@mat3ra/wode 2026.5.23-0 → 2026.6.5-0

package/src/js/context/providers/PointsPathFormDataProvider.js

@@ -1,163 +0,0 @@
-/* eslint-disable max-classes-per-file */
-/* eslint react/prop-types: 0 */
-import { JSONSchemaFormDataProvider } from "@mat3ra/ade";
-import { math as codeJSMath } from "@mat3ra/code/dist/js/math";
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-import { Made } from "@mat3ra/made";
-import s from "underscore.string";
-
-import { applicationContextMixin } from "../mixins/ApplicationContextMixin";
-import { materialContextMixin } from "../mixins/MaterialContextMixin";
-
-const defaultPoint = "Г";
-const defaultSteps = 10;
-
-export class PointsPathFormDataProvider extends JSONSchemaFormDataProvider {
-    jsonSchemaId = "context-providers-directory/points-path-data-provider";
-
-    constructor(config) {
-        super(config);
-        this.initMaterialContextMixin();
-        this.initApplicationContextMixin();
-        this.reciprocalLattice = new Made.ReciprocalLattice(this.material.lattice);
-        this.symmetryPoints = this.symmetryPointsFromMaterial;
-    }
-
-    get isEditedIsSetToFalseOnMaterialUpdate() {
-        return this.isMaterialUpdated || this.isMaterialCreatedDefault;
-    }
-
-    get defaultData() {
-        return this.reciprocalLattice.defaultKpointPath;
-    }
-
-    get symmetryPointsFromMaterial() {
-        return this.reciprocalLattice.symmetryPoints;
-    }
-
-    get jsonSchemaPatchConfig() {
-        const points = [].concat(this.symmetryPoints).map((x) => x.point);
-
-        return {
-            "items.properties.point": {
-                default: defaultPoint,
-                enum: points,
-            },
-            "items.properties.steps": {
-                default: defaultSteps,
-            },
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    get uiSchema() {
-        return {
-            items: {},
-        };
-    }
-
-    get uiSchemaStyled() {
-        return {
-            items: {
-                point: this.defaultFieldStyles,
-                steps: this.defaultFieldStyles,
-            },
-        };
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    get templates() {
-        return {};
-    }
-
-    getBrillouinZoneImageComponent(title) {
-        const hasRequiredFn = typeof this.material.getBrillouinZoneImageComponent === "function";
-        if (!hasRequiredFn) {
-            console.log(
-                "PointsPathFormDataProvider: Material class has no function" +
-                    " 'getBrillouinZoneImageComponent'! Returning empty Object instead.",
-            );
-            return null;
-        }
-        return this.material.getBrillouinZoneImageComponent(title);
-    }
-
-    get useExplicitPath() {
-        return this.application.name === "vasp";
-    }
-
-    // override yieldData to avoid storing explicit path in saved context
-    yieldDataForRendering() {
-        return this.yieldData(this.useExplicitPath);
-    }
-
-    transformData(path = [], useExplicitPath = false) {
-        const rawData = path.map((p) => {
-            const point = this.symmetryPoints.find((sp) => sp.point === p.point);
-            return { ...p, coordinates: point.coordinates };
-        });
-        const processedData = useExplicitPath ? this._convertToExplicitPath(rawData) : rawData;
-        // make coordinates into string and add formatting
-        return processedData.map((p) => {
-            const coordinates = this.is2PIBA
-                ? this.get2PIBACoordinates(p.coordinates)
-                : p.coordinates;
-            p.coordinates = coordinates.map((c) => s.sprintf("%14.9f", c));
-            return p;
-        });
-    }
-
-    get2PIBACoordinates(point) {
-        return this.reciprocalLattice.getCartesianCoordinates(point);
-    }
-
-    // Initially, path contains symmetry points with steps counts.
-    // This function explicitly calculates each point between symmetry points by step counts.
-    // eslint-disable-next-line class-methods-use-this
-    _convertToExplicitPath(path) {
-        const points = [];
-        for (let i = 0; i < path.length - 1; i++) {
-            const startPoint = path[i];
-            const endPoint = path[i + 1];
-            const middlePoints = codeJSMath.calculateSegmentsBetweenPoints3D(
-                startPoint.coordinates,
-                endPoint.coordinates,
-                startPoint.steps,
-            );
-            points.push(startPoint.coordinates);
-            points.push(...middlePoints);
-            // Include endPoint into path for the last section, otherwise it will be included by next loop iteration
-            if (path.length - 2 === i) points.push(endPoint.coordinates);
-        }
-        return points.map((x) => {
-            return {
-                coordinates: x,
-                steps: 1,
-            };
-        });
-    }
-}
-
-export class ExplicitPointsPathFormDataProvider extends PointsPathFormDataProvider {
-    // eslint-disable-next-line class-methods-use-this
-    get useExplicitPath() {
-        return true;
-    }
-}
-
-export class ExplicitPointsPath2PIBAFormDataProvider extends ExplicitPointsPathFormDataProvider {
-    // eslint-disable-next-line class-methods-use-this
-    get is2PIBA() {
-        return true;
-    }
-}
-
-materialContextMixin(PointsPathFormDataProvider.prototype);
-applicationContextMixin(PointsPathFormDataProvider.prototype);

