diff --git a/example/software_directory/modeling/espresso.json b/example/software_directory/modeling/espresso.json index 3c493d2a9..9c4bd0878 100644 --- a/example/software_directory/modeling/espresso.json +++ b/example/software_directory/modeling/espresso.json @@ -2,5 +2,5 @@ "name": "espresso", "shortName": "qe", "summary": "Quantum Espresso", - "version": "5.1.1" + "version": "7.2" } diff --git a/src/py/mat3ra/esse/data/examples.py b/src/py/mat3ra/esse/data/examples.py index 9758ee89a..e864aaeb5 100644 --- a/src/py/mat3ra/esse/data/examples.py +++ b/src/py/mat3ra/esse/data/examples.py @@ -1,2 +1,2 @@ import json -EXAMPLES = json.loads(json.dumps([{'data': {'method': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'subtype': 'gga', 'type': 'dft'}, 'path': 'model'}, {'data': {'_id': 'FPjAaKfuYAL7tiHbm', 'createdAt': '2018-11-19 06:41:46.877Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'exabyteId': 'qKtTzu9utCo6ac4n7', 'hash': 'f4fd707d2e47c15f8d786cf159040954', 'isDefault': True, 'name': 'workflow', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'properties': ['band_structure'], 'schemaVersion': '0.2.0', 'slug': 'workflow', 'subworkflows': [{'_id': 'LCthJ6E2QabYCZqf4', 'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1', 'hasAdvancedComputeOptions': True}, 'model': {'method': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'subtype': 'gga', 'type': 'dft'}, 'name': 'Band Structure', 'properties': ['band_structure'], 'units': [{'flowchartId': 'pw-scf', 'head': True, 'name': 'pw_scf', 'status': 'idle', 'type': 'execution', 'tags': ['test-tags']}]}], 'tags': ['workflow'], 'units': [{'_id': 'LCthJ6E2QabYCZqf4', 'flowchartId': '05c362dc27ff1bb98d16fd60', 'type': 'subworkflow'}]}, 'path': 'workflow'}, {'data': {'_id': 'tvFyik5699io8khi8', 'chargeRate': {'rate': 2}, 'createdAt': '2019-01-03T23:52:26.809Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'description': 'Default project', 'gid': 3000000, 'isDefault': True, 'name': 'Default', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'schemaVersion': '0.2.0', 'slug': 'exadmin-default', 'tags': [], 'updatedAt': '2019-01-04T00:12:37.316Z'}, 'path': 'project'}, {'data': {'_id': 'FPjAaKfuYAL7tiHbm', '_material': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Material', 'slug': 'silicon-fcc'}, '_project': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Project', 'slug': 'project-default'}, 'compute': {'arguments': {'nband': 1, 'npools': 1, 'ntg': 1}, 'cluster': {'fqdn': 'master-1-staging.exabyte.io', 'jid': '1234.master-1-staging.exabyte.io'}, 'email': 'demo@exabyte.io', 'errors': [{'domain': 'rupy', 'message': 'File Not Found: /home/demo/data/project1/job-123/job-config.json', 'reason': 'FileNotFound'}], 'excludeFilesPattern': '^.*.txt$', 'maxCPU': 36, 'nodes': 1, 'notify': 'abe', 'ppn': 1, 'queue': 'OF', 'timeLimit': '00:05:00'}, 'createdAt': '2018-11-19 06:41:46.877Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'name': 'job', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'schemaVersion': '0.2.0', 'slug': 'job', 'status': 'pre-submission', 'workflow': {'_id': 'FPjAaKfuYAL7tiHbm', 'createdAt': '2018-11-19 06:41:46.877Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'exabyteId': 'qKtTzu9utCo6ac4n7', 'hash': 'f4fd707d2e47c15f8d786cf159040954', 'isDefault': True, 'name': 'workflow', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'properties': ['band_structure'], 'schemaVersion': '0.2.0', 'slug': 'workflow', 'subworkflows': [{'_id': 'LCthJ6E2QabYCZqf4', 'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1', 'hasAdvancedComputeOptions': True}, 'model': {'method': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'subtype': 'gga', 'type': 'dft'}, 'name': 'Band Structure', 'properties': ['band_structure'], 'units': [{'flowchartId': 'pw-scf', 'head': True, 'name': 'pw_scf', 'status': 'idle', 'type': 'execution', 'tags': ['test-tags']}]}], 'tags': ['workflow'], 'units': [{'_id': 'LCthJ6E2QabYCZqf4', 'flowchartId': '05c362dc27ff1bb98d16fd60', 'type': 'subworkflow'}]}}, 'path': 'job'}, {'data': {'_id': 'LCthJ6E2QabYCZqf3', 'basis': {'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}], 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}], 