Benchmark Nomad Lab Parser

Binder

import sys
from nomad.client import parse, normalize_all
# match and run the parser
archive = parse('pyiron_atomistics/tests/static/vasp_test_files/outcar_samples/OUTCAR_1')[0]
Could not extract xc functional from pseudopotential for Ni (parser=parsers/vasp)
normalize_all(archive)
section_run = archive.run[0]
python_dict = section_run.m_to_dict()
python_dict
{'program': {'name': 'VASP',
  'version': '5.4.1 24Jun15 complex serial IFC91_ompi',
  'compilation_datetime': 1480924356.0},
 'method': [{'dft': {'xc_functional': {'name': 'GGA_C_PBE+GGA_X_PBE',
     'exchange': [{'name': 'GGA_X_PBE'}],
     'correlation': [{'name': 'GGA_C_PBE'}]}},
   'k_mesh': {'dimensionality': 3,
    'points': {'re': [[0.125, 0.125, 0.125],
      [0.375, 0.125, 0.125],
      [0.375, 0.375, 0.125],
      [0.375, 0.375, 0.375]],
     'im': [[0.0, 0.0, 0.0],
      [0.0, 0.0, 0.0],
      [0.0, 0.0, 0.0],
      [0.0, 0.0, 0.0]]},
    'multiplicities': [8.0, 24.0, 24.0, 8.0],
    'weights': [0.125, 0.375, 0.375, 0.125]},
   'electronic': {'method': 'DFT'},
   'scf': {'threshold_energy_change': 1.602176634e-23},
   'atom_parameters': [{'atom_number': 28,
     'n_valence_electrons': 10.0,
     'label': 'Ni',
     'mass': 9.7457037818754e-26,
     'pseudopotential': {'name': 'PAW Ni 03Mar1998',
      'type': 'PAW',
      'cutoff': 4.3197565970581195e-17}}],
   'electrons_representation': [{'native_tier': 'VASP - accurate',
     'type': 'plane waves',
     'scope': ['wavefunction'],
     'basis_set': [{'type': 'plane waves',
       'scope': ['valence'],
       'cutoff': 4.005441585e-17},
      {'type': 'plane waves',
       'scope': ['augmentation'],
       'cutoff': 8.725453948764e-17}]}]}],
 'system': [{'type': 'bulk',
   'configuration_raw_gid': 'iU3S5jEhSVfAHgASjb3vF66_iPET',
   'is_representative': True,
   'chemical_composition': 'NiNiNiNi',
   'chemical_composition_hill': 'Ni4',
   'chemical_composition_reduced': 'Ni',
   'atoms': {'species': [28, 28, 28, 28],
    'labels': ['Ni', 'Ni', 'Ni', 'Ni'],
    'positions': [[0.0, 0.0, 0.0],
     [1.85e-10, 1.85e-10, 0.0],
     [1.85e-10, 0.0, 1.85e-10],
     [0.0, 1.85e-10, 1.85e-10]],
    'lattice_vectors': [[3.7e-10, 0.0, 0.0],
     [0.0, 3.7e-10, 0.0],
     [0.0, 0.0, 3.7e-10]],
    'lattice_vectors_reciprocal': [[16981581911.296179, 0.0, 0.0],
     [0.0, 16981581911.296179, 0.0],
     [0.0, 0.0, 16981581911.296179]],
    'periodic': [True, True, True]},
   'prototype': [{'aflow_id': 'A_cF4_225_a',
     'aflow_url': 'http://www.aflowlib.org/CrystalDatabase/A_cF4_225_a.html',
     'assignment_method': 'normalized-wyckoff',
     'label': '225-Cu-cF4'}],
   'symmetry': [{'bravais_lattice': 'cF',
     'crystal_system': 'cubic',
     'hall_number': 523,
     'hall_symbol': '-F 4 2 3',
     'international_short_symbol': 'Fm-3m',
     'origin_shift': [0.0, 0.0, 0.0],
     'point_group': 'm-3m',
     'space_group_number': 225,
     'symmetry_method': 'MatID (spg)',
     'transformation_matrix': [[1.0, 0.0, 0.0],
      [0.0, 1.0, 0.0],
      [0.0, 0.0, 1.0]],
     'system_original': [{'equivalent_atoms': [0, 0, 0, 0],
       'wyckoff_letters': ['a', 'a', 'a', 'a']}],
     'system_primitive': [{'atomic_numbers': [28],
       'equivalent_atoms': [0],
       'wyckoff_letters': ['a'],
       'positions': [[0.0, 0.0, 0.0]],
       'lattice_vectors': [[0.0,
         1.8500000000000003e-10,
         1.8500000000000003e-10],
        [1.8500000000000003e-10, 0.0, 1.8500000000000003e-10],
        [1.8500000000000003e-10, 1.8500000000000003e-10, 0.0]]}],
     'system_std': [{'atomic_numbers': [28, 28, 28, 28],
       'equivalent_atoms': [0, 0, 0, 0],
       'wyckoff_letters': ['a', 'a', 'a', 'a'],
