@mat3ra/esse 2023.12.25-2

package/schema/methods_category/physical/qm/enum_options.json

@@ -0,0 +1,8 @@
+{
+    "$id": "methods-category/physical/qm/enum-options",
+    "wavefunction": {
+        "enum": [
+            "wf"
+        ]
+    }
+}

package/schema/methods_category/physical/qm/enum_options.yml

@@ -0,0 +1,3 @@
+# Tier 2 enum slugs
+wavefunction:
+  - wf # wave function category

package/schema/methods_category/physical/qm/wf/ao/dunning.json

@@ -0,0 +1,17 @@
+{
+    "$id": "methods-category/physical/qm/wf/ao/dunning",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Dunning correlation-consistent basis set category schema",
+    "allOf": [
+        {
+            "$ref": "../ao.json"
+        }
+    ],
+    "properties": {
+        "subtype": {
+            "enum": [
+                "dunning"
+            ]
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf/ao/other.json

@@ -0,0 +1,17 @@
+{
+    "$id": "methods-category/physical/qm/wf/ao/other",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Other (neither Pople nor Dunning) basis set category schema",
+    "allOf": [
+        {
+            "$ref": "../ao.json"
+        }
+    ],
+    "properties": {
+        "subtype": {
+            "enum": [
+                "other"
+            ]
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf/ao/pople.json

@@ -0,0 +1,17 @@
+{
+    "$id": "methods-category/physical/qm/wf/ao/pople",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Pople basis set category schema",
+    "allOf": [
+        {
+            "$ref": "../ao.json"
+        }
+    ],
+    "properties": {
+        "subtype": {
+            "enum": [
+                "pople"
+            ]
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf/ao.json

@@ -0,0 +1,18 @@
+{
+    "$id": "methods-category/physical/qm/wf/ao",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Approximating the electronic wave function with a atomic orbital basis",
+    "allOf": [
+        {
+            "$ref": "../wf.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "$ref": "./enum_options.json#/atomicOrbital"
+        },
+        "subtype": {
+            "$ref": "./enum_options.json#/aoTypes"
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf/enum_options.json

@@ -0,0 +1,63 @@
+{
+    "$id": "methods-category/physical/qm/wf/enum-options",
+    "planewave": {
+        "enum": [
+            "pw"
+        ]
+    },
+    "atomicOrbital": {
+        "enum": [
+            "ao"
+        ]
+    },
+    "wavelet": {
+        "enum": [
+            "wvl"
+        ]
+    },
+    "smearing": {
+        "enum": [
+            "smearing"
+        ]
+    },
+    "tetrahedron": {
+        "enum": [
+            "tetrahedron"
+        ]
+    },
+    "pseudization": {
+        "enum": [
+            "psp"
+        ]
+    },
+    "pseudoSubtypes": {
+        "enum": [
+            "us",
+            "nc",
+            "paw",
+            "coulomb"
+        ]
+    },
+    "smearingSubtypes": {
+        "enum": [
+            "gaussian",
+            "marzari-vanderbilt",
+            "methfessel-paxton",
+            "fermi-dirac"
+        ]
+    },
+    "tetrahedronSubtypes": {
+        "enum": [
+            "linear",
+            "optimized",
+            "bloechl"
+        ]
+    },
+    "aoTypes": {
+        "enum": [
+            "pople",
+            "dunning",
+            "other"
+        ]
+    }
+}

package/schema/methods_category/physical/qm/wf/enum_options.yml

@@ -0,0 +1,43 @@
+# --- Type enum slugs ---
+# Wave function types
+planewave:
+  - pw # plane waves
+atomicOrbital:
+  - ao # atomic orbital basis
+wavelet:
+  - wvl # wavelet series
+# Brillouin Zone integration
+smearing:
+  - smearing # Occupation number smearing
+tetrahedron:
+  - tetrahedron # Tetrahedron method
+
+# --- SubType enum slugs ---
+pseudization:
+  - psp # Pseudopotential Approximation
+#
+# Pseudopotential
+pseudoSubtypes:
+  - us # ultra-soft
+  - nc # norm-conserving
+  - paw # projector augmented wave
+  - coulomb # Coulomb potential
+#
+# Occupation number smearing (Brillouin zone integration)
+smearingSubtypes:
+  - gaussian
+  - marzari-vanderbilt # Marzari-Vanderbilt smearing, doi:10.1103/PhysRevLett.82.3296
+  - methfessel-paxton # Methfessel-Paxton smearing, doi:10.1103/PhysRevB.40.3616
+  - fermi-dirac # uses Fermi-Dirac distribution instead of Heaviside step function
+#
+# Tetrahedron methods (Brillouin zone integration)
+tetrahedronSubtypes:
+  - linear # original linear tetrahedron method
+  - optimized # Optimized tetrahedron method by Kawamura, doi:10.1103/PhysRevB.89.094515
+  - bloechl # Tetrahedron method with Bloechl correction, doi:10.1103/PhysRevB.49.16223
+#
+# Atomic Orbital basis types
+aoTypes:
+  - pople
+  - dunning
+  - other

package/schema/methods_category/physical/qm/wf/psp.json

@@ -0,0 +1,18 @@
+{
+    "$id": "methods-category/physical/qm/wf/psp",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Pseudopotential category schema",
+    "allOf": [
+        {
+            "$ref": "../wf.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "$ref": "./enum_options.json#/pseudization"
+        },
+        "subtype": {
+            "$ref": "./enum_options.json#/pseudoSubtypes"
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf/pw.json