'name': 'basis', 'units': 'crystal'}, 'createdAt': '2016-04-03T05:25:37.430Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'derivedProperties': [{'name': 'volume', 'units': 'angstrom^3', 'value': 131.1}, {'name': 'density', 'units': 'g/cm^3', 'value': 2.33}, {'name': 'symmetry', 'spaceGroupSymbol': 'Fd-3m', 'tolerance': {'units': 'angstrom', 'value': 0.3}}, {'degree': 10, 'name': 'p-norm', 'value': 0.71}, {'element': 'Si', 'name': 'elemental_ratio', 'value': 0.71}, {'name': 'inchi', 'value': ''}, {'name': 'inchi_key', 'value': ''}], 'exabyteId': 'RKiswuxHKkF3uvLyA', 'formula': 'Si', 'hash': '4ac3fa057e3530628eb1295c77110eaa', 'isDefault': False, 'isNonPeriodic': False, 'lattice': {'name': 'lattice', 'vectors': {'a': [5.0, 0.000121312, 0.000131415], 'alat': 1.0, 'b': [0.000121312, 5.0, 0.000121314], 'c': [0.000121313, 0.000121312, 5.0], 'units': 'angstrom'}, 'a': 5.14, 'alpha': 90.0, 'b': 5.14, 'beta': 90.0, 'c': 5.14, 'gamma': 90.0, 'type': 'CUB', 'units': {'angle': 'degree', 'length': 'angstrom'}}, 'name': 'Silicon FCC', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'scaledHash': '5bd4eb168e3530628eb1295d88221cbb', 'schemaVersion': '0.2.0', 'slug': 'silicon-fcc', 'unitCellFormula': 'Si2', 'updatedAt': '2016-04-04T17:58:42.867Z'}, 'path': 'material'}, {'data': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'path': 'method'}, {'data': {'properties': [{'name': 'atomic_radius', 'value': 4}, {'name': 'electronegativity', 'value': 1.1}, {'name': 'ionization_potential', 'value': 7.7}], 'symbol': 'Si'}, 'path': 'element'}, {'data': {'_id': 'nDAavgjrT5ezwFgod', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'title': 'My Calculation'}, 'path': 'core/reference'}, {'data': {'xDataArray': [0, 1, 2], 'yDataSeries': [[0, 0.5, 1], [0, 2.5, 5]]}, 'path': 'core/abstract/2d_data'}, {'data': [[1, 0, 0], [0, 1, 0], [0, 0, 1]], 'path': 'core/abstract/3d_tensor'}, {'data': {'dimensions': [2, 2, 2], 'shifts': [0, 0, 0]}, 'path': 'core/abstract/3d_grid'}, {'data': {'a': [5.0, 0.0, 0.0], 'b': [0.0, 5.0, 0.0], 'c': [0.0, 0.0, 5.0]}, 'path': 'core/abstract/3d_vector_basis'}, {'data': [0.0, 5.5, 0.0], 'path': 'core/abstract/point'}, {'data': {'xAxis': {'label': 'kpoint index'}, 'xDataArray': [0, 1, 2], 'yAxis': {'label': 'eigenvalues', 'units': 'eV'}, 'yDataSeries': [[0, 0.5, 1], [0, 2.5, 5]]}, 'path': 'core/abstract/2d_plot'}, {'data': [1.0, 0.0, 0.0], 'path': 'core/abstract/vector'}, {'data': [1.0, 0.0, 0.0], 'path': 'core/primitive/array_of_3_numbers'}, {'data': {'a': 5.14, 'alpha': 90.0, 'b': 5.14, 'beta': 90.0, 'c': 5.14, 'gamma': 90.0}, 'path': 'core/primitive/3d_lattice'}, {'data': [True, False, False], 'path': 'core/primitive/array_of_3_booleans'}, {'data': [[0, 0.5, 1], [0, 2.5, 5]], 'path': 'core/primitive/1d_data_series'}, {'data': {'value': 'example string'}, 'path': 'core/primitive/string'}, {'data': {'label': 'energy', 'units': 'eV'}, 'path': 'core/primitive/axis'}, {'data': [{'id': 1}, {'id': 2}], 'path': 'core/primitive/array_of_ids'}, {'data': {'value': 0.1}, 'path': 'core/primitive/scalar'}, {'data': {'authors': [{'affiliation': 'Exabyte Inc.', 'first': 'John', 'last': 'Doe'}], 'doi': '10.1000/xyz123'}, 'path': 'core/reference/literature'}, {'data': {'_id': 'nDAavgjrT5ezwFgod', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'title': 'My Calculation'}, 'path': 'core/reference/modeling'}, {'data': {'authors': [{'affiliation': 'Exabyte Inc.', 'first': 'John', 'last': 'Doe'}], 'conditions': [{'name': 'pressure', 'scalar': [{'value': '1.2'}, {'value': '3.3'}], 'units': 'kbar'}], 'method': 'DFT', 'references': [{'authors': [{'affiliation': 'Exabyte Inc.', 'first': 'John', 'last': 'Doe'}], 'doi': '10.1000/xyz123'}], 'timestamp': 141182979832, 'title': 'Experiment 1'}, 'path': 'core/reference/experiment'}, {'data': {'affiliation': 'Exabyte Inc.', 'first': 'John', 'last': 'Doe'}, 'path': 'core/reference/literature/name'}, {'data': {'end': '2', 'start': '1'}, 'path': 'core/reference/literature/pages'}, {'data': {'_id': 'nDAavgjrT5ezwFgod', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'title': 'My Calculation'}, 'path': 'core/reference/modeling/exabyte'}, {'data': {'latitude': 24.3423424, 'longitude': 43.234232}, 'path': 