       'positions': [[0.0, 0.0, 0.0],
        [0.0, 0.5, 0.5],
        [0.5, 0.0, 0.5],
        [0.5, 0.5, 0.0]],
       'lattice_vectors': [[3.7000000000000007e-10, 0.0, 0.0],
        [0.0, 3.7000000000000007e-10, 0.0],
        [0.0, 0.0, 3.7000000000000007e-10]]}]}]}],
 'calculation': [{'system_ref': '#/run/0/system/0',
   'method_ref': '#/run/0/method/0',
   'energy': {'highest_occupied': 4.8547554186834e-19,
    'lowest_unoccupied': 4.928295326184e-19,
    'total': {'value': -3.929860643857051e-18},
    'free': {'value': -3.940979576661935e-18},
    'total_t0': {'value': -3.937273266261032e-18}},
   'forces': {'total': {'value': [[-0.0, 0.0, 0.0],
      [-0.0, 0.0, 0.0],
      [0.0, 0.0, 0.0],
      [0.0, -0.0, -0.0]]}},
   'stress': {'total': {'value': [[-45593181000.0, 0.0, 0.0],
      [0.0, -45593181000.0, 0.0],
      [0.0, 0.0, -45593181000.0]]}},
   'eigenvalues': [{'kpoints': [[0.125, 0.125, 0.125],
      [0.375, 0.125, 0.125],
      [0.375, 0.375, 0.125],
      [0.375, 0.375, 0.375]],
     'kpoints_weights': [0.125, 0.375, 0.375, 0.125],
     'kpoints_multiplicities': [8.0, 24.0, 24.0, 8.0],
     'occupations': [[[2.0,
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        2.00007,
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        2.07079,
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        2.07079,
        0.56911,
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        0.56911,
        -0.0,
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        -0.0],
       [2.0,
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        1.71069,
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        1.08468,
        0.24804,
        -0.0,
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        2.00002,
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        2.06649,
        0.54407,
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       [2.0,
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        2.03855,
        2.03855,
        1.11299,
        1.11299,
        1.11299,
        -0.0,
        -0.0,
        -0.0]]],
     'energies': [[[-6.830239208405399e-19,
        -4.2778116127799997e-20,
        -4.2778116127799997e-20,
        -4.2778116127799997e-20,
        2.718893747898e-20,
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        2.1666234621582e-19,
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       [-4.658328563355e-19,
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       [-2.8031682388464e-19,
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   'scf_iteration': [{'energy': {'total': {'value': 2.6353442277773303e-17},
      'exchange': {'value': 0.0},
      'free': {'value': 2.6356360163461323e-17},
      'sum_eigenvalues': {'value': 4.9871727844422416e-17},
      'total_t0': {'value': 2.635538753489865e-17},
      'correction_hartree': {'value': -1.7113085439714434e-16}}},
    {'energy': {'total': {'value': -3.5800767464125665e-18},
      'exchange': {'value': 0.0},
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      'total_t0': {'value': -3.580416359793676e-18},
      'correction_hartree': {'value': -1.7113085439714434e-16}}},
    {'energy': {'total': {'value': -4.6468378534730794e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -4.6543938594705676e-18},
      'sum_eigenvalues': {'value': 1.887144771317603e-17},
      'total_t0': {'value': -4.651875191338797e-18},
      'correction_hartree': {'value': -1.7113085439714434e-16}}},
    {'energy': {'total': {'value': -4.65375742844842e-18},
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      'total_t0': {'value': -3.937273266261032e-18},
      'correction_hartree': {'value': -1.5893766573522206e-16}}}]}]}