package/src/js/context/providers/by_application/ExecutableContextProvider.js

@@ -1,17 +0,0 @@
-import { ContextProvider } from "@mat3ra/ade";
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-
-export default class ExecutableContextProvider extends ContextProvider {
-    jsonSchemaId = "context-provider";
-
-    constructor(config) {
-        super({
-            ...config,
-            domain: "executable",
-        });
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getSchemaById(this.jsonSchemaId);
-    }
-}

package/src/js/context/providers/by_application/espresso/QENEBContextProvider.js

@@ -1,58 +0,0 @@
-import lodash from "lodash";
-
-import { jobContextMixin } from "../../../mixins/JobContextMixin";
-import { materialContextMixin } from "../../../mixins/MaterialContextMixin";
-import { materialsContextMixin } from "../../../mixins/MaterialsContextMixin";
-import { materialsSetContextMixin } from "../../../mixins/MaterialsSetContextMixin";
-import { methodDataContextMixin } from "../../../mixins/MethodDataContextMixin";
-import { workflowContextMixin } from "../../../mixins/WorkflowContextMixin";
-import ExecutableContextProvider from "../ExecutableContextProvider";
-import QEPWXContextProvider from "./QEPWXContextProvider";
-
-export default class QENEBContextProvider extends ExecutableContextProvider {
-    jsonSchemaId = "context-providers-directory/by-application/qe-neb-context-provider";
-
-    _material = undefined;
-
-    _materials = [];
-
-    _materialsSet = undefined;
-
-    constructor(config) {
-        super(config);
-        this.initJobContextMixin();
-        this.initMaterialsContextMixin();
-        this.initMethodDataContextMixin();
-        this.initWorkflowContextMixin();
-        this.initMaterialContextMixin();
-        this.initMaterialsSetContextMixin();
-    }
-
-    getData() {
-        const sortedMaterials = this.sortMaterialsByIndexInSet(this.materials);
-        const PWXContexts = sortedMaterials.map((material) => {
-            const context = { ...this.config.context, material };
-            const config = { ...this.config, context };
-            return new QEPWXContextProvider(config).getData();
-        });
-
-        return {
-            ...lodash.omit(PWXContexts[0], [
-                "ATOMIC_POSITIONS",
-                "ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS",
-            ]),
-            FIRST_IMAGE: PWXContexts[0].ATOMIC_POSITIONS,
-            LAST_IMAGE: PWXContexts[PWXContexts.length - 1].ATOMIC_POSITIONS,
-            INTERMEDIATE_IMAGES: PWXContexts.slice(1, PWXContexts.length - 1).map(
-                (data) => data.ATOMIC_POSITIONS,
-            ),
-        };
-    }
-}
-
-materialContextMixin(QENEBContextProvider.prototype);
-materialsContextMixin(QENEBContextProvider.prototype);
-methodDataContextMixin(QENEBContextProvider.prototype);
-workflowContextMixin(QENEBContextProvider.prototype);
-jobContextMixin(QENEBContextProvider.prototype);
-materialsSetContextMixin(QENEBContextProvider.prototype);