'core/reference/experiment/location'}, {'data': {'name': 'pressure', 'scalar': [{'value': '1.2'}, {'value': '3.3'}], 'units': 'kbar'}, 'path': 'core/reference/experiment/condition'}, {'data': {'pathname': '/path/to/file/', 'basename': 'some_file.png', 'filetype': 'image'}, 'path': 'core/reusable/file_metadata'}, {'data': [{'id': 1, 'value': [0, 0, 0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}], 'path': 'core/reusable/atomic_vectors'}, {'data': {'CONTAINER': 'production-20160630-cluster-001', 'NAME': '/cluster-001-home/jrd101/data/jrd101-default/kernel-train-Cxmkj97aXKZeaRZov/Cxmkj97aXKZeaRZov.json', 'PROVIDER': 'aws', 'REGION': 'us-east-1', 'SIZE': 6582, 'TIMESTAMP': '1614217411'}, 'path': 'core/reusable/object_storage_container_data'}, {'data': {'name': 'zero_point_energy', 'units': 'eV', 'value': -0.0634}, 'path': 'core/reusable/energy'}, {'data': {'kpointConduction': [0, 0, 0], 'kpointValence': [0, 0, 0], 'name': 'band_gap', 'type': 'direct', 'units': 'rydberg', 'value': 0.0947}, 'path': 'core/reusable/band_gap'}, {'data': {'_id': 'K3McGkqXh28HJ775m', 'createdAt': '2018-11-19 06:41:46.877Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'data': {'name': 'pressure', 'units': 'kbar', 'value': -149.03}, 'group': 'qe:dft:gga:pbe', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'schemaVersion': '0.2.0', 'slug': 'pressure', 'source': {'_id': 'nDAavgjrT5ezwFgod', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'title': 'My Calculation'}}, 'path': 'property/base'}, {'data': {'&CONTROL': {'calculation': 'scf', 'title': '', 'verbosity': 'low', 'restart_mode': 'from_scratch', 'wf_collect': True, 'tstress': True, 'tprnfor': True, 'outdir': '{{ JOB_WORK_DIR }}/outdir', 'wfcdir': '{{ JOB_WORK_DIR }}/outdir', 'prefix': '__prefix__', 'pseudo_dir': '{{ JOB_WORK_DIR }}/pseudo'}, '&SYSTEM': {'ibrav': 0, 'nat': 2, 'ntyp': 2, 'ecutwfc': 40, 'ecutrho': 200, 'occupations': 'smearing', 'degauss': 0.005, 'starting_magnetization': [0.01, 0.02], 'Hubbard_occ': [[1, 1, 0.0], [1, 2, 0.02]]}, '&ELECTRONS': {'diagonalization': 'david', 'diago_david_ndim': 4, 'diago_full_acc': True, 'mixing_beta': 0.3, 'startingwfc': 'atomic+random'}, '&IONS': None, '&CELL': None, 'ATOMIC_SPECIES': {'values': [{'X': 'Cs', 'Mass_X': 132.90543, 'PseudoPot_X': 'Cs.upf'}, {'X': 'Cl', 'Mass_X': 35.4527, 'PseudoPot_X': 'Cl.upf'}]}, 'CELL_PARAMETERS': {'card_option': 'angstrom', 'values': {'v1': [4.324582724, 0.0, 2.496799], 'v2': [1.441527575, 4.077255694, 2.496799], 'v3': [0.0, 0.0, 4.993598]}}, 'K_POINTS': {'card_option': 'automatic', 'values': {'nk1': 2, 'nk2': 2, 'nk3': 2, 'sk1': 0, 'sk2': 0, 'sk3': 0}}}, 'path': '3pse/file/applications/espresso/7.2/pw.x'}, {'data': {'name': 'Methfessel-Paxton smearing', 'path': '/qm/wf/smearing/methfessel-paxton', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'smearing', 'subtype': 'methfessel-paxton'}}, 'path': 'methods_directory/physical/smearing'}, {'data': {'name': 'PAW Pseudopotential method', 'path': '/qm/wf/psp/paw', 'slug': 'pseudopotential', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'psp', 'subtype': 'paw'}, 'data': [{'slug': 'pseudopotential', 'source': {'info': {}, 'type': 'exabyte'}, 'data': {'element': 'Ru', 'hash': '3349af97451e04faae570056fb6a110b', 'filename': 'ru_pbe_dojo-oncv_0.4.upf', 'path': '/export/share/pseudo/ru/gga/pbe/dojo-oncv/0.4/nc/ru_pbe_dojo-oncv_0.4.upf', 'valenceConfiguration': [{'orbitalName': '4S', 'orbitalIndex': 1, 'principalNumber': 4, 'angularMomentum': 0, 'occupation': 2.0}, {'orbitalName': '4P', 'orbitalIndex': 2, 'principalNumber': 4, 'angularMomentum': 1, 'occupation': 6.0}, {'orbitalName': '4D', 'orbitalIndex': 3, 'principalNumber': 4, 'angularMomentum': 2, 'occupation': 7.0}, {'orbitalName': '5S', 'orbitalIndex': 4, 'principalNumber': 5, 'angularMomentum': 0, 'occupation': 1.0}], 'apps': ['espresso'], 'exchangeCorrelation': {'functional': 'pbe', 'approximation': 'gga'}, 'name': 'pseudopotential', 'source': 'dojo-oncv', 'type': 'nc', 'version': '0.4'}}]}, 'path': 'methods_directory/physical/psp'}, {'data': {'name': 'Plane wave basis', 'path': '/qm/wf/pw', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'pw'}}, 'path': 'methods_directory/physical/pw'}, {'data': {'name': 'Optimized