@mat3ra/wode 2025.10.1-0

package/dist/context/mixins/MethodDataContextMixin.js

@@ -0,0 +1,48 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.methodDataContextMixin = methodDataContextMixin;
+var _cryptoJs = _interopRequireDefault(require("crypto-js"));
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+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.default.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/dist/context/mixins/WorkflowContextMixin.js

@@ -0,0 +1,28 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.workflowContextMixin = workflowContextMixin;
+const defaultWorkflow = {
+  subworkflows: [],
+  units: [],
+  hasRelaxation: false
+};
+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/dist/context/providers/BoundaryConditionsFormDataProvider.js

@@ -0,0 +1,86 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.BoundaryConditionsFormDataProvider = void 0;
+var _JSONSchemaFormDataProvider = _interopRequireDefault(require("@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider"));
+var _made = require("@mat3ra/made");
+var _utils = require("@mat3ra/utils");
+var _MaterialContextMixin = require("../mixins/MaterialContextMixin");
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+class BoundaryConditionsFormDataProvider extends _JSONSchemaFormDataProvider.default {
+  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.Utils.clone.deepClone(this.yieldData());
+    data.boundaryConditions.offset *= _made.Made.coefficients.ANGSTROM_TO_BOHR;
+    data.boundaryConditions.targetFermiEnergy *= _made.Made.coefficients.EV_TO_RY;
+    data.boundaryConditions.electricField *= _made.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
+        }
+      }
+    };
+  }
+}
+exports.BoundaryConditionsFormDataProvider = BoundaryConditionsFormDataProvider;
+(0, _MaterialContextMixin.materialContextMixin)(BoundaryConditionsFormDataProvider.prototype);

package/dist/context/providers/CollinearMagnetizationContextProvider.js

@@ -0,0 +1,113 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.CollinearMagnetizationContextProvider = void 0;
+var _JSONSchemaFormDataProvider = _interopRequireDefault(require("@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider"));
+var _lodash = _interopRequireDefault(require("lodash"));
+var _MaterialContextMixin = require("../mixins/MaterialContextMixin");
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
+function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == typeof i ? i : i + ""; }
+function _toPrimitive(t, r) { if ("object" != typeof t || !t) return t; var e = t[Symbol.toPrimitive]; if (void 0 !== e) { var i = e.call(t, r || "default"); if ("object" != typeof i) return i; throw new TypeError("@@toPrimitive must return a primitive value."); } return ("string" === r ? String : Number)(t); }
+class CollinearMagnetizationContextProvider extends _JSONSchemaFormDataProvider.default {
+  constructor(config) {
+    super(config);
+    _defineProperty(this, "indexOfElement", element => {
+      return this.uniqueElementsWithLabels.indexOf(element) + 1;
+    });
+    _defineProperty(this, "transformData", data => {
+      const startingMagnetizationWithIndex = data.startingMagnetization.map(row => ({
+        ...row,
+        index: this.indexOfElement(row.atomicSpecies)
+      }));
+      return {
+        ...data,
+        startingMagnetization: startingMagnetizationWithIndex
+      };
+    });
+    this.initMaterialContextMixin();
+    this.firstElement = this.uniqueElementsWithLabels?.length > 0 ? this.uniqueElementsWithLabels[0] : "";
+    this.isTotalMagnetization = _lodash.default.get(this.data, "isTotalMagnetization", false);
+  }
+  get uniqueElementsWithLabels() {
+    const elementsWithLabelsArray = this.material?.Basis?.elementsWithLabelsArray || [];
+    return [...new Set(elementsWithLabelsArray)];
+  }
+  get defaultData() {
+    return {
+      startingMagnetization: [{
+        index: 1,
+        atomicSpecies: this.firstElement,
+        value: 0.0
+      }],
+      isTotalMagnetization: false,
+      totalMagnetization: 0.0
+    };
+  }
+  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
+        }
+      }
+    };
+  }
+}
+exports.CollinearMagnetizationContextProvider = CollinearMagnetizationContextProvider;
+(0, _MaterialContextMixin.materialContextMixin)(CollinearMagnetizationContextProvider.prototype);

