@mat3ra/made 2026.8.7-0 → 2026.8.18-0

package/src/js/lattice/unit_cell.ts

@@ -1,66 +0,0 @@
-import { Vector3DSchema } from "@mat3ra/esse/dist/js/types";
-
-export type UnitCellProps = [
-    number,
-    number,
-    number,
-    number,
-    number,
-    number,
-    number,
-    number,
-    number,
-    string,
-];
-
-// TODO: refactor and remove the need for UnitCell
-export class UnitCell {
-    ax: number;
-
-    ay: number;
-
-    az: number;
-
-    bx: number;
-
-    by: number;
-
-    bz: number;
-
-    cx: number;
-
-    cy: number;
-
-    cz: number;
-
-    units: string;
-
-    constructor([ax, ay, az, bx, by, bz, cx, cy, cz, units]: UnitCellProps) {
-        this.ax = ax;
-        this.ay = ay;
-        this.az = az;
-        this.bx = bx;
-        this.by = by;
-        this.bz = bz;
-        this.cx = cx;
-        this.cy = cy;
-        this.cz = cz;
-        this.units = units;
-    }
-
-    vectorA(): Vector3DSchema {
-        return [this.ax, this.ay, this.az];
-    }
-
-    vectorB(): Vector3DSchema {
-        return [this.bx, this.by, this.bz];
-    }
-
-    vectorC(): Vector3DSchema {
-        return [this.cx, this.cy, this.cz];
-    }
-
-    axes(): [Vector3DSchema, Vector3DSchema, Vector3DSchema] {
-        return [this.vectorA(), this.vectorB(), this.vectorC()];
-    }
-}

package/src/js/made.ts

@@ -1,62 +0,0 @@
-import { Basis } from "./basis/basis";
-import { Cell } from "./cell/cell";
-import { ATOMIC_COORD_UNITS, coefficients, tolerance, units } from "./constants";
-import { AtomicConstraints } from "./constraints/constraints";
-import {
-    defaultNonPeriodicMinimumLatticeSize,
-    diatomicLatticePaddingFactor,
-    Lattice,
-    molecularLatticePaddingFactor,
-} from "./lattice/lattice";
-import { DEFAULT_LATTICE_UNITS, LATTICE_TYPE_CONFIGS } from "./lattice/lattice_types";
-import { ReciprocalLattice } from "./lattice/reciprocal/lattice_reciprocal";
-import { UnitCell } from "./lattice/unit_cell";
-import { defaultMaterialConfig, Material } from "./material";
-import parsers from "./parsers/parsers";
-import tools from "./tools/index";
-
-export const Made = {
-    coefficients,
-    tolerance,
-    units,
-    ATOMIC_COORD_UNITS,
-
-    Material,
-    defaultMaterialConfig,
-    Lattice,
-    Cell,
-    UnitCell,
-    defaultNonPeriodicMinimumLatticeSize,
-    diatomicLatticePaddingFactor,
-    molecularLatticePaddingFactor,
-    ReciprocalLattice,
-    Basis,
-    AtomicConstraints,
-
-    parsers,
-    tools,
-    LATTICE_TYPE_CONFIGS,
-    DEFAULT_LATTICE_UNITS,
-};
-
-export {
-    coefficients,
-    tolerance,
-    units,
-    ATOMIC_COORD_UNITS,
-    Material,
-    defaultMaterialConfig,
-    Lattice,
-    Cell,
-    UnitCell,
-    defaultNonPeriodicMinimumLatticeSize,
-    diatomicLatticePaddingFactor,
-    molecularLatticePaddingFactor,
-    ReciprocalLattice,
-    Basis,
-    AtomicConstraints,
-    parsers,
-    tools,
-    LATTICE_TYPE_CONFIGS,
-    DEFAULT_LATTICE_UNITS,
-};