Tetrahedron method (Kawamura)', 'path': '/qm/wf/tetrahedron/optimized', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'tetrahedron', 'subtype': 'optimized'}}, 'path': 'methods_directory/physical/tetrahedron'}, {'data': {'slug': 'pseudopotential', 'source': {'info': {}, 'type': 'exabyte'}, 'data': {'element': 'Ru', 'hash': '3349af97451e04faae570056fb6a110b', 'filename': 'ru_pbe_dojo-oncv_0.4.upf', 'path': '/export/share/pseudo/ru/gga/pbe/dojo-oncv/0.4/nc/ru_pbe_dojo-oncv_0.4.upf', 'valenceConfiguration': [{'orbitalName': '4S', 'orbitalIndex': 1, 'principalNumber': 4, 'angularMomentum': 0, 'occupation': 2.0}, {'orbitalName': '4P', 'orbitalIndex': 2, 'principalNumber': 4, 'angularMomentum': 1, 'occupation': 6.0}, {'orbitalName': '4D', 'orbitalIndex': 3, 'principalNumber': 4, 'angularMomentum': 2, 'occupation': 7.0}, {'orbitalName': '5S', 'orbitalIndex': 4, 'principalNumber': 5, 'angularMomentum': 0, 'occupation': 1.0}], 'apps': ['espresso'], 'exchangeCorrelation': {'functional': 'pbe', 'approximation': 'gga'}, 'name': 'pseudopotential', 'source': 'dojo-oncv', 'type': 'nc', 'version': '0.4'}}, 'path': 'methods_directory/physical/psp/file'}, {'data': {'name': 'cc-pVTZ basis set', 'path': '/qm/wf/ao/dunning?basisSlug=cc-pvtz', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'ao', 'subtype': 'dunning'}, 'parameters': {'basisSlug': 'cc-pvtz'}}, 'path': 'methods_directory/physical/ao/dunning'}, {'data': {'data': {'dataSet': {'exabyteIds': ['LCthJ6E2QabYCZqf4', 'LCthJ6E2QabYCZqf5', 'LCthJ6E2QabYCZqf6', 'LCthJ6E2QabYCZqf7', 'LCthJ6E2QabYCZqf8', 'LCthJ6E2QabYCZqf9', 'LCthJ6E2QabYCZq10', 'LCthJ6E2QabYCZq11'], 'extra': {}}, 'perProperty': [{'intercept': 0.363, 'name': 'band_gaps:direct', 'perFeature': [{'coefficient': 0.015, 'importance': 0.134, 'name': 'atomic_radius:Ge'}, {'coefficient': 0.016, 'importance': 0.135, 'name': 'atomic_radius:Si'}]}, {'intercept': 0.364, 'name': 'band_gaps:indirect', 'perFeature': [{'coefficient': 0.016, 'importance': 0.135, 'name': 'atomic_radius:Ge'}, {'coefficient': 0.017, 'importance': 0.136, 'name': 'atomic_radius:Si'}]}]}, 'precision': {'perProperty': [{'score': 0.8, 'trainingError': 0.002}]}, 'subtype': 'least_squares', 'type': 'linear'}, 'path': 'methods_directory/legacy/regression'}, {'data': {'type': 'pseudopotential', 'subtype': 'us'}, 'path': 'methods_directory/legacy/pseudopotential'}, {'data': {'type': 'localorbital', 'subtype': 'pople'}, 'path': 'methods_directory/legacy/localorbital'}, {'data': {'type': 'unknown', 'subtype': 'unknown'}, 'path': 'methods_directory/legacy/unknown'}, {'data': {'data': {'dataSet': {'exabyteIds': ['LCthJ6E2QabYCZqf4', 'LCthJ6E2QabYCZqf5', 'LCthJ6E2QabYCZqf6', 'LCthJ6E2QabYCZqf7', 'LCthJ6E2QabYCZqf8', 'LCthJ6E2QabYCZqf9', 'LCthJ6E2QabYCZq10', 'LCthJ6E2QabYCZq11'], 'extra': {}}, 'perProperty': [{'intercept': 0.363, 'name': 'band_gaps:direct', 'perFeature': [{'coefficient': 0.015, 'importance': 0.134, 'name': 'atomic_radius:Ge'}, {'coefficient': 0.016, 'importance': 0.135, 'name': 'atomic_radius:Si'}]}, {'intercept': 0.364, 'name': 'band_gaps:indirect', 'perFeature': [{'coefficient': 0.016, 'importance': 0.135, 'name': 'atomic_radius:Ge'}, {'coefficient': 0.017, 'importance': 0.136, 'name': 'atomic_radius:Si'}]}]}, 'precision': {'perProperty': [{'score': 0.8, 'trainingError': 0.002}]}, 'categories': {'type': 'linear', 'subtype': 'least_squares'}, 'name': 'Linear least squares regression', 'path': '/linear/leastsq'}, 'path': 'methods_directory/mathematical/regression'}, {'data': {'name': 'Conjugate gradient method', 'path': '/opt/diff/ordern/cg', 'categories': {'tier1': 'opt', 'tier2': 'diff', 'tier3': 'ordern', 'type': 'cg'}}, 'path': 'methods_directory/mathematical/cg'}, {'data': {'charge': 0, 'multiplicity': 1}, 'path': 'properties_directory/electronic_configuration'}, {'data': {'name': 'ionization_potential', 'value': 7.7}, 'path': 'properties_directory/elemental/ionization_potential'}, {'data': {'name': 'electronegativity', 'value': 1.1}, 'path': 'properties_directory/elemental/electronegativity'}, {'data': {'name': 'atomic_radius', 'value': 4}, 'path': 'properties_directory/elemental/atomic_radius'}, {'data': {'data': [{'grid': {'dimensions': [1, 1, 1], 'shifts': [0, 