@mat3ra/mode 2025.11.3-0 → 2025.11.5-0

package/dist/data/model_method_map.js

@@ -1,82 +0,0 @@
-"use strict";
-
-/* eslint-disable */
-module.exports = {
-  "pb": {
-    "qm": {
-      "abin": {
-        "gw": [{
-          "path": "/qm/wf/none/pw/none"
-        }, {
-          "regex": "\\/qm\\/wf\\/none\\/psp\\/.*"
-        }, {
-          "regex": "\\/qm\\/wf\\/none\\/smearing\\/.*"
-        }, {
-          "regex": "\\/qm\\/wf\\/none\\/tetrahedron\\/.*"
-        }, {
-          "path": "/opt/diff/ordern/cg/none"
-        }, {
-          "path": "/linalg/diag/none/davidson/none"
-        }]
-      },
-      "dft": {
-        "ksdft": {
-          "lda": [{
-            "path": "/qm/wf/none/pw/none"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/psp\\/.*"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/smearing\\/.*"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/tetrahedron\\/.*"
-          }, {
-            "path": "/opt/diff/ordern/cg/none"
-          }, {
-            "path": "/linalg/diag/none/davidson/none"
-          }],
-          "gga": [{
-            "path": "/qm/wf/none/pw/none"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/psp\\/.*"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/smearing\\/.*"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/tetrahedron\\/.*"
-          }, {
-            "path": "/opt/diff/ordern/cg/none"
-          }, {
-            "path": "/linalg/diag/none/davidson/none"
-          }],
-          "hybrid": [{
-            "path": "/qm/wf/none/pw/none"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/psp\\/.*"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/smearing\\/.*"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/tetrahedron\\/.*"
-          }, {
-            "path": "/opt/diff/ordern/cg/none"
-          }, {
-            "path": "/linalg/diag/none/davidson/none"
-          }, {
-            "regex": "\\/qm\\/wf\\/none\\/ao\\/pople.*"
-          }]
-        }
-      }
-    }
-  },
-  "st": {
-    "det": {
-      "ml": {
-        "re": [{
-          "path": "/none/none/none/linear/least_squares"
-        }, {
-          "path": "/none/none/none/linear/ridge"
-        }, {
-          "path": "/none/none/none/kernel_ridge/least_squares"
-        }]
-      }
-    }
-  }
-};

package/dist/default_methods.js

@@ -1,39 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.UnknownMethodConfig = exports.PseudopotentialMethodConfig = exports.LocalOrbitalMethodConfig = void 0;
-exports.allowedSubtypes = allowedSubtypes;
-exports.allowedTypes = allowedTypes;
-var _lodash = _interopRequireDefault(require("lodash"));
-var _tree = require("./tree");
-function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-const PseudopotentialMethodConfig = exports.PseudopotentialMethodConfig = {
-  type: "pseudopotential",
-  subtype: "us"
-};
-const LocalOrbitalMethodConfig = exports.LocalOrbitalMethodConfig = {
-  type: "localorbital",
-  subtype: "pople"
-};
-const UnknownMethodConfig = exports.UnknownMethodConfig = {
-  type: "unknown",
-  subtype: "unknown"
-};
-function allowedTypes(model) {
-  return _lodash.default.keys(_lodash.default.get(_tree.MODEL_TREE, `${model.type}.${model.subtype}.methods`, [])).map(x => {
-    return {
-      slug: x,
-      name: _lodash.default.get(_tree.MODEL_NAMES, x, x)
-    };
-  });
-}
-function allowedSubtypes(model, type) {
-  return _lodash.default.get(_tree.MODEL_TREE, `${model.type}.${model.subtype}.methods.${type}`, []).map(x => {
-    return {
-      slug: x,
-      name: _lodash.default.get(_tree.MODEL_NAMES, x, x)
-    };
-  });
-}

package/dist/default_models.js

@@ -1,14 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.UnknownModelConfig = exports.DFTModelConfig = void 0;
-const DFTModelConfig = exports.DFTModelConfig = {
-  type: "dft",
-  subtype: "gga"
-};
-const UnknownModelConfig = exports.UnknownModelConfig = {
-  type: "unknown",
-  subtype: "unknown"
-};

