@mat3ra/esse 2025.4.26-0 → 2025.5.16-0

package/schema/material/reusable/repetitions.json

@@ -0,0 +1,18 @@
+{
+    "$id": "material/reusable/repetitions",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Crystal Repetitions Schema",
+    "description": "Number of unit cells to repeat in each direction for a crystal structure.",
+    "type": "array",
+    "items": {
+        "type": "integer",
+        "minimum": 1
+    },
+    "minItems": 3,
+    "maxItems": 3,
+    "default": [
+        1,
+        1,
+        1
+    ]
+}

package/schema/material/reusable/slab/enums.json

@@ -0,0 +1,11 @@
+{
+    "$id": "material/reusable/slab/enums",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Surface Types Enum",
+    "$comment": "The surface types used by passivation and surface analysis",
+    "enum": [
+        "top",
+        "bottom",
+        "both"
+    ]
+}

package/schema/material/reusable/slab/miller_indices.json

@@ -0,0 +1,17 @@
+{
+    "$id": "material/reusable/slab/miller-indices",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Miller Indices Schema",
+    "description": "Miller indices for crystallographic plane designation",
+    "type": "array",
+    "items": {
+        "type": "integer"
+    },
+    "minItems": 3,
+    "maxItems": 3,
+    "default": [
+        0,
+        0,
+        1
+    ]
+}

package/schema/material/reusable/slab/number_of_layers.json

@@ -0,0 +1,9 @@
+{
+    "$id": "material/reusable/slab/number-of-layers",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "number_of_layers Schema",
+    "description": "Number of atomic layers in a structural component",
+    "type": "integer",
+    "minimum": 1,
+    "default": 1
+}

package/schema/material/reusable/slab/termination.json

@@ -0,0 +1,23 @@
+{
+    "$id": "material/reusable/slab/termination",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Termination Schema",
+    "description": "Defines a specific termination of a slab",
+    "type": "object",
+    "required": [
+        "chemical_elements",
+        "space_group_symmetry_label"
+    ],
+    "properties": {
+        "chemical_elements": {
+            "title": "Chemical Elements",
+            "description": "Chemical elements at the termination",
+            "type": "string"
+        },
+        "space_group_symmetry_label": {
+            "title": "Space Group Symmetry Label",
+            "description": "Space group symmetry designation for the termination",
+            "type": "string"
+        }
+    }
+}

package/schema/material/reusable/slab/vacuum.json

@@ -0,0 +1,9 @@
+{
+    "$id": "material/reusable/slab/vacuum",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Vacuum Schema",
+    "description": "Vacuum thickness in Angstroms",
+    "type": "number",
+    "minimum": 0.0,
+    "default": 5.0
+}

package/schema/material/reusable/supercell_matrix_2d.json

@@ -0,0 +1,27 @@
+{
+    "$id": "material/reusable/supercell-matrix-2d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Supercell Matrix 2D Schema",
+    "description": "Supercell matrix for xy plane transformations",
+    "type": "array",
+    "items": {
+        "type": "array",
+        "items": {
+            "type": "integer"
+        },
+        "minItems": 2,
+        "maxItems": 2
+    },
+    "minItems": 2,
+    "maxItems": 2,
+    "default": [
+        [
+            1,
+            0
+        ],
+        [
+            0,
+            1
+        ]
+    ]
+}

package/schema/material/reusable/supercell_matrix_3d.json

@@ -0,0 +1,34 @@
+{
+    "$id": "material/reusable/supercell-matrix-3d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Supercell Matrix 3D Schema",
+    "description": "3x3 matrix of integers for transforming a unit cell into a supercell",
+    "type": "array",
+    "items": {
+        "type": "array",
+        "items": {
+            "type": "integer"
+        },
+        "minItems": 3,
+        "maxItems": 3
+    },
+    "minItems": 3,
+    "maxItems": 3,
+    "default": [
+        [
+            1,
+            0,
+            0
+        ],
+        [
+            0,
+            1,
+            0
+        ],
+        [
+            0,
+            0,
+            1
+        ]
+    ]
+}

package/schema/materials_category/single_material/two_dimensional/slab/configuration.json

@@ -0,0 +1,42 @@
+{
+    "$id": "materials-category/single-material/two-dimensional/slab/configuration",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Slab Configuration Schema",
+    "description": "Configuration for creating a slab from a bulk material",
+    "type": "object",
+    "properties": {
+        "bulk": {
+            "$ref": "../../../../material.json"
+        },
+        "miller_indices": {
+            "$ref": "../../../../material/reusable/slab/miller_indices.json"
+        },
+        "number_of_layers": {
+            "$ref": "../../../../material/reusable/slab/number_of_layers.json"
+        },
+        "vacuum": {
+            "$ref": "../../../../material/reusable/slab/vacuum.json"
+        },
+        "xy_supercell_matrix": {
+            "$ref": "../../../../material/reusable/supercell_matrix_2d.json"
+        },
+        "use_conventional_cell": {
+            "title": "Use Conventional Cell",
+            "description": "Whether to use conventional cell",
+            "type": "boolean",
+            "default": true
+        },
+        "use_orthogonal_z": {
+            "title": "Use Orthogonal Z",
+            "description": "Whether to make z-axis orthogonal",
+            "type": "boolean",
+            "default": false
+        },
+        "make_primitive": {
+            "title": "Make Primitive",
+            "description": "Whether to make the slab primitive",
+            "type": "boolean",
+            "default": false
+        }
+    }
+}

package/src/js/esse/JSONSchemasGenerator.ts

@@ -69,7 +69,17 @@ export default class JSONSchemasGenerator implements JSONSchemasGeneratorConfig
         const schemas = this.schemas.map((schema) => {
             console.log(`Resolving schema: ${schema.$id}`);
             const mergedSchema = skipMergeAllOff ? schema : mergeAllOf(schema, mergeAllOfConfig);
-            const idAsPath = mergedSchema.$id?.replace(/-/g, "_");
+            let idAsPath = mergedSchema.$id;
+            if (!idAsPath) {
+                throw new Error(`Schema ID is missing:
+                ${JSON.stringify(mergedSchema)}`);
+            }
+            const schemaHasDash = idAsPath.includes("-");
+            if (schemaHasDash) {
+                // replace dashes with underscores
+                idAsPath = idAsPath.replace(/-/g, "_");
+            }
+
             const fullPath = `${schemasFolder}/${idAsPath}.json`;
 
             fs.mkdirSync(path.dirname(fullPath), { recursive: true });

package/src/js/esse/utils.ts

@@ -16,12 +16,18 @@ export type JSONSchemaDefinition = JSONSchema7Definition;
  */
 export function parseIncludeReferenceStatements(filePath: string): JSONSchema {
     const jsonResolver = new JSONInclude();
-    const parsed = jsonResolver.parseIncludeStatements(filePath);
+    const parsed = jsonResolver.parseIncludeStatements(filePath) as JSONSchema;
     const dirPath = path.dirname(filePath);
+    // Store the original $id before dereferencing
+    const originalId = parsed.$id;
     let dereferenced = deref(parsed, { baseFolder: dirPath, removeIds: true });
     // handle circular references and use non-dereferenced source
     if (dereferenced instanceof Error && dereferenced.message === "Circular self reference") {
-        dereferenced = parsed as JSONSchema;
+        dereferenced = parsed;
+    }
+    // Restore the original $id after dereferencing
+    if (originalId) {
+        dereferenced.$id = originalId;
     }
     return dereferenced;
 }