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Restarting old jobs does not work anymore with the latest update #1510

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ahmedabdelkawy opened this issue Jul 3, 2024 · 5 comments
Open

Restarting old jobs does not work anymore with the latest update #1510

ahmedabdelkawy opened this issue Jul 3, 2024 · 5 comments
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bug Something isn't working

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@ahmedabdelkawy
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All restart functionality is broken for old jobs (not sure how to allow others to reproduce this)

error: rror saving warn (key /Ni111_Mo_surface_sub1_cov/input/vasp_dict/eddrmm_handling): h5io_browser doesn't support saving elements of type "<class 'str'>" to HDF!

  • switching pyiron versions to the old ones did not work
  • manually changing h5io_browser did not work
  • old problematic jobs: type(job_test['input/vasp_dict']) -> dict
  • new working jobs: type(job_test['input/vasp_dict']) -> pyiron_base.storage.hdfio.ProjectHDFio
@ahmedabdelkawy ahmedabdelkawy added the bug Something isn't working label Jul 3, 2024
@ahmedabdelkawy ahmedabdelkawy transferred this issue from pyiron/pyiron_atomistics Jul 3, 2024
@jan-janssen
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Can you be a bit more specific how old these jobs are? Which version of pyiron_atomistics did you use to create those?

@ahmedabdelkawy
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how to do that for a job? since !conda list pyiron will print out those for the loaded kernel

@jan-janssen
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Can you post the output of job.to_dict() for both the old and the new job? Maybe we can write a converter from the old format to the new one. Do you know when the old job was calculated?

@ahmedabdelkawy
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ahmedabdelkawy commented Jul 3, 2024 •
edited by jan-janssen
Loading