package/src/js/material.ts

@@ -1,458 +0,0 @@
-import { type DefaultableInMemoryEntity, InMemoryEntity } from "@mat3ra/code/dist/js/entity";
-import { defaultableEntityMixin } from "@mat3ra/code/dist/js/entity/mixins/DefaultableMixin";
-import {
-    type HasConsistencyChecks,
-    hasConsistencyChecksMixin,
-} from "@mat3ra/code/dist/js/entity/mixins/HasConsistencyChecksMixin";
-import {
-    type HasMetadata,
-    hasMetadataMixin,
-} from "@mat3ra/code/dist/js/entity/mixins/HasMetadataMixin";
-import type { AnyObject } from "@mat3ra/esse/dist/js/esse/types";
-import type {
-    AtomicConstraintsSchema,
-    ConsistencyCheck,
-    DerivedPropertiesSchema,
-    FileSourceSchema,
-    InChIRepresentationSchema,
-    LatticeSchema,
-    MaterialSchema,
-} from "@mat3ra/esse/dist/js/types";
-import CryptoJS from "crypto-js";
-
-import type { BasisConfig } from "./basis/basis";
-import { type ConstrainedBasisConfig, ConstrainedBasis } from "./basis/constrained_basis";
-import {
-    isConventionalCellSameAsPrimitiveForLatticeType,
-    PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES,
-    PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS,
-} from "./cell/conventional_cell";
-import { Constraint } from "./constraints/constraints";
-import { Lattice } from "./lattice/lattice";
-import parsers from "./parsers/parsers";
-import supercellTools from "./tools/supercell";
-
-interface Material
-    extends HasConsistencyChecks,
-        DefaultableInMemoryEntity,
-        Required<HasMetadata<MaterialSchema["metadata"]>> {}
-
-// TODO: remove in-line type creation
-type MaterialSchemaWithConsistencyChecksAsString = Omit<MaterialSchema, "consistencyChecks"> & {
-    consistencyChecks?: ConsistencyCheck[];
-};
-
-type OptionallyConstrainedBasisConfig = BasisConfig &
-    Partial<Pick<ConstrainedBasisConfig, "constraints">>;
-
-type Schema = MaterialSchemaWithConsistencyChecksAsString;
-
-export const defaultMaterialConfig: MaterialSchema = {
-    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 InMemoryEntity implements Schema {
-    declare static createDefault: () => Material;
-
-    static get defaultConfig() {
-        return defaultMaterialConfig;
-    }
-
-    static constructMaterialFileSource(
-        fileName: string,
-        fileContent: string,
-        fileExtension: string,
-    ): FileSourceSchema {
-        return {
-            extension: fileExtension,
-            filename: fileName,
-            text: fileContent,
-            hash: CryptoJS.MD5(fileContent).toString(),
-        };
-    }
-
-    get name() {
-        return this.prop("name") ?? this.formula; // if name is not set, use formula, but keep empty string
-    }
-
-    set name(name: string) {
-        this.setProp("name", name);
-    }
-
-    get src() {
-        return this.prop("src");
-    }
-
-    set src(src: FileSourceSchema | undefined) {
-        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(): boolean {
-        return this.prop("isNonPeriodic", false);
-    }
-
-    /**
-     * @summary Sets the value of isNonPeriodic based on Boolean value passed as an argument.
-     */
-    set isNonPeriodic(bool: boolean) {
-        this.setProp("isNonPeriodic", bool);
-    }
-
-    /**
-     * @summary Returns the specific derived property (as specified by name) for a material.
-     */
-    getDerivedPropertyByName(name: string) {
-        return this.getDerivedProperties().find((x) => x.name === name);
-    }
-
-    /**
-     * @summary Returns the derived properties array for a material.
-     */
-    getDerivedProperties(): DerivedPropertiesSchema {
-        return this.prop("derivedProperties", []);
-    }
-
-    /**
-     * Gets material's formula
-     */
-    get formula(): string {
-        return this.prop("formula") || this.Basis.formula;
-    }
-
-    get unitCellFormula(): string {
-        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: string | BasisConfig, format?: string, unitz?: string) {
-        let basis: BasisConfig | undefined;
-        if (typeof textOrObject === "string" && format === "xyz") {
-            basis = parsers.xyz.toBasisConfig(textOrObject, unitz);
-        } else {
-            basis = textOrObject as BasisConfig;
-        }
-        this.setProp("basis", basis);
-        this.unsetFileProps();
-        this.updateFormula();
-    }
-
-    setBasisConstraints(constraints: Constraint[]) {
-        const basisWithConstraints = {
-            ...this.basis,
-            constraints: constraints.map((c) => c.toJSON()),
-        };
-        this.setBasis(basisWithConstraints);
-    }
-
-    setBasisConstraintsFromArrayOfObjects(constraints: AtomicConstraintsSchema) {
-        const constraintsInstances = constraints.map((c) => {
-            return Constraint.fromValueAndId(c.value, c.id);
-        });
-        this.setBasisConstraints(constraintsInstances);
-    }
-
-    get basis() {
-        return this.requiredProp<OptionallyConstrainedBasisConfig>("basis");
-    }
-