package/src/js/context/providers/by_application/espresso/QEPWXContextProvider.js

@@ -1,168 +0,0 @@
-import { PERIODIC_TABLE } from "@exabyte-io/periodic-table.js";
-import path from "path";
-import s from "underscore.string";
-
-import { jobContextMixin } from "../../../mixins/JobContextMixin";
-import { materialContextMixin } from "../../../mixins/MaterialContextMixin";
-import { materialsContextMixin } from "../../../mixins/MaterialsContextMixin";
-import { methodDataContextMixin } from "../../../mixins/MethodDataContextMixin";
-import { workflowContextMixin } from "../../../mixins/WorkflowContextMixin";
-import ExecutableContextProvider from "../ExecutableContextProvider";
-
-export default class QEPWXContextProvider extends ExecutableContextProvider {
-    jsonSchemaId = "context-providers-directory/by-application/qe-pwx-context-provider";
-
-    _material = undefined;
-
-    _materials = [];
-
-    constructor(config) {
-        super(config);
-        this.initMaterialsContextMixin();
-        this.initMethodDataContextMixin();
-        this.initWorkflowContextMixin();
-        this.initJobContextMixin();
-        this.initMaterialContextMixin();
-    }
-
-    static atomSymbols(material) {
-        return material.Basis.uniqueElements;
-    }
-
-    static uniqueElementsWithLabels(material) {
-        // return unique items
-        return [...new Set(material.Basis.elementsWithLabelsArray)];
-    }
-
-    /** Returns the input text block for atomic positions WITH constraints.
-     */
-    static atomicPositionsWithConstraints(material) {
-        return material.Basis.getAtomicPositionsWithConstraintsAsStrings().join("\n");
-    }
-
-    /** Returns the input text block for atomic positions
-     *  Note: does NOT include constraints
-     */
-    static atomicPositions(material) {
-        return material.Basis.atomicPositions.join("\n");
-    }
-
-    static NAT(material) {
-        return material.Basis.atomicPositions.length;
-    }
-
-    static NTYP(material) {
-        return material.Basis.uniqueElements.length;
-    }
-
-    static NTYP_WITH_LABELS(material) {
-        return this.uniqueElementsWithLabels(material).length;
-    }
-
-    buildQEPWXContext(material) {
-        const IBRAV = 0; // use CELL_PARAMETERS to define Bravais lattice
-
-        return {
-            IBRAV,
-            RESTART_MODE: this.RESTART_MODE,
-            ATOMIC_SPECIES: this.ATOMIC_SPECIES(material),
-            ATOMIC_SPECIES_WITH_LABELS: this.ATOMIC_SPECIES_WITH_LABELS(material),
-            NAT: QEPWXContextProvider.NAT(material),
-            NTYP: QEPWXContextProvider.NTYP(material),
-            NTYP_WITH_LABELS: QEPWXContextProvider.NTYP_WITH_LABELS(material),
-            ATOMIC_POSITIONS: QEPWXContextProvider.atomicPositionsWithConstraints(material),
-            ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS: QEPWXContextProvider.atomicPositions(material),
-            CELL_PARAMETERS: QEPWXContextProvider.CELL_PARAMETERS(material),
-        };
-    }
-
-    getDataPerMaterial() {
-        if (!this.materials || this.materials.length <= 1) return {};
-        return { perMaterial: this.materials.map((material) => this.buildQEPWXContext(material)) };
-    }
-
-    /*
