npm - @mat3ra/esse - Versions diffs - 2024.3.25-2 → 2024.3.25-3 - Mend

@mat3ra/esse 2024.3.25-2 → 2024.3.25-3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (558) hide show

package/dist/js/example/properties_directory/structural/p_norm.json ADDED Viewed

@@ -0,0 +1,5 @@
+{
+    "degree": 10,
+    "name": "p-norm",
+    "value": 0.71
+}

package/dist/js/example/properties_directory/structural/symmetry.json ADDED Viewed

@@ -0,0 +1,9 @@
+{
+    "name": "symmetry",
+    "pointGroupSymbol": "C2v",
+    "spaceGroupSymbol": "Fd-3m",
+    "tolerance": {
+        "units": "angstrom",
+        "value": 0.3
+    }
+}

package/dist/js/example/properties_directory/structural/volume.json ADDED Viewed

@@ -0,0 +1,5 @@
+{
+    "name": "volume",
+    "units": "angstrom^3",
+    "value": 131.1
+}

package/dist/js/example/properties_directory/workflow/convergence/electronic.json ADDED Viewed

@@ -0,0 +1,15 @@
+{
+    "data": [
+        [
+            -123.45678,
+            -12.345678,
+            -1.2345678,
+            -0.1234567,
+            -0.0123456,
+            -0.0012345,
+            -0.0001234
+        ]
+    ],
+    "tolerance": 0.001,
+    "units": "rydberg"
+}

package/dist/js/example/properties_directory/workflow/convergence/ionic.json ADDED Viewed

@@ -0,0 +1,20 @@
+{
+    "data": [
+        {
+            "electronic": {
+                "data": [
+                    0.10303193,
+                    0.04365779,
+                    0.00051472,
+                    0.00007496,
+                    0.00000309,
+                    5.6e-7
+                ],
+                "units": "eV"
+            },
+            "energy": -123.45678
+        }
+    ],
+    "tolerance": 0.001,
+    "units": "eV"
+}

package/dist/js/example/properties_directory/workflow/convergence/kpoint.json ADDED Viewed

@@ -0,0 +1,22 @@
+{
+    "data": [
+        {
+            "grid": {
+                "dimensions": [
+                    1,
+                    1,
+                    1
+                ],
+                "shifts": [
+                    0,
+                    0,
+                    0
+                ]
+            },
+            "value": "-123.45678"
+        }
+    ],
+    "property": "total_energy",
+    "tolerance": 0.001,
+    "units": "eV"
+}

package/dist/js/example/property/base.json ADDED Viewed

@@ -0,0 +1,31 @@
+{
+    "_id": "K3McGkqXh28HJ775m",
+    "createdAt": "2018-11-19 06:41:46.877Z",
+    "creator": {
+        "_id": "HtxACY2wX4b2hS8Rv",
+        "cls": "User",
+        "slug": "exadmin"
+    },
+    "data": {
+        "name": "pressure",
+        "units": "kbar",
+        "value": -149.03
+    },
+    "group": "qe:dft:gga:pbe",
+    "owner": {
+        "_id": "HtxACY2wX4b2hS8Rv",
+        "cls": "Account",
+        "slug": "exabyte"
+    },
+    "schemaVersion": "0.2.0",
+    "slug": "pressure",
+    "source": {
+        "_id": "nDAavgjrT5ezwFgod",
+        "owner": {
+            "_id": "HtxACY2wX4b2hS8Rv",
+            "cls": "Account",
+            "slug": "exabyte"
+        },
+        "title": "My Calculation"
+    }
+}

package/dist/js/example/software/application.json ADDED Viewed

@@ -0,0 +1,7 @@
+{
+    "name": "espresso",
+    "shortName": "qe",
+    "summary": "Quantum Espresso",
+    "version": "5.1.1",
+    "hasAdvancedComputeOptions": true
+}

