matbinder / nomad-lab-vasp-parser

Benchmark Nomad Lab Parser

Home Page:https://mybinder.org/v2/gh/matbinder/nomad-lab-vasp-parser/HEAD?labpath=nomad.ipynb

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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,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.00007,
        2.00007,
        2.00023,
        2.00023,
        2.00023,
        2.07079,
        2.07079,
        2.07079,
        0.56911,
        0.56911,
        0.56911,
        -0.0,
        -0.0,
        -0.0],
       [2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.00001,
        2.0003,
        2.0003,
        2.01592,
        1.71069,
        1.08468,
        1.08468,
        0.24804,
        -0.0,
        -0.0],
       [2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.00002,
        2.0663,
        2.0663,
        2.06649,
        0.54407,
        -0.0,
        -0.0,
        -0.0],
       [2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        2.0,
        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,
        2.718893747898e-20,
        2.718893747898e-20,
        2.1666234621582e-19,
        2.5240690692036e-19,
        2.5240690692036e-19,
        3.7489331058966e-19,
        3.7489331058966e-19,
        3.8160643068612e-19,
        3.8160643068612e-19,
        3.8160643068612e-19,
        4.378588523058599e-19,
        4.378588523058599e-19,
        4.378588523058599e-19,
        4.8494682357912e-19,
        4.8494682357912e-19,
        4.8494682357912e-19,
        8.8940029306608e-19,
        8.8940029306608e-19,
        8.8940029306608e-19],
       [-4.658328563355e-19,
        -1.4204898037044e-19,
        4.364329151015999e-20,
        4.364329151015999e-20,
        8.291264080949998e-20,
        8.472310040592e-20,
        8.472310040592e-20,
        1.6337395136898e-19,
        2.1440327716188e-19,
        2.1440327716188e-19,
        2.6386246985346e-19,
        2.728506807702e-19,
        2.9047462374419996e-19,
        3.5718925878396e-19,
        3.6354990002093997e-19,
        3.8304838965672e-19,
        3.8304838965672e-19,
        4.1233617852623994e-19,
        4.6128267469494e-19,
        4.7485311078492e-19,
        4.7485311078492e-19,
        4.928295326184e-19,
        1.20850581325986e-18,
        1.20850581325986e-18],
       [-2.8031682388464e-19,
        -3.568047363918e-20,
        -3.568047363918e-20,
        3.822793448724e-20,
        1.2686034588011998e-19,
        1.3581651326418e-19,
        1.3581651326418e-19,
        1.6834069893437998e-19,
        1.89857931129e-19,
        1.89857931129e-19,
        2.0623217632847998e-19,
        2.452932426654e-19,
        2.8741446637326e-19,
        3.3089754022002e-19,
        3.3089754022002e-19,
        3.3128206261217994e-19,
        3.6803599459613995e-19,
        4.3290812650679997e-19,
        4.3290812650679997e-19,
        4.4079083554608e-19,
        4.8547554186834e-19,
        6.9073039045008e-19,
        6.9073039045008e-19,
        1.0289979431865e-18],
       [-1.8019680602598e-19,
        -6.602569908714e-20,
        -6.602569908714e-20,
        -6.602569908714e-20,
        1.9924668620424e-19,
        1.9924668620424e-19,
        1.9924668620424e-19,
        2.4466839377813995e-19,
        2.4466839377813995e-19,
        2.6458344933876e-19,
        2.6458344933876e-19,
        2.6458344933876e-19,
        2.833449377229e-19,
        2.833449377229e-19,
        2.833449377229e-19,
        2.8368139481603998e-19,
        4.459818878402399e-19,
        4.459818878402399e-19,
        4.743243924957e-19,
        4.743243924957e-19,
        4.743243924957e-19,
        7.1755082730324e-19,
        7.1755082730324e-19,
        7.1755082730324e-19]]]}],
   '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},
      'free': {'value': -3.580586166484231e-18},
      'sum_eigenvalues': {'value': 1.9938208818634368e-17},
      '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},
      'exchange': {'value': 0.0},
      'free': {'value': -4.6613839702722196e-18},
      'sum_eigenvalues': {'value': 1.886452813820069e-17},
      'total_t0': {'value': -4.658841788596169e-18},
      'correction_hartree': {'value': -1.7113085439714434e-16}}},
    {'energy': {'total': {'value': -4.653824056565922e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -4.661452070790048e-18},
      'sum_eigenvalues': {'value': 1.886446150848101e-17},
      'total_t0': {'value': -4.658909400450123e-18},
      'correction_hartree': {'value': -1.7113085439714434e-16}}},
    {'energy': {'total': {'value': -4.3347985586863034e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -4.339977216542023e-18},
      'sum_eigenvalues': {'value': -4.996893319857027e-19},
      'total_t0': {'value': -4.338250997790842e-18},
      'correction_hartree': {'value': -1.540950945846528e-16}}},
    {'energy': {'total': {'value': -3.93548105705865e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -3.947336574549249e-18},
      'sum_eigenvalues': {'value': 8.637037829614532e-18},
      'total_t0': {'value': -3.943384735385716e-18},
      'correction_hartree': {'value': -1.6053283717072305e-16}}},
    {'energy': {'total': {'value': -3.930399707400796e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -3.942039700090589e-18},
      'sum_eigenvalues': {'value': 8.492217506641905e-18},
      'total_t0': {'value': -3.938159702527325e-18},
      'correction_hartree': {'value': -1.595097068213449e-16}}},
    {'energy': {'total': {'value': -3.929820110390388e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -3.9409959348853675e-18},
      'sum_eigenvalues': {'value': 8.204060255159354e-18},
      'total_t0': {'value': -3.9372706595196485e-18},
      'correction_hartree': {'value': -1.589941157180382e-16}}},
    {'energy': {'total': {'value': -3.9299002993309195e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -3.940978218016149e-18},
      'sum_eigenvalues': {'value': 8.148612116596824e-18},
      'total_t0': {'value': -3.9372855789884645e-18},
      'correction_hartree': {'value': -1.5887708095588604e-16}}},
    {'energy': {'total': {'value': -3.929860643857051e-18},
      'exchange': {'value': 0.0},
      'free': {'value': -3.940979576661935e-18},
      'sum_eigenvalues': {'value': 8.179162773132796e-18},
      'total_t0': {'value': -3.937273266261032e-18},
      'correction_hartree': {'value': -1.5893766573522206e-16}}}]}]}

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Benchmark Nomad Lab Parser

https://mybinder.org/v2/gh/matbinder/nomad-lab-vasp-parser/HEAD?labpath=nomad.ipynb


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