@@ -0,0 +1,15 @@
+{
+    "$id": "methods-category/physical/qm/wf/pw",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Plane wave catgeory schema",
+    "allOf": [
+        {
+            "$ref": "../wf.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "$ref": "./enum_options.json#/planewave"
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf/smearing.json

@@ -0,0 +1,19 @@
+{
+    "$id": "methods-category/physical/qm/wf/smearing",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Smearing methods category schema",
+    "description": "Approximating Heaviside step function with smooth function",
+    "allOf": [
+        {
+            "$ref": "../wf.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "$ref": "enum_options.json#/smearing"
+        },
+        "subtype": {
+            "$ref": "./enum_options.json#/smearingSubtypes"
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf/tetrahedron.json

@@ -0,0 +1,18 @@
+{
+    "$id": "methods-category/physical/qm/wf/tetrahedron",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Tetrahedron method for Brillouin zone integration category schema ",
+    "allOf": [
+        {
+            "$ref": "../wf.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "$ref": "enum_options.json#/tetrahedron"
+        },
+        "subtype": {
+            "$ref": "./enum_options.json#/tetrahedronSubtypes"
+        }
+    }
+}

package/schema/methods_category/physical/qm/wf.json

@@ -0,0 +1,15 @@
+{
+    "$id": "methods-category/physical/qm/wf",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Methods related to wave functions",
+    "allOf": [
+        {
+            "$ref": "../qm.json"
+        }
+    ],
+    "properties": {
+        "tier2": {
+            "$ref": "enum_options.json#/wavefunction"
+        }
+    }
+}

package/schema/methods_category/physical/qm.json

@@ -0,0 +1,15 @@
+{
+    "$id": "methods-category/physical/qm",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "Quantum-Mechanical method category schema",
+    "allOf": [
+        {
+            "$ref": "../../core/reusable/categories.json"
+        }
+    ],
+    "properties": {
+        "tier1": {
+            "$ref": "enum_options.json#/quantumMechanical"
+        }
+    }
+}

package/schema/methods_directory/legacy/localorbital.json

@@ -0,0 +1,22 @@
+{
+    "$id": "methods-directory/legacy/localorbital",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "legacy method localorbital",
+    "allOf": [
+        {
+            "$ref": "../../method.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "enum": [
+                "localorbital"
+            ]
+        },
+        "subtype": {
+            "enum": [
+                "pople"
+            ]
+        }
+    }
+}

package/schema/methods_directory/legacy/pseudopotential.json

@@ -0,0 +1,25 @@
+{
+    "$id": "methods-directory/legacy/pseudopotential",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "legacy method pseudopotential",
+    "allOf": [
+        {
+            "$ref": "../../method.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "enum": [
+                "pseudopotential"
+            ]
+        },
+        "subtype": {
+            "enum": [
+                "paw",
+                "nc",
+                "us",
+                "any"
+            ]
+        }
+    }
+}

package/schema/methods_directory/legacy/regression.json

@@ -0,0 +1,34 @@
+{
+    "$id": "methods-directory/legacy/regression",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "legacy method regression",
+    "allOf": [
+        {
+            "$ref": "../../method.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "enum": [
+                "linear",
+                "kernel_ridge"
+            ]
+        },
+        "subtype": {
+            "enum": [
+                "least_squares",
+                "ridge"
+            ]
+        },
+        "precision": {
+            "$ref": "../mathematical/regression/precision.json"
+        },
+        "data": {
+            "$ref": "../mathematical/regression/data.json"
+        }
+    },
+    "required": [
+        "precision",
+        "data"
+    ]
+}

package/schema/methods_directory/legacy/unknown.json

@@ -0,0 +1,22 @@
+{
+    "$id": "methods-directory/legacy/unknown",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "legacy method unknown",
+    "allOf": [
+        {
+            "$ref": "../../method.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "enum": [
+                "unknown"
+            ]
+        },
+        "subtype": {
+            "enum": [
+                "unknown"
+            ]
+        }
+    }
+}

package/schema/methods_directory/mathematical/cg.json

@@ -0,0 +1,17 @@
+{
+    "$id": "methods-directory/mathematical/cg",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method conjugate gradient",
+    "description": "conjugate gradient method schema",
+    "allOf": [
+        {
+            "$ref": "../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../methods_category/mathematical/opt/diff/ordern/cg.json"
+        }
+    },
+    "required": ["categories"]
+}

package/schema/methods_directory/mathematical/davidson.json

@@ -0,0 +1,17 @@
+{
+    "$id": "methods-directory/mathematical/davidson",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method davidson",
+    "description": "Davidson diagonalization method",
+    "allOf": [
+        {
+            "$ref": "../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../methods_category/mathematical/linalg/diag/davidson.json"
+        }
+    },
+    "required": ["categories"]
+}

