SOF-6892: refactoring atomic data per orbital and orbital pair

Exabyte-io · Dec 8, 2023 · f240a45 · f240a45
1 parent c08e946
commit f240a45
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Showing 10 changed files with 101 additions and 66 deletions.
diff --git a/schema/core/reusable/atomic_data/numeric.json b/schema/core/reusable/atomic_data/numeric.json
@@ -2,21 +2,9 @@
     "$id": "core/reusable/atomic-data/numeric-data",
     "$schema": "http://json-schema.org/draft-04/schema#",
     "title": "Atomic data numeric properties",
-    "description": "Numeric fields used in atomic data",
+    "description": "Numeric value specific to atomic data",
     "type": "object",
     "properties": {
-        "id": {
-            "type": "integer",
-            "description": "Site number or index in the lattice"
-        },
-        "id2": {
-            "type": "integer",
-            "description": "Site number or index in the lattice of second site"
-        },
-        "distance": {
-            "type": "number",
-            "description": "Distance between two sites in angstrom."
-        },
         "value": {
             "type": "number",
             "description": "Value related to a specific property, e.g., Hubbard U, V etc."

diff --git a/schema/core/reusable/atomic_data/per_orbital.json b/schema/core/reusable/atomic_data/per_orbital.json
@@ -0,0 +1,22 @@
+{
+    "$id": "core/reusable/atomic-data/per-orbital",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital",
+    "description": "Atomic properties per orbital e.g., Hubbard U parameters.",
+    "type": "object",
+    "properties": {
+        "id": {
+            "type": "integer",
+            "description": "Site number or index in the lattice"
+        },
+        "atomicSpecies": {
+            "type": "string",
+            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
+            "description": "Example: Co1, Mn"
+        },
+        "orbitalName": {
+            "type": "string",
+            "pattern": "^[1-7][sSpPdDfF]$"
+        }
+    }
+}
diff --git a/schema/core/reusable/atomic_data/per_orbital_pair.json b/schema/core/reusable/atomic_data/per_orbital_pair.json
@@ -0,0 +1,39 @@
+{
+    "$id": "core/reusable/atomic-data/per-orbital-pair",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital pair",
+    "description": "Atomic properties per orbital pair e.g., Hubbard V parameters.",
+    "type": "object",
+    "properties": {
+        "id": {
+            "type": "integer",
+            "description": "Site number or index in the lattice"
+        },
+        "id2": {
+            "type": "integer",
+            "description": "Site number or index in the lattice of second site"
+        },
+        "atomicSpecies": {
+            "type": "string",
+            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
+            "description": "Example: Co1, Mn"
+        },
+        "atomicSpecies2": {
+            "type": "string",
+            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
+            "description": "Example: Co2, O"
+        },
+        "orbitalName": {
+            "type": "string",
+            "pattern": "^[1-7][sSpPdDfF]$"
+        },
+        "orbitalName2": {
+            "type": "string",
+            "pattern": "^[1-7][sSpPdDfF]$"
+        },
+        "distance": {
+            "type": "number",
+            "description": "Distance between two sites in angstrom."
+        }
+    }
+}
diff --git a/schema/core/reusable/atomic_data/string.json b/schema/core/reusable/atomic_data/string.json
@@ -2,26 +2,12 @@
     "$id": "core/reusable/atomic-data/string-data",
     "$schema": "http://json-schema.org/draft-04/schema#",
     "title": "Atomic data string properties",
-    "description": "String fields used in atomic data",
+    "description": "String value specific to atomic data",
     "type": "object",
     "properties": {
-        "atomicSpecies": {
+        "value": {
             "type": "string",
-            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
-            "description": "Example: Co1, Mn"
-        },
-        "atomicSpecies2": {
-            "type": "string",
-            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
-            "description": "Example: Co2, O"
-        },
-        "orbitalName": {
-            "type": "string",
-            "pattern": "^[1-7][sSpPdDfF]$"
-        },
-        "orbitalName2": {
-            "type": "string",
-            "pattern": "^[1-7][sSpPdDfF]$"
+            "description": "String value specific to atomic data"
         }
     }
 }
diff --git a/schema/core/reusable/atomic_data_per_orbital.json b/schema/core/reusable/atomic_data_per_orbital.json
diff --git a/schema/core/reusable/atomic_data_per_orbital_numeric.json b/schema/core/reusable/atomic_data_per_orbital_numeric.json
@@ -0,0 +1,15 @@
+{
+    "$id": "core/reusable/atomic-data-per-orbital-numeric",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital numeric",
+    "description": "Atomic properties per orbital pair with numeric value e.g., Hubbard V parameters.",
+    "type": "object",
+    "allOf":[
+        {
+            "$ref": "atomic_data/per_orbital.json"
+        },
+        {
+            "$ref": "atomic_data/numeric.json"
+        }
+    ]
+}
diff --git a/schema/core/reusable/atomic_data_per_orbital_pair.json b/schema/core/reusable/atomic_data_per_orbital_pair.json
diff --git a/schema/core/reusable/atomic_data_per_orbital_pair_numeric.json b/schema/core/reusable/atomic_data_per_orbital_pair_numeric.json
@@ -0,0 +1,15 @@
+{
+    "$id": "core/reusable/atomic-data-per-orbital-pair-numeric",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital pair numeric",
+    "description": "Atomic properties per orbital pair with numeric value e.g., Hubbard V parameters.",
+    "type": "object",
+    "allOf":[
+        {
+            "$ref": "atomic_data/per_orbital_pair.json"
+        },
+        {
+            "$ref": "atomic_data/numeric.json"
+        }
+    ]
+}
diff --git a/schema/properties_directory/non-scalar/hubbard_u.json b/schema/properties_directory/non-scalar/hubbard_u.json
@@ -16,9 +16,10 @@
                 "type": "object",
                 "allOf": [
                     {
-                        "$ref": "../../core/reusable/atomic_data_per_orbital.json"
+                        "$ref": "../../core/reusable/atomic_data_per_orbital_numeric.json"
                     }
-                ]
+                ],
+                "required": ["id", "atomicSpecies", "orbitalName", "value"]
             }
         }
     },

diff --git a/schema/properties_directory/non-scalar/hubbard_v.json b/schema/properties_directory/non-scalar/hubbard_v.json
@@ -16,9 +16,10 @@
                 "type": "object",
                 "allOf": [
                     {
-                        "$ref": "../../core/reusable/atomic_data_per_orbital_pair.json"
+                        "$ref": "../../core/reusable/atomic_data_per_orbital_pair_numeric.json"
                     }
-                ]
+                ],
+                "required": ["id", "id2", "atomicSpecies", "atomicSpecies2", "value"]
             }
         }
     },