@mat3ra/esse 2023.12.25-2

package/example/core/reference/modeling.json

@@ -0,0 +1,3 @@
+{
+    "...": "include(modeling/exabyte.json)"
+}

package/example/core/reference.json

@@ -0,0 +1,3 @@
+{
+    "...": "include(reference/modeling.json)"
+}

package/example/core/reusable/atomic_vectors.json

@@ -0,0 +1,18 @@
+[
+    {
+        "id": 1,
+        "value": [
+            0,
+            0,
+            0
+        ]
+    },
+    {
+        "id": 2,
+        "value": [
+            0.25,
+            0.25,
+            0.25
+        ]
+    }
+]

package/example/core/reusable/band_gap.json

@@ -0,0 +1,16 @@
+{
+    "kpointConduction": [
+        0,
+        0,
+        0
+    ],
+    "kpointValence": [
+        0,
+        0,
+        0
+    ],
+    "name": "band_gap",
+    "type": "direct",
+    "units": "rydberg",
+    "value": 0.0947
+}

package/example/core/reusable/energy.json

@@ -0,0 +1,5 @@
+{
+    "name": "zero_point_energy",
+    "units": "eV",
+    "value": -0.0634
+}

package/example/core/reusable/file_metadata.json

@@ -0,0 +1,5 @@
+{
+    "pathname": "/path/to/file/",
+    "basename": "some_file.png",
+    "filetype": "image"
+}

package/example/core/reusable/object_storage_container_data.json

@@ -0,0 +1,8 @@
+{
+    "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"
+}

package/example/element.json

@@ -0,0 +1,14 @@
+{
+    "properties": [
+        {
+            "...": "include(properties_directory/elemental/atomic_radius.json)"
+        },
+        {
+            "...": "include(properties_directory/elemental/electronegativity.json)"
+        },
+        {
+            "...": "include(properties_directory/elemental/ionization_potential.json)"
+        }
+    ],
+    "symbol": "Si"
+}

package/example/job/compute.json

@@ -0,0 +1,26 @@
+{
+    "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"
+}

package/example/job.json

@@ -0,0 +1,26 @@
+{
+    "_id": "FPjAaKfuYAL7tiHbm",
+    "_material": {
+        "...": "include(system/_material.json)"
+    },
+    "_project": {
+        "...": "include(system/_project.json)"
+    },
+    "compute": {
+        "...": "include(job/compute.json)"
+    },
+    "createdAt": "2018-11-19 06:41:46.877Z",
+    "creator": {
+        "...": "include(system/creator.json)"
+    },
+    "name": "job",
+    "owner": {
+        "...": "include(system/owner.json)"
+    },
+    "schemaVersion": "0.2.0",
+    "slug": "job",
+    "status": "pre-submission",
+    "workflow": {
+        "...": "include(workflow.json)"
+    }
+}

package/example/material.json

@@ -0,0 +1,94 @@
+{
+    "_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": {
+        "...": "include(system/creator.json)"
+    },
+    "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": {
+        "...": "include(properties_directory/structural/lattice.json)"
+    },
+    "name": "Silicon FCC",
+    "owner": {
+        "...": "include(system/owner.json)"
+    },
+    "scaledHash": "5bd4eb168e3530628eb1295d88221cbb",
+    "schemaVersion": "0.2.0",
+    "slug": "silicon-fcc",
+    "unitCellFormula": "Si2",
+    "updatedAt": "2016-04-04T17:58:42.867Z"
+}

package/example/method/categorized_method.json

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+{
+    "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"
+            }
+        }
+    ]
+}

package/example/method/method_parameters.json

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+{
+    "basisSlug": "6-311G"
+}

package/example/method.json

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+{
+    "data": {
+        "pseudo": []
+    },
+    "subtype": "us",
+    "type": "pseudopotential"
+}

package/example/methods_directory/legacy/localorbital.json

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+{
+    "type": "localorbital",
+    "subtype": "pople"
+}

package/example/methods_directory/legacy/pseudopotential.json

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+{
+    "type": "pseudopotential",
+    "subtype": "us"
+}

