@mat3ra/esse 2023.12.25-2

package/example/properties_directory/non-scalar/total_energy_contributions.json

@@ -0,0 +1,44 @@
+{
+    "PAWDoubleCounting2": {
+        "name": "PAW_double-counting_correction_2",
+        "value": 12658.30538857
+    },
+    "PAWDoubleCounting3": {
+        "name": "PAW_double-counting_correction_3",
+        "value": -12074.85364512
+    },
+    "alphaZ": {
+        "name": "alphaZ",
+        "value": 1056.91493097
+    },
+    "atomicEnergy": {
+        "name": "atomic_energy",
+        "value": 15740.5725788
+    },
+    "eigenvalues": {
+        "name": "eigenvalues",
+        "value": -577.80127102
+    },
+    "ewald": {
+        "name": "ewald",
+        "value": 128376.45871064
+    },
+    "exchange": {
+        "name": "exchange",
+        "value": 0
+    },
+    "exchangeCorrelation": {
+        "name": "exchange_correlation",
+        "value": 41.63693035
+    },
+    "hartree": {
+        "name": "hartree",
+        "value": -145344.66902862
+    },
+    "name": "total_energy_contributions",
+    "temperatureEntropy": {
+        "name": "temperature_entropy",
+        "value": -0.00032545
+    },
+    "units": "eV"
+}

package/example/properties_directory/non-scalar/vibrational_spectrum.json

@@ -0,0 +1,25 @@
+{
+    "name": "vibrational_spectrum",
+    "xAxis": {
+        "label": "wavenumber",
+        "units": "cm-1"
+    },
+    "xDataArray": [
+        [
+            1625.972,
+            3631.832,
+            3735.535
+        ]
+    ],
+    "yAxis": {
+        "label": "Absorption coefficient",
+        "units": "km/mol"
+    },
+    "yDataSeries": [
+        [
+            46.681,
+            1.139,
+            14.281
+        ]
+    ]
+}

package/example/properties_directory/scalar/electron_affinity.json

@@ -0,0 +1,5 @@
+{
+    "name": "electron_affinity",
+    "units": "eV",
+    "value": 2.5
+}

package/example/properties_directory/scalar/fermi_energy.json

@@ -0,0 +1,5 @@
+{
+    "name": "fermi_energy",
+    "units": "eV",
+    "value": -1.2
+}

package/example/properties_directory/scalar/formation_energy.json

@@ -0,0 +1,5 @@
+{
+    "name": "formation_energy",
+    "units": "eV",
+    "value": -123.43573079
+}

package/example/properties_directory/scalar/ionization_potential.json

@@ -0,0 +1,5 @@
+{
+    "name": "ionization_potential",
+    "units": "eV",
+    "value": 14.0
+}

package/example/properties_directory/scalar/pressure.json

@@ -0,0 +1,5 @@
+{
+    "name": "pressure",
+    "units": "kbar",
+    "value": -27.345
+}

package/example/properties_directory/scalar/reaction_energy_barrier.json

@@ -0,0 +1,5 @@
+{
+    "name": "reaction_energy_barrier",
+    "units": "eV",
+    "value": -123.43573079
+}

package/example/properties_directory/scalar/surface_energy.json

@@ -0,0 +1,5 @@
+{
+    "name": "surface_energy",
+    "units": "eV/A^2",
+    "value": 0.02
+}

package/example/properties_directory/scalar/total_energy.json

@@ -0,0 +1,5 @@
+{
+    "name": "total_energy",
+    "units": "eV",
+    "value": -123.43573079
+}

package/example/properties_directory/scalar/total_force.json

@@ -0,0 +1,5 @@
+{
+    "name": "total_force",
+    "units": "eV/angstrom",
+    "value": 1e-06
+}

package/example/properties_directory/scalar/valence_band_offset.json

@@ -0,0 +1,5 @@
+{
+    "name": "valence_band_offset",
+    "units": "eV",
+    "value": 0.245
+}

package/example/properties_directory/scalar/zero_point_energy.json

@@ -0,0 +1,5 @@
+{
+    "name": "zero_point_energy",
+    "units": "eV",
+    "value": -123.43573079
+}

package/example/properties_directory/structural/atomic_forces.json

@@ -0,0 +1,22 @@
+{
+    "name": "atomic_forces",
+    "units": "eV/bohr",
+    "values": [
+        {
+            "id": 1,
+            "value": [
+                -3.9e-07,
+                -2.4e-07,
+                0.0
+            ]
+        },
+        {
+            "id": 2,
+            "value": [
+                3.9e-07,
+                2.4e-07,
+                0.0
+            ]
+        }
+    ]
+}

package/example/properties_directory/structural/basis/atomic_constraints.json

@@ -0,0 +1,21 @@
+{
+    "name": "atomic_constraints",
+    "values": [
+        {
+            "id": 1,
+            "value": [
+                true,
+                false,
+                true
+            ]
+        },
+        {
+            "id": 2,
+            "value": [
+                false,
+                false,
+                true
+            ]
+        }
+    ]
+}

package/example/properties_directory/structural/basis/atomic_coordinate.json

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

package/example/properties_directory/structural/basis/atomic_coordinates.json

@@ -0,0 +1,21 @@
+{
+    "name": "atomic_coordinates",
+    "values": [
+        {
+            "id": 1,
+            "value": [
+                0,
+                0,
+                0
+            ]
+        },
+        {
+            "id": 2,
+            "value": [
+                0.25,
+                0.25,
+                0.25
+            ]
+        }
+    ]
+}