Old job -> restart not working -> creation date: 2024-01-03

{'NAME': 'Vasp',
 'TYPE': "<class 'pyiron_atomistics.vasp.vasp.Vasp'>",
 'OBJECT': 'Vasp',
 'DICT_VERSION': '0.1.0',
 'VERSION': '6.4.0_mpi',
 'HDF_VERSION': '0.2.0',
 'status': 'finished',
 'input/generic_dict': {'restart_file_list': [],
  'restart_file_dict': {},
  'exclude_nodes_hdf': [],
  'exclude_groups_hdf': []},
 'server': {'NAME': 'Server',
  'TYPE': "<class 'pyiron_base.jobs.job.extension.server.generic.Server'>",
  'OBJECT': 'Server',
  'DICT_VERSION': '0.1.0',
  'user': 'aabdelkawy',
  'host': 'cmti001',
  'run_mode': 'queue',
  'queue': 'cm',
  'qid': 6803227,
  'cores': 80,
  'threads': 1,
  'new_h5': True,
  'structure_id': None,
  'run_time': None,
  'memory_limit': None,
  'accept_crash': False},
 'executable': {'NAME': 'Executable',
  'TYPE': "<class 'pyiron_base.jobs.job.extension.executable.Executable'>",
  'OBJECT': 'Executable',
  'DICT_VERSION': '0.1.0',
  'executable': {'NAME': 'DataContainer',
   'TYPE': "<class 'pyiron_base.storage.datacontainer.DataContainer'>",
   'OBJECT': 'DataContainer',
   'HDF_VERSION': '0.2.0',
   'VERSION': '0.1.0',
   'READ_ONLY': False,
   'version': '6.4.0_mpi',
   'name': 'vasp',
   'operation_system_nt': 0,
   'executable': None,
   'mpi': 1,
   'accepted_return_codes': [0]}},
 'input/generic/NAME': 'GenericInput',
 'input/generic/TYPE': "<class 'pyiron_atomistics.atomistics.job.atomistic.GenericInput'>",
 'input/generic/OBJECT': 'GenericInput',
 'input/generic/DICT_VERSION': '0.1.0',
 'input/generic/VERSION': '0.1',
 'input/generic/data_dict': {'Parameter': ['calc_mode',
   'structure',
   'fix_symmetry',
   'k_mesh_spacing',
   'k_mesh_center_shift',
   'reduce_kpoint_symmetry',
   'max_iter',
   'pressure'],
  'Value': ['minimize', 'atoms', 'True', 'None', 'None', 'True', None, None],
  'Comment': ['static, minimize, md',
   'atoms, continue_final',
   '',
   '',
   '',
   '',
   '',
   '']},
 'input/structure/TYPE': "<class 'pyiron_atomistics.atomistics.structure.atoms.Atoms'>",
 'input/structure/units': {'length': 'A', 'mass': 'u'},
 'input/structure/dimension': 3,
 'input/structure/positions': array([[ 0.        ,  0.        ,  0.        ],
        [ 2.4876017 ,  1.43621752,  2.03111828],
        [ 1.24380078,  0.71810871,  4.05734758],
        [ 0.        ,  0.        ,  6.08684106],
        [ 2.4876017 ,  1.43621752,  8.11469364],
        [ 1.24380078,  0.71810871, 10.11913593],
        [ 1.24380083,  2.15432623,  0.        ],
        [ 3.73140253,  3.59054375,  2.03111828],
        [ 2.48760161,  2.87243494,  4.05734758],
        [ 1.24380083,  2.15432623,  6.08684106],
        [ 3.73140253,  3.59054375,  8.11469364],
        [ 2.48760161,  2.87243494, 10.11913593],
        [ 2.48760166,  4.30865246,  0.        ],
        [ 4.97520336,  5.74486998,  2.03111828],
        [ 3.73140243,  5.02676117,  4.05734758],
        [ 2.48760166,  4.30865246,  6.08684106],
        [ 4.97520336,  5.74486998,  8.11469364],
        [ 3.73140243,  5.02676117, 10.11913593],
        [ 3.73140248,  6.46297869,  0.        ],
        [ 6.21900419,  7.89919621,  2.03111828],
        [ 4.97520326,  7.1810874 ,  4.05734758],
        [ 3.73140248,  6.46297869,  6.08684106],
        [ 6.21900419,  7.89919621,  8.11469364],
        [ 4.97520326,  7.1810874 , 10.11913593],
        [ 2.48760166,  0.        ,  0.        ],
        [ 4.97520336,  1.43621752,  2.03111828],
        [ 3.73140243,  0.71810871,  4.05734758],
        [ 2.48760166,  0.        ,  6.08684106],
        [ 4.97520336,  1.43621752,  8.11469364],
        [ 3.73140243,  0.71810871, 10.11913593],