0, 0]}, 'value': '-123.45678'}], 'property': 'total_energy', 'tolerance': 0.001, 'units': 'eV'}, 'path': 'properties_directory/workflow/convergence/kpoint'}, {'data': {'data': [[-123.45678, -12.345678, -1.2345678, -0.1234567, -0.0123456, -0.0012345, -0.0001234]], 'tolerance': 0.001, 'units': 'rydberg'}, 'path': 'properties_directory/workflow/convergence/electronic'}, {'data': {'data': [{'electronic': {'data': [0.10303193, 0.04365779, 0.00051472, 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'/cluster-001-home/jrd101/data/jrd101-default/kernel-train-Cxmkj97aXKZeaRZov/Cxmkj97aXKZeaRZov.json', 'PROVIDER': 'aws', 'REGION': 'us-east-1', 'SIZE': 6582, 'TIMESTAMP': '1614217411'}}, 'path': 'workflow/unit/io/object_storage'}, {'data': {'endpoint': 'data-frame', 'endpoint_options': {'data': {'features': ['elemental_ratio:Si', 'elemental_ratio:Ge', 'ionization_potential:Ge', 'ionization_potential:Si'], 'ids': ['KuAsBRwofzGfHPWiT'], 'targets': ['band_gaps:indirect', 'band_gaps:direct']}, 'headers': {'X-Auth-Token': '', 'X-User-Id': ''}, 'method': 'POST', 'params': {'query': {'formula': 'SiGe'}}}, 'name': 'DATA'}, 'path': 'workflow/unit/io/api'}, {'data': {'features': ['elemental_ratio:Si', 'elemental_ratio:Ge', 'ionization_potential:Ge', 'ionization_potential:Si'], 'ids': ['KuAsBRwofzGfHPWiT'], 'targets': ['band_gaps:indirect', 'band_gaps:direct']}, 'path': 'workflow/unit/io/db'}, {'data': {'monitors': [{'name': 'standard_output'}], 'postProcessors': [], 'preProcessors': [], 'results': [{'name': 'atomic_forces'}]}, 'path': 'workflow/unit/runtime/runtime_items'}, {'data': {'name': 'PZ+U (magnetism)', 'categories': {'tier1': {'name': 'physics-based', 'slug': 'pb'}, 'tier2': {'name': 'quantum-mechanical', 'slug': 'qm'}, 'tier3': {'name': 'density functional theory', 'slug': 'dft'}, 'type': {'name': 'Kohn-Sham DFT', 'slug': 'ksdft'}, 'subtype': {'name': 'Local Density Approximation', 'slug': 'lda'}}, 'parameters': {'functional': 'pz', 'spinPolarization': 'collinear', 'hubbardType': 'U'}, 'method': {'name': 'PW-NCPP (Davidson Diagonalization, Gaussian Smearing)', 'path': '/qm/wf/pw:/qm/wf/psp/nc?functional=pbe:/qm/wf/smearing/gaussian:/linalg/diag/davidson', 'units': [{'name': 'Plane-wave', 'path': '/qm/wf/pw', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'pw'}}, {'name': 'Norm-conserving PSP', 'path': '/qm/wf/psp/nc?functional=pbe', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'psp', 'subtype': 'nc'}, 'parameters': {'functional': 'pbe'}}, {'name': 'Gaussian Smearing method', 'path': '/qm/wf/smearing/gaussian', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'smearing', 'subtype': 'gaussian'}}, {'name': 'Davidson Diagonalization', 'path': '/linalg/diag/davidson', 'categories': {'tier1': 'linalg', 'tier2': 'diag', 'type': 'davidson'}}]}}, 'path': 'model/categorized_model'}, {'data': {'functional': 'pbe', 'dispersionCorrection': 'dft-d3', 'hubbardType': 'u', 'spinPolarization': 'collinear', 'spinOrbitCoupling': True}, 'path': 'model/model_parameters'}, {'data': {'arguments': {'nband': 1, 'npools': 1, 'ntg': 1}, 'cluster': {'fqdn': 'master-1-staging.exabyte.io', 'jid': '1234.master-1-staging.exabyte.io'}, 'email': 'demo@exabyte.io', 'errors': [{'domain': 'rupy', 'message': 'File Not Found: /home/demo/data/project1/job-123/job-config.json', 'reason': 'FileNotFound'}], 'excludeFilesPattern': '^.*.txt$', 'maxCPU': 36, 'nodes': 1, 'notify': 'abe', 'ppn': 1, 'queue': 'OF', 'timeLimit': '00:05:00'}, 'path': 'job/compute'}, {'data': {'exec': 'jupyter', 'flavor': 'notebook', 'name': 'jupyterLab', 'shortName': 'jl', 'summary': 'Jupyter Lab', 'version': '0.33.12'}, 'path': 'software_directory/scripting/jupyter-lab'}, {'data': {'exec': 'sh', 'flavor': 'sh', 'name': 'shell', 'shortName': 'sh', 'summary': 'Shell Script', 'version': '4.2.46'}, 'path': 'software_directory/scripting/shell'}, {'data': {'exec': 'python', 'flavor': 'python2', 'name': 'python', 'shortName': 'py', 'summary': 'Python Script', 'version': '2.7.5'}, 'path': 'software_directory/scripting/python'}, {'data': {'application': {'exec': 'python', 'flavor': 'python2', 'name': 'python', 'shortName': 'py', 'summary': 'Python Script', 'version': '2.7.5'}, 'compute': None, 'flowchartId': 