@mat3ra/made 2026.8.7-0 → 2026.8.13-0

package/dist/js/material.d.ts

@@ -1,169 +0,0 @@
-import { type DefaultableInMemoryEntity, InMemoryEntity } from "@mat3ra/code/dist/js/entity";
-import { type HasConsistencyChecks } from "@mat3ra/code/dist/js/entity/mixins/HasConsistencyChecksMixin";
-import { type HasMetadata } from "@mat3ra/code/dist/js/entity/mixins/HasMetadataMixin";
-import type { AnyObject } from "@mat3ra/esse/dist/js/esse/types";
-import type { AtomicConstraintsSchema, ConsistencyCheck, DerivedPropertiesSchema, FileSourceSchema, LatticeSchema, MaterialSchema } from "@mat3ra/esse/dist/js/types";
-import type { BasisConfig } from "./basis/basis";
-import { type ConstrainedBasisConfig, ConstrainedBasis } from "./basis/constrained_basis";
-import { Constraint } from "./constraints/constraints";
-import { Lattice } from "./lattice/lattice";
-interface Material extends HasConsistencyChecks, DefaultableInMemoryEntity, Required<HasMetadata<MaterialSchema["metadata"]>> {
-}
-type MaterialSchemaWithConsistencyChecksAsString = Omit<MaterialSchema, "consistencyChecks"> & {
-    consistencyChecks?: ConsistencyCheck[];
-};
-type OptionallyConstrainedBasisConfig = BasisConfig & Partial<Pick<ConstrainedBasisConfig, "constraints">>;
-type Schema = MaterialSchemaWithConsistencyChecksAsString;
-export declare const defaultMaterialConfig: MaterialSchema;
-declare class Material extends InMemoryEntity implements Schema {
-    static createDefault: () => Material;
-    static get defaultConfig(): MaterialSchema;
-    static constructMaterialFileSource(fileName: string, fileContent: string, fileExtension: string): FileSourceSchema;
-    get name(): string;
-    set name(name: string);
-    get src(): FileSourceSchema | undefined;
-    set src(src: FileSourceSchema | undefined);
-    updateFormula(): void;
-    /**
-     * Gets Bolean value for whether or not a material is non-periodic vs periodic.
-     * False = periodic, True = non-periodic
-     */
-    get isNonPeriodic(): boolean;
-    /**
-     * @summary Sets the value of isNonPeriodic based on Boolean value passed as an argument.
-     */
-    set isNonPeriodic(bool: boolean);
-    /**
-     * @summary Returns the specific derived property (as specified by name) for a material.
-     */
-    getDerivedPropertyByName(name: string): {
-        name?: "volume";
-        units?: "angstrom^3";
-        value: number;
-    } | {
-        name?: "density";
-        units?: "g/cm^3";
-        value: number;
-    } | {
-        pointGroupSymbol?: string;
-        spaceGroupSymbol?: string;
-        tolerance?: {
-            units?: "angstrom";
-            value: number;
-        };
-        name?: "symmetry";
-    } | {
-        name?: "elemental_ratio";
-        value: number;
-        element?: string;
-    } | {
-        name?: "p-norm";
-        degree?: number;
-        value: number;
-    } | {
-        name?: "inchi";
-        value: string;
-    } | {
-        name?: "inchi_key";
-        value: string;
-    } | undefined;
-    /**
-     * @summary Returns the derived properties array for a material.
-     */
-    getDerivedProperties(): DerivedPropertiesSchema;
-    /**
-     * Gets material's formula
-     */
-    get formula(): string;
-    get unitCellFormula(): string;
-    unsetFileProps(): void;
-    /**
-     * @param textOrObject Basis text or JSON object.
-     * @param format Format (xyz, etc.)
-     * @param unitz crystal/cartesian
-     */
-    setBasis(textOrObject: string | BasisConfig, format?: string, unitz?: string): void;
-    setBasisConstraints(constraints: Constraint[]): void;
-    setBasisConstraintsFromArrayOfObjects(constraints: AtomicConstraintsSchema): void;
-    get basis(): OptionallyConstrainedBasisConfig;
-    get Basis(): ConstrainedBasis;
-    /**
-     * High-level access to unique elements from material instead of basis.