        [ 3.73140248,  2.15432623,  0.        ],
        [ 6.21900419,  3.59054375,  2.03111828],
        [ 4.97520326,  2.87243494,  4.05734758],
        [ 3.73140248,  2.15432623,  6.08684106],
        [ 6.21900419,  3.59054375,  8.11469364],
        [ 4.97520326,  2.87243494, 10.11913593],
        [ 4.97520331,  4.30865246,  0.        ],
        [ 7.46280501,  5.74486998,  2.03111828],
        [ 6.21900409,  5.02676117,  4.05734758],
        [ 4.97520331,  4.30865246,  6.08684106],
        [ 7.46280501,  5.74486998,  8.11469364],
        [ 6.21900409,  5.02676117, 10.11913593],
        [ 6.21900414,  6.46297869,  0.        ],
        [ 8.70660584,  7.89919621,  2.03111828],
        [ 7.46280492,  7.1810874 ,  4.05734758],
        [ 6.21900414,  6.46297869,  6.08684106],
        [ 8.70660584,  7.89919621,  8.11469364],
        [ 7.46280492,  7.1810874 , 10.11913593],
        [ 4.97520331,  0.        ,  0.        ],
        [ 7.46280501,  1.43621752,  2.03111828],
        [ 6.21900409,  0.71810871,  4.05734758],
        [ 4.97520331,  0.        ,  6.08684106],
        [ 7.46280501,  1.43621752,  8.11469364],
        [ 6.21900409,  0.71810871, 10.11913593],
        [ 6.21900414,  2.15432623,  0.        ],
        [ 8.70660584,  3.59054375,  2.03111828],
        [ 7.46280492,  2.87243494,  4.05734758],
        [ 6.21900414,  2.15432623,  6.08684106],
        [ 8.70660584,  3.59054375,  8.11469364],
        [ 7.46280492,  2.87243494, 10.11913593],
        [ 7.46280497,  4.30865246,  0.        ],
        [ 9.95040667,  5.74486998,  2.03111828],
        [ 8.70660574,  5.02676117,  4.05734758],
        [ 7.46280497,  4.30865246,  6.08684106],
        [ 9.95040667,  5.74486998,  8.11469364],
        [ 8.70660574,  5.02676117, 10.11913593],
        [ 8.70660579,  6.46297869,  0.        ],
        [11.1942075 ,  7.89919621,  2.03111828],
        [ 9.95040657,  7.1810874 ,  4.05734758],
        [ 8.70660579,  6.46297869,  6.08684106],
        [11.1942075 ,  7.89919621,  8.11469364],
        [ 9.95040657,  7.1810874 , 10.11913593],
        [ 7.46280496,  0.        ,  0.        ],
        [ 9.95040667,  1.43621752,  2.03111828],
        [ 8.70660574,  0.71810871,  4.05734758],
        [ 7.46280496,  0.        ,  6.08684106],
        [ 9.95040667,  1.43621752,  8.11469364],
        [ 8.70660574,  0.71810871, 10.11913593],
        [ 8.70660579,  2.15432623,  0.        ],
        [11.1942075 ,  3.59054375,  2.03111828],
        [ 9.95040657,  2.87243494,  4.05734758],
        [ 8.70660579,  2.15432623,  6.08684106],
        [11.1942075 ,  3.59054375,  8.11469364],
        [ 9.95040657,  2.87243494, 10.11913593],
        [ 9.95040662,  4.30865246,  0.        ],
        [12.43800832,  5.74486998,  2.03111828],
        [11.1942074 ,  5.02676117,  4.05734758],
        [ 9.95040662,  4.30865246,  6.08684106],
        [12.43800832,  5.74486998,  8.11469364],
        [11.1942074 ,  5.02676117, 10.11913593],
        [11.19420745,  6.46297869,  0.        ],
        [13.68180915,  7.89919621,  2.03111828],
        [12.43800823,  7.1810874 ,  4.05734758],
        [11.19420745,  6.46297869,  6.08684106],
        [13.68180915,  7.89919621,  8.11469364],
        [12.43800823,  7.1810874 , 10.11913593]]),
 'input/structure/info': {},
 'input/structure/species': ['Ni', 'Mo'],
 'input/structure/indices': array([0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
        0, 0, 0, 0, 0, 0, 0, 0]),
 'input/structure/tags/initial_magmoms': [0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.0,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
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  0.635,