package/dist/index.js

@@ -1,69 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "DFTModel", {
-  enumerable: true,
-  get: function () {
-    return _dft.DFTModel;
-  }
-});
-Object.defineProperty(exports, "Method", {
-  enumerable: true,
-  get: function () {
-    return _method.Method;
-  }
-});
-Object.defineProperty(exports, "MethodConversionHandler", {
-  enumerable: true,
-  get: function () {
-    return _methodConversionHandler.MethodConversionHandler;
-  }
-});
-Object.defineProperty(exports, "MethodFactory", {
-  enumerable: true,
-  get: function () {
-    return _factory.MethodFactory;
-  }
-});
-Object.defineProperty(exports, "Model", {
-  enumerable: true,
-  get: function () {
-    return _model.Model;
-  }
-});
-Object.defineProperty(exports, "ModelConversionHandler", {
-  enumerable: true,
-  get: function () {
-    return _modelConversionHandler.ModelConversionHandler;
-  }
-});
-Object.defineProperty(exports, "ModelFactory", {
-  enumerable: true,
-  get: function () {
-    return _factory2.ModelFactory;
-  }
-});
-Object.defineProperty(exports, "PseudopotentialMethod", {
-  enumerable: true,
-  get: function () {
-    return _pseudopotential.PseudopotentialMethod;
-  }
-});
-exports.tree = exports.default_models = exports.default_methods = void 0;
-var default_methods = _interopRequireWildcard(require("./default_methods"));
-exports.default_methods = default_methods;
-var default_models = _interopRequireWildcard(require("./default_models"));
-exports.default_models = default_models;
-var _method = require("./method");
-var _methodConversionHandler = require("./methodConversionHandler");
-var _factory = require("./methods/factory");
-var _pseudopotential = require("./methods/pseudopotential");
-var _model = require("./model");
-var _modelConversionHandler = require("./modelConversionHandler");
-var _dft = require("./models/dft");
-var _factory2 = require("./models/factory");
-var tree = _interopRequireWildcard(require("./tree"));
-exports.tree = tree;
-function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }

package/dist/method.js

@@ -1,84 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.Method = void 0;
-var _entity = require("@mat3ra/code/dist/js/entity");
-var _utils = require("@mat3ra/code/dist/js/utils");
-var _lodash = _interopRequireDefault(require("lodash"));
-var _default_methods = require("./default_methods");
-function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-class Method extends _entity.InMemoryEntity {
-  constructor(config) {
-    const data = config.data || {};
-    super({
-      ...config,
-      data
-    });
-  }
-  cloneWithoutData() {
-    const clone = this.clone();
-    clone.setData({});
-    return clone;
-  }
-  get type() {
-    return this.prop("type");
-  }
-  get subtype() {
-    return this.prop("subtype");
-  }
-  setSubtype(subtype) {
-    // TODO: add proper handling of method data subscriptions on type/subtype change
-    this.setProp("subtype", subtype);
-  }
-  static get defaultConfig() {
-    return _default_methods.PseudopotentialMethodConfig;
-  }
-  get precision() {
-    return this.prop("precision");
-  }
-  get data() {
-    return this.prop("data");
-  }
-  get searchText() {
-    return this.prop("data.searchText", "");
-  }
-
-  // used to narrow down the list of methodData items available for selection
-  // utilizing "data" field as a "blackbox" container for searchText
-  setSearchText(searchText) {
-    this.setData({
-      ...this.prop("data"),
-      searchText
-    });
-  }
-  setData(data = {}) {
-    this.setProp("data", data);
-  }
-  get omitInHashCalculation() {
-    const data = this.prop("data");
-    return !data.searchText && _lodash.default.isEmpty(_lodash.default.omit(data, "searchText"));
-  }
-
-  // data without client-only fields
-  cleanData(fieldsToExclude = []) {
-    const filteredData = {
-      ...this.prop("data")
-    };
-    fieldsToExclude.forEach(f => {
-      delete filteredData[f];
-    });
-    return filteredData;
-  }
-
-  // override in child class if needed
-  toJSONWithCleanData(fieldsToExclude = []) {
-    const json = {
-      ...this._json,
-      data: this.cleanData(fieldsToExclude)
-    };
-    return (0, _utils.deepClone)(json);
-  }
-}
-exports.Method = Method;

