mat3ra-esse 2024.4.19.post0__tar.gz → 2024.4.19.post1__tar.gz

{mat3ra_esse-2024.4.19.post0 → mat3ra_esse-2024.4.19.post1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mat3ra-esse
-Version: 2024.4.19.post0
+Version: 2024.4.19.post1
 Summary: Excellent Source of Schemas and Examples.
 Author-email: "Exabyte Inc." <info@mat3ra.com>
 License: # LICENSE

{mat3ra_esse-2024.4.19.post0 → mat3ra_esse-2024.4.19.post1}/schema/methods_category/physical/qm/wf/enum_options.json

@@ -34,6 +34,7 @@
         "enum": [
             "us",
             "nc",
+            "nc-fr",
             "paw",
             "coulomb"
         ]

{mat3ra_esse-2024.4.19.post0 → mat3ra_esse-2024.4.19.post1}/schema/methods_category/physical/qm/wf/enum_options.yml

@@ -20,6 +20,7 @@ pseudization:
 pseudoSubtypes:
   - us # ultra-soft
   - nc # norm-conserving
+  - nc-fr # norm-conserving full-relativistic
   - paw # projector augmented wave
   - coulomb # Coulomb potential
 #

mat3ra_esse-2024.4.19.post1/src/py/mat3ra/esse/data/examples.py

@@ -0,0 +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': [{'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1', 'hasAdvancedComputeOptions': True}, 'compute': None, 'executable': {'advancedComputeOptions': True, 'applicationId': ['eaJepm4AWfqpaCw59'], 'isDefault': True, 'monitors': [{'name': 'standard_output'}], 'name': 'pw.x', 'postProcessors': [], 'preProcessors': [], 'results': [{'name': 'atomic_forces'}]}, 'flavor': {'executableId': '4987JFJ3kKbwvFSG7', 'input': [{'templateId': 'dJ7HYz5pQ4AuN5qc9'}], 'name': 'pw_scf'}, 'flowchartId': 'execution', 'head': True, 'input': [{'content': 'K_POINTS automatic\n2 2 2 0 0 0', 'name': 'pw_scf.in'}], 'monitors': [{'name': 'scf_accuracy'}, {'name': 'standard_output'}], 'name': 'execution', 'next': 'pw-bands', 'postProcessors': [], 'preProcessors': [], 'results': [{'name': 'harris_foulkes_estimate'}], 'status': 'idle', 'type': 'execution'}]}], 'tags': ['workflow'], 'units': [{'_id': 'LCthJ6E2QabYCZqf4', 'flowchartId': '05c362dc27ff1bb98d16fd60', 'type': 'subworkflow', 'name': 'subworkflow unit'}]}, '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': [{'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1', 'hasAdvancedComputeOptions': True}, 'compute': None, 'executable': {'advancedComputeOptions': True, 'applicationId': ['eaJepm4AWfqpaCw59'], 'isDefault': True, 'monitors': [{'name': 'standard_output'}], 'name': 'pw.x', 'postProcessors': [], 'preProcessors': [], 'results': [{'name': 'atomic_forces'}]}, 'flavor': {'executableId': '4987JFJ3kKbwvFSG7', 'input': [{'templateId': 'dJ7HYz5pQ4AuN5qc9'}], 'name': 'pw_scf'}, 'flowchartId': 'execution', 'head': True, 'input': [{'content': 'K_POINTS automatic\n2 2 2 0 0 0', 'name': 'pw_scf.in'}], 'monitors': [{'name': 'scf_accuracy'}, {'name': 'standard_output'}], 'name': 'execution', 'next': 'pw-bands', 'postProcessors': [], 'preProcessors': [], 'results': [{'name': 'harris_foulkes_estimate'}], 'status': 'idle', 'type': 'execution'}]}], 'tags': ['workflow'], 'units': [{'_id': 'LCthJ6E2QabYCZqf4', 