-     */
-    get uniqueElements(): ("H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "S" | "Cl" | "Ar" | "K" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og" | "X" | "Vac")[];
-    get lattice(): LatticeSchema;
-    set lattice(config: LatticeSchema);
-    get Lattice(): Lattice;
-    /**
-     * Returns the inchi string from the derivedProperties for a non-periodic material, or throws an error if the
-     *  inchi cannot be found.
-     *  @returns {String}
-     */
-    getInchiStringForHash(): string;
-    /**
-     * Calculates hash from basis and lattice. Algorithm expects the following:
-     * - asserts lattice units to be angstrom
-     * - asserts basis units to be crystal
-     * - asserts basis coordinates and lattice measurements are rounded to hash precision
-     * - forms strings for lattice and basis
-     * - creates MD5 hash from basisStr + latticeStr + salt
-     * @param salt Salt for hashing, empty string by default.
-     * @param isScaled Whether to scale the lattice parameter 'a' to 1.
-     */
-    calculateHash(salt?: string, isScaled?: boolean, bypassNonPeriodicCheck?: boolean): string;
-    set hash(hash: string);
-    get hash(): string;
-    /**
-     * Calculates hash from basis and lattice as above + scales lattice properties to make lattice.a = 1
-     */
-    get scaledHash(): string;
-    get external(): MaterialSchema["external"];
-    set external(external: MaterialSchema["external"]);
-    /**
-     * Converts basis to crystal/fractional coordinates.
-     */
-    toCrystal(): void;
-    /**
-     * Converts current material's basis coordinates to cartesian.
-     * No changes if coordinates already cartesian.
-     */
-    toCartesian(): void;
-    /**
-     * Returns material's basis in XYZ format.
-     */
-    getBasisAsXyz(fractional?: boolean): string;
-    /**
-     * Returns material in Quantum Espresso output format:
-     * ```
-     *    CELL_PARAMETERS (angstroms)
-     *    -0.543131284  -0.000000000   0.543131284
-     *    -0.000000000   0.543131284   0.543131284
-     *    -0.543131284   0.543131284   0.000000000
-     *
-     *    ATOMIC_POSITIONS (crystal)
-     *    Si       0.000000000   0.000000000  -0.000000000
-     *    Si       0.250000000   0.250000000   0.250000000
-     * ```
-     */
-    getAsQEFormat(): string;
-    /**
-     * Returns material in POSCAR format. Pass `true` to ignore original poscar source and re-serialize.
-     */
-    getAsPOSCAR(ignoreOriginal?: boolean, omitConstraints?: boolean): string;
-    /**
-     * Returns a copy of the material with conventional cell constructed instead of primitive.
-     */
-    getACopyWithConventionalCell(): this;
-    /**
-     * @summary a series of checks for the material and returns an array of results in ConsistencyChecks format.
-     * @returns Array of checks results
-     */
-    getConsistencyChecks(): ConsistencyCheck[];
-    /**
-     * @summary a series of checks for the material's basis and returns an array of results in ConsistencyChecks format.