package/dist/methodConversionHandler.js

@@ -1,128 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.MethodConversionHandler = void 0;
-exports.safelyGetSlug = safelyGetSlug;
-var _default_methods = require("./default_methods");
-function safelyGetSlug(slugObj) {
-  return typeof slugObj === "string" ? slugObj : slugObj.slug;
-}
-
-/**
- * The method interface converts between the legacy method data structure (type, subtype)
- * and the categorized method data structure (units with tier1, tier2, ...).
- */
-class MethodConversionHandler {
-  static convertToSimple(cm) {
-    if (!cm) return this.convertUnknownToSimple();
-    const pspUnits = cm.units.filter(u => u.categories.type === "psp");
-    const aoUnit = cm.units.find(u => u.categories.type === "ao");
-    const reUnit = cm.units.find(u => u.name && u.name.includes("regression"));
-    if (pspUnits.length) return this.convertPspUnitsToSimple(pspUnits);
-    if (aoUnit) return this.convertAoUnitToSimple();
-    if (reUnit) return this.convertRegressionUnitToSimple(reUnit);
-    return this.convertRegressionUnitToSimple(reUnit);
-  }
-  static convertUnknownToSimple() {
-    return _default_methods.UnknownMethodConfig;
-  }
-  static convertPspUnitsToSimple(cm) {
-    const [firstPspUnit, ...otherUnits] = cm;
-    if (!firstPspUnit || !firstPspUnit.categories?.subtype) return this.convertUnknownToSimple();
-    const subtype = otherUnits?.length ? "any" : firstPspUnit.categories.subtype;
-    return {
-      type: "pseudopotential",
-      subtype
-    };
-  }
-  static convertAoUnitToSimple() {
-    return _default_methods.LocalOrbitalMethodConfig;
-  }
-  static convertRegressionUnitToSimple(cm) {
-    const type = cm.categories.type || "linear";
-    const subtype = cm.categories.subtype || "least_squares";
-    return {
-      type: safelyGetSlug(type),
-      subtype: safelyGetSlug(subtype),
-      data: cm.data,
-      precision: cm.precision
-    };
-  }
-  static convertToCategorized(sm, allMethods = []) {
-    switch (sm?.type) {
-      case "pseudopotential":
-        return this.convertPspToCategorized(sm, allMethods);
-      case "localorbital":
-        return this.convertAoToCategorized(sm);
-      case "linear":
-        return this.convertRegressionToCategorized(sm);
-      case "kernel_ridge":
-        return this.convertRegressionToCategorized(sm);
-      default:
-        return undefined;
-    }
-  }
-  static convertPspToCategorized(sm, allMethods = []) {
-    const subtype = safelyGetSlug(sm.subtype);
-    // the "any" subtype is equivalent to the method representing all planewave-pseudopotential
-    // methods. All other subtypes are equivalent to using a specific PW-PSP method.
-    const path = subtype === "any" ? "/qm/wf/none/psp/us::/qm/wf/none/psp/nc::/qm/wf/none/psp/nc-fr::/qm/wf/none/psp/paw::/qm/wf/none/pw/none" : `/qm/wf/none/smearing/gaussian::/linalg/diag/none/davidson/none::/qm/wf/none/psp/${subtype}::/qm/wf/none/pw/none`;
-    return allMethods.find(catMethod => {
-      return catMethod.path === path;
-    });
-  }
-  static convertAoToCategorized(sm) {
-    const subtype = safelyGetSlug(sm.subtype);
-    return {
-      units: [{
-        parameters: {
-          basisSlug: "6-31G"
-        },
-        categories: {
-          tier1: "qm",
-          tier2: "wf",
-          type: "ao",
-          subtype
-        },
-        tags: ["atomic orbital"],
-        name: "Wave function: LCAO - Pople basis set (6-31G)",
-        path: "/qm/wf/none/ao/pople?basisSlug=6-31G"
-      }],
-      name: "Wave function: LCAO - Pople basis set (6-31G)",
-      path: "/qm/wf/none/ao/pople?basisSlug=6-31G"
-    };
-  }
-  static convertRegressionToCategorized(sm) {
-    const type = safelyGetSlug(sm.type);
-    const subtype = safelyGetSlug(sm.subtype);
-    const {
-      precision,
-      data
-    } = sm;
-    const path = `/none/none/none/${type}/${subtype}`;
-    const nameMap = {
-      kernel_ridge: "Kernel ridge",
-      linear: "Linear",
-      least_squares: "least squares",
-      ridge: "ridge"
-    };
-    const name = `${nameMap[type]} ${nameMap[subtype]} regression`;
-    return {
-      units: [{
-        categories: {
-          type,
-          subtype
-        },
-        name,
-        path,
-        precision,
-        data
-      }],
-      name,
-      path
-    };
-  }
-}
-exports.MethodConversionHandler = MethodConversionHandler;

