@mat3ra/esse 2025.4.26-0 → 2025.5.13-0

package/dist/js/types.d.ts

@@ -1600,6 +1600,12 @@ export interface DimensionalGridSchema {
      */
     shifts: [number, number, number];
 }
+/** Schema dist/js/schema/core/abstract/coordinate_2d.json */
+/**
+ * @minItems 2
+ * @maxItems 2
+ */
+export type Coordinate2DSchema = [number, number];
 /** Schema dist/js/schema/core/abstract/coordinate_3d.json */
 /**
  * @minItems 3
@@ -6151,6 +6157,64 @@ export interface MaterialConsistencyCheckSchema {
 export interface MaterialConventionalSchema {
     conventional?: {};
 }
+/** Schema dist/js/schema/material/reusable/repetitions.json */
+/**
+ * Number of unit cells to repeat in each direction for a crystal structure.
+ *
+ * @minItems 3
+ * @maxItems 3
+ */
+export type CrystalRepetitionsSchema = [number, number, number];
+/** Schema dist/js/schema/material/reusable/slab/enums.json */
+export type SurfaceTypesEnum = "top" | "bottom" | "both";
+/** Schema dist/js/schema/material/reusable/slab/miller_indices.json */
+/**
+ * Miller indices for crystallographic plane designation
+ *
+ * @minItems 3
+ * @maxItems 3
+ */
+export type MillerIndicesSchema = [number, number, number];
+/** Schema dist/js/schema/material/reusable/slab/number_of_layers.json */
+/**
+ * Number of atomic layers in a structural component
+ */
+export type NumberOfLayersSchema = number;
+/** Schema dist/js/schema/material/reusable/slab/termination.json */
+/**
+ * Defines a specific termination of a slab
+ */
+export interface TerminationSchema {
+    /**
+     * Chemical elements at the termination
+     */
+    chemical_elements: string;
+    /**
+     * Space group symmetry designation for the termination
+     */
+    space_group_symmetry_label: string;
+}
+/** Schema dist/js/schema/material/reusable/slab/vacuum.json */
+/**
+ * Vacuum thickness in Angstroms
+ */
+export type VacuumSchema = number;
+/** Schema dist/js/schema/material/reusable/supercell_matrix_2d.json */
+/**
+ * Supercell matrix for xy plane transformations
+ *
+ * @minItems 2
+ * @maxItems 2
+ */
+export type SupercellMatrix2DSchema = [[number, number], [number, number]];
+/** Schema dist/js/schema/material/reusable/supercell_matrix_3d.json */
+/**
+ * 3x3 matrix of integers for transforming a unit cell into a supercell
+ *
+ * @minItems 3
+ * @maxItems 3
+ */
+export type SupercellMatrix3DSchema = [[number, number, number], [number, number, number], [number, number, number]];
 /** Schema dist/js/schema/material.json */
 export interface MaterialSchema {
     /**
@@ -6408,6 +6472,302 @@ export interface MaterialSchema {
     isDefault?: boolean;
     metadata?: {};
 }
+/** Schema dist/js/schema/materials_category/single_material/two_dimensional/slab/configuration.json */
+/**
+ * Configuration for creating a slab from a bulk material
+ */
+export interface SlabConfigurationSchema {
+    bulk?: {
+        /**
+         * reduced chemical formula
+         */
+        formula?: string;
+        /**
+         * chemical formula based on the number of atoms of each element in the supercell
+         */
+        unitCellFormula?: string;
+        basis: {
+            /**
+             * atomic elements schema
+             */
+            elements: {
+                /**
+                 * value of this entry
+                 */
+                value: string;
+                /**
+                 * integer id of this entry
+                 */
+                id: number;
+            }[];
+            /**
+             * atomic coordinates schema
+             */
+            coordinates: {
+                /**
+                 * value of this entry
+                 *
+                 * @minItems 3
+                 * @maxItems 3
+                 */
+                value: [number, number, number];
+                /**
+                 * integer id of this entry
+                 */
+                id: number;
+            }[];
+            units?: "crystal" | "cartesian";
+            /**
+             * atomic labels schema
+             */
+            labels?: {
+                /**
+                 * value of this entry
+                 */
+                value: (number | string | number) | number;
+                /**
+                 * integer id of this entry
+                 */
+                id: number;
+            }[];
+        };
+        lattice: {
+            /**
+             * length of the first lattice vector
+             */
+            a: number;
+            /**
+             * length of the second lattice vector
+             */
+            b: number;
+            /**
+             * length of the third lattice vector
+             */
+            c: number;
+            /**
+             * angle between first and second lattice vector
+             */
+            alpha: number;
+            /**
+             * angle between second and third lattice vector
+             */
+            beta: number;
+            /**
+             * angle between first and third lattice vector
+             */
+            gamma: number;
+            vectors?: {
+                /**
+                 * @minItems 3
+                 * @maxItems 3
+                 */
+                a: [number, number, number];
+                /**
+                 * @minItems 3
+                 * @maxItems 3
+                 */
+                b: [number, number, number];
+                /**
+                 * @minItems 3
+                 * @maxItems 3
+                 */
+                c: [number, number, number];
+                /**
+                 * lattice parameter for fractional coordinates
+                 */
+                alat?: number;
+                units?: "angstrom" | "bohr";
+            };
+            type?: "CUB" | "BCC" | "FCC" | "TET" | "MCL" | "ORC" | "ORCC" | "ORCF" | "ORCI" | "HEX" | "BCT" | "TRI" | "MCLC" | "RHL";