package/example/methods_directory/legacy/regression.json

@@ -0,0 +1,61 @@
+{
+    "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"
+}

package/example/methods_directory/legacy/unknown.json

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+{
+    "type": "unknown",
+    "subtype": "unknown"
+}

package/example/methods_directory/mathematical/cg.json

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+{
+    "name": "Conjugate gradient method",
+    "path": "/opt/diff/ordern/cg",
+    "categories": {
+        "tier1": "opt",
+        "tier2": "diff",
+        "tier3": "ordern",
+        "type": "cg"
+    }
+}

package/example/methods_directory/mathematical/regression.json

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+{
+    "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"
+}

package/example/methods_directory/physical/ao/dunning.json

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+{
+    "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"
+    }
+}

package/example/methods_directory/physical/psp/file.json

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+{
+    "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"
+    }
+}

package/example/methods_directory/physical/psp.json

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+{
+    "name": "PAW Pseudopotential method",
+    "path": "/qm/wf/psp/paw",
+    "slug": "pseudopotential",
+    "categories": {
+        "tier1": "qm",
+        "tier2": "wf",
+        "type": "psp",
+        "subtype": "paw"
+    },
+    "data": [
+        {
+            "...": "include(psp/file.json)"
+        }
+    ]
+}

package/example/methods_directory/physical/pw.json

@@ -0,0 +1,9 @@
+{
+    "name": "Plane wave basis",
+    "path": "/qm/wf/pw",
+    "categories": {
+        "tier1": "qm",
+        "tier2": "wf",
+        "type": "pw"
+    }
+}

package/example/methods_directory/physical/smearing.json

@@ -0,0 +1,10 @@
+{
+    "name": "Methfessel-Paxton smearing",
+    "path": "/qm/wf/smearing/methfessel-paxton",
+    "categories": {
+        "tier1": "qm",
+        "tier2": "wf",
+        "type": "smearing",
+        "subtype": "methfessel-paxton"
+    }
+}

package/example/methods_directory/physical/tetrahedron.json

@@ -0,0 +1,10 @@
+{
+    "name": "Optimized Tetrahedron method (Kawamura)",
+    "path": "/qm/wf/tetrahedron/optimized",
+    "categories": {
+        "tier1": "qm",
+        "tier2": "wf",
+        "type": "tetrahedron",
+        "subtype": "optimized"
+    }
+}

package/example/model/categorized_model.json

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+{
+    "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": {
+        "...": "include(../method/categorized_method.json)"
+    }
+}

package/example/model/model_parameters.json

@@ -0,0 +1,7 @@
+{
+    "functional": "pbe",
+    "dispersionCorrection": "dft-d3",
+    "hubbardType": "u",
+    "spinPolarization": "collinear",
+    "spinOrbitCoupling": true
+}

package/example/model.json

@@ -0,0 +1,7 @@
+{
+    "method": {
+        "...": "include(method.json)"
+    },
+    "subtype": "gga",
+    "type": "dft"
+}

package/example/models_category/pb/qm/abin/gw.json

@@ -0,0 +1,7 @@
+{
+        "tier1": "pb",
+        "tier2": "qm",
+        "tier3": "abin",
+        "type": "gw",
+        "subtype": "evgw"
+    }

package/example/models_category/pb/qm/dft/ksdft.json

@@ -0,0 +1,6 @@
+{
+    "tier1": "pb",
+    "tier2": "qm",
+    "tier3": "dft",
+    "type": "ksdft"
+}

package/example/models_category/pb/qm/semp.json

@@ -0,0 +1,5 @@
+{
+    "tier1": "pb",
+    "tier2": "qm",
+    "tier3": "semp"
+}

package/example/models_directory/gga.json

@@ -0,0 +1,15 @@
+{
+    "name": "PBE-D3 (SOC)",
+    "categories": {
+        "tier1": "pb",
+        "tier2": "qm",
+        "tier3": "dft",
+        "type": "ksdft",
+        "subtype": "gga"
+    },
+    "parameters": {
+        "functional": "pbe",
+        "spinOrbitCoupling": true,
+        "dispersionCorrection": "DFT-D3"
+    }
+}