Problems with the new VASP parser
This time its really about the new VASP parser.
There are still two important issue types:
- Some of the materials project data (27k entries) the run XML is invalid. A few closing tags missing. In the old parser, we somehow ignored the XML parser errors and could still process the files. Try to mimic the same. Example: https://nomad-lab.eu/prod/rae/reprocess/gui/entry/id/uiNy_zS0S7Kx-Ru-rAlSNA/phFMspmymFkaFA7n6XFrLFx5jeuI/logs
- For a lot of entries (32k) the parse creates a system with site coordinates, but the atom labels are missing. Example: https://nomad-lab.eu/prod/rae/reprocess/gui/entry/id/nHo8kktjSviBVsqMt0BLuw/wHrB0Pk-p0pypeE0pzNQaWf1RcN8/archive/section_workflow/calculation_result_ref/single_configuration_calculation_to_system_ref/atom_positions
Otherwise, these are the results from the reprocessing with your last fixes:
- 480, parsers/vasp, v_XEJQ1ATCmRv6xutSXbzg:mNrUgVAN0brYiQDt8lw_ksRBarRP
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/vaspparser/vasp_parser.py", line 1101, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 885, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 639, in atom_info
self._atom_info['n_atoms'] = sum(ions)
TypeError: unsupported operand type(s) for +: 'int' and 'str'- 34, parsers/vasp, wS4nTynCRVinVLoXPp283w:xru7dr5W31rwqfDUroffjJLLPbww
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/vaspparser/vasp_parser.py", line 1103, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1072, in parse_configurations
parse_dos(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1037, in parse_dos
dos, fields = self.parser.get_partial_dos(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 756, in get_partial_dos
n_atoms = self.atom_info['n_atoms']
KeyError: 'n_atoms'- 1, parsers/vasp, N6rQDIFJT36PituBeUrqEA:JNHBGOZn-kSVR29iavzBvae19G_C
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/celery/worker/consumer/consumer.py", line 318, in start
blueprint.start(self)
File "/usr/local/lib/python3.7/site-packages/celery/bootsteps.py", line 119, in start
step.start(parent)
File "/usr/local/lib/python3.7/site-packages/celery/worker/consumer/consumer.py", line 599, in start
c.loop(*c.loop_args())
File "/usr/local/lib/python3.7/site-packages/celery/worker/loops.py", line 83, in asynloop
next(loop)
File "/usr/local/lib/python3.7/site-packages/kombu/asynchronous/hub.py", line 303, in create_loop
poll_timeout = fire_timers(propagate=propagate) if scheduled else 1
File "/usr/local/lib/python3.7/site-packages/kombu/asynchronous/hub.py", line 145, in fire_timers
entry()
File "/usr/local/lib/python3.7/site-packages/kombu/asynchronous/timer.py", line 68, in __call__
return self.fun(*self.args, **self.kwargs)
File "/usr/local/lib/python3.7/site-packages/kombu/asynchronous/timer.py", line 130, in _reschedules
return fun(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/kombu/connection.py", line 313, in heartbeat_check
return self.transport.heartbeat_check(self.connection, rate=rate)
File "/usr/local/lib/python3.7/site-packages/kombu/transport/pyamqp.py", line 149, in heartbeat_check
return connection.heartbeat_tick(rate=rate)
File "/usr/local/lib/python3.7/site-packages/amqp/connection.py", line 744, in heartbeat_tick
self.send_heartbeat()
File "/usr/local/lib/python3.7/site-packages/amqp/connection.py", line 695, in send_heartbeat
self.frame_writer(8, 0, None, None, None)
File "/usr/local/lib/python3.7/site-packages/amqp/method_framing.py", line 189, in write_frame
write(view[:offset])
File "/usr/local/lib/python3.7/site-packages/amqp/transport.py", line 305, in write
self._write(s)
ConnectionResetError: [Errno 104] Connection reset by peer
During handling of the above exception, another exception occurred:
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/vaspparser/vasp_parser.py", line 1101, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 885, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 639, in atom_info
self._atom_info['n_atoms'] = sum(ions)
TypeError: unsupported operand type(s) for +: 'int' and 'str'- 1, parsers/vasp, LX65oD_mSI-zJYP4ttIChg:kJV30wnielD5VE6_tW3eVlK5_Dhq
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/vaspparser/vasp_parser.py", line 1101, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 885, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 416, in atom_info
array_info[fields[i]].append(val[i])
TypeError: 'NoneType' object is not subscriptableOld issue:
- 9372, in normalizer, 8Y5OzjCbQKCAPH9OSJftfA:_W-3vpvD5mfmH0VpDIqRbxItHwZw
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 301, in symmetry_analysis
space_group_number = symm.get_space_group_number()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 114, in get_space_group_number
dataset = self.get_symmetry_dataset()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 566, in get_symmetry_dataset
'Spglib error when finding symmetry dataset.')