-    // returns the instance of {ConstrainedBasis} class
-    get Basis() {
-        const basisData = this.basis;
-
-        return new 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(): LatticeSchema {
-        return this.prop("lattice") as LatticeSchema;
-    }
-
-    set lattice(config: LatticeSchema) {
-        const originalIsInCrystalUnits = this.Basis.isInCrystalUnits;
-        const basis = this.Basis;
-        basis.toCartesian();
-
-        const newLattice = new 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(): Lattice {
-        return new 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(): string {
-        const inchi = this.getDerivedPropertyByName("inchi");
-        if (inchi) {
-            return (inchi as InChIRepresentationSchema).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): string {
-        let message;
-        if (!this.isNonPeriodic || bypassNonPeriodicCheck) {
-            message =
-                this.Basis.hashString + "#" + this.Lattice.getHashString(isScaled) + "#" + salt;
-        } else {
-            message = this.getInchiStringForHash();
-        }
-        return CryptoJS.MD5(message).toString();
-    }
-
-    set hash(hash: string) {
-        this.setProp("hash", hash);
-    }
-
-    get hash(): string {
-        return this.prop("hash") as string;
-    }
-
-    /**
-     * Calculates hash from basis and lattice as above + scales lattice properties to make lattice.a = 1
-     */
-    get scaledHash(): string {
-        return this.calculateHash("", true);
-    }
-
-    get external() {
-        return this.prop<MaterialSchema["external"]>("external");
-    }
-
-    set external(external: MaterialSchema["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): string {
-        return parsers.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(): string {
-        return parsers.espresso.toEspressoFormat(this.toJSON());
-    }
-
-    /**
-     * Returns material in POSCAR format. Pass `true` to ignore original poscar source and re-serialize.
-     */
-    getAsPOSCAR(ignoreOriginal = false, omitConstraints = false): string {
-        // By default return original source if exists
-        if (this.src?.extension === "poscar" && !ignoreOriginal) {
-            return this.src.text;
-        }
-        return parsers.poscar.toPoscar(this.toJSON(), omitConstraints);
-    }
-
-    /**
-     * Returns a copy of the material with conventional cell constructed instead of primitive.
-     */
-    getACopyWithConventionalCell(): this {
-        const material = this.clone();
-
-        // if conventional and primitive cells are the same => return a copy.
-        if (isConventionalCellSameAsPrimitiveForLatticeType(this.Lattice.type)) {
-            return material;
-        }
-
-        const conventionalSupercellMatrix =
-            PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[this.Lattice.type];
-        const conventionalLatticeType =
-            PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES[this.Lattice.type];
-        const config = supercellTools.generateConfig(this, conventionalSupercellMatrix);
-
-        config.lattice.type = conventionalLatticeType;
-        config.name = `${this.name} - conventional cell`;
-
-        // @ts-expect-error
-        return new this.constructor(config) as this;
-    }
-
-    /**
-     * @summary a series of checks for the material and returns an array of results in ConsistencyChecks format.
-     * @returns Array of checks results
-     */
-    getConsistencyChecks(): ConsistencyCheck[] {
-        const basisChecks = this.getBasisConsistencyChecks();
-
-        // any other Material checks can be added here
-
-        return basisChecks;
-    }
-
-    /**
-     * @summary a series of checks for the material's basis and returns an array of results in ConsistencyChecks format.
-     * @returns Array of checks results
-     */
-    getBasisConsistencyChecks(): ConsistencyCheck[] {
-        const checks: ConsistencyCheck[] = [];
-        const limit = 1000;
-        const basis = this.Basis;
-
-        if (this.Basis.elements.length < limit) {
-            const overlappingAtomsGroups = basis.getOverlappingAtoms();
-            overlappingAtomsGroups.forEach(({ id1, id2, element1, element2 }) => {
-                checks.push(
-                    {
-                        key: `basis.coordinates.${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(): MaterialSchema & AnyObject {
-        // validation intoJSON() method will fail if name is not set in _json
-        this.name = this.name || this.formula;
-
-        return {
-            ...(super.toJSON() as MaterialSchema & AnyObject),
-            lattice: this.Lattice.toJSON(),
-            basis: this.Basis.toJSON(),
-            isNonPeriodic: this.isNonPeriodic,
-        };
-    }
-}
-
-defaultableEntityMixin(Material);
-hasConsistencyChecksMixin(Material.prototype);
-hasMetadataMixin(Material.prototype);
-
-export { Material };