-     * @returns Array of checks results
-     */
-    getBasisConsistencyChecks(): ConsistencyCheck[];
-    toJSON(): MaterialSchema & AnyObject;
-}
-export { Material };

package/dist/js/material.js

@@ -1,362 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Material = exports.defaultMaterialConfig = void 0;
-const entity_1 = require("@mat3ra/code/dist/js/entity");
-const DefaultableMixin_1 = require("@mat3ra/code/dist/js/entity/mixins/DefaultableMixin");
-const HasConsistencyChecksMixin_1 = require("@mat3ra/code/dist/js/entity/mixins/HasConsistencyChecksMixin");
-const HasMetadataMixin_1 = require("@mat3ra/code/dist/js/entity/mixins/HasMetadataMixin");
-const crypto_js_1 = __importDefault(require("crypto-js"));
-const constrained_basis_1 = require("./basis/constrained_basis");
-const conventional_cell_1 = require("./cell/conventional_cell");
-const constraints_1 = require("./constraints/constraints");
-const lattice_1 = require("./lattice/lattice");
-const parsers_1 = __importDefault(require("./parsers/parsers"));
-const supercell_1 = __importDefault(require("./tools/supercell"));
-exports.defaultMaterialConfig = {
-    name: "Silicon FCC",
-    basis: {
-        elements: [
-            {
-                id: 0,
-                value: "Si",
-            },
-            {
-                id: 1,
-                value: "Si",
-            },
-        ],
-        coordinates: [
-            {
-                id: 0,
-                value: [0.0, 0.0, 0.0],
-            },
-            {
-                id: 1,
-                value: [0.25, 0.25, 0.25],
-            },
-        ],
-        units: "crystal",
-    },
-    lattice: {
-        // Primitive cell for Diamond FCC Silicon at ambient conditions
-        type: "FCC",
-        a: 3.867,
-        b: 3.867,
-        c: 3.867,
-        alpha: 60,
-        beta: 60,
-        gamma: 60,
-        units: {
-            length: "angstrom",
-            angle: "degree",
-        },
-    },
-    metadata: {},
-};
-class Material extends entity_1.InMemoryEntity {
-    static get defaultConfig() {
-        return exports.defaultMaterialConfig;
-    }
-    static constructMaterialFileSource(fileName, fileContent, fileExtension) {
-        return {
-            extension: fileExtension,
-            filename: fileName,
-            text: fileContent,
-            hash: crypto_js_1.default.MD5(fileContent).toString(),
-        };
-    }
-    get name() {
-        var _a;
-        return (_a = this.prop("name")) !== null && _a !== void 0 ? _a : this.formula; // if name is not set, use formula, but keep empty string
-    }
-    set name(name) {
-        this.setProp("name", name);
-    }
-    get src() {
-        return this.prop("src");
-    }
-    set src(src) {
-        this.setProp("src", src);
-    }
-    updateFormula() {
-        this.setProp("formula", this.Basis.formula);
-        this.setProp("unitCellFormula", this.Basis.unitCellFormula);
-    }
-    /**
-     * Gets Bolean value for whether or not a material is non-periodic vs periodic.
-     * False = periodic, True = non-periodic
-     */
-    get isNonPeriodic() {
-        return this.prop("isNonPeriodic", false);
-    }
-    /**
-     * @summary Sets the value of isNonPeriodic based on Boolean value passed as an argument.
-     */
-    set isNonPeriodic(bool) {
-        this.setProp("isNonPeriodic", bool);
-    }
-    /**
-     * @summary Returns the specific derived property (as specified by name) for a material.
-     */
-    getDerivedPropertyByName(name) {
-        return this.getDerivedProperties().find((x) => x.name === name);
-    }
-    /**
-     * @summary Returns the derived properties array for a material.
-     */
-    getDerivedProperties() {
-        return this.prop("derivedProperties", []);
-    }
-    /**
-     * Gets material's formula
-     */
-    get formula() {
-        return this.prop("formula") || this.Basis.formula;
-    }
-    get unitCellFormula() {
-        return this.prop("unitCellFormula") || this.Basis.unitCellFormula;
-    }
-    unsetFileProps() {
-        this.unsetProp("src");
-        this.unsetProp("icsdId");
-        this.unsetProp("external");
-    }
-    /**
-     * @param textOrObject Basis text or JSON object.
-     * @param format Format (xyz, etc.)
