@mat3ra/wode 2026.4.9-0 → 2026.5.29-0

package/src/js/context/mixins/MethodDataContextMixin.js

@@ -1,48 +0,0 @@
-import CryptoJS from "crypto-js";
-
-export function methodDataContextMixin(item) {
-    const properties = {
-        _methodData: undefined,
-
-        isEdited: false,
-
-        methodDataHash: undefined,
-
-        extraData: undefined,
-
-        initMethodDataContextMixin() {
-            this._methodData = (this.config.context && this.config.context.methodData) || {};
-            this.isEdited = Boolean(this.config.isEdited);
-        },
-
-        /* @summary Replace the logic in constructor with this in order to enable passing `methodDataHash` between
-         *          subsequent initializations of the derived class. Not used at present and kept for the record.
-         */
-        _initMethodDataHash() {
-            this.methodDataHash = CryptoJS.MD5(JSON.stringify(this.methodData)).toString();
-            this.extraData = { methodDataHash: this.methodDataHash };
-            if (!this._methodData) {
-                this._methodData = {};
-                this.isEdited = false;
-                // Commented out to reduce effect on performance. Uncomment for debugging purposes.
-                // TODO: remove on next refactoring or convert to log
-                // console.warn("MethodDataContextMixin: methodData is undefined or null");
-            } else if (this.isMethodDataUpdated) {
-                this.isEdited = false;
-            } else {
-                // eslint-disable-next-line no-undef
-                this.isEdited = config.isEdited;
-            }
-        },
-
-        get methodData() {
-            return this._methodData;
-        },
-
-        get isMethodDataUpdated() {
-            return Boolean(this.extraData && this.extraData.methodDataHash !== this.methodDataHash);
-        },
-    };
-
-    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
-}

package/src/js/context/mixins/WorkflowContextMixin.js

@@ -1,25 +0,0 @@
-const defaultWorkflow = {
-    subworkflows: [],
-    units: [],
-    hasRelaxation: false,
-};
-
-export function workflowContextMixin(item) {
-    const properties = {
-        isEdited: false,
-
-        _workflow: defaultWorkflow,
-
-        get workflow() {
-            return this._workflow;
-        },
-
-        initWorkflowContextMixin() {
-            const { config } = this; // as WorkflowConfig;
-            this._workflow = (config.context && config.context.workflow) || defaultWorkflow;
-            this.isEdited = false; // we always get the `defaultData` (recalculated from scratch, not persistent)
-        },
-    };
-
-    Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
-}

package/src/js/context/providers/BoundaryConditionsFormDataProvider.js

@@ -1,72 +0,0 @@
-import { JSONSchemaFormDataProvider } from "@mat3ra/ade";
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-import { Made } from "@mat3ra/made";
-import { Utils } from "@mat3ra/utils";
-
-import { materialContextMixin } from "../mixins/MaterialContextMixin";
-
-export class BoundaryConditionsFormDataProvider extends JSONSchemaFormDataProvider {
-    jsonSchemaId = "context-providers-directory/boundary-conditions-data-provider";
-
-    constructor(config) {
-        super(config);
-        this.initMaterialContextMixin();
-    }
-
-    get boundaryConditions() {
-        return this.material.metadata.boundaryConditions || {};
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    get defaultData() {
-        return {
-            type: this.boundaryConditions.type || "pbc",
-            offset: this.boundaryConditions.offset || 0,
-            electricField: 0,
-            targetFermiEnergy: 0,
-        };
-    }
-
-    get jsonSchemaPatchConfig() {
-        const defaults = this.defaultData;
-        return {
-            type: { default: defaults.type },
-            offset: { default: defaults.offset },
-            electricField: { default: defaults.electricField },
-            targetFermiEnergy: { default: defaults.targetFermiEnergy },
-        };
-    }
-
-    // TODO: MOVE to WA/wove instantiation
-    // eslint-disable-next-line class-methods-use-this
-    get uiSchema() {
-        return {
-            type: { "ui:disabled": true },
-            offset: { "ui:disabled": true },
-            electricField: {},
-            targetFermiEnergy: {},
-        };
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    get humanName() {
-        return "Boundary Conditions";
-    }
-
-    yieldDataForRendering() {
-        const data = Utils.clone.deepClone(this.yieldData());
-        data.boundaryConditions.offset *= Made.coefficients.ANGSTROM_TO_BOHR;
-        data.boundaryConditions.targetFermiEnergy *= Made.coefficients.EV_TO_RY;
-        data.boundaryConditions.electricField *= Made.coefficients.EV_A_TO_RY_BOHR;
-        return data;
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}
-
-materialContextMixin(BoundaryConditionsFormDataProvider.prototype);