matid.exceptions.CellNormalizationError: Spglib error when finding symmetry dataset.- 562, parsers/vasp, 6jR5WJQvSVSrflHsGFx4JA:c5MNoko2F5JRyd21ng1M4R4N2CrV
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/vaspparser/vasp_parser.py", line 1086, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 870, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 628, in atom_info
self._atom_info['n_atoms'] = sum(ions)
TypeError: unsupported operand type(s) for +: 'int' and 'str'- 125, parsers/vasp, 6Jsud_OzS06cVDUunSLKtQ:idG3yalNgMALlY5L2mUN_-mhPylM
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/vaspparser/vasp_parser.py", line 1086, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 870, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 411, in atom_info
array_info[fields[i]].append(val[i])
TypeError: 'NoneType' object is not subscriptable- 105, in normalizer, 1lW8mBSbTii8wIBpaQaRtg:WTvXT5LHquxyhxQ5lFbDih3t6y2b
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/celery/worker/consumer/consumer.py", line 318, in start
blueprint.start(self)
File "/usr/local/lib/python3.7/site-packages/celery/bootsteps.py", line 119, in start
step.start(parent)
File "/usr/local/lib/python3.7/site-packages/celery/worker/consumer/consumer.py", line 599, in start
c.loop(*c.loop_args())
File "/usr/local/lib/python3.7/site-packages/celery/worker/loops.py", line 83, in asynloop
next(loop)
File "/usr/local/lib/python3.7/site-packages/kombu/asynchronous/hub.py", line 301, in create_loop
item()
File "/usr/local/lib/python3.7/site-packages/vine/promises.py", line 170, in __call__
return self.throw()
File "/usr/local/lib/python3.7/site-packages/vine/promises.py", line 167, in __call__
retval = fun(*final_args, **final_kwargs)
File "/usr/local/lib/python3.7/site-packages/kombu/transport/base.py", line 218, in _read
raise RecoverableConnectionError('Socket was disconnected')
amqp.exceptions.RecoverableConnectionError: Socket was disconnected
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 301, in symmetry_analysis
space_group_number = symm.get_space_group_number()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 114, in get_space_group_number
dataset = self.get_symmetry_dataset()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 566, in get_symmetry_dataset
'Spglib error when finding symmetry dataset.')
matid.exceptions.CellNormalizationError: Spglib error when finding symmetry dataset.- 86, parsers/vasp, 6Jsud_OzS06cVDUunSLKtQ:nYUkIOLtmqvxVDZdSh6KwePYl0eF
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/vaspparser/vasp_parser.py", line 1088, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1054, in parse_configurations
parse_eigenvalues(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 954, in parse_eigenvalues
eigenvalues = self.parser.get_eigenvalues(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 443, in get_eigenvalues
n_kpts = len(self.kpoints_info.get('k_mesh_points', []))
TypeError: object of type 'NoneType' has no len()- 35, in normalizer, -VXrWVKjQIOHNVoU8Ft40Q:tsBC1IaYWFKfPbXlHB_ERQlx1LBh
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 195, in normalize_system
atoms.set_positions(1e10 * atom_positions.magnitude)
File "/usr/local/lib/python3.7/site-packages/ase/atoms.py", line 662, in set_positions
self.set_array('positions', newpositions, shape=(3,))
File "/usr/local/lib/python3.7/site-packages/ase/atoms.py", line 475, in set_array
(name, a.shape, b.shape))
ValueError: Array "positions" has wrong shape (0,) != (0, 3).- 34, in normalizer, yPkSfxx8RVSOcTQNKwhQJw:nslOUAQgpEUrfbMrtuQPU4YftT-z
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 303, in normalize
self.fill(context)
File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 205, in fill
struct.normalize(context)
File "/app/nomad/normalizing/encyclopedia/material.py", line 740, in normalize
prim_atoms = symmetry_analyzer.get_primitive_system()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 272, in get_primitive_system
conv_sys = self.get_conventional_system()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 305, in get_conventional_system
spglib_conv_sys = self._get_spglib_conventional_system()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 582, in _get_spglib_conventional_system
dataset = self.get_symmetry_dataset()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 566, in get_symmetry_dataset
'Spglib error when finding symmetry dataset.')
matid.exceptions.CellNormalizationError: Spglib error when finding symmetry dataset.- 24, in normalizer, 5IvJz3uWTeu7Sgf197BSnw:YrIvxg5rzU9_y0HZIPP5hWXjvBIA
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 303, in normalize
self.fill(context)
File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 205, in fill
struct.normalize(context)
File "/app/nomad/normalizing/encyclopedia/material.py", line 522, in normalize
spg_number = symmetry_analyzer.get_space_group_number()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 114, in get_space_group_number
dataset = self.get_symmetry_dataset()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 566, in get_symmetry_dataset
'Spglib error when finding symmetry dataset.')
