@mat3ra/wode 2025.10.1-0

package/src/context/providers/BoundaryConditionsFormDataProvider.js

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+import JSONSchemaFormDataProvider from "@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider";
+import { Made } from "@mat3ra/made";
+import { Utils } from "@mat3ra/utils";
+
+import { materialContextMixin } from "../mixins/MaterialContextMixin";
+
+export class BoundaryConditionsFormDataProvider extends JSONSchemaFormDataProvider {
+    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,
+        };
+    }
+
+    // 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 {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            type: "object",
+            properties: {
+                type: {
+                    type: "string",
+                    title: "Type",
+                    default: this.defaultData.type,
+                },
+                offset: {
+                    type: "number",
+                    title: "Offset (A)",
+                    default: this.defaultData.offset,
+                },
+                electricField: {
+                    type: "number",
+                    title: "Electric Field (eV/A)",
+                    default: this.defaultData.electricField,
+                },
+                targetFermiEnergy: {
+                    type: "number",
+                    title: "Target Fermi Energy (eV)",
+                    default: this.defaultData.targetFermiEnergy,
+                },
+            },
+        };
+    }
+}
+
+materialContextMixin(BoundaryConditionsFormDataProvider.prototype);

package/src/context/providers/CollinearMagnetizationContextProvider.js

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+import JSONSchemaFormDataProvider from "@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider";
+import lodash from "lodash";
+
+import { materialContextMixin } from "../mixins/MaterialContextMixin";
+
+export class CollinearMagnetizationContextProvider extends JSONSchemaFormDataProvider {
+    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,
+        };
+    }
+
+    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 {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            title: "",
+            description: "Set starting magnetization, can have values in the range [-1, +1].",
+            type: "object",
+            properties: {
+                startingMagnetization: {
+                    type: "array",
+                    maxItems: this.uniqueElementsWithLabels.length,
+                    items: {
+                        type: "object",
+                        properties: {
+                            atomicSpecies: {
+                                type: "string",
+                                title: "Atomic species",
+                                enum: this.uniqueElementsWithLabels,
+                                default: this.firstElement,
+                            },
+                            value: {
+                                type: "number",
+                                title: "Starting magnetization",
+                                default: 0.0,
+                                minimum: -1.0,
+                                maximum: 1.0,
+                            },
+                        },
+                    },
+                },
+                isTotalMagnetization: {
+                    type: "boolean",
+                    title: "Set total magnetization instead",
+                    default: false,
+                },
+                totalMagnetization: {
+                    type: "number",
+                    title: "Total magnetization",
+                    default: 0.0,
+                },
+            },
+        };
+    }
+}
+
+materialContextMixin(CollinearMagnetizationContextProvider.prototype);

package/src/context/providers/HubbardContextProviderLegacy.js

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+import { HubbardUContextProvider } from "./HubbardUContextProvider";
+
+const defaultHubbardConfig = {
+    hubbardUValue: 1.0,
+};
+
+export class HubbardContextProviderLegacy extends HubbardUContextProvider {
+    get defaultData() {
+        return [
+            {
+                ...defaultHubbardConfig,
+                atomicSpecies: this.firstElement,
+                atomicSpeciesIndex: this.uniqueElementsWithLabels?.length > 0 ? 1 : null,
+            },
+        ];
+    }
+
+    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 {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            title: "",
+            description: "Hubbard parameters for DFT+U calculation.",
+            type: "array",
+            uniqueItems: true,
+            minItems: 1,
+            items: {
+                type: "object",
+                properties: {
+                    atomicSpecies: {
+                        type: "string",
+                        title: "Atomic species",
+                        enum: this.uniqueElementsWithLabels,
+                    },
+                    atomicSpeciesIndex: {
+                        type: "integer",
+                        title: "Species index",
+                    },
+                    hubbardUValue: {
+                        type: "number",
+                        title: "Hubbard U (eV)",
+                        default: defaultHubbardConfig.hubbardUValue,
+                    },
+                },
+            },
+        };
+    }
+}