package/src/js/parsers/cif.ts

@@ -1,25 +0,0 @@
-export interface Meta {
-    icsdId?: number;
-}
-
-/**
- * Extracts meta information from a CIF file
- * @param txt - CIF file text.
- */
-function parseMeta(txt: string): Meta {
-    const REGEX = {
-        ICSD_ID: /_database_code_ICSD\s+(\d+)/,
-    };
-    const meta: Meta = {};
-    const groups = txt.match(REGEX.ICSD_ID);
-
-    if (groups) {
-        meta.icsdId = Number(groups[1]);
-    }
-
-    return meta;
-}
-
-export default {
-    parseMeta,
-};

package/src/js/parsers/errors.ts

@@ -1,6 +0,0 @@
-export class InvalidLineError extends Error {
-    constructor(num: number, content: string) {
-        super(`Invalid line: ${num}`);
-        console.log(`Invalid line: ${num}, content: ${content}`);
-    }
-}

package/src/js/parsers/espresso.ts

@@ -1,30 +0,0 @@
-import { MaterialSchema } from "@mat3ra/esse/dist/js/types";
-import { map } from "lodash";
-import s from "underscore.string";
-
-import { Lattice } from "../lattice/lattice";
-import xyz from "./xyz";
-
-/**
- * Construct textual representation of a materialOrConfig according to Quantum ESPRESSO pw.x input format.
- * @param materialOrConfig - material class instance or its config object
- */
-function toEspressoFormat(materialOrConfig: MaterialSchema): string {
-    const l = new Lattice(materialOrConfig.lattice);
-    const vectors = l.vectorArrays;
-    const vectorsAsString = map(vectors, (v) => {
-        return `${s.sprintf("%14.9f", v[0])}\t${s.sprintf("%14.9f", v[1])}\t${s.sprintf(
-            "%14.9f",
-            v[2],
-        )}`;
-    }).join("\n");
-    return s.sprintf(
-        "CELL_PARAMETERS (angstroms)\n%s\n\nATOMIC_POSITIONS (crystal)\n%s",
-        vectorsAsString,
-        xyz.fromMaterial(materialOrConfig),
-    );
-}
-
-export default {
-    toEspressoFormat,
-};

package/src/js/parsers/native_format_parsers.ts

@@ -1,51 +0,0 @@
-import Poscar from "./poscar";
-
-const NATIVE_FORMAT = {
-    JSON: "json",
-    POSCAR: "poscar",
-    CIF: "cif",
-    PWX: "pwx",
-    XYZ: "xyz",
-    UNKNOWN: "unknown",
-};
-
-/**
- * @summary Detects the format of the input string
- * @throws {Error} - If the input string is unknown format
- * @param {string} text -  input string to detect format
- * @returns {NATIVE_FORMAT} - Format of the input string
- */
-function detectFormat(text: string) {
-    const jsonRegex = /^\s*\{/;
-    if (jsonRegex.test(text)) return NATIVE_FORMAT.JSON;
-    if (Poscar.isPoscar(text)) return NATIVE_FORMAT.POSCAR;
-
-    return NATIVE_FORMAT.UNKNOWN;
-}
-
-/**
- * @summary Function to handle conversion from native formats
- * @param {String} text - input string to detect format and convert
- * @throws {Error} - If the input string is of unknown format
- * @return {Object} - Material config
- */
-function convertFromNativeFormat(text: string) {
-    const format = detectFormat(text);
-
-    switch (format) {
-        case NATIVE_FORMAT.JSON:
-            return JSON.parse(text);
-        case NATIVE_FORMAT.POSCAR:
-            return Poscar.fromPoscar(text);
-        case NATIVE_FORMAT.UNKNOWN:
-            throw new Error(`Unknown format`);
-        // TODO:  add more formats
-        default:
-            throw new Error(`Unsupported format: ${format}`);
-    }
-}
-
-export default {
-    detectFormat,
-    convertFromNativeFormat,
-};