@mat3ra/mode 2025.10.2-0

package/dist/tree.js

@@ -0,0 +1,165 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.MODEL_TREE = exports.MODEL_NAMES = exports.METHODS = void 0;
+exports.filterMethodsByModel = filterMethodsByModel;
+exports.treeSlugToNamedObject = exports.getTreeByApplicationNameAndVersion = exports.getPseudopotentialTypesFromTree = exports.getDefaultModelTypeForApplication = exports.getDFTFunctionalsFromTree = exports.getDFTFunctionalsByApproximation = void 0;
+var _utils = require("@mat3ra/code/dist/js/utils");
+var _standata = require("@mat3ra/standata");
+var _lodash = _interopRequireDefault(require("lodash"));
+var _underscore = _interopRequireDefault(require("underscore"));
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+// TODO: migrate to use manifest instead
+
+const METHODS = exports.METHODS = {
+  pseudopotential: "pseudopotential",
+  localorbital: "localorbital",
+  unknown: "unknown"
+};
+const methods = {
+  [METHODS.pseudopotential]: ["paw", "nc", "nc-fr", "us"],
+  // TODO: Add additional basis set options, once user choice of specific (i.e 3-21G vs cc-pVDZ) is implemented.
+  [METHODS.localorbital]: ["pople"],
+  [METHODS.unknown]: ["unknown"]
+};
+const getPseudopotentialTypesFromTree = () => methods[METHODS.pseudopotential];
+
+// DFT-specific
+exports.getPseudopotentialTypesFromTree = getPseudopotentialTypesFromTree;
+const DFTModelRefiners = ["hse", "g0w0"];
+const DFTModelModifiers = ["soc", "magn"];
+const DFTModelTree = {
+  gga: {
+    refiners: DFTModelRefiners,
+    modifiers: DFTModelModifiers,
+    methods,
+    functionals: ["pbe", "pbesol", "pw91", "other"]
+  },
+  lda: {
+    refiners: DFTModelRefiners,
+    modifiers: DFTModelModifiers,
+    methods,
+    functionals: ["pz", "pw", "vwn", "other"]
+  },
+  hybrid: {
+    methods,
+    functionals: ["b3lyp", "hse06"]
+  },
+  other: {
+    methods,
+    functionals: ["other"]
+  }
+};
+const getDFTFunctionalsFromTree = () => Object.keys(DFTModelTree);
+exports.getDFTFunctionalsFromTree = getDFTFunctionalsFromTree;
+const getDFTFunctionalsByApproximation = approximation => {
+  const branch = DFTModelTree[approximation];
+  return branch && branch.functionals;
+};
+
+// GENERAL
+exports.getDFTFunctionalsByApproximation = getDFTFunctionalsByApproximation;
+const MODEL_TREE = exports.MODEL_TREE = {
+  dft: DFTModelTree,
+  ml: {
+    re: {
+      methods: {
+        linear: ["least_squares", "ridge"],
+        kernel_ridge: ["least_squares"]
+      }
+    }
+  },
+  unknown: {
+    unknown: {
+      methods: {
+        unknown: ["unknown"]
+      }
+    }
+  }
+};
+const MODEL_NAMES = exports.MODEL_NAMES = {
+  dft: "density functional theory",
+  lda: "local density approximation",
+  gga: "generalized gradient approximation",
+  hybrid: "hybrid functional",
+  ml: "machine learning",
+  re: "regression"
+};
+const treeSlugToNamedObject = modelSlug => {
+  return {
+    slug: modelSlug,
+    name: _lodash.default.get(MODEL_NAMES, modelSlug, modelSlug)
+  };
+};
+
+// TODO: find a better way to handle application-specific model-method combination
+// must be a subset of the MODEL_TREE above
+// demonstrate how tree can be modified
+// VASP_MODELS_TREE.gga.functionals = _.omit(VASP_MODELS_TREE.gga.functionals);
+exports.treeSlugToNamedObject = treeSlugToNamedObject;
+const VASP_MODELS_TREE = (0, _utils.deepClone)(_underscore.default.pick(MODEL_TREE, "dft"));
+const ESPRESSO_MODELS_TREE = (0, _utils.deepClone)(_underscore.default.pick(MODEL_TREE, "dft"));
+const NWCHEM_MODELS_TREE = (0, _utils.deepClone)(_underscore.default.pick(MODEL_TREE, "dft"));
+["gga", "lda"].forEach(approximation => {
+  // pick "paw" for vasp
+  VASP_MODELS_TREE.dft[approximation].methods.pseudopotential = VASP_MODELS_TREE.dft[approximation].methods.pseudopotential.splice(0, 1);
+
+  // assert "us" is the first option
+  ESPRESSO_MODELS_TREE.dft[approximation].methods.pseudopotential = ESPRESSO_MODELS_TREE.dft[approximation].methods.pseudopotential.reverse();
+});
+const UNKNOWN_MODELS_TREE = _underscore.default.pick(MODEL_TREE, "unknown");
+// const ML_MODELS_TREE = _.pick(MODEL_TREE, "ml");
+
+const MODELS_TREE_CONFIGS_BY_APPLICATION_NAME_VERSION = [{
+  name: "vasp",
+  tree: VASP_MODELS_TREE
+}, {
+  name: "espresso",
+  tree: ESPRESSO_MODELS_TREE
+}, {
+  name: "python",
+  tree: UNKNOWN_MODELS_TREE
+}, {
+  name: "shell",
+  tree: UNKNOWN_MODELS_TREE
+}, {
+  name: "jupyterLab",
+  tree: UNKNOWN_MODELS_TREE
+}, {
+  name: "nwchem",
+  tree: NWCHEM_MODELS_TREE
+}, {
+  name: "deepmd",
+  tree: UNKNOWN_MODELS_TREE
+}];
+const getTreeByApplicationNameAndVersion = ({
+  name,
+  // eslint-disable-next-line no-unused-vars
+  version
+}) => {
+  // TODO: add logic to filter by version when necessary
+  const cfgs = MODELS_TREE_CONFIGS_BY_APPLICATION_NAME_VERSION.filter(cfg => cfg.name === name).map(x => x.tree);
+  return Object.assign({}, ...cfgs);
+};
+exports.getTreeByApplicationNameAndVersion = getTreeByApplicationNameAndVersion;
+const getDefaultModelTypeForApplication = application => {
+  return Object.keys(getTreeByApplicationNameAndVersion(application))[0];
+};
+
+/**
+ * Filter list of method configs based on model
+ * @param {Object[]} methodList - Array of method configs
+ * @param {Object} model - Model config for which methods should be filtered
+ * @return {Object[]}
+ */
+exports.getDefaultModelTypeForApplication = getDefaultModelTypeForApplication;
+function filterMethodsByModel({
+  methodList,
+  model
+}) {
+  if (!model) return [];
+  const modelMethodFilter = new _standata.ModelMethodFilter();
+  return modelMethodFilter.getCompatibleMethods(model, methodList);
+}