matid.exceptions.CellNormalizationError: Spglib error when finding symmetry dataset.- 18, parsers/vasp, plbG1LdbQ2aYp6eiB7ol8g:PjVZ8C35JZM5w8G_rlLaIhC0weTh
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/vaspparser/vasp_parser.py", line 1086, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 847, in parse_method
incar_parameters = self.parser.get_incar()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 539, in get_incar
self.parser.mainfile).strip('OUTCAR'))
File "/usr/local/lib/python3.7/posixpath.py", line 146, in basename
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType- 9, in normalizer, 5IvJz3uWTeu7Sgf197BSnw:oBh5MiHjYXmDT8SkDoRN49tDdCW_
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 81, in wrap_positions
np.asarray(positions).T).T - shift
File "<__array_function__ internals>", line 6, in solve
File "/usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 393, in solve
r = gufunc(a, b, signature=signature, extobj=extobj)
File "/usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix- 9, in normalizer, 28T0hCzfQuCZ50gH-QeKAw:lP2LexSZzBoxD8OMTkF-YM0AN-KG
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 303, in normalize
self.fill(context)
File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 205, in fill
struct.normalize(context)
File "/app/nomad/normalizing/encyclopedia/material.py", line 760, in normalize
self.lattice_parameters(ideal, std_atoms, ideal.periodicity)
File "/app/nomad/normalizing/encyclopedia/material.py", line 573, in lattice_parameters
a = np.linalg.norm(cell[periodic_indices[0], :]) * 1e-10
IndexError: index 0 is out of bounds for axis 0 with size 0- 5, parsers/vasp, plbG1LdbQ2aYp6eiB7ol8g:EYiQm81mGpHxIShi9y8Ub_F5c-VI
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/vaspparser/vasp_parser.py", line 1088, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1057, in parse_configurations
parse_dos(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1001, in parse_dos
energies, values, integrated, e_fermi = self.parser.get_total_dos(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 724, in get_total_dos
n_dos = int(line.split()[2])
ValueError: invalid literal for int() with base 10: '5.08315306'- 5, in normalizer, 4SFPVdb5Sj6Kn4U_cwWohg:f_qztS81ukPrLObA41RnC5i7JVZu
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/celery/worker/consumer/consumer.py", line 318, in start
blueprint.start(self)
File "/usr/local/lib/python3.7/site-packages/celery/bootsteps.py", line 119, in start
step.start(parent)
File "/usr/local/lib/python3.7/site-packages/celery/worker/consumer/consumer.py", line 599, in start
c.loop(*c.loop_args())
File "/usr/local/lib/python3.7/site-packages/celery/worker/loops.py", line 83, in asynloop
next(loop)
File "/usr/local/lib/python3.7/site-packages/kombu/asynchronous/hub.py", line 364, in create_loop
cb(*cbargs)
File "/usr/local/lib/python3.7/site-packages/kombu/transport/base.py", line 238, in on_readable
reader(loop)
File "/usr/local/lib/python3.7/site-packages/kombu/transport/base.py", line 218, in _read
raise RecoverableConnectionError('Socket was disconnected')
amqp.exceptions.RecoverableConnectionError: Socket was disconnected
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 301, in symmetry_analysis
space_group_number = symm.get_space_group_number()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 114, in get_space_group_number
dataset = self.get_symmetry_dataset()
File "/usr/local/lib/python3.7/site-packages/matid/symmetry/symmetryanalyzer.py", line 566, in get_symmetry_dataset
'Spglib error when finding symmetry dataset.')