package/dist/js/example/software/executable.json ADDED Viewed

@@ -0,0 +1,20 @@
+{
+    "advancedComputeOptions": true,
+    "applicationId": [
+        "eaJepm4AWfqpaCw59"
+    ],
+    "isDefault": true,
+    "monitors": [
+        {
+            "name": "standard_output"
+        }
+    ],
+    "name": "pw.x",
+    "postProcessors": [],
+    "preProcessors": [],
+    "results": [
+        {
+            "name": "atomic_forces"
+        }
+    ]
+}

package/dist/js/example/software/flavor.json ADDED Viewed

@@ -0,0 +1,9 @@
+{
+    "executableId": "4987JFJ3kKbwvFSG7",
+    "input": [
+        {
+            "templateId": "dJ7HYz5pQ4AuN5qc9"
+        }
+    ],
+    "name": "pw_scf"
+}

package/dist/js/example/software/template.json ADDED Viewed

@@ -0,0 +1,14 @@
+{
+    "applicationName": "espresso",
+    "applicationVersions": [
+        "6.0"
+    ],
+    "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
+    "contextProviders": [
+        {
+            "name": "KGridManagerMixin"
+        }
+    ],
+    "executableName": "pw.x",
+    "name": "kpoints_grid"
+}

package/dist/js/example/software_directory/ml/exabyteml.json ADDED Viewed

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

package/dist/js/example/software_directory/ml/unit/execution/evaluate/cross_validate.json ADDED Viewed

@@ -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/dist/js/example/software_directory/ml/unit/execution/initialize.json ADDED Viewed

@@ -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/dist/js/example/software_directory/ml/unit/execution/score.json ADDED Viewed

@@ -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/dist/js/example/software_directory/ml/unit/execution/train.json ADDED Viewed

@@ -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/dist/js/example/software_directory/ml/unit/processing/data_transformation/manipulation.json ADDED Viewed

@@ -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/dist/js/example/software_directory/ml/unit/processing/data_transformation/scale_and_reduce.json ADDED Viewed

@@ -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/dist/js/example/software_directory/ml/unit/processing/feature_selection/filter_based.json ADDED Viewed

@@ -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/dist/js/example/software_directory/modeling/espresso/arguments.json ADDED Viewed

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

package/dist/js/example/software_directory/modeling/espresso.json ADDED Viewed

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

package/dist/js/example/software_directory/modeling/nwchem.json ADDED Viewed

@@ -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/dist/js/example/software_directory/modeling/unit/execution.json ADDED Viewed

@@ -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/dist/js/example/software_directory/modeling/vasp.json ADDED Viewed

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

package/dist/js/example/software_directory/scripting/jupyter_lab.json ADDED Viewed

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

package/dist/js/example/software_directory/scripting/python.json ADDED Viewed

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

package/dist/js/example/software_directory/scripting/shell.json ADDED Viewed

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

package/dist/js/example/software_directory/scripting/unit/execution.json ADDED Viewed

@@ -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/dist/js/example/system/_material.json ADDED Viewed

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

package/dist/js/example/system/_parent_job.json ADDED Viewed

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

package/dist/js/example/system/_project.json ADDED Viewed

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

package/dist/js/example/system/consistency_check.json ADDED Viewed

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

package/dist/js/example/system/creator.json ADDED Viewed

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

package/dist/js/example/system/entity_reference.json ADDED Viewed

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

package/dist/js/example/system/file_source.json ADDED Viewed

@@ -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/dist/js/example/system/iframe_message.json ADDED Viewed

@@ -0,0 +1,9 @@
+{
+    "type": "from-iframe-to-host",
+    "action": "set-data",
+    "payload": {
+        "property": {
+            "name": "material"
+        }
+    }
+}

package/dist/js/example/system/message.json ADDED Viewed

@@ -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/dist/js/example/system/owner.json ADDED Viewed

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

package/dist/js/example/workflow/subworkflow.json ADDED Viewed

@@ -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/dist/js/example/workflow/unit/assignment.json ADDED Viewed

@@ -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/dist/js/example/workflow/unit/condition.json ADDED Viewed

@@ -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"
+}