@mat3ra/esse 2024.3.25-2 → 2024.3.25-3

package/dist/js/example/workflow/unit/execution.json

@@ -0,0 +1,66 @@
+{
+    "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"
+}

package/dist/js/example/workflow/unit/input/_inputItemScope.json

@@ -0,0 +1,4 @@
+{
+    "name": "N_K_y",
+    "scope": "global"
+}

package/dist/js/example/workflow/unit/io/api.json

@@ -0,0 +1,31 @@
+{
+    "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"
+}

package/dist/js/example/workflow/unit/io/db.json

@@ -0,0 +1,15 @@
+{
+    "features": [
+        "elemental_ratio:Si",
+        "elemental_ratio:Ge",
+        "ionization_potential:Ge",
+        "ionization_potential:Si"
+    ],
+    "ids": [
+        "KuAsBRwofzGfHPWiT"
+    ],
+    "targets": [
+        "band_gaps:indirect",
+        "band_gaps:direct"
+    ]
+}

package/dist/js/example/workflow/unit/io/object_storage.json

@@ -0,0 +1,12 @@
+{
+    "basename": "index.html",
+    "overwrite": true,
+    "objectData": {
+        "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/dist/js/example/workflow/unit/io.json

@@ -0,0 +1,41 @@
+{
+    "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"
+}

package/dist/js/example/workflow/unit/map.json

@@ -0,0 +1,16 @@
+{
+    "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"
+}

package/dist/js/example/workflow/unit/processing.json

@@ -0,0 +1,13 @@
+{
+    "flowchartId": "data_transformation_manipulation",
+    "inputData": {
+        "cleanMissingData": true,
+        "removeDuplicateRows": true,
+        "replaceNoneValuesWith": 0
+    },
+    "name": "data_transformation_manipulation",
+    "operation": "data_transformation",
+    "operationType": "manipulation",
+    "status": "idle",
+    "type": "processing"
+}

package/dist/js/example/workflow/unit/reduce.json

@@ -0,0 +1,16 @@
+{
+    "flowchartId": "reduce",
+    "head": true,
+    "input": [
+        {
+            "arguments": [
+                "band_gaps"
+            ],
+            "operation": "aggregate"
+        }
+    ],
+    "mapFlowchartId": "1",
+    "name": "reduce",
+    "status": "idle",
+    "type": "reduce"
+}

package/dist/js/example/workflow/unit/runtime/runtime_items.json

@@ -0,0 +1,14 @@
+{
+    "monitors": [
+        {
+            "name": "standard_output"
+        }
+    ],
+    "postProcessors": [],
+    "preProcessors": [],
+    "results": [
+        {
+            "name": "atomic_forces"
+        }
+    ]
+}

package/dist/js/example/workflow.json

@@ -0,0 +1,129 @@
+{
+    "_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/dist/js/schema/3pse/db/nist_jarvis/2024.3.13/atoms.json

@@ -0,0 +1,79 @@
+{
+    "$id": "3pse/db/nist-jarvis/2024.3.13/atoms",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "NIST J.A.R.V.I.S. db entry `atoms` key schema. Based on https://figshare.com/articles/dataset/Monolayer_data_for_heterostructure/22344571",
+    "type": "object",
+    "additionalProperties": false,
+    "properties": {
+        "lattice_mat": {
+            "type": "array",
+            "description": "Crystal lattice vectors as a 3x3 matrix, in Angstroms",
+            "minItems": 3,
+            "maxItems": 3,
+            "items": {
+                "$schema": "http://json-schema.org/draft-07/schema#",
+                "title": "array of 3 number elements schema",
+                "type": "array",
+                "minItems": 3,
+                "maxItems": 3,
+                "items": {
+                    "type": "number"
+                }
+            }
+        },
+        "coords": {
+            "type": "array",
+            "description": "Atomic coordinates for each atom in the unit cell",
+            "minItems": 1,
+            "items": {
+                "$schema": "http://json-schema.org/draft-07/schema#",
+                "title": "array of 3 number elements schema",
+                "type": "array",
+                "minItems": 3,
+                "maxItems": 3,
+                "items": {
+                    "type": "number"
+                }
+            }
+        },
+        "elements": {
+            "type": "array",
+            "description": "Atomic elements for each atom in the unit cell in the same order as `coords`",
+            "minItems": 1,
+            "items": {
+                "type": "string"
+            }
+        },
+        "abc": {
+            "$schema": "http://json-schema.org/draft-07/schema#",
+            "title": "array of 3 number elements schema",
+            "type": "array",
+            "minItems": 3,
+            "maxItems": 3,
+            "items": {
+                "type": "number"
+            }
+        },
+        "angles": {
+            "$schema": "http://json-schema.org/draft-07/schema#",
+            "title": "array of 3 number elements schema",
+            "type": "array",
+            "minItems": 3,
+            "maxItems": 3,
+            "items": {
+                "type": "number"
+            }
+        },
+        "cartesian": {
+            "type": "boolean",
+            "description": "True if the coordinates are in Cartesian space, false if in fractional space"
+        },
+        "props": {
+            "type": "array",
+            "description": "Additional properties for each of the atoms",
+            "items": {
+                "type": "string"
+            }
+        }
+    }
+}