package/dist/methods/factory.js

@@ -1,24 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.MethodFactory = void 0;
-var _method = require("../method");
-var _pseudopotential = require("./pseudopotential");
-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 MethodFactory {
-  static create(config) {
-    switch (config.type) {
-      case "pseudopotential":
-        return new this.PseudopotentialMethod(config);
-      default:
-        return new this.Method(config);
-    }
-  }
-}
-exports.MethodFactory = MethodFactory;
-_defineProperty(MethodFactory, "Method", _method.Method);
-_defineProperty(MethodFactory, "PseudopotentialMethod", _pseudopotential.PseudopotentialMethod);

package/dist/methods/pseudopotential.js

@@ -1,100 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.PseudopotentialMethod = void 0;
-var _utils = require("@mat3ra/code/dist/js/utils");
-var _underscore = _interopRequireDefault(require("underscore"));
-var _method = require("../method");
-function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-class PseudopotentialMethod extends _method.Method {
-  constructor(config) {
-    super(config);
-    this.PseudopotentialCls = null;
-  }
-
-  // "Unique" or "selected" pseudopotentials - one per element
-  get pseudo() {
-    return this.prop("data.pseudo", []);
-  }
-
-  // "All" or "non-unique" pseudopotentials available for a choice
-  get allPseudo() {
-    return this.prop("data.allPseudo", []);
-  }
-  get pseudopotentials() {
-    return this.pseudo.map(x => new this.PseudopotentialCls(x));
-  }
-  get allPseudopotentials() {
-    return this.allPseudo.map(x => new this.PseudopotentialCls(x));
-  }
-  static extractExchangeCorrelationFromSubworkflow(subworkflow) {
-    const {
-      model
-    } = subworkflow;
-    const approximation = model.subtype;
-    const functional = model.functional ? model.functional.slug || model.functional : "";
-    return {
-      approximation,
-      functional
-    };
-  }
-  hasPseudopotentialFor(element) {
-    return Boolean(this.pseudopotentials.find(x => x.element === element));
-  }
-
-  /**
-   * @summary Sets one pseudopotential per element. Subsequent applications will override previous.
-   * @param pseudo {Pseudopotential}
-   */
-  setPseudopotentialPerElement(pseudo) {
-    if (!pseudo) {
-      this.setPseudopotentials([]);
-      return;
-    }
-    const arr = this.pseudopotentials.filter(x => x.element !== pseudo.element);
-    arr.push(pseudo);
-    this.setPseudopotentials(arr);
-  }
-
-  // add new pseudopotentials to the list of all pseudopotentials
-  addToAllPseudos(pseudos) {
-    // eslint-disable-next-line no-param-reassign
-    pseudos = (0, _utils.safeMakeArray)(pseudos);
-    const allPseudos = this.allPseudopotentials;
-    allPseudos.push(...pseudos);
-    this.setAllPseudopotentials(allPseudos);
-  }
-
-  /**
-   * @param pseudopotentials {Pseudopotential[]}
-   */
-  setPseudopotentials(pseudopotentials) {
-    // sort by alphabetical order to ensure elements order consistency in VASP POSCAR/POTCAR
-    this.setData({
-      ...this.data,
-      pseudo: _underscore.default.sortBy(pseudopotentials, "element").map(x => x.toJSON())
-    });
-  }
-
-  /**
-   * @param pseudopotentials {Pseudopotential[]}
-   */
-  setAllPseudopotentials(pseudopotentials) {
-    // sort by alphabetical order to ensure elements order consistency in VASP POSCAR/POTCAR
-    this.setData({
-      ...this.data,
-      allPseudo: _underscore.default.sortBy(pseudopotentials, "element").map(x => x.toJSON())
-    });
-  }
-
-  // override default `toJSONWithCleanData` method to avoid saving `allPseudo` inside the workflow
-  // TODO: revise after implementing Pseudopotential Sets
-  toJSONWithCleanData(exclude = []) {
-    return super.toJSONWithCleanData(exclude.concat(["allPseudo"
-    // 'pseudo' - not cleaning the field to save it in `Job.workflow`
-    ]));
-  }
-}
-exports.PseudopotentialMethod = PseudopotentialMethod;

