FHI-vibes parser/processing

This should be the used workflow parsers version

sigkill 9 problems are usually due to using too much memory.

10 entries (1 uploads) x parsers/fhi-vibes: 3VtDWp0ZSt6KCATZ6SiAuQ/aiGK_methods/MgO/nve.3/greenkubo_eff.nc (v1)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1047, in parsing
    self._parser_results, logger=logger)
  File "/app/nomad/parsing/parser.py", line 249, in parse
    self.mainfile_parser.parse(mainfile, archive, logger)
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/fhivibes/parser.py", line 382, in parse
    self.parse_configurations()
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/fhivibes/parser.py", line 180, in parse_configurations
    for n_frame in range(self.n_frames):
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/fhivibes/parser.py", line 110, in n_frames
    return len(self.parser.get('positions'))
TypeError: object of type 'NoneType' has no len()

10 entries (1 uploads) x parsers/fhi-vibes: 3VtDWp0ZSt6KCATZ6SiAuQ/aiGK_methods/CuI/nve.1/trajectory.nc (v1)

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: 2536.

4 entries (1 uploads) x parsers/phonopy: 3VtDWp0ZSt6KCATZ6SiAuQ/aiGK_methods/CuI/phono3py/phono3py/output/disp_fc3.yaml (v1)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1047, in parsing
    self._parser_results, logger=logger)
  File "/app/nomad/parsing/parser.py", line 249, in parse
    self.mainfile_parser.parse(mainfile, archive, logger)
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 393, in parse
    phonopy_obj = self.phonopy_obj
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 247, in phonopy_obj
    self._build_phonopy_object_vasp()
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 255, in _build_phonopy_object_vasp
    phonopy_obj = phonopy.load(self.mainfile)
  File "/usr/local/lib/python3.7/site-packages/phonopy/cui/load.py", line 292, in load
    log_level=log_level)
  File "/usr/local/lib/python3.7/site-packages/phonopy/cui/load_helper.py", line 207, in set_dataset_and_force_constants
    log_level)
  File "/usr/local/lib/python3.7/site-packages/phonopy/cui/load_helper.py", line 233, in _produce_force_constants
    fc_calculator_options=fc_calculator_options)
  File "/usr/local/lib/python3.7/site-packages/phonopy/api_phonopy.py", line 961, in produce_force_constants
    raise RuntimeError("Forces are not yet set.")
RuntimeError: Forces are not yet set.

4 entries (1 uploads) x parsers/fhi-vibes: 3VtDWp0ZSt6KCATZ6SiAuQ/aiGK_methods/MgO/nvt.p.1/trajectory.nc (v1)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1047, in parsing
    self._parser_results, logger=logger)
  File "/app/nomad/parsing/parser.py", line 249, in parse
    self.mainfile_parser.parse(mainfile, archive, logger)
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/fhivibes/parser.py", line 368, in parse
    sec_run.program = Program(name='FHI-vibes', version=metadata['vibes']['version'])
KeyError: 'vibes'

3 entries (1 uploads) x parsers/phonopy: 3VtDWp0ZSt6KCATZ6SiAuQ/aiGK_methods/MgO/phonopy/output/thermal_properties.yaml (v1)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1047, in parsing
    self._parser_results, logger=logger)
  File "/app/nomad/parsing/parser.py", line 249, in parse
    self.mainfile_parser.parse(mainfile, archive, logger)
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 393, in parse
    phonopy_obj = self.phonopy_obj
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 247, in phonopy_obj
    self._build_phonopy_object_vasp()
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 255, in _build_phonopy_object_vasp
    phonopy_obj = phonopy.load(self.mainfile)
  File "/usr/local/lib/python3.7/site-packages/phonopy/cui/load.py", line 266, in load
    log_level=log_level)
  File "/usr/local/lib/python3.7/site-packages/phonopy/api_phonopy.py", line 149, in __init__
    self._unitcell = PhonopyAtoms(atoms=unitcell)
  File "/usr/local/lib/python3.7/site-packages/phonopy/structure/atoms.py", line 269, in __init__
    pbc=True)
  File "/usr/local/lib/python3.7/site-packages/phonopy/structure/atoms.py", line 68, in __init__
    scaled_positions=scaled_positions)
  File "/usr/local/lib/python3.7/site-packages/phonopy/structure/atoms.py", line 198, in _set_cell_and_positions
    self._set_cell(cell)
  File "/usr/local/lib/python3.7/site-packages/phonopy/structure/atoms.py", line 171, in _set_cell
    raise TypeError("Array shape of cell is not 3x3.")
TypeError: Array shape of cell is not 3x3.

2 entries (1 uploads) x parsers/phonopy: 3VtDWp0ZSt6KCATZ6SiAuQ/aiGK_methods/MgO/phonopy/output/band.yaml (v1)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1047, in parsing
    self._parser_results, logger=logger)
  File "/app/nomad/parsing/parser.py", line 249, in parse
    self.mainfile_parser.parse(mainfile, archive, logger)
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 393, in parse
    phonopy_obj = self.phonopy_obj
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 247, in phonopy_obj
    self._build_phonopy_object_vasp()
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/phonopy/parser.py", line 255, in _build_phonopy_object_vasp
    phonopy_obj = phonopy.load(self.mainfile)
  File "/usr/local/lib/python3.7/site-packages/phonopy/cui/load.py", line 292, in load
    log_level=log_level)
  File "/usr/local/lib/python3.7/site-packages/phonopy/cui/load_helper.py", line 179, in set_dataset_and_force_constants
    _fc = _read_force_constants_file(phonon, "FORCE_CONSTANTS")
  File "/usr/local/lib/python3.7/site-packages/phonopy/cui/load_helper.py", line 220, in _read_force_constants_file
    p2s_map=p2s_map)
  File "/usr/local/lib/python3.7/site-packages/phonopy/file_IO.py", line 390, in parse_FORCE_CONSTANTS
    check_force_constants_indices(idx, idx1, p2s_map, filename)
  File "/usr/local/lib/python3.7/site-packages/phonopy/file_IO.py", line 435, in check_force_constants_indices
    raise RuntimeError(text)
RuntimeError: FORCE_CONSTANTS file is inconsistent with the calculation setting. PRIMITIVE_AXIS may not be set correctly.

1 entries (1 uploads) x parsers/fhi-vibes: 3VtDWp0ZSt6KCATZ6SiAuQ/aiGK_methods/MgO/nve.1/test.nc (v1)

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 1047, in parsing
    self._parser_results, logger=logger)
  File "/app/nomad/parsing/parser.py", line 249, in parse
    self.mainfile_parser.parse(mainfile, archive, logger)
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/fhivibes/parser.py", line 362, in parse
    for _ in range(self.n_frames):
  File "/usr/local/lib/python3.7/site-packages/workflowparsers/fhivibes/parser.py", line 110, in n_frames
    return len(self.parser.get('positions'))
TypeError: object of type 'NoneType' has no len()

Edited Jan 09, 2023 by Alvin Noe Ladines