matid.exceptions.CellNormalizationError: Spglib error when finding symmetry dataset.- 5, in normalizer, iGLjoQSPRc6d9IPJMGpxvg:ogRag81kOdbI2LCn0HFNsBk_sPp-
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 212, in classify
return_factors=True
File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 676, in get_displacement_tensor
D, D_len, factors = find_mic(flattened_disp, cell, pbc, max_distance)
File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 725, in find_mic
Dr = np.dot(D, np.linalg.inv(cell))
File "<__array_function__ internals>", line 6, in inv
File "/usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 545, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
File "/usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix- 4, in normalizer, mBb0_3cyTR6eJoN4qX-bGg:zVHAXa8GKnEZTBsLibSwd3iiNeJu
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 212, in classify
return_factors=True
File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 676, in get_displacement_tensor
D, D_len, factors = find_mic(flattened_disp, cell, pbc, max_distance)
File "/usr/local/lib/python3.7/site-packages/matid/geometry.py", line 750, in find_mic
tvecs = np.dot(tvec_factors, cell)
File "<__array_function__ internals>", line 6, in dot
ValueError: On entry to DGEMM parameter number 4 had an illegal value- 4, parsers/vasp, VshkgA9fRVaBUM1A99_pTA:-CjT6qeDr5dhnp50fV3uGVp-RnMJ
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/vaspparser/vasp_parser.py", line 1088, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1049, in parse_configurations
sec_system = parse_system(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 906, in parse_system
structure = self.parser.get_structure(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 658, in get_structure
positions = pint.Quantity(np.dot(positions, cell), 'angstrom')
File "<__array_function__ internals>", line 6, in dot
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'- 55, in normalizer, 2jFT-SBtT4mnxQg06pgJOA:SzG3VquLpYI9AqsHd-_qXGZdcYBN
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 662, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 703, in write_archive
raise e
File "/app/nomad/processing/data.py", line 696, in write_archive
return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
File "/app/nomad/files.py", line 354, in write_archive
raise e
File "/app/nomad/files.py", line 348, in write_archive
write_archive(archive_file_object.os_path, 1, data=[(calc_id, data)])
File "/app/nomad/archive.py", line 540, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive.py", line 203, in __exit__
raise exc_val
File "/app/nomad/archive.py", line 540, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive.py", line 238, in add
packed = self._toc_packer.pack(data)
File "/app/nomad/archive.py", line 103, in pack
result = super().pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 848, in pack
self._pack(obj)
File "/app/nomad/archive.py", line 119, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive.py", line 142, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive.py", line 119, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive.py", line 142, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive.py", line 116, in _pack
pack_result = self._buffer.write(packb(obj))
File "/app/nomad/archive.py", line 55, in packb
return __packer.pack(o)
File "msgpack/_packer.pyx", line 284, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 290, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 287, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 281, in msgpack._packer.Packer._pack
TypeError: can't serialize array([[ 0. , 0. , 0. ],
[ 0.16666667, 0. , 0. ],
[ 0.33333333, 0. , 0. ],
[ 0.5 , 0. , 0. ],
[ 0. , 0.16666667, -0. ],
[ 0.16666667, 0.16666667, 0. ],
[ 0.33333333, 0.16666667, 0. ],
[ 0.5 , 0.16666667, 0. ],
[-0.33333333, 0.16666667, 0. ],
[-0.16666667, 0.16666667, -0. ],
[ 0. , 0.33333333, -0. ],
[ 0.16666667, 0.33333333, 0. ],
[ 0.33333333, 0.33333333, -0. ],
[ 0.5 , 0.33333333, 0. ],
[-0.33333333, 0.33333333, -0. ],
[-0.16666667, 0.33333333, -0. ],
[ 0. , 0.5 , -0. ],
[ 0.16666667, 0.5 , 0. ],
[ 0.33333333, 0.5 , -0. ],
[ 0.5 , 0.5 , 0. ],
[ 0. , 0. , 0.16666667],
[ 0.16666667, 0. , 0.16666667],
[ 0.33333333, 0. , 0.16666667],
[ 0.5 , 0. , 0.16666667],