-     * @NOTE: Overriding getData makes this provider "stateless", ie. delivering data from scratch each time and not
-     *        considering the content of `this.data`, and `this.isEdited` field(s).
-     */
-    getData() {
-        // the below values are read from PlanewaveDataManager instead
-        // ECUTWFC = 40;
-        // ECUTRHO = 200;
-
-        return {
-            ...this.buildQEPWXContext(this.material),
-            ...this.getDataPerMaterial(),
-        };
-    }
-
-    get RESTART_MODE() {
-        return this.job.parentJob || this.workflow.hasRelaxation ? "restart" : "from_scratch";
-    }
-
-    getPseudoBySymbol(symbol) {
-        return (this.methodData.pseudo || []).find((p) => p.element === symbol);
-    }
-
-    /** Builds ATOMIC SPECIES block of pw.x input in the format
-     *  X   Mass_X   PseudoPot_X
-     *  where X            is the atom label
-     *        Mass_X       is the mass of element X [amu]
-     *        PseudoPot_X  is the pseudopotential filename associated with element X
-     *
-     *  Note: assumes this.methodData is defined
-     */
-    ATOMIC_SPECIES(material) {
-        return QEPWXContextProvider.atomSymbols(material)
-            .map((symbol) => {
-                const pseudo = this.getPseudoBySymbol(symbol);
-                return QEPWXContextProvider.symbolToAtomicSpecie(symbol, pseudo);
-            })
-            .join("\n");
-    }
-
-    ATOMIC_SPECIES_WITH_LABELS(material) {
-        return QEPWXContextProvider.uniqueElementsWithLabels(material)
-            .map((symbol) => {
-                const symbolWithoutLabel = symbol.replace(/\d$/, "");
-                const label = symbol.match(/\d$/g) ? symbol.match(/\d$/g)?.[0] : "";
-                const pseudo = this.getPseudoBySymbol(symbolWithoutLabel);
-                return QEPWXContextProvider.elementAndPseudoToAtomicSpecieWithLabels(
-                    symbolWithoutLabel,
-                    pseudo,
-                    label,
-                );
-            })
-            .join("\n");
-    }
-
-    static CELL_PARAMETERS(material) {
-        return material.Lattice.vectorArrays
-            .map((x) => {
-                return x
-                    .map((y) => {
-                        return s.sprintf("%14.9f", y).trim();
-                    })
-                    .join(" ");
-            })
-            .join("\n");
-    }
-
-    static symbolToAtomicSpecie(symbol, pseudo) {
-        const el = PERIODIC_TABLE[symbol];
-        const filename = pseudo?.filename || path.basename(pseudo?.path || "");
-        return s.sprintf("%s %f %s", symbol, el.atomic_mass, filename) || "";
-    }
-
-    static elementAndPseudoToAtomicSpecieWithLabels(symbol, pseudo, label = "") {
-        const el = PERIODIC_TABLE[symbol];
-        const filename = pseudo?.filename || path.basename(pseudo?.path || "");
-        return s.sprintf("%s%s %f %s", symbol, label, el.atomic_mass, filename) || "";
-    }
-}
-
-materialContextMixin(QEPWXContextProvider.prototype);
-materialsContextMixin(QEPWXContextProvider.prototype);
-methodDataContextMixin(QEPWXContextProvider.prototype);
-workflowContextMixin(QEPWXContextProvider.prototype);
-jobContextMixin(QEPWXContextProvider.prototype);

