Merge branch 'dev' into feature/SOF-7053

Exabyte-io · Oct 31, 2023 · 955b182 · 955b182
2 parents f9ed5fa + d8dfefb
commit 955b182
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Showing 44 changed files with 525 additions and 59 deletions.
diff --git a/example/method/method_parameters.json b/example/method/method_parameters.json
@@ -0,0 +1,3 @@
+{
+    "basisSlug": "6-311G"
+}
diff --git a/example/methods_directory/legacy/localorbital.json b/example/methods_directory/legacy/localorbital.json
@@ -0,0 +1,4 @@
+{
+    "type": "localorbital",
+    "subtype": "pople"
+}
diff --git a/example/methods_directory/legacy/pseudopotential.json b/example/methods_directory/legacy/pseudopotential.json
@@ -0,0 +1,4 @@
+{
+    "type": "pseudopotential",
+    "subtype": "us"
+}
diff --git a/example/methods_directory/legacy/regression.json b/example/methods_directory/legacy/regression.json
@@ -0,0 +1,61 @@
+{
+    "data": {
+        "dataSet": {
+            "exabyteIds": [
+                "LCthJ6E2QabYCZqf4",
+                "LCthJ6E2QabYCZqf5",
+                "LCthJ6E2QabYCZqf6",
+                "LCthJ6E2QabYCZqf7",
+                "LCthJ6E2QabYCZqf8",
+                "LCthJ6E2QabYCZqf9",
+                "LCthJ6E2QabYCZq10",
+                "LCthJ6E2QabYCZq11"
+            ],
+            "extra": {}
+        },
+        "perProperty": [
+            {
+                "intercept": 0.363,
+                "name": "band_gaps:direct",
+                "perFeature": [
+                    {
+                        "coefficient": 0.015,
+                        "importance": 0.134,
+                        "name": "atomic_radius:Ge"
+                    },
+                    {
+                        "coefficient": 0.016,
+                        "importance": 0.135,
+                        "name": "atomic_radius:Si"
+                    }
+                ]
+            },
+            {
+                "intercept": 0.364,
+                "name": "band_gaps:indirect",
+                "perFeature": [
+                    {
+                        "coefficient": 0.016,
+                        "importance": 0.135,
+                        "name": "atomic_radius:Ge"
+                    },
+                    {
+                        "coefficient": 0.017,
+                        "importance": 0.136,
+                        "name": "atomic_radius:Si"
+                    }
+                ]
+            }
+        ]
+    },
+    "precision": {
+        "perProperty": [
+            {
+                "score": 0.8,
+                "trainingError": 0.002
+            }
+        ]
+    },
+    "subtype": "least_squares",
+    "type": "linear"
+}
diff --git a/example/methods_directory/legacy/unknown.json b/example/methods_directory/legacy/unknown.json
@@ -0,0 +1,4 @@
+{
+    "type": "unknown",
+    "subtype": "unknown"
+}
diff --git a/example/model/model_parameters.json b/example/model/model_parameters.json
@@ -0,0 +1,7 @@
+{
+    "functional": "pbe",
+    "dispersionCorrection": "dft-d3",
+    "hubbardType": "u",
+    "spinPolarization": "collinear",
+    "spinOrbitCoupling": true
+}
diff --git a/example/models_directory/legacy/dft.json b/example/models_directory/legacy/dft.json
@@ -0,0 +1,8 @@
+{
+    "type": "dft",
+    "subtype": "gga",
+    "functional": "pbe",
+    "method": {
+        "...": "include(../../method.json)"
+    }
+}
diff --git a/example/models_directory/legacy/ml.json b/example/models_directory/legacy/ml.json
@@ -0,0 +1,7 @@
+{
+    "type": "ml",
+    "subtype": "re",
+    "method": {
+        "...": "include(../../method.json)"
+    }
+}
diff --git a/example/models_directory/legacy/unknown.json b/example/models_directory/legacy/unknown.json
@@ -0,0 +1,7 @@
+{
+    "type": "unknown",
+    "subtype": "unknown",
+    "method": {
+        "...": "include(../../method.json)"
+    }
+}
diff --git a/schema/core/reusable/categories.json b/schema/core/reusable/categories.json
@@ -1,7 +1,7 @@
 {
     "$id": "core/reusable/categories",
     "$schema": "http://json-schema.org/draft-04/schema#",
-    "title": "categories schema",
+    "title": "categories",
     "description": "Used to categorize entities such as models and methods",
     "type": "object",
     "properties": {

diff --git a/schema/method.json b/schema/method.json
@@ -1,7 +1,7 @@
 {
     "$id": "method",
     "$schema": "http://json-schema.org/draft-04/schema#",
-    "title": "method schema (base)",
+    "title": "base method",
     "properties": {
         "type": {
             "description": "general type of this method, eg. `pseudopotential`",

diff --git a/schema/method/categorized_method.json b/schema/method/categorized_method.json
@@ -1,19 +1,16 @@
 {
     "$id": "method/categorized-method",
     "$schema": "http://json-schema.org/draft-04/schema#",
-    "title": "categorized method schema",
+    "title": "categorized method",
     "allOf": [
         {
-            "$ref": "../system/name.json"
+            "$ref": "../system/path_entity.json"
         },
         {
             "$ref": "../system/tags.json"
         }
     ],
     "properties": {
-        "path": {
-            "$ref": "../core/reusable/category_path.json"
-        },
         "units": {
             "type": "array",
             "items": {