package/dist/js/schema/3pse/db/nist_jarvis/2024.3.13/db_entry.json

@@ -0,0 +1,91 @@
+{
+    "$id": "3pse/db/nist-jarvis/2024.3.13/db-entry",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "NIST J.A.R.V.I.S. db entry schema. Based on https://figshare.com/articles/dataset/Monolayer_data_for_heterostructure/22344571",
+    "type": "object",
+    "additionalProperties": true,
+    "properties": {
+        "atoms": {
+            "$schema": "http://json-schema.org/draft-07/schema#",
+            "title": "NIST J.A.R.V.I.S. db entry `atoms` key schema. Based on https://figshare.com/articles/dataset/Monolayer_data_for_heterostructure/22344571",
+            "type": "object",
+            "additionalProperties": false,
+            "properties": {
+                "lattice_mat": {
+                    "type": "array",
+                    "description": "Crystal lattice vectors as a 3x3 matrix, in Angstroms",
+                    "minItems": 3,
+                    "maxItems": 3,
+                    "items": {
+                        "$schema": "http://json-schema.org/draft-07/schema#",
+                        "title": "array of 3 number elements schema",
+                        "type": "array",
+                        "minItems": 3,
+                        "maxItems": 3,
+                        "items": {
+                            "type": "number"
+                        }
+                    }
+                },
+                "coords": {
+                    "type": "array",
+                    "description": "Atomic coordinates for each atom in the unit cell",
+                    "minItems": 1,
+                    "items": {
+                        "$schema": "http://json-schema.org/draft-07/schema#",
+                        "title": "array of 3 number elements schema",
+                        "type": "array",
+                        "minItems": 3,
+                        "maxItems": 3,
+                        "items": {
+                            "type": "number"
+                        }
+                    }
+                },
+                "elements": {
+                    "type": "array",
+                    "description": "Atomic elements for each atom in the unit cell in the same order as `coords`",
+                    "minItems": 1,
+                    "items": {
+                        "type": "string"
+                    }
+                },
+                "abc": {
+                    "$schema": "http://json-schema.org/draft-07/schema#",
+                    "title": "array of 3 number elements schema",
+                    "type": "array",
+                    "minItems": 3,
+                    "maxItems": 3,
+                    "items": {
+                        "type": "number"
+                    }
+                },
+                "angles": {
+                    "$schema": "http://json-schema.org/draft-07/schema#",
+                    "title": "array of 3 number elements schema",
+                    "type": "array",
+                    "minItems": 3,
+                    "maxItems": 3,
+                    "items": {
+                        "type": "number"
+                    }
+                },
+                "cartesian": {
+                    "type": "boolean",
+                    "description": "True if the coordinates are in Cartesian space, false if in fractional space"
+                },
+                "props": {
+                    "type": "array",
+                    "description": "Additional properties for each of the atoms",
+                    "items": {
+                        "type": "string"
+                    }
+                }
+            }
+        },
+        "jid": {
+            "type": "string",
+            "description": "The id of the entry in the database, e.g. JVASP-677"
+        }
+    }
+}

package/dist/js/schema/3pse/file/applications/espresso/7.2/pw.x/atomic_positions.json

@@ -0,0 +1,72 @@
+{
+    "$id": "3pse/file/applications/espresso/7.2/pw.x/atomic-positions",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "atomic positions schema",
+    "description": "https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm1493",
+    "type": "object",
+    "additionalProperties": false,
+    "properties": {
+        "card_option": {
+            "type": "string",
+            "enum": [
+                "alat",
+                "bohr",
+                "angstrom",
+                "crystal",
+                "crystal_sg"
+            ],
+            "default": "alat"
+        },
+        "values": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "required": [
+                    "x",
+                    "y",
+                    "z"
+                ],
+                "additionalProperties": false,
+                "properties": {
+                    "X": {
+                        "type": "string",
+                        "description": "label of the atom as specified in ATOMIC_SPECIES"
+                    },
+                    "x": {
+                        "type": "number",
+                        "description": "atomic positions"
+                    },
+                    "y": {
+                        "type": "number",
+                        "description": "atomic positions"
+                    },
+                    "z": {
+                        "type": "number",
+                        "description": "atomic positions"
+                    },
+                    "if_pos(1)": {
+                        "$schema": "http://json-schema.org/draft-07/schema#",
+                        "title": "integer one or zero",
+                        "type": "integer",
+                        "minimum": 0,
+                        "maximum": 1
+                    },
+                    "if_pos(2)": {
+                        "$schema": "http://json-schema.org/draft-07/schema#",
+                        "title": "integer one or zero",
+                        "type": "integer",
+                        "minimum": 0,
+                        "maximum": 1
+                    },
+                    "if_pos(3)": {
+                        "$schema": "http://json-schema.org/draft-07/schema#",
+                        "title": "integer one or zero",
+                        "type": "integer",
+                        "minimum": 0,
+                        "maximum": 1
+                    }
+                }
+            }
+        }
+    }
+}

package/dist/js/schema/3pse/file/applications/espresso/7.2/pw.x/atomic_species.json

@@ -0,0 +1,30 @@
+{
+    "$id": "3pse/file/applications/espresso/7.2/pw.x/atomic-species",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "atomic species schema",
+    "type": "object",
+    "additionalProperties": false,
+    "properties": {
+        "values": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "additionalProperties": false,
+                "properties": {
+                    "X": {
+                        "type": "string",
+                        "description": "label of the atom. Acceptable syntax: chemical symbol X (1 or 2 characters, case-insensitive) or chemical symbol plus a number or a letter, as in \"Xn\" (e.g. Fe1) or \"X_*\" or \"X-*\" (e.g. C1, C_h; max total length cannot exceed 3 characters)"
+                    },
+                    "Mass_X": {
+                        "type": "number",
+                        "description": "mass of the atomic species [amu: mass of C = 12]. Used only when performing Molecular Dynamics run or structural optimization runs using Damped MD. Not actually used in all other cases (but stored in data files, so phonon calculations will use these values unless other values are provided)"
+                    },
+                    "PseudoPot_X": {
+                        "type": "string",
+                        "description": "PseudoPot_X"
+                    }
+                }
+            }
+        }
+    }
+}