package/example/properties_directory/structural/basis/atomic_element.json

@@ -0,0 +1,4 @@
+{
+    "id": 1,
+    "value": "Si"
+}

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

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

package/example/properties_directory/structural/basis.json

@@ -0,0 +1,19 @@
+{
+    "bonds": [
+        {
+            "...": "include(basis/bonds.json)"
+        }
+    ],
+    "coordinates": [
+        {
+            "...": "include(basis/atomic_coordinate.json)"
+        }
+    ],
+    "elements": [
+        {
+            "...": "include(basis/atomic_element.json)"
+        }
+    ],
+    "name": "basis",
+    "units": "crystal"
+}

package/example/properties_directory/structural/density.json

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

package/example/properties_directory/structural/elemental_ratio.json

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

package/example/properties_directory/structural/inchi.json

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

package/example/properties_directory/structural/inchi_key.json

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

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

@@ -0,0 +1,13 @@
+{
+    "a": 5.14,
+    "alpha": 90.0,
+    "b": 5.14,
+    "beta": 90.0,
+    "c": 5.14,
+    "gamma": 90.0,
+    "type": "CUB",
+    "units": {
+        "angle": "degree",
+        "length": "angstrom"
+    }
+}

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

@@ -0,0 +1,19 @@
+{
+    "a": [
+        5.0,
+        0.000121312,
+        0.000131415
+    ],
+    "alat": 1.0,
+    "b": [
+        0.000121312,
+        5.0,
+        0.000121314
+    ],
+    "c": [
+        0.000121313,
+        0.000121312,
+        5.0
+    ],
+    "units": "angstrom"
+}

package/example/properties_directory/structural/lattice.json

@@ -0,0 +1,7 @@
+{
+    "...": "include(lattice/lattice_bravais.json)",
+    "name": "lattice",
+    "vectors": {
+        "...": "include(lattice/lattice_vectors.json)"
+    }
+}

package/example/properties_directory/structural/magnetic_moments.json

@@ -0,0 +1,22 @@
+{
+    "name": "magnetic_moments",
+    "units": "uB",
+    "values": [
+        {
+            "id": 1,
+            "value": [
+                0.0,
+                0.0,
+                1.235
+            ]
+        },
+        {
+            "id": 2,
+            "value": [
+                0.0,
+                0.0,
+                -1.235
+            ]
+        }
+    ]
+}

package/example/properties_directory/structural/molecular_pattern.json

@@ -0,0 +1,71 @@
+[
+    {
+        "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/example/properties_directory/structural/p-norm.json

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

package/example/properties_directory/structural/symmetry.json

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

package/example/properties_directory/structural/volume.json

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

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

@@ -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/example/properties_directory/workflow/convergence/ionic.json

@@ -0,0 +1,20 @@
+{
+    "data": [
+        {
+            "electronic": {
+                "data": [
+                    0.10303193,
+                    0.04365779,
+                    0.00051472,
+                    7.496e-05,
+                    3.09e-06,
+                    5.6e-07
+                ],
+                "units": "eV"
+            },
+            "energy": -123.45678
+        }
+    ],
+    "tolerance": 0.001,
+    "units": "eV"
+}

package/example/properties_directory/workflow/convergence/kpoint.json

@@ -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/example/property/base.json

@@ -0,0 +1,21 @@
+{
+    "_id": "K3McGkqXh28HJ775m",
+    "createdAt": "2018-11-19 06:41:46.877Z",
+    "creator": {
+        "...": "include(../system/creator.json)"
+    },
+    "data": {
+        "name": "pressure",
+        "units": "kbar",
+        "value": -149.03
+    },
+    "group": "qe:dft:gga:pbe",
+    "owner": {
+        "...": "include(../system/owner.json)"
+    },
+    "schemaVersion": "0.2.0",
+    "slug": "pressure",
+    "source": {
+        "...": "include(../core/reference.json)"
+    }
+}

package/example/software/application.json

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

package/example/software/executable.json

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

package/example/software/flavor.json

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

package/example/software/template.json

@@ -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/example/software_directory/ml/exabyteml.json

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

package/example/software_directory/ml/unit/execution/evaluate/cross-validate.json

@@ -0,0 +1,17 @@
+{
+    "application": {
+        "...": "include(../../../exabyteml.json)"
+    },
+    "flavor": {
+        "executableId": "4987JFJ3kKbwvFSG7",
+        "name": "cross-validate"
+    },
+    "flowchartId": "evaluate",
+    "head": true,
+    "input": {
+        "nSplits": 3
+    },
+    "name": "evaluate",
+    "status": "idle",
+    "type": "execution"
+}

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

@@ -0,0 +1,20 @@
+{
+    "application": {
+        "...": "include(../../exabyteml.json)"
+    },
+    "flavor": {
+        "executableId": "4987JFJ3kKbwvFSG7",
+        "name": "initialize"
+    },
+    "flowchartId": "initialize",
+    "head": true,
+    "input": {
+        "targets": [
+            "band_gaps:indirect",
+            "band_gaps:direct"
+        ]
+    },
+    "name": "initialize",
+    "status": "idle",
+    "type": "execution"
+}

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

@@ -0,0 +1,15 @@
+{
+    "application": {
+        "...": "include(../../exabyteml.json)"
+    },
+    "flavor": {
+        "executableId": "4987JFJ3kKbwvFSG7",
+        "name": "score"
+    },
+    "flowchartId": "score",
+    "head": true,
+    "input": {},
+    "name": "score",
+    "status": "idle",
+    "type": "execution"
+}