package/src/js/context/providers/CollinearMagnetizationContextProvider.js

@@ -1,105 +0,0 @@
-import { JSONSchemaFormDataProvider } from "@mat3ra/ade";
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-import lodash from "lodash";
-
-import { materialContextMixin } from "../mixins/MaterialContextMixin";
-
-export class CollinearMagnetizationContextProvider extends JSONSchemaFormDataProvider {
-    jsonSchemaId = "context-providers-directory/collinear-magnetization-context-provider";
-
-    constructor(config) {
-        super(config);
-
-        this.initMaterialContextMixin();
-
-        this.firstElement =
-            this.uniqueElementsWithLabels?.length > 0 ? this.uniqueElementsWithLabels[0] : "";
-        this.isTotalMagnetization = lodash.get(this.data, "isTotalMagnetization", false);
-    }
-
-    get uniqueElementsWithLabels() {
-        const elementsWithLabelsArray = this.material?.Basis?.elementsWithLabelsArray || [];
-        return [...new Set(elementsWithLabelsArray)];
-    }
-
-    indexOfElement = (element) => {
-        return this.uniqueElementsWithLabels.indexOf(element) + 1;
-    };
-
-    get defaultData() {
-        return {
-            startingMagnetization: [
-                {
-                    index: 1,
-                    atomicSpecies: this.firstElement,
-                    value: 0.0,
-                },
-            ],
-            isTotalMagnetization: false,
-            totalMagnetization: 0.0,
-        };
-    }
-
-    get jsonSchemaPatchConfig() {
-        return {
-            "properties.startingMagnetization": {
-                maxItems: this.uniqueElementsWithLabels.length,
-            },
-            "properties.startingMagnetization.items.properties.atomicSpecies": {
-                enum: this.uniqueElementsWithLabels,
-                default: this.firstElement,
-            },
-            "properties.startingMagnetization.items.properties.value": {
-                default: 0.0,
-            },
-            "properties.isTotalMagnetization": {
-                default: false,
-            },
-            "properties.totalMagnetization": {
-                default: 0.0,
-            },
-        };
-    }
-
-    transformData = (data) => {
-        const startingMagnetizationWithIndex = data.startingMagnetization.map((row) => ({
-            ...row,
-            index: this.indexOfElement(row.atomicSpecies),
-        }));
-
-        return {
-            ...data,
-            startingMagnetization: startingMagnetizationWithIndex,
-        };
-    };
-
-    get uiSchemaStyled() {
-        return {
-            startingMagnetization: {
-                items: {
-                    atomicSpecies: {
-                        "ui:classNames": "col-xs-3",
-                    },
-                    value: {
-                        "ui:classNames": "col-xs-6",
-                    },
-                },
-                "ui:readonly": this.isTotalMagnetization,
-            },
-            isTotalMagnetization: {},
-            totalMagnetization: {
-                "ui:classNames": "col-xs-6",
-                "ui:readonly": !this.isTotalMagnetization,
-            },
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}
-
-materialContextMixin(CollinearMagnetizationContextProvider.prototype);

package/src/js/context/providers/HubbardContextProviderLegacy.js

@@ -1,67 +0,0 @@
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-
-import { HubbardUContextProvider } from "./HubbardUContextProvider";
-
-const defaultHubbardConfig = {
-    hubbardUValue: 1.0,
-};
-
-export class HubbardContextProviderLegacy extends HubbardUContextProvider {
-    jsonSchemaId = "context-providers-directory/hubbard-legacy-context-provider";
-
-    get defaultData() {
-        return [
-            {
-                ...defaultHubbardConfig,
-                atomicSpecies: this.firstElement,
-                atomicSpeciesIndex: this.uniqueElementsWithLabels?.length > 0 ? 1 : null,
-            },
-        ];
-    }
-
-    get jsonSchemaPatchConfig() {
-        return {
-            "items.properties.atomicSpecies": {
-                enum: this.uniqueElementsWithLabels,
-            },
-            "items.properties.hubbardUValue": {
-                default: defaultHubbardConfig.hubbardUValue,
-            },
-        };
-    }
-
-    speciesIndexFromSpecies = (species) => {
-        return this.uniqueElementsWithLabels?.length > 0
-            ? this.uniqueElementsWithLabels.indexOf(species) + 1
-            : null;
-    };
-
-    transformData = (data) => {
-        return data.map((row) => ({
-            ...row,
-            atomicSpeciesIndex: this.speciesIndexFromSpecies(row.atomicSpecies),
-        }));
-    };
-
-    get uiSchemaStyled() {
-        return {
-            "ui:options": {
-                addable: true,
-                orderable: false,
-                removable: true,
-            },
-            items: {
-                atomicSpecies: this.defaultFieldStyles,
-                atomicSpeciesIndex: { ...this.defaultFieldStyles, "ui:readonly": true },
-                hubbardUValue: this.defaultFieldStyles,
-            },
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}