[-0.33333333, 0. , 0.16666667],
[-0.16666667, -0. , 0.16666667],
[ 0. , 0.16666667, 0.16666667],
[ 0.16666667, 0.16666667, 0.16666667],
[ 0.33333333, 0.16666667, 0.16666667],
[ 0.5 , 0.16666667, 0.16666667],
[-0.33333333, 0.16666667, 0.16666667],
[-0.16666667, 0.16666667, 0.16666667],
[ 0. , 0.33333333, 0.16666667],
[ 0.16666667, 0.33333333, 0.16666667],
[ 0.33333333, 0.33333333, 0.16666667],
[ 0.5 , 0.33333333, 0.16666667],
[-0.33333333, 0.33333333, 0.16666667],
[-0.16666667, 0.33333333, 0.16666667],
[ 0. , 0.5 , 0.16666667],
[ 0.16666667, 0.5 , 0.16666667],
[ 0.33333333, 0.5 , 0.16666667],
[ 0.5 , 0.5 , 0.16666667],
[-0.33333333, 0.5 , 0.16666667],
[-0.16666667, 0.5 , 0.16666667],
[ 0. , -0.33333333, 0.16666667],
[ 0.16666667, -0.33333333, 0.16666667],
[ 0.33333333, -0.33333333, 0.16666667],
[ 0.5 , -0.33333333, 0.16666667],
[-0.33333333, -0.33333333, 0.16666667],
[-0.16666667, -0.33333333, 0.16666667],
[ 0. , -0.16666667, 0.16666667],
[ 0.16666667, -0.16666667, 0.16666667],
[ 0.33333333, -0.16666667, 0.16666667],
[ 0.5 , -0.16666667, 0.16666667],
[-0.33333333, -0.16666667, 0.16666667],
[-0.16666667, -0.16666667, 0.16666667],
[ 0. , 0. , 0.33333333],
[ 0.16666667, 0. , 0.33333333],
[ 0.33333333, 0. , 0.33333333],
[ 0.5 , 0. , 0.33333333],
[-0.33333333, 0. , 0.33333333],
[-0.16666667, -0. , 0.33333333],
[ 0. , 0.16666667, 0.33333333],
[ 0.16666667, 0.16666667, 0.33333333],
[ 0.33333333, 0.16666667, 0.33333333],
[ 0.5 , 0.16666667, 0.33333333],
[-0.33333333, 0.16666667, 0.33333333],
[-0.16666667, 0.16666667, 0.33333333],
[ 0. , 0.33333333, 0.33333333],
[ 0.16666667, 0.33333333, 0.33333333],
[ 0.33333333, 0.33333333, 0.33333333],
[ 0.5 , 0.33333333, 0.33333333],
[-0.33333333, 0.33333333, 0.33333333],
[-0.16666667, 0.33333333, 0.33333333],
[ 0. , 0.5 , 0.33333333],
[ 0.16666667, 0.5 , 0.33333333],
[ 0.33333333, 0.5 , 0.33333333],
[ 0.5 , 0.5 , 0.33333333],
[-0.33333333, 0.5 , 0.33333333],
[-0.16666667, 0.5 , 0.33333333],
[ 0. , -0.33333333, 0.33333333],
[ 0.16666667, -0.33333333, 0.33333333],
[ 0.33333333, -0.33333333, 0.33333333],
[ 0.5 , -0.33333333, 0.33333333],
[-0.33333333, -0.33333333, 0.33333333],
[-0.16666667, -0.33333333, 0.33333333],
[ 0. , -0.16666667, 0.33333333],
[ 0.16666667, -0.16666667, 0.33333333],
[ 0.33333333, -0.16666667, 0.33333333],
[ 0.5 , -0.16666667, 0.33333333],
[-0.33333333, -0.16666667, 0.33333333],
[-0.16666667, -0.16666667, 0.33333333],
[ 0. , 0. , 0.5 ],
[ 0.16666667, 0. , 0.5 ],
[ 0.33333333, 0. , 0.5 ],
[ 0.5 , 0. , 0.5 ],
[ 0. , 0.16666667, 0.5 ],
[ 0.16666667, 0.16666667, 0.5 ],
[ 0.33333333, 0.16666667, 0.5 ],
[ 0.5 , 0.16666667, 0.5 ],
[-0.33333333, 0.16666667, 0.5 ],
[-0.16666667, 0.16666667, 0.5 ],
[ 0. , 0.33333333, 0.5 ],
[ 0.16666667, 0.33333333, 0.5 ],
[ 0.33333333, 0.33333333, 0.5 ],
[ 0.5 , 0.33333333, 0.5 ],
[-0.33333333, 0.33333333, 0.5 ],
[-0.16666667, 0.33333333, 0.5 ],
[ 0. , 0.5 , 0.5 ],
[ 0.16666667, 0.5 , 0.5 ],
[ 0.33333333, 0.5 , 0.5 ],
[ 0.5 , 0.5 , 0.5 ]])
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 423, in on_fail
self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 703, in write_archive
raise e
File "/app/nomad/processing/data.py", line 696, in write_archive
return self.upload_files.write_archive(self.calc_id, archive.m_to_dict())
File "/app/nomad/files.py", line 354, in write_archive
raise e
File "/app/nomad/files.py", line 348, in write_archive
write_archive(archive_file_object.os_path, 1, data=[(calc_id, data)])
File "/app/nomad/archive.py", line 540, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive.py", line 203, in __exit__
raise exc_val
File "/app/nomad/archive.py", line 540, in write_archive
writer.add(uuid, entry)
File "/app/nomad/archive.py", line 238, in add
packed = self._toc_packer.pack(data)
File "/app/nomad/archive.py", line 103, in pack
result = super().pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 848, in pack
self._pack(obj)
File "/app/nomad/archive.py", line 119, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive.py", line 142, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive.py", line 119, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 839, in _pack
nest_limit - 1)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 941, in _pack_map_pairs
self._pack(v, nest_limit - 1)
File "/app/nomad/archive.py", line 142, in _pack