'flowchartId': '05c362dc27ff1bb98d16fd60', 'type': 'subworkflow', 'name': 'subworkflow unit'}]}}, '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': {'phi': {'nelect': 48, 'phi': 4.73414095269429, 'scf_vbm': -1.6519, 'scf_cbm': -1.6472, 'Ef': -1.97822464, 'scf_gap': 0.0, 'avg_max': 2.7559163126942896, 'scf_dir': False}, 'atoms': {'lattice_mat': [[3.353617811446221, 0.0, 0.0], [0.0, 6.273423021773385, 0.0], [0.0, 0.0, 33.313518]], 'coords': [[0.0, 0.6004615456553349, 0.2002745956304112], [0.5, 0.9651745521229684, 0.205389889617873], [0.0, 0.8600702878546368, 0.2642586539633663], [0.5, 0.3508476059345406, 0.2471701152668883], [0.5, 0.7055702442093444, 0.1414059027438078], [0.0, 0.2147957642231673, 0.1584938427776558]], 'elements': ['Mo', 'Mo', 'Te', 'Te', 'Te', 'Te'], 'abc': [3.35362, 6.27342, 33.31352], 'angles': [90.0, 90.0, 90.0], 'cartesian': False, 'props': ['', '', '', '', '', '']}, 'jid': 'JVASP-677'}, 'path': '3pse/db/nist_jarvis/2024.3.13/db_entry'}, {'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, 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'workflow/unit/assignment'}, {'data': {'flowchartId': 'data_transformation_manipulation', 'inputData': {'cleanMissingData': True, 'removeDuplicateRows': True, 'replaceNoneValuesWith': 0}, 'name': 'data_transformation_manipulation', 'operation': 'data_transformation', 'operationType': 'manipulation', 'status': 'idle', 'type': 'processing'}, 'path': 'workflow/unit/processing'}, {'data': {'flowchartId': 'reduce', 'head': True, 'input': [{'arguments': ['band_gaps'], 'operation': 'aggregate'}], 'mapFlowchartId': '1', 'name': 'reduce', 'status': 'idle', 'type': 'reduce'}, 'path': 'workflow/unit/reduce'}, {'data': {'flowchartId': 'io', 'head': True, 'input': [{'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': 'io', 'source': 'api', 'status': 'idle', 'subtype': 'input', 'type': 'io'}, 'path': 'workflow/unit/io'}, {'data': {'flowchartId': 'map', 'head': True, 'input': {'target': 'MAP_K_POINTS_1', 'values': ['2 2 2 0 0 0', '3 3 3 0 0 0', '4 4 4 0 0 0']}, 'name': 'map', 'status': 'idle', 'type': 'map', 'workflowId': 'zxjhEiaQvwWwvB3oM'}, 'path': 'workflow/unit/map'}, {'data': {'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '5.1.1', 'hasAdvancedComputeOptions': True}, 'compute': None, 'executable': {'advancedComputeOptions': True, 'applicationId': ['eaJepm4AWfqpaCw59'], 'isDefault': True, 'monitors': [{'name': 'standard_output'}], 'name': 'pw.x', 'postProcessors': [], 'preProcessors': [], 'results': [{'name': 'atomic_forces'}]}, 'flavor': {'executableId': '4987JFJ3kKbwvFSG7', 'input': [{'templateId': 'dJ7HYz5pQ4AuN5qc9'}], 'name': 'pw_scf'}, 'flowchartId': 'execution', 'head': True, 'input': [{'content': 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{'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', 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'software_directory/modeling/vasp'}, {'data': {'application': {'name': 'espresso', 'shortName': 'qe', 'summary': 'Quantum Espresso', 'version': '7.2'}, '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'}]))