'scripting', 'head': True, 'input': [{'content': "print('Hello World!')", 'name': 'script.py'}], 'name': 'scripting', 'status': 'idle', 'type': 'execution'}, 'path': 'software_directory/scripting/unit/execution'}, {'data': {'name': 'NWChem', 'summary': 'NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations', 'version': '6.6', 'exec': 'nwchem'}, 'path': 'software_directory/modeling/nwchem'}, {'data': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1'}, 'path': 'software_directory/modeling/espresso'}, {'data': {'name': 'vasp', 'shortName': 'vasp', 'summary': 'vienna ab-initio simulation package', 'version': '5.3.5'}, 'path': 'software_directory/modeling/vasp'}, {'data': {'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1'}, 'flowchartId': 'modeling', 'head': True, 'input': [{'content': 'K_POINTS automatic\n2 2 2 0 0 0', 'name': 'pw_scf.in'}], 'name': 'modeling', 'status': 'idle', 'type': 'execution'}, 'path': 'software_directory/modeling/unit/execution'}, {'data': {'nband': 1, 'npools': 1, 'ntg': 1}, 'path': 'software_directory/modeling/espresso/arguments'}, {'data': {'name': 'exabyteml', 'shortName': 'ml', 'summary': 'exabyte machine learning engine', 'version': '0.2.0'}, 'path': 'software_directory/ml/exabyteml'}, {'data': {'flowchartId': 'data_transformation', 'head': True, 'inputData': {'cleanMissingData': True, 'removeDuplicateRows': True, 'replaceNoneValuesWith': 0}, 'name': 'data_transformation', 'operation': 'data_transformation', 'operationType': 'manipulation', 'status': 'idle', 'type': 'processing'}, 'path': 'software_directory/ml/unit/processing/data_transformation/manipulation'}, {'data': {'flowchartId': 'data_transformation', 'head': True, 'inputData': {'perFeature': [{'mean': 0.156, 'name': 'atomic_radius:Ge', 'scale': 1.5, 'variance': 0.1}, {'mean': 0.155, 'name': 'atomic_radius:Si', 'scale': 1.4, 'variance': 0.11}], 'scaler': 'standard_scaler'}, 'name': 'data_transformation', 'operation': 'data_transformation', 'operationType': 'scale_and_reduce', 'status': 'idle', 'type': 'processing'}, 'path': 'software_directory/ml/unit/processing/data_transformation/scale_and_reduce'}, {'data': {'flowchartId': 'feature_selection', 'head': True, 'inputData': {'algorithm': 'f_regression', 'nFeatures': 100}, 'name': 'feature_selection', 'operation': 'feature_selection', 'operationType': 'filter_based', 'status': 'idle', 'type': 'processing'}, 'path': 'software_directory/ml/unit/processing/feature_selection/filter_based'}, {'data': {'application': {'name': 'exabyteml', 'shortName': 'ml', 'summary': 'exabyte machine learning engine', 'version': '0.2.0'}, 'flavor': {'executableId': '4987JFJ3kKbwvFSG7', 'name': 'score'}, 'flowchartId': 'score', 'head': True, 'input': {}, 'name': 'score', 'status': 'idle', 'type': 'execution'}, 'path': 'software_directory/ml/unit/execution/score'}, {'data': {'application': {'name': 'exabyteml', 'shortName': 'ml', 'summary': 'exabyte machine learning engine', 'version': '0.2.0'}, 'flavor': {'executableId': '4987JFJ3kKbwvFSG7', 'name': 'train'}, 'flowchartId': 'train', 'head': True, 'input': {'features': ['elemental_ratio:Si', 'elemental_ratio:Ge', 'ionization_potential:Ge', 'ionization_potential:Si'], 'targets': ['band_gaps:indirect', 'band_gaps:direct']}, 'name': 'train', 'status': 'idle', 'type': 'execution'}, 'path': 'software_directory/ml/unit/execution/train'}, {'data': {'application': {'name': 'exabyteml', 'shortName': 'ml', 'summary': 'exabyte machine learning engine', 'version': '0.2.0'}, 'flavor': {'executableId': '4987JFJ3kKbwvFSG7', 'name': 'initialize'}, 'flowchartId': 'initialize', 'head': True, 'input': {'targets': ['band_gaps:indirect', 'band_gaps:direct']}, 'name': 'initialize', 'status': 'idle', 'type': 'execution'}, 'path': 'software_directory/ml/unit/execution/initialize'}, {'data': {'application': {'name': 'exabyteml', 'shortName': 'ml', 'summary': 'exabyte machine learning engine', 'version': '0.2.0'}, 'flavor': {'executableId': '4987JFJ3kKbwvFSG7', 'name': 'cross-validate'}, 'flowchartId': 'evaluate', 'head': True, 'input': {'nSplits': 3}, 'name': 'evaluate', 'status': 'idle', 'type': 'execution'}, 'path': 'software_directory/ml/unit/execution/evaluate/cross-validate'}, {'data': {'name': 