pack_result = super()._pack(obj, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/msgpack/fallback.py", line 835, in _pack
self._pack(obj[i], nest_limit - 1)
File "/app/nomad/archive.py", line 116, in _pack
pack_result = self._buffer.write(packb(obj))
File "/app/nomad/archive.py", line 55, in packb
return __packer.pack(o)
File "msgpack/_packer.pyx", line 284, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 290, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 287, in msgpack._packer.Packer.pack
File "msgpack/_packer.pyx", line 234, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 263, in msgpack._packer.Packer._pack
File "msgpack/_packer.pyx", line 281, in msgpack._packer.Packer._pack
TypeError: can't serialize array([[ 0. , 0. , 0. ],
[ 0.16666667, 0. , 0. ],
[ 0.33333333, 0. , 0. ],
[ 0.5 , 0. , 0. ],
[ 0. , 0.16666667, -0. ],
[ 0.16666667, 0.16666667, 0. ],
[ 0.33333333, 0.16666667, 0. ],
[ 0.5 , 0.16666667, 0. ],
[-0.33333333, 0.16666667, 0. ],
[-0.16666667, 0.16666667, -0. ],
[ 0. , 0.33333333, -0. ],
[ 0.16666667, 0.33333333, 0. ],
[ 0.33333333, 0.33333333, -0. ],
[ 0.5 , 0.33333333, 0. ],
[-0.33333333, 0.33333333, -0. ],
[-0.16666667, 0.33333333, -0. ],
[ 0. , 0.5 , -0. ],
[ 0.16666667, 0.5 , 0. ],
[ 0.33333333, 0.5 , -0. ],
[ 0.5 , 0.5 , 0. ],
[ 0. , 0. , 0.16666667],
[ 0.16666667, 0. , 0.16666667],
[ 0.33333333, 0. , 0.16666667],
[ 0.5 , 0. , 0.16666667],
[-0.33333333, 0. , 0.16666667],
[-0.16666667, -0. , 0.16666667],
[ 0. , 0.16666667, 0.16666667],
[ 0.16666667, 0.16666667, 0.16666667],
[ 0.33333333, 0.16666667, 0.16666667],
[ 0.5 , 0.16666667, 0.16666667],
[-0.33333333, 0.16666667, 0.16666667],
[-0.16666667, 0.16666667, 0.16666667],
[ 0. , 0.33333333, 0.16666667],
[ 0.16666667, 0.33333333, 0.16666667],
[ 0.33333333, 0.33333333, 0.16666667],
[ 0.5 , 0.33333333, 0.16666667],
[-0.33333333, 0.33333333, 0.16666667],
[-0.16666667, 0.33333333, 0.16666667],
[ 0. , 0.5 , 0.16666667],
[ 0.16666667, 0.5 , 0.16666667],
[ 0.33333333, 0.5 , 0.16666667],
[ 0.5 , 0.5 , 0.16666667],
[-0.33333333, 0.5 , 0.16666667],
[-0.16666667, 0.5 , 0.16666667],
[ 0. , -0.33333333, 0.16666667],
[ 0.16666667, -0.33333333, 0.16666667],
[ 0.33333333, -0.33333333, 0.16666667],
[ 0.5 , -0.33333333, 0.16666667],
[-0.33333333, -0.33333333, 0.16666667],
[-0.16666667, -0.33333333, 0.16666667],
[ 0. , -0.16666667, 0.16666667],
[ 0.16666667, -0.16666667, 0.16666667],
[ 0.33333333, -0.16666667, 0.16666667],
[ 0.5 , -0.16666667, 0.16666667],
[-0.33333333, -0.16666667, 0.16666667],
[-0.16666667, -0.16666667, 0.16666667],
[ 0. , 0. , 0.33333333],
[ 0.16666667, 0. , 0.33333333],
[ 0.33333333, 0. , 0.33333333],
[ 0.5 , 0. , 0.33333333],
[-0.33333333, 0. , 0.33333333],
[-0.16666667, -0. , 0.33333333],
[ 0. , 0.16666667, 0.33333333],
[ 0.16666667, 0.16666667, 0.33333333],
[ 0.33333333, 0.16666667, 0.33333333],
[ 0.5 , 0.16666667, 0.33333333],
[-0.33333333, 0.16666667, 0.33333333],
[-0.16666667, 0.16666667, 0.33333333],
[ 0. , 0.33333333, 0.33333333],
[ 0.16666667, 0.33333333, 0.33333333],
[ 0.33333333, 0.33333333, 0.33333333],
[ 0.5 , 0.33333333, 0.33333333],
[-0.33333333, 0.33333333, 0.33333333],
[-0.16666667, 0.33333333, 0.33333333],
[ 0. , 0.5 , 0.33333333],
[ 0.16666667, 0.5 , 0.33333333],
[ 0.33333333, 0.5 , 0.33333333],
[ 0.5 , 0.5 , 0.33333333],
[-0.33333333, 0.5 , 0.33333333],
[-0.16666667, 0.5 , 0.33333333],
[ 0. , -0.33333333, 0.33333333],
[ 0.16666667, -0.33333333, 0.33333333],
[ 0.33333333, -0.33333333, 0.33333333],
[ 0.5 , -0.33333333, 0.33333333],
[-0.33333333, -0.33333333, 0.33333333],
[-0.16666667, -0.33333333, 0.33333333],
[ 0. , -0.16666667, 0.33333333],
[ 0.16666667, -0.16666667, 0.33333333],
[ 0.33333333, -0.16666667, 0.33333333],
[ 0.5 , -0.16666667, 0.33333333],
[-0.33333333, -0.16666667, 0.33333333],
[-0.16666667, -0.16666667, 0.33333333],
[ 0. , 0. , 0.5 ],
[ 0.16666667, 0. , 0.5 ],
[ 0.33333333, 0. , 0.5 ],
[ 0.5 , 0. , 0.5 ],
[ 0. , 0.16666667, 0.5 ],
[ 0.16666667, 0.16666667, 0.5 ],
[ 0.33333333, 0.16666667, 0.5 ],
[ 0.5 , 0.16666667, 0.5 ],
[-0.33333333, 0.16666667, 0.5 ],
[-0.16666667, 0.16666667, 0.5 ],
[ 0. , 0.33333333, 0.5 ],
[ 0.16666667, 0.33333333, 0.5 ],
[ 0.33333333, 0.33333333, 0.5 ],
[ 0.5 , 0.33333333, 0.5 ],
[-0.33333333, 0.33333333, 0.5 ],
[-0.16666667, 0.33333333, 0.5 ],
[ 0. , 0.5 , 0.5 ],
[ 0.16666667, 0.5 , 0.5 ],