+            units?: {
+                length?: "angstrom" | "bohr";
+                angle?: "degree" | "radian";
+            };
+        };
+        derivedProperties?: ({
+            name?: "volume";
+            units?: "angstrom^3";
+            value: number;
+        } | {
+            name?: "density";
+            units?: "g/cm^3";
+            value: number;
+        } | {
+            /**
+             * point group symbol in Schoenflies notation
+             */
+            pointGroupSymbol?: string;
+            /**
+             * space group symbol in Hermann–Mauguin notation
+             */
+            spaceGroupSymbol?: string;
+            /**
+             * tolerance used for symmetry calculation
+             */
+            tolerance?: {
+                units?: "angstrom";
+                value: number;
+            };
+            name?: "symmetry";
+        } | {
+            name?: "elemental_ratio";
+            value: number;
+            /**
+             * the element this ratio is for
+             */
+            element?: string;
+        } | {
+            name?: "p-norm";
+            /**
+             * degree of the dimensionality of the norm
+             */
+            degree?: number;
+            value: number;
+        } | {
+            name?: "inchi";
+            value: string;
+        } | {
+            name?: "inchi_key";
+            value: string;
+        })[];
+        /**
+         * information about a database source
+         */
+        external?: {
+            /**
+             * ID string for the materials uploaded from a third party source inside the third party source. For materialsproject.org an example ID is mp-32
+             */
+            id: string | number;
+            /**
+             * Third party source name, e.g. materials project, 2dmatpedia, ICSD, etc.
+             */
+            source: string;
+            /**
+             * Deprecated. To be removed. A flag that is true when material is initially imported from a third party * (as opposed to being independently designed from scratch).
+             */
+            origin: boolean;
+            /**
+             * Original response from external source.
+             */
+            data?: {};
+            /**
+             * Digital Object Identifier, e.g. 10.1088/0953-8984/25/10/105506
+             */
+            doi?: string;
+            /**
+             * The URL of the original record, e.g. https://next-gen.materialsproject.org/materials/mp-48; ToDo: update to use URI type per https://json-schema.org/understanding-json-schema/reference/string#resource-identifiers
+             */
+            url?: string;
+        };
+        /**
+         * file source with the information inside
+         */
+        src?: {
+            /**
+             * file extension
+             */
+            extension?: string;
+            /**
+             * file name without extension
+             */
+            filename: string;
+            /**
+             * file content as raw text
+             */
+            text: string;
+            /**
+             * MD5 hash based on file content
+             */
+            hash: string;
+        };
+        /**
+         * Hash string for a scaled structure with lattice vector a set to 1 (eg. for materials under pressure).
+         */
+        scaledHash?: string;
+        /**
+         * Corresponding ICSD id of the material
+         */
+        icsdId?: number;
+        /**
+         * Whether to work in the finite molecular picture (usually with atomic orbital basis)
+         */
+        isNonPeriodic?: boolean;
+        consistencyChecks?: {
+            /**
+             * Name of the consistency check that is performed, which is listed in an enum.
+             */
+            name: "default" | "atomsTooClose" | "atomsOverlap";
+            /**
+             * Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
+             */
+            key: string;
+            /**
+             * Severity level of the problem, which is used in UI to differentiate.
+             */
+            severity: "info" | "warning" | "error";
+            /**
+             * Message generated by the consistency check describing the problem.
+             */
+            message: string;
+        }[];
+        /**
+         * entity identity
+         */
+        _id?: string;
+        /**
+         * entity slug
+         */
+        slug?: string;
+        systemName?: string;
+        /**
+         * entity's schema version. Used to distinct between different schemas.
+         */
+        schemaVersion?: string;
+        /**
+         * entity name
+         */
+        name?: string;
+        /**
+         * Identifies that entity is defaultable
+         */
+        isDefault?: boolean;
+        metadata?: {};
+    };
+    /**
+     * Miller indices for crystallographic plane designation
+     *
+     * @minItems 3
+     * @maxItems 3
+     */
+    miller_indices?: [number, number, number];
+    /**
+     * Number of atomic layers in a structural component
+     */
+    number_of_layers?: number;
+    /**
+     * Vacuum thickness in Angstroms
+     */
+    vacuum?: number;
+    /**
+     * Supercell matrix for xy plane transformations
+     *
+     * @minItems 2
+     * @maxItems 2
+     */
+    xy_supercell_matrix?: [[number, number], [number, number]];
+    /**
+     * Whether to use conventional cell
+     */
+    use_conventional_cell?: boolean;
+    /**
+     * Whether to make z-axis orthogonal
+     */
+    use_orthogonal_z?: boolean;
+    /**
+     * Whether to make the slab primitive
+     */
+    make_primitive?: boolean;
+}
 /** Schema dist/js/schema/method/categorized_method.json */
 export interface CategorizedMethod {
     units: {