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  0.636,
  0.59,
  0.59,
  0.635,
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  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634],
 'input/structure/tags/selective_dynamics': [[False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [False, False, False],
  [False, False, False],
  [True, True, True],
  [True, True, True],
  [True, True, True],
  [True, True, True]],
 'input/structure/tags/spin': [0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.0,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
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  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
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  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
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  0.636,
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  0.59,
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  0.59,
  0.635,
  0.634,
  0.634,
  0.636,
  0.59,
  0.59,
  0.635,
  0.634],
 'input/structure/cell/cell': array([[ 9.95040662,  0.        ,  0.        ],
        [ 4.97520331,  8.61730492,  0.        ],
        [ 0.        ,  0.        , 25.15559124]]),
 'input/structure/cell/pbc': array([ True,  True,  True]),
 'input/structure/spins': array([0.634, 0.636, 0.59 , 0.59 , 0.635, 0.   , 0.634, 0.636, 0.59 ,
        0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
        0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
        0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
        0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
        0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
        0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
        0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
        0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
        0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
        0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634]),
 'input/vasp_dict/eddrmm_handling': 'warn',
 'input/incar/NAME': 'Incar',
 'input/incar/TYPE': "<class 'pyiron_atomistics.vasp.base.Incar'>",
 'input/incar/OBJECT': 'Incar',
 'input/incar/DICT_VERSION': '0.1.0',
 'input/incar/VERSION': '0.1',
 'input/incar/data_dict': {'Parameter': ['SYSTEM',
   'PREC',
   'ALGO',
   'LREAL',
   'LWAVE',
   'LORBIT',
   'ENCUT',
   'ISPIN',
   'MAGMOM',
   'NCORE',
   'ISIF',
   'IBRION',
   'NELM',
   'NSW',
   'EDIFFG',
   'EDIFF'],
  'Value': ['Ni111_Mo_surface_sub1_cov',
   'Accurate',
   'Normal',
   'Auto',
   False,
   '11',
   450,
   2,
   '1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ',
   8,
   2,
   2,
   400,
   100,
   '-0.01',
   1e-06],
  'Comment': ['jobname',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '',
   '']},
 'input/kpoints/NAME': 'Kpoints',
 'input/kpoints/TYPE': "<class 'pyiron_atomistics.vasp.base.Kpoints'>",
 'input/kpoints/OBJECT': 'Kpoints',
 'input/kpoints/DICT_VERSION': '0.1.0',
 'input/kpoints/VERSION': '0.1',
 'input/kpoints/data_dict': {'Parameter': ['', '', '', '', ''],
  'Value': ['Kpoints file generated with pyiron_atomistics',
   '0',
   'Monkhorst_Pack',
   '2 2 1',
   '0 0 0'],
  'Comment': ['', '', '', '', '']},
 'input/potcar/NAME': 'Potcar',
 'input/potcar/TYPE': "<class 'pyiron_atomistics.vasp.potential.Potcar'>",
 'input/potcar/OBJECT': 'Potcar',
 'input/potcar/DICT_VERSION': '0.1.0',
 'input/potcar/VERSION': '0.1',
 'input/potcar/data_dict': {'Parameter': ['xc'],
  'Value': ['GGA'],
  'Comment': ['LDA, GGA']},
 'input/potential_dict': {'Mo': None, 'Ni': None}}