[ 0.33333333, 0.5 , 0.5 ],
[ 0.5 , 0.5 , 0.5 ]])The old issue:
@ladinesa ideally you would prioritise this (at least the first 5).
- 1252, parsers/vasp, yJ_Jq-c_SzKd7OmSJChQ3A:tLuoZg0AlBPDXXyR0b5kox_Ncim-
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/vaspparser/vasp_parser.py", line 1076, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 860, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 625, in atom_info
assert len(ions) == len(species)
AssertionError- 935, parsers/vasp, yJ_Jq-c_SzKd7OmSJChQ3A:kBmXMBOGS90-cRB6f2O6fYGiA1Wl
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/vaspparser/vasp_parser.py", line 1078, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1039, in parse_configurations
sec_system = parse_system(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 896, in parse_system
structure = self.parser.get_structure(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 656, in get_structure
positions = pint.Quantity(np.dot(positions, cell), 'angstrom')
File "<__array_function__ internals>", line 6, in dot
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'- 588, parsers/vasp, xwA0ep9zRgSypxxkCokJ1w:rT8lZLyJCz5ZvXe3S2LrQTTCrgO8
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/vaspparser/vasp_parser.py", line 1078, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1047, in parse_configurations
parse_dos(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1014, in parse_dos
sec_dos.dos_values_lm = pint.Quantity(dos, '1/eV').to('1/joule').magnitude
UnboundLocalError: local variable 'sec_dos' referenced before assignment- 483, parsers/vasp, yJ_Jq-c_SzKd7OmSJChQ3A:wrEVx9FRKpR8JV_fFXi0mJpO8MKE
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/vaspparser/vasp_parser.py", line 1076, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 860, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 626, in atom_info
self._atom_info['n_atoms'] = sum(ions)
TypeError: unsupported operand type(s) for +: 'int' and 'str'- 73, parsers/vasp, vez_1F7xRxyLBw-aw6dWPw:ynnk4mILRzZGDjsnA-bsV4oscC2X
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/vaspparser/vasp_parser.py", line 1078, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1044, in parse_configurations
parse_eigenvalues(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 944, in parse_eigenvalues
eigenvalues = self.parser.get_eigenvalues(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 692, in get_eigenvalues
eigenvalues = np.reshape(eigenvalues, (n_eigs, self.ispin, n_kpts, self.n_bands, 3))
File "<__array_function__ internals>", line 6, in reshape
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 299, in reshape
return _wrapfunc(a, 'reshape', newshape, order=order)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 55, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 44, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: cannot reshape array of size 12204 into shape (0,1,228,18,3)- 64, parsers/vasp, kuWccrUZQFyoy5TCrabBsA:0v83TNUp3MjSsF6wBWDZdquATszi
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/vaspparser/vasp_parser.py", line 1078, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1021, in parse_configurations
for n_scf in range(self.parser.get_n_scf(n)):
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 416, in get_n_scf
return len(self._calculation_parsers[n_calc].get('scstep/'))
TypeError: object of type 'NoneType' has no len()- 17, parsers/vasp, kuWccrUZQFyoy5TCrabBsA:0aFQOX4UZ9ze2oyG-qiXPmdN-0cA
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/vaspparser/vasp_parser.py", line 1076, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 860, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 411, in atom_info
array_info[fields[i]].append(val[i])
TypeError: 'NoneType' object is not subscriptable- 8, parsers/vasp, kuWccrUZQFyoy5TCrabBsA:1YEsYLq1CQjR1VQPyynpL2f-BGhI
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/vaspparser/vasp_parser.py", line 1076, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 860, in parse_method
atomtypes = self.parser.atom_info.get('atomtypes', {})
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 401, in atom_info
e.get('name', None) for e in self.parser.get('atominfo/array/')]
TypeError: 'NoneType' object is not iterable- 1, parsers/vasp, mn3D9gABQd6FBNVvwnoH0A:9qDsS4sG-2e6oPjYrMLsh8qCYUL-