diff --git a/schema/method/method_parameters.json b/schema/method/method_parameters.json
@@ -0,0 +1,20 @@
+{
+    "$id": "method/method-parameters",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "MethodParameters",
+    "allOf": [
+        {
+            "oneOf": [
+                {
+                    "$ref": "../methods_directory/physical/ao/dunning.json#/definitions/ao-basis-dunning"
+                },
+                {
+                    "$ref": "../methods_directory/physical/ao/pople.json#/definitions/ao-basis-pople"
+                },
+                {
+                    "$ref": "../methods_directory/physical/ao/other.json#/definitions/ao-basis-other"
+                }
+            ]
+        }
+    ]
+}
diff --git a/schema/method/unit_method.json b/schema/method/unit_method.json
@@ -1,10 +1,10 @@
 {
     "$id": "method/unit-method",
     "$schema": "http://json-schema.org/draft-04/schema#",
-    "title": "unit method schema (base)",
+    "title": "categorized unit method",
     "allOf": [
         {
-            "$ref": "../system/name.json"
+            "$ref": "../system/path_entity.json"
         },
         {
             "$ref": "../system/tags.json"
@@ -15,10 +15,6 @@
             "description": "Method categories",
             "$ref": "../core/reusable/categories.json"
         },
-        "path": {
-            "description": "URL-like method path, e.g. physical/pw",
-            "$ref": "../core/reusable/category_path.json"
-        },
         "parameters": {
             "description": "Instructive parameters defining the method",
             "type": "object"

diff --git a/schema/methods_directory/legacy/localorbital.json b/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": [
+        {
+            "$ref": "../../method.json"
+        }
+    ],
+    "properties": {
+        "type": {
+            "enum": [
+                "localorbital"
+            ]
+        },
+        "subtype": {
+            "enum": [
+                "pople"
+            ]
+        }
+    }
+}
diff --git a/schema/methods_directory/legacy/pseudopotential.json b/schema/methods_directory/legacy/pseudopotential.json
@@ -0,0 +1,25 @@
+{
+    "$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"
+            ]
+        }
+    }
+}
diff --git a/schema/methods_directory/legacy/regression.json b/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": {
+            "$ref": "../mathematical/regression/data.json"
+        }
+    },
+    "required": [
+        "precision",
+        "data"
+    ]
+}
diff --git a/schema/methods_directory/legacy/unknown.json b/schema/methods_directory/legacy/unknown.json
@@ -0,0 +1,22 @@
+{
+    "$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"
+            ]
+        }
+    }
+}
diff --git a/schema/methods_directory/mathematical/cg.json b/schema/methods_directory/mathematical/cg.json
@@ -1,6 +1,7 @@
 {
     "$id": "methods-directory/mathematical/cg",
     "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method conjugate gradient",
     "description": "conjugate gradient method schema",
     "allOf": [
         {
@@ -11,5 +12,6 @@
         "categories": {
             "$ref": "../../methods_category/mathematical/opt/diff/ordern/cg.json"
         }
-    }
+    },
+    "required": ["categories"]
 }
diff --git a/schema/methods_directory/mathematical/davidson.json b/schema/methods_directory/mathematical/davidson.json
@@ -1,6 +1,7 @@
 {
     "$id": "methods-directory/mathematical/davidson",
     "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method davidson",
     "description": "Davidson diagonalization method",
     "allOf": [
         {
@@ -11,5 +12,6 @@
         "categories": {
             "$ref": "../../methods_category/mathematical/linalg/diag/davidson.json"
         }
-    }
+    },
+    "required": ["categories"]
 }
diff --git a/schema/methods_directory/mathematical/regression.json b/schema/methods_directory/mathematical/regression.json
@@ -1,7 +1,7 @@
 {
     "$id": "methods-directory/mathematical/regression",
     "$schema": "http://json-schema.org/draft-04/schema#",
-    "title": "linear methods schema",
+    "title": "unit method regression",
     "allOf": [
         {
             "$ref": "../../method/unit_method.json"
@@ -19,6 +19,7 @@
         }
     },
     "required": [
+        "categories",
         "precision",
         "data"
     ]

diff --git a/schema/methods_directory/physical/ao/dunning.json b/schema/methods_directory/physical/ao/dunning.json
@@ -1,6 +1,7 @@
 {
     "$id": "methods-directory/physical/ao/dunning",
     "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "unit method ao dunning",
     "description": "Dunning correlation-consistent basis set unit method",
     "allOf": [
         {
@@ -14,13 +15,19 @@
         "parameters": {
             "allOf": [
                 {
-                    "properties": {
-                        "basisSlug": {
-                            "$ref": "./enum_options.json#/dunningAoBasis"
-                        }
-                    }
+                    "$ref": "#/definitions/ao-basis-dunning"
                 }
             ]
         }
+    },
+    "required": ["categories"],
+    "definitions": {
+        "ao-basis-dunning": {
+            "properties": {
+                "basisSlug": {
+                    "$ref": "./enum_options.json#/dunningAoBasis"
+                }
+            }
+        }
     }
 }