'PW-NCPP (Davidson Diagonalization, Gaussian Smearing)', 'path': '/qm/wf/pw:/qm/wf/psp/nc?functional=pbe:/qm/wf/smearing/gaussian:/linalg/diag/davidson', 'units': [{'name': 'Plane-wave', 'path': '/qm/wf/pw', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'pw'}}, {'name': 'Norm-conserving PSP', 'path': '/qm/wf/psp/nc?functional=pbe', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'psp', 'subtype': 'nc'}, 'parameters': {'functional': 'pbe'}}, {'name': 'Gaussian Smearing method', 'path': '/qm/wf/smearing/gaussian', 'categories': {'tier1': 'qm', 'tier2': 'wf', 'type': 'smearing', 'subtype': 'gaussian'}}, {'name': 'Davidson Diagonalization', 'path': '/linalg/diag/davidson', 'categories': {'tier1': 'linalg', 'tier2': 'diag', 'type': 'davidson'}}]}, 'path': 'method/categorized_method'}, {'data': {'basisSlug': '6-311G'}, 'path': 'method/method_parameters'}])) \ No newline at end of file +EXAMPLES = json.loads(json.dumps([{'data': {'method': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'subtype': 'gga', 'type': 'dft'}, 'path': 'model'}, {'data': {'_id': 'FPjAaKfuYAL7tiHbm', 'createdAt': '2018-11-19 06:41:46.877Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'exabyteId': 'qKtTzu9utCo6ac4n7', 'hash': 'f4fd707d2e47c15f8d786cf159040954', 'isDefault': True, 'name': 'workflow', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'properties': ['band_structure'], 'schemaVersion': '0.2.0', 'slug': 'workflow', 'subworkflows': [{'_id': 'LCthJ6E2QabYCZqf4', 'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1', 'hasAdvancedComputeOptions': True}, 'model': {'method': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'subtype': 'gga', 'type': 'dft'}, 'name': 'Band Structure', 'properties': ['band_structure'], 'units': [{'flowchartId': 'pw-scf', 'head': True, 'name': 'pw_scf', 'status': 'idle', 'type': 'execution', 'tags': ['test-tags']}]}], 'tags': ['workflow'], 'units': [{'_id': 'LCthJ6E2QabYCZqf4', 'flowchartId': '05c362dc27ff1bb98d16fd60', 'type': 'subworkflow'}]}, 'path': 'workflow'}, {'data': {'_id': 'tvFyik5699io8khi8', 'chargeRate': {'rate': 2}, 'createdAt': '2019-01-03T23:52:26.809Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'description': 'Default project', 'gid': 3000000, 'isDefault': True, 'name': 'Default', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'schemaVersion': '0.2.0', 'slug': 'exadmin-default', 'tags': [], 'updatedAt': '2019-01-04T00:12:37.316Z'}, 'path': 'project'}, {'data': {'_id': 'FPjAaKfuYAL7tiHbm', '_material': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Material', 'slug': 'silicon-fcc'}, '_project': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Project', 'slug': 'project-default'}, 'compute': {'arguments': {'nband': 1, 'npools': 1, 'ntg': 1}, 'cluster': {'fqdn': 'master-1-staging.exabyte.io', 'jid': '1234.master-1-staging.exabyte.io'}, 'email': 'demo@exabyte.io', 'errors': [{'domain': 'rupy', 'message': 'File Not Found: /home/demo/data/project1/job-123/job-config.json', 'reason': 'FileNotFound'}], 'excludeFilesPattern': '^.*.txt$', 'maxCPU': 36, 'nodes': 1, 'notify': 'abe', 'ppn': 1, 'queue': 'OF', 'timeLimit': '00:05:00'}, 'createdAt': '2018-11-19 06:41:46.877Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'name': 'job', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'schemaVersion': '0.2.0', 'slug': 'job', 'status': 'pre-submission', 'workflow': {'_id': 'FPjAaKfuYAL7tiHbm', 'createdAt': '2018-11-19 06:41:46.877Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'exabyteId': 'qKtTzu9utCo6ac4n7', 'hash': 'f4fd707d2e47c15f8d786cf159040954', 'isDefault': True, 'name': 'workflow', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'properties': ['band_structure'], 'schemaVersion': '0.2.0', 'slug': 'workflow', 'subworkflows': [{'_id': 'LCthJ6E2QabYCZqf4', 'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1', 'hasAdvancedComputeOptions': True}, 'model': {'method': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'subtype': 'gga', 'type': 'dft'}, 'name': 'Band Structure', 'properties': ['band_structure'], 'units': [{'flowchartId': 'pw-scf', 'head': True, 'name': 'pw_scf', 'status': 'idle', 'type': 'execution', 'tags': ['test-tags']}]}], 'tags': ['workflow'], 