@mat3ra/esse 2024.2.6-0 → 2024.2.19-0

package/lib/js/example/3pse/file/applications/espresso/7.2/pw.x.json

@@ -0,0 +1,94 @@
+{
+    "&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
+            ],
+            [
+                1,
+                2,
+                0.02
+            ]
+        ]
+    },
+    "&ELECTRONS": {
+        "diagonalization": "david",
+        "diago_david_ndim": 4,
+        "diago_full_acc": true,
+        "mixing_beta": 0.3,
+        "startingwfc": "atomic+random"
+    },
+    "&IONS": null,
+    "&CELL": null,
+    "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,
+                2.496799
+            ],
+            "v2": [
+                1.441527575,
+                4.077255694,
+                2.496799
+            ],
+            "v3": [
+                0,
+                0,
+                4.993598
+            ]
+        }
+    },
+    "K_POINTS": {
+        "card_option": "automatic",
+        "values": {
+            "nk1": 2,
+            "nk2": 2,
+            "nk3": 2,
+            "sk1": 0,
+            "sk2": 0,
+            "sk3": 0
+        }
+    }
+}

package/lib/js/example/core/abstract/2d_data.json

@@ -0,0 +1,19 @@
+{
+    "xDataArray": [
+        0,
+        1,
+        2
+    ],
+    "yDataSeries": [
+        [
+            0,
+            0.5,
+            1
+        ],
+        [
+            0,
+            2.5,
+            5
+        ]
+    ]
+}

package/lib/js/example/core/abstract/2d_plot.json

@@ -0,0 +1,26 @@
+{
+    "xAxis": {
+        "label": "kpoint index"
+    },
+    "xDataArray": [
+        0,
+        1,
+        2
+    ],
+    "yAxis": {
+        "label": "eigenvalues",
+        "units": "eV"
+    },
+    "yDataSeries": [
+        [
+            0,
+            0.5,
+            1
+        ],
+        [
+            0,
+            2.5,
+            5
+        ]
+    ]
+}

package/lib/js/example/core/abstract/3d_grid.json

@@ -0,0 +1,12 @@
+{
+    "dimensions": [
+        2,
+        2,
+        2
+    ],
+    "shifts": [
+        0,
+        0,
+        0
+    ]
+}

package/lib/js/example/core/abstract/3d_tensor.json

@@ -0,0 +1,17 @@
+[
+    [
+        1,
+        0,
+        0
+    ],
+    [
+        0,
+        1,
+        0
+    ],
+    [
+        0,
+        0,
+        1
+    ]
+]

package/lib/js/example/core/abstract/3d_vector_basis.json

@@ -0,0 +1,17 @@
+{
+    "a": [
+        5,
+        0,
+        0
+    ],
+    "b": [
+        0,
+        5,
+        0
+    ],
+    "c": [
+        0,
+        0,
+        5
+    ]
+}

package/lib/js/example/core/abstract/point.json

@@ -0,0 +1,5 @@
+[
+    0,
+    5.5,
+    0
+]

package/lib/js/example/core/abstract/vector.json

@@ -0,0 +1,5 @@
+[
+    1,
+    0,
+    0
+]

package/lib/js/example/core/primitive/1d_data_series.json

@@ -0,0 +1,12 @@
+[
+    [
+        0,
+        0.5,
+        1
+    ],
+    [
+        0,
+        2.5,
+        5
+    ]
+]

package/lib/js/example/core/primitive/3d_lattice.json

@@ -0,0 +1,8 @@
+{
+    "a": 5.14,
+    "alpha": 90,
+    "b": 5.14,
+    "beta": 90,
+    "c": 5.14,
+    "gamma": 90
+}

package/lib/js/example/core/primitive/array_of_3_booleans.json

@@ -0,0 +1,5 @@
+[
+    true,
+    false,
+    false
+]

package/lib/js/example/core/primitive/array_of_3_numbers.json

@@ -0,0 +1,5 @@
+[
+    1,
+    0,
+    0
+]

package/lib/js/example/core/primitive/array_of_ids.json

@@ -0,0 +1,8 @@
+[
+    {
+        "id": 1
+    },
+    {
+        "id": 2
+    }
+]

package/lib/js/example/core/primitive/axis.json

@@ -0,0 +1,4 @@
+{
+    "label": "energy",
+    "units": "eV"
+}

package/lib/js/example/core/primitive/scalar.json

@@ -0,0 +1,3 @@
+{
+    "value": 0.1
+}

package/lib/js/example/core/primitive/string.json

@@ -0,0 +1,3 @@
+{
+    "value": "example string"
+}

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

@@ -0,0 +1,12 @@
+{
+    "name": "pressure",
+    "scalar": [
+        {
+            "value": "1.2"
+        },
+        {
+            "value": "3.3"
+        }
+    ],
+    "units": "kbar"
+}

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

@@ -0,0 +1,4 @@
+{
+    "latitude": 24.3423424,
+    "longitude": 43.234232
+}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

package/lib/js/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/lib/js/example/element.json

@@ -0,0 +1,17 @@
+{
+    "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

@@ -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/lib/js/example/job.json

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