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Issue created by Markus Scheidgen@mscheidgOwner3 of 4 checklist items completed3/4 checklist items

Problems in the OLD VASP parser

I did a mistake and this was done for the OLD VASP parser!!!

I reprocesses all AFLOW calculations. Overall it run pretty smoothly. Performance was good. There have been a few exceptions. @ladinesa can you have a look, even though they are not coming from the parser it self. Most of them are probably more data problems that parser problems and the normalisers are just lacking some exception handling that you could add. The first one, might be an indication that the parser produced bad DOS data.

I continue to re-process the rest of VASP. Which is more diverse and will show us more errors probably.

Traceback (most recent call last):
  File "/app/nomad/normalizing/dos.py", line 149, 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
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 572, in normalizing
    normalizer(self._parser_results).normalize(logger=logger)
  File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 286, in normalize
    self.fill(context)
  File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 188, in fill
    struct.normalize(context)
  File "/app/nomad/normalizing/encyclopedia/material.py", line 392, in normalize
    wyckoff_sets = symmetry_analyzer.get_wyckoff_sets_conventional(return_parameters=True)
  File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 508, in get_wyckoff_sets_conventional
    return_parameters=return_parameters,
  File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 1406, in _get_wyckoff_sets
    .format(wset.wyckoff_letter, wset.space_group, wset.element, wset.indices)
ValueError: Could not resolve the free Wyckoff parameters for Wyckoff letter 'b' in space group 178. Problem in determining variables for element 'Cl' at indices '[0, 1, 2, 3, 4, 5]'.
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 572, in normalizing
    normalizer(self._parser_results).normalize(logger=logger)
  File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 286, in normalize
    self.fill(context)
  File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 188, in fill
    struct.normalize(context)
  File "/app/nomad/normalizing/encyclopedia/material.py", line 512, in normalize
    symmetry_analyzer = self.get_symmetry_analyzer(repr_atoms)
  File "/app/nomad/normalizing/encyclopedia/material.py", line 482, in get_symmetry_analyzer
    raise ValueError("Could not detect the periodic dimensions in a 2D system.")
ValueError: Could not detect the periodic dimensions in a 2D system.
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 318, in classify
    dist_matrix_radii_pbc
  File "/usr/local/lib/python3.7/site-packages/matid/classification/classifier.py", line 463, in cross_validate_region
    dist_matrix_radii_pbc,
  File "/usr/local/lib/python3.7/site-packages/matid/classification/periodicfinder.py", line 134, in get_region
    bond_threshold
  File "/usr/local/lib/python3.7/site-packages/matid/classification/periodicfinder.py", line 586, in _find_proto_cell
    offset = proto_cell.get_positions()[seed_group_index]
IndexError: index 1 is out of bounds for axis 0 with size 1
Edited by Markus Scheidgen