@mat3ra/esse 2024.3.20-0 → 2024.3.25-0

package/lib/js/example/core/reference/experiment.json

@@ -1,38 +0,0 @@
-{
-    "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"
-}

package/lib/js/example/core/reference/literature/name.json

@@ -1,5 +0,0 @@
-{
-    "affiliation": "Exabyte Inc.",
-    "first": "John",
-    "last": "Doe"
-}

package/lib/js/example/core/reference/literature/pages.json

@@ -1,4 +0,0 @@
-{
-    "end": "2",
-    "start": "1"
-}

package/lib/js/example/core/reference/literature.json

@@ -1,10 +0,0 @@
-{
-    "authors": [
-        {
-            "affiliation": "Exabyte Inc.",
-            "first": "John",
-            "last": "Doe"
-        }
-    ],
-    "doi": "10.1000/xyz123"
-}

package/lib/js/example/core/reference/modeling/exabyte.json

@@ -1,9 +0,0 @@
-{
-    "_id": "nDAavgjrT5ezwFgod",
-    "owner": {
-        "_id": "HtxACY2wX4b2hS8Rv",
-        "cls": "Account",
-        "slug": "exabyte"
-    },
-    "title": "My Calculation"
-}

package/lib/js/example/core/reference/modeling.json

@@ -1,9 +0,0 @@
-{
-    "_id": "nDAavgjrT5ezwFgod",
-    "owner": {
-        "_id": "HtxACY2wX4b2hS8Rv",
-        "cls": "Account",
-        "slug": "exabyte"
-    },
-    "title": "My Calculation"
-}

package/lib/js/example/core/reference.json

@@ -1,9 +0,0 @@
-{
-    "_id": "nDAavgjrT5ezwFgod",
-    "owner": {
-        "_id": "HtxACY2wX4b2hS8Rv",
-        "cls": "Account",
-        "slug": "exabyte"
-    },
-    "title": "My Calculation"
-}

package/lib/js/example/core/reusable/atomic_vectors.json

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

package/lib/js/example/core/reusable/band_gap.json

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

package/lib/js/example/core/reusable/energy.json

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

package/lib/js/example/core/reusable/file_metadata.json

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

package/lib/js/example/core/reusable/object_storage_container_data.json

@@ -1,8 +0,0 @@
-{
-    "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/lib/js/example/element.json

@@ -1,17 +0,0 @@
-{
-    "properties": [
-        {
-            "name": "atomic_radius",
-            "value": 4
-        },
-        {
-            "name": "electronegativity",
-            "value": 1.1
-        },
-        {
-            "name": "ionization_potential",
-            "value": 7.7
-        }
-    ],
-    "symbol": "Si"
-}

package/lib/js/example/job/compute.json

@@ -1,26 +0,0 @@
-{
-    "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/lib/js/example/job.json

@@ -1,183 +0,0 @@
-{
-    "_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": null,
-                        "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"
-            }
-        ]
-    }
-}

package/lib/js/example/material.json

@@ -1,128 +0,0 @@
-{
-    "_id": "LCthJ6E2QabYCZqf3",
-    "basis": {
-        "coordinates": [
-            {
-                "id": 1,
-                "value": [
-                    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,
-                0.000121312,
-                0.000131415
-            ],
-            "alat": 1,
-            "b": [
-                0.000121312,
-                5,
-                0.000121314
-            ],
-            "c": [
-                0.000121313,
-                0.000121312,
-                5
-            ],
-            "units": "angstrom"
-        },
-        "a": 5.14,
-        "alpha": 90,
-        "b": 5.14,
-        "beta": 90,
-        "c": 5.14,
-        "gamma": 90,
-        "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"
-}

package/lib/js/example/method/categorized_method.json

@@ -1,47 +0,0 @@
-{
-    "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/lib/js/example/method/method_parameters.json

@@ -1,3 +0,0 @@
-{
-    "basisSlug": "6-311G"
-}

package/lib/js/example/method.json

@@ -1,7 +0,0 @@
-{
-    "data": {
-        "pseudo": []
-    },
-    "subtype": "us",
-    "type": "pseudopotential"
-}

package/lib/js/example/methods_directory/legacy/localorbital.json

@@ -1,4 +0,0 @@
-{
-    "type": "localorbital",
-    "subtype": "pople"
-}

package/lib/js/example/methods_directory/legacy/pseudopotential.json

@@ -1,4 +0,0 @@
-{
-    "type": "pseudopotential",
-    "subtype": "us"
-}

package/lib/js/example/methods_directory/legacy/regression.json

@@ -1,61 +0,0 @@
-{
-    "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/lib/js/example/methods_directory/legacy/unknown.json

@@ -1,4 +0,0 @@
-{
-    "type": "unknown",
-    "subtype": "unknown"
-}

package/lib/js/example/methods_directory/mathematical/cg.json

@@ -1,10 +0,0 @@
-{
-    "name": "Conjugate gradient method",
-    "path": "/opt/diff/ordern/cg",
-    "categories": {
-        "tier1": "opt",
-        "tier2": "diff",
-        "tier3": "ordern",
-        "type": "cg"
-    }
-}