@mat3ra/esse 2024.3.20-0 → 2024.3.25-0

package/lib/js/example/properties_directory/structural/basis/bonds.json

@@ -1,24 +0,0 @@
-[
-    {
-        "atomPair": [
-            {
-                "id": 1
-            },
-            {
-                "id": 2
-            }
-        ],
-        "bondType": "single"
-    },
-    {
-        "atomPair": [
-            {
-                "id": 3
-            },
-            {
-                "id": 4
-            }
-        ],
-        "bondType": "double"
-    }
-]

package/lib/js/example/properties_directory/structural/basis.json

@@ -1,46 +0,0 @@
-{
-    "bonds": [
-        {
-            "0": {
-                "atomPair": [
-                    {
-                        "id": 1
-                    },
-                    {
-                        "id": 2
-                    }
-                ],
-                "bondType": "single"
-            },
-            "1": {
-                "atomPair": [
-                    {
-                        "id": 3
-                    },
-                    {
-                        "id": 4
-                    }
-                ],
-                "bondType": "double"
-            }
-        }
-    ],
-    "coordinates": [
-        {
-            "id": 1,
-            "value": [
-                0,
-                0,
-                0
-            ]
-        }
-    ],
-    "elements": [
-        {
-            "id": 1,
-            "value": "Si"
-        }
-    ],
-    "name": "basis",
-    "units": "crystal"
-}

package/lib/js/example/properties_directory/structural/density.json

@@ -1,5 +0,0 @@
-{
-    "name": "density",
-    "units": "g/cm^3",
-    "value": 2.33
-}

package/lib/js/example/properties_directory/structural/elemental_ratio.json

@@ -1,5 +0,0 @@
-{
-    "element": "Si",
-    "name": "elemental_ratio",
-    "value": 0.71
-}

package/lib/js/example/properties_directory/structural/inchi.json

@@ -1,4 +0,0 @@
-{
-    "name": "inchi",
-    "value": "1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
-}

package/lib/js/example/properties_directory/structural/inchi_key.json

@@ -1,4 +0,0 @@
-{
-    "name": "inchi_key",
-    "value": "UHOVQNZJYSORNB-UHFFFAOYSA-N"
-}

package/lib/js/example/properties_directory/structural/lattice/lattice_bravais.json

@@ -1,13 +0,0 @@
-{
-    "a": 5.14,
-    "alpha": 90,
-    "b": 5.14,
-    "beta": 90,
-    "c": 5.14,
-    "gamma": 90,
-    "type": "CUB",
-    "units": {
-        "angle": "degree",
-        "length": "angstrom"
-    }
-}

package/lib/js/example/properties_directory/structural/lattice/lattice_vectors.json

@@ -1,19 +0,0 @@
-{
-    "a": [
-        5,
-        0.000121312,
-        0.000131415
-    ],
-    "alat": 1,
-    "b": [
-        0.000121312,
-        5,
-        0.000121314
-    ],
-    "c": [
-        0.000121313,
-        0.000121312,
-        5
-    ],
-    "units": "angstrom"
-}

package/lib/js/example/properties_directory/structural/lattice.json

@@ -1,33 +0,0 @@
-{
-    "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"
-    }
-}

package/lib/js/example/properties_directory/structural/magnetic_moments.json

@@ -1,22 +0,0 @@
-{
-    "name": "magnetic_moments",
-    "units": "uB",
-    "values": [
-        {
-            "id": 1,
-            "value": [
-                0,
-                0,
-                1.235
-            ]
-        },
-        {
-            "id": 2,
-            "value": [
-                0,
-                0,
-                -1.235
-            ]
-        }
-    ]
-}

package/lib/js/example/properties_directory/structural/molecular_pattern.json

@@ -1,71 +0,0 @@
-[
-    {
-        "SMARTS": "[O&D1]-C(=O)[#6X3]",
-        "atoms": [
-            {
-                "id": 1,
-                "isConnector": false
-            },
-            {
-                "id": 2,
-                "isConnector": false
-            },
-            {
-                "id": 3,
-                "isConnector": false
-            },
-            {
-                "id": 4,
-                "isConnector": true
-            }
-        ],
-        "name": "functional_group"
-    },
-    {
-        "atoms": [
-            {
-                "id": 1,
-                "isConnector": true
-            },
-            {
-                "id": 2,
-                "isConnector": false
-            },
-            {
-                "id": 3,
-                "isConnector": true
-            }
-        ],
-        "name": "special_bond"
-    },
-    {
-        "atoms": [
-            {
-                "id": 1,
-                "isConnector": false
-            },
-            {
-                "id": 2,
-                "isConnector": false
-            },
-            {
-                "id": 3,
-                "isConnector": false
-            },
-            {
-                "id": 4,
-                "isConnector": false
-            },
-            {
-                "id": 5,
-                "isConnector": false
-            },
-            {
-                "id": 6,
-                "isConnector": true
-            }
-        ],
-        "isAromatic": true,
-        "name": "ring"
-    }
-]

package/lib/js/example/properties_directory/structural/p_norm.json

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

package/lib/js/example/properties_directory/structural/symmetry.json

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

package/lib/js/example/properties_directory/structural/volume.json

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

package/lib/js/example/properties_directory/workflow/convergence/electronic.json

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

package/lib/js/example/properties_directory/workflow/convergence/ionic.json

@@ -1,20 +0,0 @@
-{
-    "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/lib/js/example/properties_directory/workflow/convergence/kpoint.json

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

package/lib/js/example/property/base.json

@@ -1,31 +0,0 @@
-{
-    "_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/lib/js/example/software/application.json

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

package/lib/js/example/software/executable.json

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

package/lib/js/example/software/flavor.json

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

package/lib/js/example/software/template.json

@@ -1,14 +0,0 @@
-{
-    "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/lib/js/example/software_directory/ml/exabyteml.json

@@ -1,6 +0,0 @@
-{
-    "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

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

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

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

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

@@ -1,14 +0,0 @@
-{
-    "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

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

@@ -1,13 +0,0 @@
-{
-    "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

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

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

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

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

@@ -1,6 +0,0 @@
-{
-    "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

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

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

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

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

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

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