package/dist/model.js

@@ -1,123 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.Model = void 0;
-var _entity = require("@mat3ra/code/dist/js/entity");
-var _lodash = _interopRequireDefault(require("lodash"));
-var _default_models = require("./default_models");
-var _method = require("./method");
-var _factory = require("./methods/factory");
-var _tree = require("./tree");
-function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-class Model extends _entity.InMemoryEntity {
-  constructor({
-    application,
-    ...config
-  }) {
-    super(config);
-    this._application = application;
-    this._MethodFactory = _factory.MethodFactory;
-  }
-  get type() {
-    return this.prop("type", this.defaultType);
-  }
-  get subtype() {
-    return this.prop("subtype", this.defaultSubtype);
-  }
-  setSubtype(subtype) {
-    this.setProp("subtype", subtype);
-    this.setMethod(this._MethodFactory.create(this.defaultMethodConfig));
-  }
-  get allowedTypes() {
-    return Object.keys(this.tree).map(modelSlug => (0, _tree.treeSlugToNamedObject)(modelSlug));
-  }
-  get allowedSubtypes() {
-    return Object.keys(this.treeBranchForType).map(slug => (0, _tree.treeSlugToNamedObject)(slug));
-  }
-  get defaultType() {
-    return this.allowedTypes[0]?.slug;
-  }
-  get defaultSubtype() {
-    return this.allowedSubtypes[0]?.slug;
-  }
-  get tree() {
-    return this._application && this.treeByApplicationNameAndVersion || _tree.MODEL_TREE;
-  }
-  get treeBranchForType() {
-    return this.tree[this.type] || {};
-  }
-  get treeBranchForSubType() {
-    return this.treeBranchForType[this.subtype] || {};
-  }
-  get treeByApplicationNameAndVersion() {
-    const [name, version] = [this._application.name, this._application.version];
-    return (0, _tree.getTreeByApplicationNameAndVersion)({
-      name,
-      version
-    });
-  }
-  get groupSlug() {
-    return `${this._application.shortName}:${this.type}:${this.subtype}`;
-  }
-  get method() {
-    if (!this._method) {
-      const method = this.prop("method") || this.defaultMethodConfig;
-      this._method = this._MethodFactory.create(method);
-    }
-    return this._method;
-  }
-  setMethod(method) {
-    this._method = method;
-  }
-
-  // Consider moving the below to `Method`
-  get methodsFromTree() {
-    return this.treeBranchForSubType.methods || {};
-  }
-  get methodTypes() {
-    return Object.keys(this.methodsFromTree).map(m => (0, _tree.treeSlugToNamedObject)(m));
-  }
-  get methodSubtypes() {
-    return this.methodsFromTree[this.method.type].map(m => (0, _tree.treeSlugToNamedObject)(m)) || [];
-  }
-  get defaultMethodConfig() {
-    const type = Object.keys(this.methodsFromTree)[0];
-    const subtype = (this.methodsFromTree[type] || [])[0];
-    return {
-      type,
-      subtype
-    };
-  }
-  static get defaultConfig() {
-    return {
-      ..._default_models.DFTModelConfig,
-      method: _method.Method.defaultConfig
-    };
-  }
-  static get allTypes() {
-    return Object.keys(this.tree).map(modelSlug => (0, _tree.treeSlugToNamedObject)(modelSlug));
-  }
-  toJSON() {
-    return {
-      ...super.toJSON(),
-      type: this.type,
-      subtype: this.subtype,
-      // TODO: use schema-based cleaning instead
-      method: this.method.toJSONWithCleanData()
-    };
-  }
-
-  // to be used with extra properties
-  // eslint-disable-next-line class-methods-use-this
-  _stringToSlugifiedObject(slug) {
-    return _lodash.default.isString(slug) ? {
-      slug
-    } : slug;
-  }
-  get isUnknown() {
-    return this.type === "unknown";
-  }
-}
-exports.Model = Model;