids/arg/Dipeptide/bare/conf_0403/FHIaims.out'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1001, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
```
- [ ] 1 x
[**parsers/fhi-aims**: *vZFlWi73QF2OmB6W5PKTfQ/AminoAcids/argH/Dipeptide/Ba/conf_0152/FHIaims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/vZFlWi73QF2OmB6W5PKTfQ/U_mWIfCYNcsxieL0CiPiGbtIa8fI),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/vZFlWi73QF2OmB6W5PKTfQ/U_mWIfCYNcsxieL0CiPiGbtIa8fI/raw)
```
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 953, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 704, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 766, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'AminoAcids/argH/Dipeptide/Ba/conf_0152/FHIaims.out'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1001, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
```
- [ ] 1 x
[**parsers/fhi-aims**: *vZFlWi73QF2OmB6W5PKTfQ/AminoAcids/argH/Dipeptide/Ca/conf_0402/FHIaims.out* (v1)](https://nomad-lab.eu/prod/v1/gui/search/entries/entry/id/vZFlWi73QF2OmB6W5PKTfQ/uywGpW_4QxuNgHxM3jBUDp9cdKc6),
[raw files (v0)](https://nomad-lab.eu/prod/rae/gui/entry/id/vZFlWi73QF2OmB6W5PKTfQ/uywGpW_4QxuNgHxM3jBUDp9cdKc6/raw)
```
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 953, in process_calc
self._initialize_metadata_for_processing()
File "/app/nomad/processing/data.py", line 704, in _initialize_metadata_for_processing
self._apply_metadata_from_process(self._entry_metadata)
File "/app/nomad/processing/data.py", line 766, in _apply_metadata_from_process
entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
File "/app/nomad/files.py", line 1048, in calc_hash
for filepath in self.calc_files(mainfile):
File "/app/nomad/files.py", line 1011, in calc_files
raise KeyError(mainfile)
KeyError: 'AminoAcids/argH/Dipeptide/Ca/conf_0402/FHIaims.out'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1001, in on_fail
self._entry_metadata.apply_archvie_metadata(self._parser_results)
File "/app/nomad/datamodel/datamodel.py", line 683, in apply_archvie_metadata
for section, property_def, _ in archive.m_traverse():
AttributeError: 'NoneType' object has no attribute 'm_traverse'
```
issue