package/src/js/context/providers/HubbardJContextProvider.js

@@ -1,65 +0,0 @@
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-
-import { HubbardUContextProvider } from "./HubbardUContextProvider";
-
-const defaultHubbardConfig = {
-    paramType: "U",
-    atomicSpecies: "",
-    atomicOrbital: "2p",
-    value: 1.0,
-};
-
-export class HubbardJContextProvider extends HubbardUContextProvider {
-    jsonSchemaId = "context-providers-directory/hubbard-j-context-provider";
-
-    get defaultData() {
-        return [
-            {
-                ...defaultHubbardConfig,
-                atomicSpecies: this.firstElement,
-            },
-        ];
-    }
-
-    get jsonSchemaPatchConfig() {
-        return {
-            "items.properties.paramType": {
-                default: defaultHubbardConfig.paramType,
-            },
-            "items.properties.atomicSpecies": {
-                enum: this.uniqueElementsWithLabels,
-                default: this.firstElement,
-            },
-            "items.properties.atomicOrbital": {
-                enum: this.orbitalList,
-                default: defaultHubbardConfig.atomicOrbital,
-            },
-            "items.properties.value": {
-                default: defaultHubbardConfig.value,
-            },
-        };
-    }
-
-    get uiSchemaStyled() {
-        return {
-            "ui:options": {
-                addable: true,
-                orderable: true,
-                removable: true,
-            },
-            items: {
-                paramType: this.defaultFieldStyles,
-                atomicSpecies: this.defaultFieldStyles,
-                atomicOrbital: this.defaultFieldStyles,
-                value: this.defaultFieldStyles,
-            },
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}

package/src/js/context/providers/HubbardUContextProvider.js

@@ -1,95 +0,0 @@
-import { JSONSchemaFormDataProvider } from "@mat3ra/ade";
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-
-import { materialContextMixin } from "../mixins/MaterialContextMixin";
-
-const defaultHubbardConfig = {
-    atomicSpecies: "",
-    atomicOrbital: "2p",
-    hubbardUValue: 1.0,
-};
-
-export class HubbardUContextProvider extends JSONSchemaFormDataProvider {
-    jsonSchemaId = "context-providers-directory/hubbard-u-context-provider";
-
-    constructor(config) {
-        super(config);
-
-        this.initMaterialContextMixin();
-
-        this.uniqueElements = this.material?.Basis?.uniqueElements || [];
-        this.orbitalList = [
-            "2p",
-            "3s",
-            "3p",
-            "3d",
-            "4s",
-            "4p",
-            "4d",
-            "4f",
-            "5s",
-            "5p",
-            "5d",
-            "5f",
-            "6s",
-            "6p",
-            "6d",
-            "7s",
-            "7p",
-            "7d",
-        ];
-        const _elementsWithLabels = this.material?.Basis?.elementsWithLabelsArray || [];
-        this.uniqueElementsWithLabels = [...new Set(_elementsWithLabels)];
-        this.firstElement =
-            this.uniqueElementsWithLabels?.length > 0 ? this.uniqueElementsWithLabels[0] : "";
-    }
-
-    get defaultData() {
-        return [
-            {
-                ...defaultHubbardConfig,
-                atomicSpecies: this.firstElement,
-            },
-        ];
-    }
-
-    get jsonSchemaPatchConfig() {
-        return {
-            "items.properties.atomicSpecies": {
-                enum: this.uniqueElementsWithLabels,
-                default: this.firstElement,
-            },
-            "items.properties.atomicOrbital": {
-                enum: this.orbitalList,
-                default: defaultHubbardConfig.atomicOrbital,
-            },
-            "items.properties.hubbardUValue": {
-                default: defaultHubbardConfig.hubbardUValue,
-            },
-        };
-    }
-
-    get uiSchemaStyled() {
-        return {
-            "ui:options": {
-                addable: true,
-                orderable: false,
-                removable: true,
-            },
-            items: {
-                atomicSpecies: this.defaultFieldStyles,
-                atomicOrbital: this.defaultFieldStyles,
-                hubbardUValue: this.defaultFieldStyles,
-            },
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}
-
-materialContextMixin(HubbardUContextProvider.prototype);