package/src/js/context/providers/by_application/nwchem/NWChemTotalEnergyContextProvider.js

@@ -1,89 +0,0 @@
-import { PERIODIC_TABLE } from "@exabyte-io/periodic-table.js";
-import lodash from "lodash";
-import _ from "underscore";
-import s from "underscore.string";
-
-import { jobContextMixin } from "../../../mixins/JobContextMixin";
-import { materialContextMixin } from "../../../mixins/MaterialContextMixin";
-import { methodDataContextMixin } from "../../../mixins/MethodDataContextMixin";
-import { workflowContextMixin } from "../../../mixins/WorkflowContextMixin";
-import ExecutableContextProvider from "../ExecutableContextProvider";
-
-export default class NWChemTotalEnergyContextProvider extends ExecutableContextProvider {
-    jsonSchemaId =
-        "context-providers-directory/by-application/nwchem-total-energy-context-provider";
-
-    _material = undefined;
-
-    constructor(config) {
-        super(config);
-        this.initMethodDataContextMixin();
-        this.initWorkflowContextMixin();
-        this.initJobContextMixin();
-        this.initMaterialContextMixin();
-    }
-
-    get atomicPositionsWithoutConstraints() {
-        return this.material.Basis.atomicPositions;
-    }
-
-    get atomicPositions() {
-        const basis = this.material.Basis;
-        basis.toCartesian();
-        return basis.getAtomicPositionsWithConstraintsAsStrings();
-    }
-
-    get atomSymbols() {
-        return this.material.Basis.uniqueElements;
-    }
-
-    get cartesianAtomicPositions() {
-        return this.material.Basis.toCartesian !== undefined;
-    }
-
-    get ATOMIC_SPECIES() {
-        return _.map(this.atomSymbols, (symbol) => {
-            return NWChemTotalEnergyContextProvider.symbolToAtomicSpecies(symbol);
-        }).join("\n");
-    }
-
-    /*
-     * @NOTE: Overriding getData makes this provider "stateless", ie. delivering data from scratch each time and not
-     *        considering the content of `this.data`, and `this.isEdited` field(s).
-     */
-    getData() {
-        /*
-        TODO: Create ability for user to define CHARGE, MULT, BASIS and FUNCTIONAL parameters.
-         */
-        const CHARGE = 0;
-        const MULT = 1;
-        const BASIS = "6-31G";
-        const FUNCTIONAL = "B3LYP";
-
-        return {
-            CHARGE,
-            MULT,
-            BASIS,
-            NAT: this.atomicPositions.length,
-            NTYP: this.atomSymbols.length,
-            ATOMIC_POSITIONS: this.atomicPositions.join("\n"),
-            ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS: this.atomicPositionsWithoutConstraints.join("\n"),
-            ATOMIC_SPECIES: this.ATOMIC_SPECIES,
-            FUNCTIONAL,
-            CARTESIAN: this.cartesianAtomicPositions,
-        };
-    }
-
-    static symbolToAtomicSpecies(symbol, pseudo) {
-        const el = PERIODIC_TABLE[symbol];
-        const filename = pseudo
-            ? lodash.get(pseudo, "filename", s.strRightBack(pseudo.path || "", "/"))
-            : "";
-        return el ? s.sprintf("%s %f %s", symbol, el.atomic_mass, filename) : undefined;
-    }
-}
-
-materialContextMixin(NWChemTotalEnergyContextProvider.prototype);
-methodDataContextMixin(NWChemTotalEnergyContextProvider.prototype);
-workflowContextMixin(NWChemTotalEnergyContextProvider.prototype);
-jobContextMixin(NWChemTotalEnergyContextProvider.prototype);

package/src/js/context/providers/by_application/vasp/VASPContextProvider.js

@@ -1,58 +0,0 @@
-import { jobContextMixin } from "../../../mixins/JobContextMixin";
-import { materialContextMixin } from "../../../mixins/MaterialContextMixin";
-import { materialsContextMixin } from "../../../mixins/MaterialsContextMixin";
-import { methodDataContextMixin } from "../../../mixins/MethodDataContextMixin";
-import { workflowContextMixin } from "../../../mixins/WorkflowContextMixin";
-import ExecutableContextProvider from "../ExecutableContextProvider";
-
-export default class VASPContextProvider extends ExecutableContextProvider {
-    jsonSchemaId = "context-providers-directory/by-application/vasp-context-provider";
-
-    _material = undefined;
-
-    _materials = [];
-
-    constructor(config) {
-        super(config);
-        this.initJobContextMixin();
-        this.initMaterialsContextMixin();
-        this.initMethodDataContextMixin();
-        this.initWorkflowContextMixin();
-        this.initMaterialContextMixin();
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    buildVASPContext(material) {
-        return {
-            // TODO: figure out whether we need two separate POSCARS, maybe one is enough
-            POSCAR: material.getAsPOSCAR(true, true),
-            POSCAR_WITH_CONSTRAINTS: material.getAsPOSCAR(true),
-        };
-    }
-
-    getDataPerMaterial() {
-        if (!this.materials || this.materials.length <= 1) return {};
-        return { perMaterial: this.materials.map((material) => this.buildVASPContext(material)) };
-    }
-
-    /*
-     * @NOTE: Overriding getData makes this provider "stateless", ie. delivering data from scratch each time and not
-     *        considering the content of `this.data`, and `this.isEdited` field(s).
-     */
-    getData() {
-        // consider adjusting so that below values are read from PlanewaveDataManager
-        // ECUTWFC;
-        // ECUTRHO;
-
-        return {
-            ...this.buildVASPContext(this.material),
-            ...this.getDataPerMaterial(),
-        };
-    }
-}
-
-materialContextMixin(VASPContextProvider.prototype);
-materialsContextMixin(VASPContextProvider.prototype);
-methodDataContextMixin(VASPContextProvider.prototype);
-workflowContextMixin(VASPContextProvider.prototype);
-jobContextMixin(VASPContextProvider.prototype);