-     * @param unitz crystal/cartesian
-     */
-    setBasis(textOrObject, format, unitz) {
-        let basis;
-        if (typeof textOrObject === "string" && format === "xyz") {
-            basis = parsers_1.default.xyz.toBasisConfig(textOrObject, unitz);
-        }
-        else {
-            basis = textOrObject;
-        }
-        this.setProp("basis", basis);
-        this.unsetFileProps();
-        this.updateFormula();
-    }
-    setBasisConstraints(constraints) {
-        const basisWithConstraints = {
-            ...this.basis,
-            constraints: constraints.map((c) => c.toJSON()),
-        };
-        this.setBasis(basisWithConstraints);
-    }
-    setBasisConstraintsFromArrayOfObjects(constraints) {
-        const constraintsInstances = constraints.map((c) => {
-            return constraints_1.Constraint.fromValueAndId(c.value, c.id);
-        });
-        this.setBasisConstraints(constraintsInstances);
-    }
-    get basis() {
-        return this.requiredProp("basis");
-    }
-    // returns the instance of {ConstrainedBasis} class
-    get Basis() {
-        const basisData = this.basis;
-        return new constrained_basis_1.ConstrainedBasis({
-            ...basisData,
-            cell: this.Lattice.vectors,
-            constraints: basisData.constraints || [],
-        });
-    }
-    /**
-     * High-level access to unique elements from material instead of basis.
-     */
-    get uniqueElements() {
-        return this.Basis.uniqueElements;
-    }
-    get lattice() {
-        return this.prop("lattice");
-    }
-    set lattice(config) {
-        const originalIsInCrystalUnits = this.Basis.isInCrystalUnits;
-        const basis = this.Basis;
-        basis.toCartesian();
-        const newLattice = new lattice_1.Lattice(config);
-        basis.cell = newLattice.vectors;
-        if (originalIsInCrystalUnits)
-            basis.toCrystal();
-        // Preserve all properties from the original basis to ensure constraints are included
-        const newBasisConfig = basis.toJSON();
-        this.setProp("basis", newBasisConfig);
-        this.setProp("lattice", config);
-        this.unsetFileProps();
-    }
-    get Lattice() {
-        return new lattice_1.Lattice(this.lattice);
-    }
-    /**
-     * Returns the inchi string from the derivedProperties for a non-periodic material, or throws an error if the
-     *  inchi cannot be found.
-     *  @returns {String}
-     */
-    getInchiStringForHash() {
-        const inchi = this.getDerivedPropertyByName("inchi");
-        if (inchi) {
-            return inchi.value;
-        }
-        throw new Error("Hash cannot be created. Missing InChI string in derivedProperties");
-    }
-    /**
-     * Calculates hash from basis and lattice. Algorithm expects the following:
-     * - asserts lattice units to be angstrom
-     * - asserts basis units to be crystal
-     * - asserts basis coordinates and lattice measurements are rounded to hash precision
-     * - forms strings for lattice and basis
-     * - creates MD5 hash from basisStr + latticeStr + salt
-     * @param salt Salt for hashing, empty string by default.
-     * @param isScaled Whether to scale the lattice parameter 'a' to 1.
-     */
-    calculateHash(salt = "", isScaled = false, bypassNonPeriodicCheck = false) {
-        let message;
-        if (!this.isNonPeriodic || bypassNonPeriodicCheck) {
-            message =
-                this.Basis.hashString + "#" + this.Lattice.getHashString(isScaled) + "#" + salt;
-        }
-        else {
-            message = this.getInchiStringForHash();
-        }
-        return crypto_js_1.default.MD5(message).toString();
-    }
-    set hash(hash) {
-        this.setProp("hash", hash);
-    }
-    get hash() {
-        return this.prop("hash");
-    }
-    /**
-     * Calculates hash from basis and lattice as above + scales lattice properties to make lattice.a = 1
-     */
-    get scaledHash() {
-        return this.calculateHash("", true);
-    }
-    get external() {
-        return this.prop("external");
-    }
-    set external(external) {
-        this.setProp("external", external);
-    }
-    /**
-     * Converts basis to crystal/fractional coordinates.
-     */
-    toCrystal() {
-        const basis = this.Basis;
-        basis.toCrystal();
-        this.setProp("basis", basis.toJSON());
-    }
-    /**
-     * Converts current material's basis coordinates to cartesian.
-     * No changes if coordinates already cartesian.
-     */
-    toCartesian() {
-        const basis = this.Basis;
-        basis.toCartesian();
-        this.setProp("basis", basis.toJSON());
-    }
-    /**
-     * Returns material's basis in XYZ format.