package/package.json

@@ -0,0 +1,81 @@
+{
+    "name": "@mat3ra/mode",
+    "version": "2025.10.2-0",
+    "description": "MOdel and method DEfinitions",
+    "scripts": {
+        "test": "nyc --reporter=text mocha --recursive --bail --require @babel/register/lib --require tests/setup.js tests",
+        "lint": "eslint src tests && prettier --write src tests",
+        "lint:fix": "eslint --fix --cache src tests && prettier --write src tests",
+        "transpile": "babel --out-dir dist src",
+        "postinstall": "npm run transpile",
+        "prettier": "prettier --check src tests",
+        "prepare": "husky install || exit 0",
+        "prepublishOnly": "rm -rf dist; npm run transpile"
+    },
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/Exabyte-io/mode.git"
+    },
+    "main": "dist/index.js",
+    "files": [
+        "/dist",
+        "/src",
+        ".babelrc"
+    ],
+    "author": "Exabyte Inc.",
+    "bugs": {
+        "url": "https://github.com/Exabyte-io/mode/issues"
+    },
+    "license": "Apache-2.0",
+    "homepage": "https://github.com/Exabyte-io/mode",
+    "dependencies": {
+        "@babel/cli": "7.16.0",
+        "@babel/core": "7.16.0",
+        "@babel/eslint-parser": "7.16.3",
+        "@babel/plugin-proposal-class-properties": "7.16.0",
+        "@babel/preset-env": "7.16.4",
+        "@babel/preset-react": "7.16.7",
+        "@babel/register": "^7.16.0",
+        "@babel/runtime-corejs3": "7.16.8",
+        "ajv": "^8.12.0",
+        "js-yaml": "^4.1.0",
+        "lodash": "^4.17.21",
+        "mixwith": "^0.1.1",
+        "underscore": "^1.13.3",
+        "underscore.string": "^3.3.4"
+    },
+    "devDependencies": {
+        "@exabyte-io/eslint-config": "^2022.11.17-0",
+        "@mat3ra/esse": "2024.4.19-1",
+        "@mat3ra/standata": "2025.10.2-0",
+        "@mat3ra/code": "2024.3.25-3",
+        "chai": "^4.3.4",
+        "eslint": "7.32.0",
+        "eslint-config-airbnb": "19.0.2",
+        "eslint-config-prettier": "^8.5.0",
+        "eslint-import-resolver-exports": "^1.0.0-beta.2",
+        "eslint-plugin-import": "2.25.3",
+        "eslint-plugin-jsdoc": "37.1.0",
+        "eslint-plugin-jsx-a11y": "6.5.1",
+        "eslint-plugin-prettier": "^4.2.1",
+        "eslint-plugin-react": "7.30.0",
+        "eslint-plugin-simple-import-sort": "7.0.0",
+        "husky": "^7.0.4",
+        "lint-staged": "^12.1.2",
+        "mocha": "^9.1.3",
+        "nyc": "^15.1.0",
+        "prettier": "^2.7.1"
+    },
+    "peerDependencies": {
+        "@mat3ra/esse": "*",
+        "@mat3ra/standata": "*",
+        "@mat3ra/code": "*"
+    },
+    "engines": {
+        "node": ">20.0.0"
+    },
+    "lint-staged": {
+        "*.js": "eslint --cache --fix",
+        "*.{js,css}": "prettier --write"
+    }
+}