mat3ra_esse-2024.4.19.post1/src/py/mat3ra/esse/data/properties.py

@@ -0,0 +1,3 @@
+import json
+PROPERTIES_MANIFEST = json.loads(json.dumps({'convergence_ionic': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/workflow/convergence/ionic', 'isMonitor': True}, 'convergence_electronic': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/workflow/convergence/electronic', 'isMonitor': True}, 'pressure': {'defaults': {'units': 'kbar'}, 'schemaId': 'properties-directory/scalar/pressure', 'isResult': True}, 'total_energy': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/scalar/total-energy', 'isResult': True}, 'surface_energy': {'defaults': {'units': 'eV/A^2'}, 'schemaId': 'properties-directory/scalar/surface-energy', 'isResult': True}, 'fermi_energy': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/scalar/fermi-energy', 'isResult': True}, 'total_force': {'defaults': {'units': 'eV/angstrom'}, 'schemaId': 'properties-directory/scalar/total-force', 'isResult': True}, 'zero_point_energy': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/scalar/zero-point-energy', 'isResult': True}, 'reaction_energy_barrier': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/scalar/reaction-energy-barrier', 'isResult': True}, 'electron_affinity': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/scalar/electron-affinity', 'isResult': True}, 'ionization_potential': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/scalar/ionization-potential', 'isResult': True}, 'valence_band_offset': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/scalar/valence-band-offset'}, 'phonon_dos': {'defaults': {'xAxis': {'label': 'frequency', 'units': 'cm-1'}, 'yAxis': {'label': 'Phonon DOS', 'units': 'states/cm-1'}}, 'schemaId': 'properties-directory/non-scalar/phonon-dos', 'isResult': True}, 'phonon_dispersions': {'defaults': {'xAxis': {'label': 'qpoints', 'units': 'crystal'}, 'yAxis': {'label': 'frequency', 'units': 'cm-1'}}, 'schemaId': 'properties-directory/non-scalar/phonon-dispersions', 'isResult': True}, 'total_energy_contributions': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/non-scalar/total-energy-contributions', 'isResult': True}, 'band_gaps': {'types': ['direct', 'indirect'], 'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/non-scalar/band-gaps', 'isResult': True}, 'stress_tensor': {'defaults': {'units': 'kbar'}, 'schemaId': 'properties-directory/non-scalar/stress-tensor', 'isResult': True}, 'band_structure': {'defaults': {'xAxis': {'label': 'kpoints', 'units': 'crystal'}, 'yAxis': {'label': 'energy', 'units': 'eV'}}, 'schemaId': 'properties-directory/non-scalar/band-structure', 'isResult': True}, 'density_of_states': {'defaults': {'xAxis': {'label': 'energy', 'units': 'eV'}, 'yAxis': {'label': 'density of states', 'units': 'states/unitcell'}}, 'schemaId': 'properties-directory/non-scalar/density-of-states', 'isResult': True}, 'reaction_energy_profile': {'defaults': {'xAxis': {'label': 'reaction coordinate'}, 'yAxis': {'label': 'energy', 'units': 'eV'}}, 'schemaId': 'properties-directory/non-scalar/reaction-energy-profile', 'isResult': True}, 'potential_profile': {'defaults': {'xAxis': {'label': 'z coordinate'}, 'yAxis': {'label': 'energy', 'units': 'eV'}}, 'schemaId': 'properties-directory/non-scalar/potential-profile', 'isResult': True}, 'charge_density_profile': {'defaults': {'xAxis': {'label': 'z coordinate'}, 'yAxis': {'label': 'charge density', 'units': 'e/A'}}, 'schemaId': 'properties-directory/non-scalar/charge-density-profile', 'isResult': True}, 'vibrational_spectrum': {'defaults': {'xAxis': {'label': 'wavenumber', 'units': 'cm-1'}, 'yAxis': {'label': 'Absorption coefficient', 'units': 'km/mol'}}, 'schemaId': 'properties-directory/non-scalar/vibrational-spectrum', 'isResult': True}, 'file_content': {'schemaId': 'properties-directory/non-scalar/file-content', 'isResult': True}, 'average_potential_profile': {'defaults': {'xAxis': {'label': 'z coordinate', 'units': 'angstrom'}, 'yAxis': {'label': 'energy', 'units': 'eV'}}, 'schemaId': 'properties-directory/non-scalar/average-potential-profile', 'isResult': True}, 'dielectric_tensor': {'schemaId': 'properties-directory/non-scalar/dielectric-tensor', 'isResult': True}, 'basis': {'defaults': {'units': 'angstrom'}, 'schemaId': 'properties-directory/structural/basis'}, 'lattice': {'defaults': {'units': 'angstrom'}, 'schemaId': 'properties-directory/structural/lattice'}, 'atomic_forces': {'defaults': {'units': 'eV/angstrom'}, 'schemaId': 'properties-directory/structural/atomic-forces', 'isResult': True}, 'atomic_constraints': {'schemaId': 'properties-directory/structural/basis/atomic-constraints'}, 'p-norm': {'schemaId': 'properties-directory/structural/p-norm'}, 'volume': {'defaults': {'units': 'angstrom^3'}, 'schemaId': 'properties-directory/structural/volume'}, 'symmetry': {'defaults': {'units': 'angstrom'}, 'schemaId': 'properties-directory/structural/symmetry'}, 'elemental_ratio': {'schemaId': 'properties-directory/structural/elemental-ratio'}, 'density': {'defaults': {'units': 'g/cm^3'}, 'schemaId': 'properties-directory/structural/density'}, 'magnetic_moments': {'defaults': {'units': 'uB'}, 'schemaId': 'properties-directory/structural/magnetic-moments', 'isResult': True}, 'bonds': {'defaults': {'units': 'angstrom'}, 'schemaId': 'properties-directory/structural/basis/bonds'}, 'inchi': {'schemaId': 'properties-directory/structural/inchi'}, 'inchi_key': {'schemaId': 'properties-directory/structural/inchi-key'}, 'material': {'schemaId': 'material'}, 'hubbard_u': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/non-scalar/hubbard-u', 'isResult': True}, 'hubbard_v': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/non-scalar/hubbard-v', 'isResult': True}, 'hubbard_v_nn': {'defaults': {'units': 'eV'}, 'schemaId': 'properties-directory/non-scalar/hubbard-v-nn', 'isResult': True}}))
+RESULTS = json.loads(json.dumps(['pressure', 'total_energy', 'surface_energy', 'fermi_energy', 'total_force', 'zero_point_energy', 'reaction_energy_barrier', 'electron_affinity', 'ionization_potential', 'phonon_dos', 'phonon_dispersions', 'total_energy_contributions', 'band_gaps', 'stress_tensor', 'band_structure', 'density_of_states', 'reaction_energy_profile', 'potential_profile', 'charge_density_profile', 'vibrational_spectrum', 'file_content', 'average_potential_profile', 'dielectric_tensor', 'atomic_forces', 'magnetic_moments', 'hubbard_u', 'hubbard_v', 'hubbard_v_nn']))