'units': [{'_id': 'LCthJ6E2QabYCZqf4', 'flowchartId': '05c362dc27ff1bb98d16fd60', 'type': 'subworkflow'}]}}, 'path': 'job'}, {'data': {'_id': 'LCthJ6E2QabYCZqf3', 'basis': {'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}], 'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}], 'name': 'basis', 'units': 'crystal'}, 'createdAt': '2016-04-03T05:25:37.430Z', 'creator': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'User', 'slug': 'exadmin'}, 'derivedProperties': [{'name': 'volume', 'units': 'angstrom^3', 'value': 131.1}, {'name': 'density', 'units': 'g/cm^3', 'value': 2.33}, {'name': 'symmetry', 'spaceGroupSymbol': 'Fd-3m', 'tolerance': {'units': 'angstrom', 'value': 0.3}}, {'degree': 10, 'name': 'p-norm', 'value': 0.71}, {'element': 'Si', 'name': 'elemental_ratio', 'value': 0.71}, {'name': 'inchi', 'value': ''}, {'name': 'inchi_key', 'value': ''}], 'exabyteId': 'RKiswuxHKkF3uvLyA', 'formula': 'Si', 'hash': '4ac3fa057e3530628eb1295c77110eaa', 'isDefault': False, 'isNonPeriodic': False, 'lattice': {'name': 'lattice', 'vectors': {'a': [5.0, 0.000121312, 0.000131415], 'alat': 1.0, 'b': [0.000121312, 5.0, 0.000121314], 'c': [0.000121313, 0.000121312, 5.0], 'units': 'angstrom'}, 'a': 5.14, 'alpha': 90.0, 'b': 5.14, 'beta': 90.0, 'c': 5.14, 'gamma': 90.0, 'type': 'CUB', 'units': {'angle': 'degree', 'length': 'angstrom'}}, 'name': 'Silicon FCC', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'scaledHash': '5bd4eb168e3530628eb1295d88221cbb', 'schemaVersion': '0.2.0', 'slug': 'silicon-fcc', 'unitCellFormula': 'Si2', 'updatedAt': '2016-04-04T17:58:42.867Z'}, 'path': 'material'}, {'data': {'data': {'pseudo': []}, 'subtype': 'us', 'type': 'pseudopotential'}, 'path': 'method'}, {'data': {'properties': [{'name': 'atomic_radius', 'value': 4}, {'name': 'electronegativity', 'value': 1.1}, {'name': 'ionization_potential', 'value': 7.7}], 'symbol': 'Si'}, 'path': 'element'}, {'data': {'_id': 'nDAavgjrT5ezwFgod', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'title': 'My Calculation'}, 'path': 'core/reference'}, {'data': {'xDataArray': [0, 1, 2], 'yDataSeries': [[0, 0.5, 1], [0, 2.5, 5]]}, 'path': 'core/abstract/2d_data'}, {'data': [[1, 0, 0], [0, 1, 0], [0, 0, 1]], 'path': 'core/abstract/3d_tensor'}, {'data': {'dimensions': [2, 2, 2], 'shifts': [0, 0, 0]}, 'path': 'core/abstract/3d_grid'}, {'data': {'a': [5.0, 0.0, 0.0], 'b': [0.0, 5.0, 0.0], 'c': [0.0, 0.0, 5.0]}, 'path': 'core/abstract/3d_vector_basis'}, {'data': [0.0, 5.5, 0.0], 'path': 'core/abstract/point'}, {'data': {'xAxis': {'label': 'kpoint index'}, 'xDataArray': [0, 1, 2], 'yAxis': {'label': 'eigenvalues', 'units': 'eV'}, 'yDataSeries': [[0, 0.5, 1], [0, 2.5, 5]]}, 'path': 'core/abstract/2d_plot'}, {'data': [1.0, 0.0, 0.0], 'path': 'core/abstract/vector'}, {'data': [1.0, 0.0, 0.0], 'path': 'core/primitive/array_of_3_numbers'}, {'data': {'a': 5.14, 'alpha': 90.0, 'b': 5.14, 'beta': 90.0, 'c': 5.14, 'gamma': 90.0}, 'path': 'core/primitive/3d_lattice'}, {'data': [True, False, False], 'path': 'core/primitive/array_of_3_booleans'}, {'data': [[0, 0.5, 1], [0, 2.5, 5]], 'path': 'core/primitive/1d_data_series'}, {'data': {'value': 'example string'}, 'path': 'core/primitive/string'}, {'data': {'label': 'energy', 'units': 'eV'}, 'path': 'core/primitive/axis'}, {'data': [{'id': 1}, {'id': 2}], 'path': 'core/primitive/array_of_ids'}, {'data': {'value': 0.1}, 'path': 'core/primitive/scalar'}, {'data': {'authors': [{'affiliation': 'Exabyte Inc.', 'first': 'John', 'last': 'Doe'}], 'doi': '10.1000/xyz123'}, 'path': 'core/reference/literature'}, {'data': {'_id': 'nDAavgjrT5ezwFgod', 'owner': {'_id': 'HtxACY2wX4b2hS8Rv', 'cls': 'Account', 'slug': 'exabyte'}, 'title': 'My Calculation'}, 'path': 'core/reference/modeling'}, {'data': {'authors': [{'affiliation': 'Exabyte Inc.', 'first': 'John', 'last': 'Doe'}], 'conditions': [{'name': 'pressure', 'scalar': [{'value': '1.2'}, {'value': '3.3'}], 'units': 'kbar'}], 'method': 'DFT', 'references': [{'authors': [{'affiliation': 'Exabyte Inc.', 'first': 'John', 'last': 'Doe'}], 'doi': '10.1000/xyz123'}], 'timestamp': 141182979832, 'title': 'Experiment 1'}, 'path': 'core/reference/experiment'}, {'data': 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