package/example/material/reusable/repetitions.json

@@ -0,0 +1 @@
+[1, 2, 3]

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

@@ -0,0 +1,5 @@
+[
+    0,
+    0,
+    1
+]

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

@@ -0,0 +1 @@
+3

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

@@ -0,0 +1,4 @@
+{
+    "chemical_elements": "Si",
+    "space_group_symmetry_label": "P4/mmm_2"
+}

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

@@ -0,0 +1 @@
+15.0

package/example/material/reusable/supercell_matrix_2d.json

@@ -0,0 +1,10 @@
+[
+    [
+        2,
+        0
+    ],
+    [
+        0,
+        2
+    ]
+]

package/example/material/reusable/supercell_matrix_3d.json

@@ -0,0 +1,5 @@
+[
+  [1, 0, 0],
+  [0, 2, 0],
+  [0, 0, 3]
+] 

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

@@ -0,0 +1,25 @@
+{
+    "bulk": {
+        "...": "include(../../../../material.json)"
+    },
+    "miller_indices": [
+        0,
+        0,
+        1
+    ],
+    "number_of_layers": 3,
+    "vacuum": 15.0,
+    "xy_supercell_matrix": [
+        [
+            1,
+            0
+        ],
+        [
+            0,
+            1
+        ]
+    ],
+    "use_conventional_cell": true,
+    "use_orthogonal_z": true,
+    "make_primitive": true
+}

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/esse",
-    "version": "2025.4.26-0",
+    "version": "2025.5.13-0",
     "description": "Mat3ra's Excellent Source of Schemas and Examples (ESSE) for Digital Materials R&D",
     "scripts": {
         "transpile": "tsc -p tsconfig-transpile.json",
@@ -27,7 +27,7 @@
     },
     "homepage": "https://github.com/Exabyte-io/esse",
     "devDependencies": {
-        "@exabyte-io/eslint-config": "^2025.1.15-0",
+        "@exabyte-io/eslint-config": "2025.5.13-0",
         "@mat3ra/tsconfig": "^2024.6.3-0",
         "@typescript-eslint/eslint-plugin": "^5.62.0",
         "@typescript-eslint/parser": "^5.62.0",
@@ -40,6 +40,7 @@
         "eslint-import-resolver-node": "^0.3.9",
         "eslint-plugin-import": "^2.31.0",
         "eslint-plugin-jsdoc": "^50.6.9",
+        "eslint-plugin-jsonc": "^2.20.0",
         "eslint-plugin-jsx-a11y": "^6.10.2",
         "eslint-plugin-mui-path-imports": "0.0.15",
         "eslint-plugin-prettier": "^4.2.1",
@@ -83,8 +84,13 @@
         "node": ">=14.0.0"
     },
     "lint-staged": {
-        "*.js,!dist/**/*": "eslint --cache --fix",
-        "*.{js,css},!dist/**/*": "prettier --write"
+        "src/**/*.js": [
+            "eslint --cache --fix",
+            "prettier --write"
+        ],
+        "src/**/*.css": "prettier --write",
+        "schemas/**/*.json": "eslint --cache --fix --no-ignore",
+        "example/**/*.json": "eslint --cache --fix --no-ignore"
     },
     "exports": {
         "./dist/js/schema/*.json": "./dist/js/schema/*.json",

package/schema/core/abstract/coordinate_2d.json

@@ -0,0 +1,11 @@
+{
+    "$id": "core/abstract/coordinate-2d",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "coordinate 2d schema",
+    "type": "array",
+    "items": {
+        "type": "number"
+    },
+    "minItems": 2,
+    "maxItems": 2
+}

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
+        ]
+    ]
+}