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/vaspparser/vasp_parser.py", line 1078, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1047, in parse_configurations
parse_dos(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1012, in parse_dos
dos, fields = self.parser.get_partial_dos(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 770, in get_partial_dos
dos = np.reshape(dos, (n_lm, self.ispin, n_atoms, n_dos))
File "<__array_function__ internals>", line 6, in reshape
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 299, in reshape
return _wrapfunc(a, 'reshape', newshape, order=order)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 58, in _wrapfunc
return bound(*args, **kwds)
ValueError: cannot reshape array of size 1203 into shape (601,2,4,301)The origin issue:
Performance is fine. I am through the first third of the AFLOW calcs (2,5 million). There are errors, but it seems mostly the same cause:
- 10684, parsers/vasp, MQUEA7eSRxaNAxRtWP1ciw:UK41Lt_FMJ-q1PwzVo7gQx4pExGT
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/vaspparser/vasp_parser.py", line 1056, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1025, in parse_configurations
parse_dos(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 975, in parse_dos
energies, values, integrated, e_fermi = self.parser.get_total_dos(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 460, in get_total_dos
dos = np.array([e.text.split() for e in dos], dtype=float)
ValueError: could not convert string to float: '********'- 1967, parsers/vasp, LKZi3yswQ9u2Bau6wleiEw:yYyBxunitnqYWsgC3TYfHzQ_a8KL
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/vaspparser/vasp_parser.py", line 1056, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1022, in parse_configurations
parse_eigenvalues(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 933, in parse_eigenvalues
eigenvalues = self.parser.get_eigenvalues(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 448, in get_eigenvalues
eigenvalues = np.array([e.text.split() for e in eigenvalues], dtype=float)
ValueError: could not convert string to float: '********'- 1001, parsers/vasp, LNy7pWuzQ96uYCTkDGq4MQ:u2-u5CeXo4CHfMS90y4cMnsEEaWd
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/vaspparser/vasp_parser.py", line 1056, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1025, in parse_configurations
parse_dos(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 996, in parse_dos
dos, fields = self.parser.get_partial_dos(n_calc)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 485, in get_partial_dos
dos = np.array([e.text.split() for e in dos], dtype=float)
ValueError: could not convert string to float: '********'- 8, in normalizer, H7uVs_JbThiWMCyb0lYhhA:busgM6i7Bg-v8F2Bx72ZwqftQLyO
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 303, in normalize
self.fill(context)
File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 205, 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.- 7, parsers/vasp, MDgZ4Hx_SlqflIAB-Zh4BQ:GOjXhYSa3RoH5_FJtEYdqK7kUTVM
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/vaspparser/vasp_parser.py", line 1056, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1011, in parse_configurations
sec_scc.atom_forces = pint.Quantity(forces, 'eV/angstrom')
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: could not convert string to float: '****************'- 4, parsers/vasp, FjiYy5-ETRCrs5ktzJA55w:RHIPXUiH563rwAzEoOueSfW_c5Fs
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/vaspparser/vasp_parser.py", line 1056, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 1022, in parse_configurations
parse_eigenvalues(n)
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 945, in parse_eigenvalues
occs[i] >= 0.5)]) for i in range(len(eigs))]
File "/usr/local/lib/python3.7/site-packages/vaspparser/vasp_parser.py", line 945, in <listcomp>
occs[i] >= 0.5)]) for i in range(len(eigs))]
ValueError: max() arg is an empty sequence- 2, in normalizer, F0mY7hOAR8iXpkl4lOdnng:WkAte4KiVai15-sFchLn4b-OBSL7
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 303, in normalize
self.fill(context)
File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 205, 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 'Hf' at indices '[18, 19, 20, 21, 22, 23]'.