package/src/js/context/providers/HubbardVContextProvider.js

@@ -1,96 +0,0 @@
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-
-import { HubbardUContextProvider } from "./HubbardUContextProvider";
-
-const defaultHubbardConfig = {
-    atomicSpecies: "",
-    atomicOrbital: "2p",
-    atomicSpecies2: "",
-    atomicOrbital2: "2p",
-    siteIndex: 1,
-    siteIndex2: 1,
-    hubbardVValue: 1.0,
-};
-
-export class HubbardVContextProvider extends HubbardUContextProvider {
-    jsonSchemaId = "context-providers-directory/hubbard-v-context-provider";
-
-    get defaultData() {
-        return [
-            {
-                ...defaultHubbardConfig,
-                atomicSpecies: this.firstSpecies,
-                atomicSpecies2: this.secondSpecies,
-                siteIndex2:
-                    this.uniqueElementsWithLabels?.length > 1 ? 2 : defaultHubbardConfig.siteIndex2,
-            },
-        ];
-    }
-
-    get firstSpecies() {
-        return this.firstElement;
-    }
-
-    get secondSpecies() {
-        return this.uniqueElementsWithLabels?.length > 1
-            ? this.uniqueElementsWithLabels[1]
-            : this.firstSpecies;
-    }
-
-    get jsonSchemaPatchConfig() {
-        return {
-            "items.properties.atomicSpecies": {
-                enum: this.uniqueElementsWithLabels,
-                default: this.firstSpecies,
-            },
-            "items.properties.siteIndex": {
-                default: defaultHubbardConfig.siteIndex,
-            },
-            "items.properties.atomicOrbital": {
-                enum: this.orbitalList,
-                default: defaultHubbardConfig.atomicOrbital,
-            },
-            "items.properties.atomicSpecies2": {
-                enum: this.uniqueElementsWithLabels,
-                default: this.secondSpecies,
-            },
-            "items.properties.siteIndex2": {
-                default:
-                    this.uniqueElementsWithLabels?.length > 1 ? 2 : defaultHubbardConfig.siteIndex2,
-            },
-            "items.properties.atomicOrbital2": {
-                enum: this.orbitalList,
-                default: defaultHubbardConfig.atomicOrbital,
-            },
-            "items.properties.hubbardVValue": {
-                default: defaultHubbardConfig.hubbardVValue,
-            },
-        };
-    }
-
-    get uiSchemaStyled() {
-        return {
-            "ui:options": {
-                addable: true,
-                orderable: true,
-                removable: true,
-            },
-            items: {
-                atomicSpecies: this.defaultFieldStyles,
-                atomicOrbital: this.defaultFieldStyles,
-                atomicSpecies2: this.defaultFieldStyles,
-                atomicOrbital2: this.defaultFieldStyles,
-                siteIndex: this.defaultFieldStyles,
-                siteIndex2: this.defaultFieldStyles,
-                hubbardVValue: this.defaultFieldStyles,
-            },
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}

package/src/js/context/providers/IonDynamicsContextProvider.js

@@ -1,44 +0,0 @@
-import { JSONSchemaFormDataProvider } from "@mat3ra/ade";
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-
-const defaultMDConfig = {
-    numberOfSteps: 100,
-    timeStep: 5.0,
-    electronMass: 100.0,
-    temperature: 300.0,
-};
-
-export class IonDynamicsContextProvider extends JSONSchemaFormDataProvider {
-    jsonSchemaId = "context-providers-directory/ion-dynamics-context-provider";
-
-    // eslint-disable-next-line class-methods-use-this
-    get defaultData() {
-        return defaultMDConfig;
-    }
-
-    get jsonSchemaPatchConfig() {
-        return {
-            numberOfSteps: { default: this.defaultData.numberOfSteps },
-            timeStep: { default: this.defaultData.timeStep },
-            electronMass: { default: this.defaultData.electronMass },
-            temperature: { default: this.defaultData.temperature },
-        };
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    get uiSchema() {
-        return {
-            numberOfSteps: {},
-            timeStep: {},
-            electronMass: {},
-            temperature: {},
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}

package/src/js/context/providers/MLSettingsContextProvider.js

@@ -1,45 +0,0 @@
-import { ContextProvider } from "@mat3ra/ade";
-import JSONSchemasInterface from "@mat3ra/esse/dist/js/esse/JSONSchemasInterface";
-
-import { applicationContextMixin } from "../mixins/ApplicationContextMixin";
-
-export class MLSettingsContextProvider extends ContextProvider {
-    jsonSchemaId = "context-providers-directory/ml-settings-context-provider";
-
-    constructor(config) {
-        super(config);
-        this.initApplicationContextMixin();
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    get uiSchema() {
-        return {
-            target_column_name: {},
-            problem_category: {},
-        };
-    }
-
-    // eslint-disable-next-line class-methods-use-this
-    get defaultData() {
-        return {
-            target_column_name: "target",
-            problem_category: "regression",
-        };
-    }
-
-    get jsonSchemaPatchConfig() {
-        return {
-            target_column_name: { default: this.defaultData.target_column_name },
-            problem_category: { default: this.defaultData.problem_category },
-        };
-    }
-
-    get jsonSchema() {
-        return JSONSchemasInterface.getPatchedSchemaById(
-            this.jsonSchemaId,
-            this.jsonSchemaPatchConfig,
-        );
-    }
-}
-
-applicationContextMixin(MLSettingsContextProvider.prototype);