-     */
-    getBasisAsXyz(fractional = false) {
-        return parsers_1.default.xyz.fromMaterial(this.toJSON(), fractional);
-    }
-    /**
-     * Returns material in Quantum Espresso output format:
-     * ```
-     *    CELL_PARAMETERS (angstroms)
-     *    -0.543131284  -0.000000000   0.543131284
-     *    -0.000000000   0.543131284   0.543131284
-     *    -0.543131284   0.543131284   0.000000000
-     *
-     *    ATOMIC_POSITIONS (crystal)
-     *    Si       0.000000000   0.000000000  -0.000000000
-     *    Si       0.250000000   0.250000000   0.250000000
-     * ```
-     */
-    getAsQEFormat() {
-        return parsers_1.default.espresso.toEspressoFormat(this.toJSON());
-    }
-    /**
-     * Returns material in POSCAR format. Pass `true` to ignore original poscar source and re-serialize.
-     */
-    getAsPOSCAR(ignoreOriginal = false, omitConstraints = false) {
-        var _a;
-        // By default return original source if exists
-        if (((_a = this.src) === null || _a === void 0 ? void 0 : _a.extension) === "poscar" && !ignoreOriginal) {
-            return this.src.text;
-        }
-        return parsers_1.default.poscar.toPoscar(this.toJSON(), omitConstraints);
-    }
-    /**
-     * Returns a copy of the material with conventional cell constructed instead of primitive.
-     */
-    getACopyWithConventionalCell() {
-        const material = this.clone();
-        // if conventional and primitive cells are the same => return a copy.
-        if ((0, conventional_cell_1.isConventionalCellSameAsPrimitiveForLatticeType)(this.Lattice.type)) {
-            return material;
-        }
-        const conventionalSupercellMatrix = conventional_cell_1.PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[this.Lattice.type];
-        const conventionalLatticeType = conventional_cell_1.PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES[this.Lattice.type];
-        const config = supercell_1.default.generateConfig(this, conventionalSupercellMatrix);
-        config.lattice.type = conventionalLatticeType;
-        config.name = `${this.name} - conventional cell`;
-        // @ts-expect-error
-        return new this.constructor(config);
-    }
-    /**
-     * @summary a series of checks for the material and returns an array of results in ConsistencyChecks format.
-     * @returns Array of checks results
-     */
-    getConsistencyChecks() {
-        const basisChecks = this.getBasisConsistencyChecks();
-        // any other Material checks can be added here
-        return basisChecks;
-    }
-    /**
-     * @summary a series of checks for the material's basis and returns an array of results in ConsistencyChecks format.
-     * @returns Array of checks results
-     */
-    getBasisConsistencyChecks() {
-        const checks = [];
-        const limit = 1000;
-        const basis = this.Basis;
-        if (this.Basis.elements.length < limit) {
-            const overlappingAtomsGroups = basis.getOverlappingAtoms();
-            overlappingAtomsGroups.forEach(({ id1, id2, element1, element2 }) => {
-                checks.push({
-                    key: `basis.coordinates.${id1}`,
-                    name: "atomsOverlap",
-                    severity: "warning",
-                    message: `Atom ${element1} is too close to ${element2} at position ${id2 + 1}`,
-                }, {
-                    key: `basis.coordinates.${id2}`,
-                    name: "atomsOverlap",
-                    severity: "warning",
-                    message: `Atom ${element2} is too close to ${element1} at position ${id1 + 1}`,
-                });
-            });
-        }
-        return checks;
-    }
-    toJSON() {
-        // validation intoJSON() method will fail if name is not set in _json
-        this.name = this.name || this.formula;
-        return {
-            ...super.toJSON(),
-            lattice: this.Lattice.toJSON(),
-            basis: this.Basis.toJSON(),
-            isNonPeriodic: this.isNonPeriodic,
-        };
-    }
-}
-exports.Material = Material;
-(0, DefaultableMixin_1.defaultableEntityMixin)(Material);
-(0, HasConsistencyChecksMixin_1.hasConsistencyChecksMixin)(Material.prototype);
-(0, HasMetadataMixin_1.hasMetadataMixin)(Material.prototype);