package/src/context/providers/HubbardJContextProvider.js

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+import { HubbardUContextProvider } from "./HubbardUContextProvider";
+
+const defaultHubbardConfig = {
+    paramType: "U",
+    atomicSpecies: "",
+    atomicOrbital: "2p",
+    value: 1.0,
+};
+
+export class HubbardJContextProvider extends HubbardUContextProvider {
+    get defaultData() {
+        return [
+            {
+                ...defaultHubbardConfig,
+                atomicSpecies: this.firstElement,
+            },
+        ];
+    }
+
+    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 {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            title: "",
+            description: "Hubbard parameters for DFT+U+J calculation.",
+            type: "array",
+            items: {
+                type: "object",
+                properties: {
+                    paramType: {
+                        type: "string",
+                        title: "Species",
+                        enum: ["U", "J", "B", "E2", "E3"],
+                        default: defaultHubbardConfig.paramType,
+                    },
+                    atomicSpecies: {
+                        type: "string",
+                        title: "Species",
+                        enum: this.uniqueElementsWithLabels,
+                        default: this.firstElement,
+                    },
+                    atomicOrbital: {
+                        type: "string",
+                        title: "Orbital",
+                        enum: this.orbitalList,
+                        default: defaultHubbardConfig.atomicOrbital,
+                    },
+                    value: {
+                        type: "number",
+                        title: "Value (eV)",
+                        default: defaultHubbardConfig.value,
+                    },
+                },
+            },
+            minItems: 1,
+        };
+    }
+}

package/src/context/providers/HubbardUContextProvider.js

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+import JSONSchemaFormDataProvider from "@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider";
+
+import { materialContextMixin } from "../mixins/MaterialContextMixin";
+
+const defaultHubbardConfig = {
+    atomicSpecies: "",
+    atomicOrbital: "2p",
+    hubbardUValue: 1.0,
+};
+
+export class HubbardUContextProvider extends JSONSchemaFormDataProvider {
+    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 uiSchemaStyled() {
+        return {
+            "ui:options": {
+                addable: true,
+                orderable: false,
+                removable: true,
+            },
+            items: {
+                atomicSpecies: this.defaultFieldStyles,
+                atomicOrbital: this.defaultFieldStyles,
+                hubbardUValue: this.defaultFieldStyles,
+            },
+        };
+    }
+
+    get jsonSchema() {
+        return {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            title: "",
+            description: "Hubbard U parameters for DFT+U or DFT+U+V calculation.",
+            type: "array",
+            items: {
+                type: "object",
+                properties: {
+                    atomicSpecies: {
+                        type: "string",
+                        title: "Atomic species",
+                        enum: this.uniqueElementsWithLabels,
+                        default: this.firstElement,
+                    },
+                    atomicOrbital: {
+                        type: "string",
+                        title: "Atomic orbital",
+                        enum: this.orbitalList,
+                        default: defaultHubbardConfig.atomicOrbital,
+                    },
+                    hubbardUValue: {
+                        type: "number",
+                        title: "Hubbard U (eV)",
+                        default: defaultHubbardConfig.hubbardUValue,
+                    },
+                },
+            },
+        };
+    }
+}
+
+materialContextMixin(HubbardUContextProvider.prototype);