package/dist/context/providers/HubbardContextProviderLegacy.js

@@ -0,0 +1,81 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.HubbardContextProviderLegacy = void 0;
+var _HubbardUContextProvider = require("./HubbardUContextProvider");
+function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
+function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == typeof i ? i : i + ""; }
+function _toPrimitive(t, r) { if ("object" != typeof t || !t) return t; var e = t[Symbol.toPrimitive]; if (void 0 !== e) { var i = e.call(t, r || "default"); if ("object" != typeof i) return i; throw new TypeError("@@toPrimitive must return a primitive value."); } return ("string" === r ? String : Number)(t); }
+const defaultHubbardConfig = {
+  hubbardUValue: 1.0
+};
+class HubbardContextProviderLegacy extends _HubbardUContextProvider.HubbardUContextProvider {
+  constructor(...args) {
+    super(...args);
+    _defineProperty(this, "speciesIndexFromSpecies", species => {
+      return this.uniqueElementsWithLabels?.length > 0 ? this.uniqueElementsWithLabels.indexOf(species) + 1 : null;
+    });
+    _defineProperty(this, "transformData", data => {
+      return data.map(row => ({
+        ...row,
+        atomicSpeciesIndex: this.speciesIndexFromSpecies(row.atomicSpecies)
+      }));
+    });
+  }
+  get defaultData() {
+    return [{
+      ...defaultHubbardConfig,
+      atomicSpecies: this.firstElement,
+      atomicSpeciesIndex: this.uniqueElementsWithLabels?.length > 0 ? 1 : null
+    }];
+  }
+  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
+          }
+        }
+      }
+    };
+  }
+}
+exports.HubbardContextProviderLegacy = HubbardContextProviderLegacy;

package/dist/context/providers/HubbardJContextProvider.js

@@ -0,0 +1,74 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.HubbardJContextProvider = void 0;
+var _HubbardUContextProvider = require("./HubbardUContextProvider");
+const defaultHubbardConfig = {
+  paramType: "U",
+  atomicSpecies: "",
+  atomicOrbital: "2p",
+  value: 1.0
+};
+class HubbardJContextProvider extends _HubbardUContextProvider.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
+    };
+  }
+}
+exports.HubbardJContextProvider = HubbardJContextProvider;

package/dist/context/providers/HubbardUContextProvider.js

@@ -0,0 +1,77 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.HubbardUContextProvider = void 0;
+var _JSONSchemaFormDataProvider = _interopRequireDefault(require("@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider"));
+var _MaterialContextMixin = require("../mixins/MaterialContextMixin");
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+const defaultHubbardConfig = {
+  atomicSpecies: "",
+  atomicOrbital: "2p",
+  hubbardUValue: 1.0
+};
+class HubbardUContextProvider extends _JSONSchemaFormDataProvider.default {
+  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
+          }
+        }
+      }
+    };
+  }
+}
+exports.HubbardUContextProvider = HubbardUContextProvider;
+(0, _MaterialContextMixin.materialContextMixin)(HubbardUContextProvider.prototype);

package/dist/context/providers/HubbardVContextProvider.js

@@ -0,0 +1,104 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.HubbardVContextProvider = void 0;
+var _HubbardUContextProvider = require("./HubbardUContextProvider");
+const defaultHubbardConfig = {
+  atomicSpecies: "",
+  atomicOrbital: "2p",
+  atomicSpecies2: "",
+  atomicOrbital2: "2p",
+  siteIndex: 1,
+  siteIndex2: 1,
+  hubbardVValue: 1.0
+};
+class HubbardVContextProvider extends _HubbardUContextProvider.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
+    };
+  }
+}
+exports.HubbardVContextProvider = HubbardVContextProvider;

package/dist/context/providers/IonDynamicsContextProvider.js

@@ -0,0 +1,62 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.IonDynamicsContextProvider = void 0;
+var _JSONSchemaFormDataProvider = _interopRequireDefault(require("@exabyte-io/ade.js/dist/js/context/JSONSchemaFormDataProvider"));
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+const defaultMDConfig = {
+  numberOfSteps: 100,
+  timeStep: 5.0,
+  electronMass: 100.0,
+  temperature: 300.0
+};
+class IonDynamicsContextProvider extends _JSONSchemaFormDataProvider.default {
+  // 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
+        }
+      }
+    };
+  }
+}
+exports.IonDynamicsContextProvider = IonDynamicsContextProvider;