package/schema/methods_directory/mathematical/regression/data.json

@@ -0,0 +1,24 @@
+{
+    "$id": "methods-directory/mathematical/regression/data",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "regression data",
+    "type": "object",
+    "properties": {
+        "perProperty": {
+            "type": "array",
+            "items": {
+                "oneOf": [
+                    {
+                        "$ref": "linear/data_per_property.json"
+                    },
+                    {
+                        "$ref": "kernel_ridge/data_per_property.json"
+                    }
+                ]
+            }
+        },
+        "dataSet": {
+            "$ref": "dataset.json"
+        }
+    }
+}

package/schema/methods_directory/mathematical/regression/dataset.json

@@ -0,0 +1,21 @@
+{
+    "$id": "methods-directory/mathematical/regression/dataset",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "description": "dataset for ml",
+    "type": "object",
+    "properties": {
+        "exabyteIds": {
+            "description": "array of exabyteIds for materials in dataset",
+            "type": "array",
+            "items": {
+                "type": "string"
+            }
+        },
+        "extra": {
+            "description": "holder for any extra information, eg. coming from user-uploaded CSV file"
+        }
+    },
+    "required": [
+        "exabyteIds"
+    ]
+}

package/schema/methods_directory/mathematical/regression/kernel_ridge/data_per_property.json

@@ -0,0 +1,27 @@
+{
+    "$id": "methods-directory/mathematical/regression/kernel-ridge/data-per-property",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "kernel-ridge regression parameters schema",
+    "properties": {
+        "xFit": {
+            "description": "training data",
+            "type": "array"
+        },
+        "dualCoefficients": {
+            "description": "dual coefficients",
+            "type": "array"
+        },
+        "perFeature": {
+            "type": "array",
+            "description": "per-feature (property used for training the ML method/model) parameters",
+            "items": {
+                "$ref": "../per_feature_item.json"
+            }
+        }
+    },
+    "required": [
+        "xFit",
+        "dualCoefficients",
+        "perFeature"
+    ]
+}

package/schema/methods_directory/mathematical/regression/linear/data_per_property.json

@@ -0,0 +1,22 @@
+{
+    "$id": "methods-directory/mathematical/regression/linear/data-per-property",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "linear regression parameters schema",
+    "properties": {
+        "intercept": {
+            "description": "intercept (shift) from the linear or non-linear fit of data points",
+            "type": "number"
+        },
+        "perFeature": {
+            "type": "array",
+            "description": "per-feature (property used for training the ML method/model) parameters",
+            "items": {
+                "$ref": "../per_feature_item.json"
+            }
+        }
+    },
+    "required": [
+        "intercept",
+        "perFeature"
+    ]
+}

package/schema/methods_directory/mathematical/regression/per_feature_item.json

@@ -0,0 +1,22 @@
+{
+    "$id": "methods-directory/mathematical/regression/per-feature-item",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "per-feature (property used for training the ML method/model) parameters schema",
+    "properties": {
+        "coefficient": {
+            "description": "coefficient in linear regression",
+            "type": "number"
+        },
+        "name": {
+            "description": "feature name",
+            "type": "string"
+        },
+        "importance": {
+            "description": "pvalue: https://en.wikipedia.org/wiki/P-value",
+            "type": "number"
+        }
+    },
+    "required": [
+        "name"
+    ]
+}

package/schema/methods_directory/mathematical/regression/precision.json

@@ -0,0 +1,14 @@
+{
+    "$id": "methods-directory/mathematical/regression/precision",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "regression precision",
+    "type": "object",
+    "properties": {
+        "perProperty": {
+            "type": "array",
+            "items": {
+                "$ref": "precision_per_property.json"
+            }
+        }
+    }
+}

package/schema/methods_directory/mathematical/regression/precision_per_property.json

@@ -0,0 +1,23 @@
+{
+    "$id": "methods-directory/mathematical/regression/precision-per-property",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "regression precision per property schema",
+    "type": "object",
+    "properties": {
+        "name": {
+            "description": "property name in 'flattened' format",
+            "type": "string"
+        },
+        "trainingError": {
+            "description": "training error of the estimator",
+            "type": "number"
+        },
+        "score": {
+            "description": "prediction score of the estimator. Eg: r2_score",
+            "type": "number"
+        }
+    },
+    "required": [
+        "trainingError"
+    ]
+}

package/schema/methods_directory/mathematical/regression.json

@@ -0,0 +1,26 @@
+{
+    "$id": "methods-directory/mathematical/regression",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method regression",
+    "allOf": [
+        {
+            "$ref": "../../method/unit_method.json"
+        }
+    ],
+    "properties": {
+        "categories": {
+            "$ref": "../../methods_category/mathematical/regression.json"
+        },
+        "precision": {
+            "$ref": "regression/precision.json"
+        },
+        "data": {
+            "$ref": "regression/data.json"
+        }
+    },
+    "required": [
+        "categories",
+        "precision",
+        "data"
+    ]
+}