@mat3ra/esse 2024.2.6-0 → 2024.2.19-0

package/lib/js/example/software_directory/ml/exabyteml.json

@@ -0,0 +1,6 @@
+{
+    "name": "exabyteml",
+    "shortName": "ml",
+    "summary": "exabyte machine learning engine",
+    "version": "0.2.0"
+}

package/lib/js/example/software_directory/ml/unit/execution/evaluate/cross_validate.json

@@ -0,0 +1,20 @@
+{
+    "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"
+}

package/lib/js/example/software_directory/ml/unit/execution/initialize.json

@@ -0,0 +1,23 @@
+{
+    "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"
+}

package/lib/js/example/software_directory/ml/unit/execution/score.json

@@ -0,0 +1,18 @@
+{
+    "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"
+}

package/lib/js/example/software_directory/ml/unit/execution/train.json

@@ -0,0 +1,29 @@
+{
+    "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"
+}

package/lib/js/example/software_directory/ml/unit/processing/data_transformation/manipulation.json

@@ -0,0 +1,14 @@
+{
+    "flowchartId": "data_transformation",
+    "head": true,
+    "inputData": {
+        "cleanMissingData": true,
+        "removeDuplicateRows": true,
+        "replaceNoneValuesWith": 0
+    },
+    "name": "data_transformation",
+    "operation": "data_transformation",
+    "operationType": "manipulation",
+    "status": "idle",
+    "type": "processing"
+}

package/lib/js/example/software_directory/ml/unit/processing/data_transformation/scale_and_reduce.json

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

package/lib/js/example/software_directory/ml/unit/processing/feature_selection/filter_based.json

@@ -0,0 +1,13 @@
+{
+    "flowchartId": "feature_selection",
+    "head": true,
+    "inputData": {
+        "algorithm": "f_regression",
+        "nFeatures": 100
+    },
+    "name": "feature_selection",
+    "operation": "feature_selection",
+    "operationType": "filter_based",
+    "status": "idle",
+    "type": "processing"
+}

package/lib/js/example/software_directory/modeling/espresso/arguments.json

@@ -0,0 +1,5 @@
+{
+    "nband": 1,
+    "npools": 1,
+    "ntg": 1
+}

package/lib/js/example/software_directory/modeling/espresso.json

@@ -0,0 +1,6 @@
+{
+    "name": "espresso",
+    "shortName": "qe",
+    "summary": "Quantum Espresso",
+    "version": "7.2"
+}

package/lib/js/example/software_directory/modeling/nwchem.json

@@ -0,0 +1,6 @@
+{
+    "name": "NWChem",
+    "summary": "NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations",
+    "version": "6.6",
+    "exec": "nwchem"
+}

package/lib/js/example/software_directory/modeling/unit/execution.json

@@ -0,0 +1,19 @@
+{
+    "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"
+}

package/lib/js/example/software_directory/modeling/vasp.json

@@ -0,0 +1,6 @@
+{
+    "name": "vasp",
+    "shortName": "vasp",
+    "summary": "vienna ab-initio simulation package",
+    "version": "5.3.5"
+}

package/lib/js/example/software_directory/scripting/jupyter_lab.json

@@ -0,0 +1,8 @@
+{
+    "exec": "jupyter",
+    "flavor": "notebook",
+    "name": "jupyterLab",
+    "shortName": "jl",
+    "summary": "Jupyter Lab",
+    "version": "0.33.12"
+}

package/lib/js/example/software_directory/scripting/python.json

@@ -0,0 +1,8 @@
+{
+    "exec": "python",
+    "flavor": "python2",
+    "name": "python",
+    "shortName": "py",
+    "summary": "Python Script",
+    "version": "2.7.5"
+}

package/lib/js/example/software_directory/scripting/shell.json

@@ -0,0 +1,8 @@
+{
+    "exec": "sh",
+    "flavor": "sh",
+    "name": "shell",
+    "shortName": "sh",
+    "summary": "Shell Script",
+    "version": "4.2.46"
+}