package/src/context/providers/HubbardVContextProvider.js

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+import { HubbardUContextProvider } from "./HubbardUContextProvider";
+
+const defaultHubbardConfig = {
+    atomicSpecies: "",
+    atomicOrbital: "2p",
+    atomicSpecies2: "",
+    atomicOrbital2: "2p",
+    siteIndex: 1,
+    siteIndex2: 1,
+    hubbardVValue: 1.0,
+};
+
+export class HubbardVContextProvider extends HubbardUContextProvider {
+    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 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 {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            title: "",
+            description: "Hubbard V parameters for DFT+U+V calculation.",
+            type: "array",
+            items: {
+                type: "object",
+                properties: {
+                    atomicSpecies: {
+                        type: "string",
+                        title: "Species 1",
+                        enum: this.uniqueElementsWithLabels,
+                        default: this.firstSpecies,
+                    },
+                    siteIndex: {
+                        type: "integer",
+                        title: "Site no 1",
+                        default: defaultHubbardConfig.siteIndex,
+                    },
+                    atomicOrbital: {
+                        type: "string",
+                        title: "Orbital 1",
+                        enum: this.orbitalList,
+                        default: defaultHubbardConfig.atomicOrbital,
+                    },
+                    atomicSpecies2: {
+                        type: "string",
+                        title: "Species 2",
+                        enum: this.uniqueElementsWithLabels,
+                        default: this.secondSpecies,
+                    },
+                    siteIndex2: {
+                        type: "integer",
+                        title: "Site no 2",
+                        default:
+                            this.uniqueElementsWithLabels?.length > 1
+                                ? 2
+                                : defaultHubbardConfig.siteIndex2,
+                    },
+                    atomicOrbital2: {
+                        type: "string",
+                        title: "Orbital 2",
+                        enum: this.orbitalList,
+                        default: defaultHubbardConfig.atomicOrbital,
+                    },
+                    hubbardVValue: {
+                        type: "number",
+                        title: "V (eV)",
+                        default: defaultHubbardConfig.hubbardVValue,
+                    },
+                },
+            },
+            minItems: 1,
+        };
+    }
+}

package/src/context/providers/IonDynamicsContextProvider.js

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+import JSONSchemaFormDataProvider from "@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider";
+
+const defaultMDConfig = {
+    numberOfSteps: 100,
+    timeStep: 5.0,
+    electronMass: 100.0,
+    temperature: 300.0,
+};
+
+export class IonDynamicsContextProvider extends JSONSchemaFormDataProvider {
+    // eslint-disable-next-line class-methods-use-this
+    get defaultData() {
+        return defaultMDConfig;
+    }
+
+    // eslint-disable-next-line class-methods-use-this
+    get uiSchema() {
+        return {
+            numberOfSteps: {},
+            timeStep: {},
+            electronMass: {},
+            temperature: {},
+        };
+    }
+
+    // eslint-disable-next-line class-methods-use-this
+    get jsonSchema() {
+        return {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            type: "object",
+            description: "Important parameters for molecular dynamics calculation",
+            properties: {
+                numberOfSteps: {
+                    type: "integer",
+                    title: "numberOfSteps",
+                    default: defaultMDConfig.numberOfSteps,
+                },
+                timeStep: {
+                    type: "number",
+                    title: "timeStep (Hartree a.u.)",
+                    default: defaultMDConfig.timeStep,
+                },
+                electronMass: {
+                    type: "number",
+                    title: "Effective electron mass",
+                    default: defaultMDConfig.electronMass,
+                },
+                temperature: {
+                    type: "number",
+                    title: "Ionic temperature (K)",
+                    default: defaultMDConfig.temperature,
+                },
+            },
+        };
+    }
+}

package/src/context/providers/MLSettingsContextProvider.js

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+import ContextProvider from "@exabyte-io/ade.js/dist/js/context/ContextProvider";
+
+import { applicationContextMixin } from "../mixins/ApplicationContextMixin";
+
+export class MLSettingsContextProvider extends ContextProvider {
+    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 jsonSchema() {
+        return {
+            $schema: "http://json-schema.org/draft-07/schema#",
+            title: " ",
+            description: "Settings important to machine learning runs.",
+            type: "object",
+            properties: {
+                target_column_name: {
+                    type: "string",
+                    default: this.defaultData.target_column_name,
+                },
+                problem_category: {
+                    type: "string",
+                    default: this.defaultData.problem_category,
+                    enum: ["regression", "classification", "clustering"],
+                },
+            },
+        };
+    }
+}
+
+applicationContextMixin(MLSettingsContextProvider.prototype);