@ahmedabdelkawy
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ahmedabdelkawy commented Jul 3, 2024 •
edited
Loading

New job -> restart is working -> created today (different structure/setup just a test job)

{'NAME': 'Vasp',
 'TYPE': "<class 'pyiron_atomistics.vasp.vasp.Vasp'>",
 'OBJECT': 'Vasp',
 'DICT_VERSION': '0.1.0',
 'VERSION': '6.4.0_mpi',
 'HDF_VERSION': '0.2.0',
 'status': 'finished',
 'input/generic_dict': {'restart_file_list': [],
  'restart_file_dict': {},
  'exclude_nodes_hdf': [],
  'exclude_groups_hdf': []},
 'server': {'NAME': 'Server',
  'TYPE': "<class 'pyiron_base.jobs.job.extension.server.generic.Server'>",
  'OBJECT': 'Server',
  'DICT_VERSION': '0.1.0',
  'user': 'aabdelkawy',
  'host': 'cmti001',
  'run_mode': 'queue',
  'queue': 'cmti',
  'qid': 8332741,
  'cores': 10,
  'threads': 1,
  'new_h5': True,
  'structure_id': None,
  'run_time': None,
  'memory_limit': None,
  'accept_crash': False},
 'executable': {'NAME': 'Executable',
  'TYPE': "<class 'pyiron_base.jobs.job.extension.executable.Executable'>",
  'OBJECT': 'Executable',
  'DICT_VERSION': '0.1.0',
  'executable': {'NAME': 'DataContainer',
   'TYPE': "<class 'pyiron_base.storage.datacontainer.DataContainer'>",
   'OBJECT': 'DataContainer',
   'HDF_VERSION': '0.2.0',
   'VERSION': '0.1.0',
   'READ_ONLY': False,
   'version': '6.4.0_mpi',
   'name': 'vasp',
   'operation_system_nt': False,
   'executable': None,
   'mpi': True,
   'accepted_return_codes': [0]}},
 'input/generic/NAME': 'GenericInput',
 'input/generic/TYPE': "<class 'pyiron_atomistics.atomistics.job.atomistic.GenericInput'>",
 'input/generic/OBJECT': 'GenericInput',
 'input/generic/DICT_VERSION': '0.1.0',
 'input/generic/VERSION': '0.1',
 'input/generic/data_dict': OrderedDict([('Parameter',
               ['calc_mode',
                'structure',
                'fix_symmetry',
                'k_mesh_spacing',
                'k_mesh_center_shift',
                'reduce_kpoint_symmetry']),
              ('Value', ['static', 'atoms', 'True', None, None, True]),
              ('Comment',
               ['static, minimize, md',
                'atoms, continue_final',
                '',
                '',
                '',
                ''])]),
 'input/structure/TYPE': "<class 'pyiron_atomistics.atomistics.structure.atoms.Atoms'>",
 'input/structure/units': {'length': 'A', 'mass': 'u'},
 'input/structure/dimension': 3,
 'input/structure/positions': array([[0.   , 0.   , 0.   ],
        [0.   , 2.025, 2.025],
        [2.025, 0.   , 2.025],
        [2.025, 2.025, 0.   ]]),
 'input/structure/info': {},
 'input/structure/species': ['Al'],
 'input/structure/indices': array([0, 0, 0, 0]),
 'input/structure/cell/cell': array([[4.05, 0.  , 0.  ],
        [0.  , 4.05, 0.  ],
        [0.  , 0.  , 4.05]]),
 'input/structure/cell/pbc': array([ True,  True,  True]),
 'input/vasp_dict/eddrmm_handling': 'ignore',
 'input/incar/NAME': 'Incar',
 'input/incar/TYPE': "<class 'pyiron_atomistics.vasp.base.Incar'>",
 'input/incar/OBJECT': 'Incar',
 'input/incar/DICT_VERSION': '0.1.0',
 'input/incar/VERSION': '0.1',
 'input/incar/data_dict': OrderedDict([('Parameter',
               ['SYSTEM',
                'PREC',
                'ALGO',
                'LREAL',
                'LWAVE',
                'LORBIT',
                'IBRION',
                'NELM',
                'NSW']),
              ('Value',
               ['test_job',
                'Accurate',
                'Fast',
                False,
                False,
                '0',
                -1,
                100,
                0]),
              ('Comment', ['jobname', '', '', '', '', '', '', '', ''])]),
 'input/kpoints/NAME': 'Kpoints',
 'input/kpoints/TYPE': "<class 'pyiron_atomistics.vasp.base.Kpoints'>",
 'input/kpoints/OBJECT': 'Kpoints',
 'input/kpoints/DICT_VERSION': '0.1.0',
 'input/kpoints/VERSION': '0.1',
 'input/kpoints/data_dict': OrderedDict([('Parameter', ['', '', '', '', '']),
              ('Value',
               ['Kpoints file generated with pyiron_atomistics',
                '0',
                'Monkhorst_Pack',
                '4 4 4',
                '0 0 0']),
              ('Comment', ['', '', '', '', ''])]),
 'input/potcar/NAME': 'Potcar',
 'input/potcar/TYPE': "<class 'pyiron_atomistics.vasp.potential.Potcar'>",
 'input/potcar/OBJECT': 'Potcar',
 'input/potcar/DICT_VERSION': '0.1.0',
 'input/potcar/VERSION': '0.1',
 'input/potcar/data_dict': OrderedDict([('Parameter', ['xc', 'Al', 'pot_0']),
              ('Value',
               ['GGA',
                'Al-gga-pbe',
                '/cmmc/u/aabdelkawy/pyiron-resources-cmmc/vasp/potentials/potpaw_PBE/Al/POTCAR']),
              ('Comment', ['LDA, GGA', '', ''])]),
 'input/potential_dict': {'Al': None}}

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@jan-janssen @ahmedabdelkawy