package/src/js/context/providers/by_application/vasp/VASPNEBContextProvider.js

@@ -1,48 +0,0 @@
-import { jobContextMixin } from "../../../mixins/JobContextMixin";
-import { materialContextMixin } from "../../../mixins/MaterialContextMixin";
-import { materialsContextMixin } from "../../../mixins/MaterialsContextMixin";
-import { materialsSetContextMixin } from "../../../mixins/MaterialsSetContextMixin";
-import { methodDataContextMixin } from "../../../mixins/MethodDataContextMixin";
-import { workflowContextMixin } from "../../../mixins/WorkflowContextMixin";
-import ExecutableContextProvider from "../ExecutableContextProvider";
-import VASPContextProvider from "./VASPContextProvider";
-
-export default class VASPNEBContextProvider extends ExecutableContextProvider {
-    jsonSchemaId = "context-providers-directory/by-application/vasp-neb-context-provider";
-
-    _materials = [];
-
-    constructor(config) {
-        super(config);
-        this.initMaterialContextMixin();
-        this.initMaterialsContextMixin();
-        this.initMaterialsSetContextMixin();
-        this.initMethodDataContextMixin();
-        this.initWorkflowContextMixin();
-        this.initJobContextMixin();
-    }
-
-    getData() {
-        const sortedMaterials = this.sortMaterialsByIndexInSet(this.materials);
-        const VASPContexts = sortedMaterials.map((material) => {
-            const context = { ...this.config.context, material };
-            const config = { ...this.config, context };
-            return new VASPContextProvider(config).getData();
-        });
-
-        return {
-            FIRST_IMAGE: VASPContexts[0].POSCAR_WITH_CONSTRAINTS,
-            LAST_IMAGE: VASPContexts[VASPContexts.length - 1].POSCAR_WITH_CONSTRAINTS,
-            INTERMEDIATE_IMAGES: VASPContexts.slice(1, VASPContexts.length - 1).map(
-                (data) => data.POSCAR_WITH_CONSTRAINTS,
-            ),
-        };
-    }
-}
-
-materialContextMixin(VASPNEBContextProvider.prototype);
-materialsContextMixin(VASPNEBContextProvider.prototype);
-materialsSetContextMixin(VASPNEBContextProvider.prototype);
-methodDataContextMixin(VASPNEBContextProvider.prototype);
-workflowContextMixin(VASPNEBContextProvider.prototype);
-jobContextMixin(VASPNEBContextProvider.prototype);

package/src/js/context/providers/settings.js

@@ -1,38 +0,0 @@
-import { Application } from "@mat3ra/ade";
-import { Made } from "@mat3ra/made";
-
-class GlobalSettings {
-    "PointsGridFormDataProvider.defaultKPPRA" = 5;
-
-    Material = Made.Material;
-
-    Application = Application;
-
-    constructor() {
-        this.resetDefaults();
-    }
-
-    get defaultKPPRA() {
-        return this["PointsGridFormDataProvider.defaultKPPRA"];
-    }
-
-    setApplication(application) {
-        this.Application = application;
-    }
-
-    setMaterial(material) {
-        this.Material = material;
-    }
-
-    setDefaultKPPRA(kppra) {
-        this["PointsGridFormDataProvider.defaultKPPRA"] = kppra;
-    }
-
-    resetDefaults() {
-        this.Material = Made.Material;
-        this.Application = Application;
-        this["PointsGridFormDataProvider.defaultKPPRA"] = 5;
-    }
-}
-
-export const globalSettings = new GlobalSettings();