package/lib/js/example/software_directory/scripting/unit/execution.json

@@ -0,0 +1,22 @@
+{
+    "application": {
+        "exec": "python",
+        "flavor": "python2",
+        "name": "python",
+        "shortName": "py",
+        "summary": "Python Script",
+        "version": "2.7.5"
+    },
+    "compute": null,
+    "flowchartId": "scripting",
+    "head": true,
+    "input": [
+        {
+            "content": "print('Hello World!')",
+            "name": "script.py"
+        }
+    ],
+    "name": "scripting",
+    "status": "idle",
+    "type": "execution"
+}

package/lib/js/example/system/_material.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Material",
+    "slug": "silicon-fcc"
+}

package/lib/js/example/system/_parent_job.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Job",
+    "slug": "parent-job"
+}

package/lib/js/example/system/_project.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Project",
+    "slug": "project-default"
+}

package/lib/js/example/system/consistency_check.json

@@ -0,0 +1,6 @@
+{
+    "key": "basis.coordinates.0",
+    "name": "atomsTooClose",
+    "severity": "warning",
+    "message": "Atom 0 is too close to atom X"
+}

package/lib/js/example/system/creator.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "User",
+    "slug": "exadmin"
+}

package/lib/js/example/system/entity_reference.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Class",
+    "slug": "Slug"
+}

package/lib/js/example/system/file_source.json

@@ -0,0 +1,6 @@
+{
+    "extension": "poscar",
+    "filename": "POSCAR.mp-546794_SiO2.poscar",
+    "text": "Si4 O8\n1.0\n5.073173 0.000000 0.000000\n0.000000 5.073173 0.000000\n0.000000 0.000000 7.359653\nSi O\n4 8\ndirect\n0.000000 0.500000 0.250000 Si\n0.500000 0.500000 0.500000 Si\n0.500000 0.000000 0.750000 Si\n0.000000 0.000000 0.000000 Si\n0.750000 0.584672 0.375000 O\n0.915328 0.250000 0.125000 O\n0.084672 0.750000 0.125000 O\n0.250000 0.415328 0.375000 O\n0.250000 0.084672 0.875000 O\n0.415328 0.750000 0.625000 O\n0.584672 0.250000 0.625000 O\n0.750000 0.915328 0.875000 O",
+    "hash": "fce4c03798763a9ed8bf64d762c7fbfd"
+}

package/lib/js/example/system/message.json

@@ -0,0 +1,16 @@
+{
+    "header": {
+        "entity": {
+            "_id": "FPjAaKfuYAL7tiHbm",
+            "flowchartId": "pw_scf",
+            "name": "unit"
+        },
+        "timestamp": 1234923492.12,
+        "version": "0.2.0"
+    },
+    "payload": {
+        "name": "total_energy",
+        "units": "eV",
+        "value": -123.43573079
+    }
+}

package/lib/js/example/system/owner.json

@@ -0,0 +1,5 @@
+{
+    "_id": "HtxACY2wX4b2hS8Rv",
+    "cls": "Account",
+    "slug": "exabyte"
+}

package/lib/js/example/workflow/subworkflow.json

@@ -0,0 +1,93 @@
+{
+    "_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"
+        }
+    ]
+}

package/lib/js/example/workflow/unit/assignment.json

@@ -0,0 +1,19 @@
+{
+    "flowchartId": "assignment",
+    "head": true,
+    "input": [
+        {
+            "name": "N_K_x",
+            "scope": "global"
+        },
+        {
+            "name": "N_K_y",
+            "scope": "global"
+        }
+    ],
+    "name": "assignment",
+    "operand": "N_K_x",
+    "status": "idle",
+    "type": "assignment",
+    "value": "N_K_x+N_K_y+1"
+}

package/lib/js/example/workflow/unit/condition.json

@@ -0,0 +1,22 @@
+{
+    "else": "sample_id_6",
+    "flowchartId": "condition",
+    "head": true,
+    "input": [
+        {
+            "name": "x",
+            "scope": "global"
+        },
+        {
+            "name": "total_energy",
+            "scope": "sample_id_2"
+        }
+    ],
+    "maxOccurrences": 100,
+    "name": "condition",
+    "statement": "abs(x-total_energy) < 1e-5",
+    "status": "idle",
+    "then": "sample_id_4",
+    "throwException": true,
+    "type": "condition"
+}

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

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

package/lib/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/lib/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/lib/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/lib/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"
+}