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BUG: cclib TaskDocument is missing molecule field #342

Closed
Andrew-S-Rosen opened this issue May 17, 2023 · 0 comments · Fixed by #353
Closed

BUG: cclib TaskDocument is missing molecule field #342

Andrew-S-Rosen opened this issue May 17, 2023 · 0 comments · Fixed by #353

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@Andrew-S-Rosen
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Andrew-S-Rosen commented May 17, 2023 •
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The cclib TaskDocument seems to always have None as the molecule field. That said, the final molecule is always present in attributes.final_molecule.

My proposal is to make the molecule field the same object as what is currently attributes.final_molecule and then simply not include the duplicate attributes.final_molecule.

Reproduce

from atomate2.common.schemas.cclib import TaskDocument
summary = TaskDocument.from_logfile(dir_name=".",logfile_extensions=".log")
print(summary)

Gaussian.log.txt

The full output:

{'builder_meta': {'emmet_version': '0.55.1',
  'pymatgen_version': '2023.5.10',
  'pull_request': None,
  'database_version': None,
  'build_date': datetime.datetime(2023, 5, 17, 18, 32, 44, 783214)},
 'charge': -2,
 'spin_multiplicity': 1,
 'natoms': 6,
 'elements': [Element Cl, Element Mo, Element O],
 'nelements': 3,
 'nelectrons': 120,
 'composition': Comp: Mo1 Cl4 O1,
 'composition_reduced': Comp: Mo1 Cl4 O1,
 'formula_alphabetical': 'Cl4 Mo1 O1',
 'formula_pretty': 'MoCl4O',
 'formula_anonymous': 'ABC4',
 'chemsys': 'Cl-Mo-O',
 'symmetry': {'point_group': 'C4v',
  'rotation_number': 4.0,
  'linear': False,
  'tolerance': 0.3,
  'eigen_tolerance': 0.01,
  'matrix_tolerance': 0.1},
 'molecule': None,
 'energy': -5516.118738093933,
 'dir_name': 'rosen.:/mnt/c/Users/asros/github/quacc/tests/schemas/gaussian_run1',
 'logfile': 'rosen.:/mnt/c/Users/asros/github/quacc/tests/schemas/gaussian_run1/Gaussian.log',
 'attributes': {'aonames': ['Mo1_1S',
   'Mo1_2S',
   'Mo1_3PX',
   'Mo1_3PY',
   'Mo1_3PZ',
   'Mo1_4PX',
   'Mo1_4PY',
   'Mo1_4PZ',
   'Mo1_5D 0',
   'Mo1_5D+1',
   'Mo1_5D-1',
   'Mo1_5D+2',
   'Mo1_5D-2',
   'O2_1S',
   'O2_2S',
   'O2_2PX',
   'O2_2PY',
   'O2_2PZ',
   'O2_3S',
   'O2_3PX',
   'O2_3PY',
   'O2_3PZ',
   'O2_4D 0',
   'O2_4D+1',
   'O2_4D-1',
   'O2_4D+2',
   'O2_4D-2',
   'Cl3_1S',
   'Cl3_2PX',
   'Cl3_2PY',
   'Cl3_2PZ',
   'Cl4_1S',
   'Cl4_2PX',
   'Cl4_2PY',
   'Cl4_2PZ',
   'Cl5_1S',
   'Cl5_2PX',
   'Cl5_2PY',
   'Cl5_2PZ',
   'Cl6_1S',
   'Cl6_2PX',
   'Cl6_2PY',
   'Cl6_2PZ'],
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    'A"',
    'A"',
    "A'",
    'A"',
    "A'",
    "A'",
    "A'",
    "A'",
    "A'",
    'A"',
    'A"',
    "A'",
    "A'",
    "A'",
    'A"',
    "A'",
    "A'",
    'A"',
    "A'"]],
  'nbasis': 43,
  'nmo': 43,
  'scfenergies': [-5516.118738093933],
  'scftargets': [[1e-08, 1e-06, 1e-06]],
  'scfvalues': [[[0.0571, 0.912, nan],
    [0.0214, 0.175, -0.144],
    [0.0244, 0.181, -0.163],
    [0.0126, 0.145, 0.361],
    [0.00525, 0.0557, -0.492],
    [0.000963, 0.00828, -0.0194],
    [5.39e-05, 0.000701, -0.000875],
    [5.38e-05, 0.000736, -1.73e-05],
    [4.87e-06, 7.6e-05, -8.82e-06],
    [9.98e-07, 7.67e-06, -5.37e-08],
    [1.77e-07, 2.6e-06, -1.32e-09],
    [1.2e-08, 1.68e-07, -2.57e-11],
    [2.31e-09, 2.63e-08, -1.31e-12]]],
  'molecule_initial': Molecule Summary
  Site: Mo (0.0000, 0.2957, 0.0000)
  Site: O (0.0000, 1.9854, 0.0000)
  Site: Cl (2.4202, -0.4162, 0.0000)
  Site: Cl (0.0000, -0.4162, 2.4202)
  Site: Cl (-2.4202, -0.4162, 0.0000)
  Site: Cl (0.0000, -0.4162, -2.4202),
  'molecule_final': Molecule Summary
  Site: Mo (0.0000, 0.2957, 0.0000)
  Site: O (0.0000, 1.9854, 0.0000)
  Site: Cl (2.4202, -0.4162, 0.0000)
  Site: Cl (0.0000, -0.4162, 2.4202)
  Site: Cl (-2.4202, -0.4162, 0.0000)
  Site: Cl (0.0000, -0.4162, -2.4202),
  'homo_energies': [3.643060230494],
  'lumo_energies': [6.7535936555594995],
  'homo_lumo_gaps': [3.1105334250654995],
  'min_homo_lumo_gap': 3.1105334250654995},
 'metadata': {'package': 'Gaussian',
  'methods': ['DFT'],
  'success': True,
  'legacy_package_version': '16revisionA.03',
  'package_version': '2016+A.03',
  'platform': 'ES64L',
  'symmetry_detected': 'cs',
  'symmetry_used': 'cs',
  'functional': 'B3LYP',
  'cpu_time': ['0:00:00'],
  'wall_time': ['0:00:00']},
 'task_label': None,
 'tags': None,
 'last_updated': '2023-05-17 18:32:44.783622'}
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Add missing molecule field to cclib TaskDocument
Add missing molecule field to cclib TaskDocument
1 participant
@Andrew-S-Rosen