package/src/data/method_list.js

@@ -0,0 +1,2 @@
+/* eslint-disable */
+module.exports = {allMethods: [{"units":[{"categories":{"subtype":"us","tier1":"qm","tier2":"wf","type":"psp"},"tags":["pseudopotential"],"name":"Ultra-soft Pseudopotential","path":"/qm/wf/none/psp/us"},{"categories":{"subtype":"nc","tier1":"qm","tier2":"wf","type":"psp"},"tags":["pseudopotential"],"name":"Norm-conserving Pseudopotential","path":"/qm/wf/none/psp/nc"},{"categories":{"subtype":"nc-fr","tier1":"qm","tier2":"wf","type":"psp"},"tags":["pseudopotential"],"name":"Norm-conserving Fully-relativistic Pseudopotential","path":"/qm/wf/none/psp/nc-fr"},{"categories":{"subtype":"paw","tier1":"qm","tier2":"wf","type":"psp"},"tags":["pseudopotential"],"name":"Projector-augmented wave Pseudopotential","path":"/qm/wf/none/psp/paw"},{"categories":{"tier1":"qm","tier2":"wf","type":"pw"},"tags":["plane wave"],"name":"Wave function: Plane wave","path":"/qm/wf/none/pw/none"}],"name":"Any Plane-wave Pseudopotential Method","path":"/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"},{"units":[{"categories":{"subtype":"least_squares","type":"linear"},"tags":["exabyteML"],"name":"Linear least squares regression","path":"/none/none/none/linear/least_squares"}],"name":"Linear least squares regression","path":"/none/none/none/linear/least_squares"},{"units":[{"categories":{"subtype":"ridge","type":"linear"},"tags":["exabyteML"],"name":"Linear ridge regression","path":"/none/none/none/linear/ridge"}],"name":"Linear ridge regression","path":"/none/none/none/linear/ridge"},{"units":[{"categories":{"type":"kernel_ridge","subtype":"least_squares"},"tags":["exabyteML"],"name":"Kernel Ridge least squares regression","path":"/none/none/none/kernel_ridge/least_squares"}],"name":"Kernel Ridge least squares regression","path":"/none/none/none/kernel_ridge/least_squares"},{"units":[{"parameters":{"basisSlug":"6-31G"},"categories":{"tier1":"qm","tier2":"wf","type":"ao","subtype":"pople"},"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"},{"units":[{"categories":{"subtype":"gaussian","tier1":"qm","tier2":"wf","type":"smearing"},"tags":["occupation number"],"name":"Gaussian Smearing","path":"/qm/wf/none/smearing/gaussian"},{"categories":{"tier1":"opt","tier2":"diff","tier3":"ordern","type":"cg"},"tags":["diagonalization"],"name":"Conjugate Gradient Diagonalization","path":"/opt/diff/ordern/cg/none"},{"categories":{"subtype":"us","tier1":"qm","tier2":"wf","type":"psp"},"tags":["pseudopotential"],"name":"Ultra-soft 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package/src/data/model_list.js

@@ -0,0 +1,2 @@
+/* eslint-disable */
+module.exports = {allModels: [{"parameters":{"spinOrbitCoupling":true,"dispersionCorrection":"dft-d3","functional":"pbe"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"gga"},"tags":["density functional theory"],"name":"DFT GGA PBE-D3 (SOC)","path":"/pb/qm/dft/ksdft/gga?spinOrbitCoupling=true&dispersionCorrection=dft-d3&functional=pbe"},{"parameters":{"spinPolarization":"collinear","dispersionCorrection":"dft-d3","functional":"pbe"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"gga"},"tags":["density functional theory"],"name":"DFT GGA PBE-D3 (collinear)","path":"/pb/qm/dft/ksdft/gga?spinPolarization=collinear&dispersionCorrection=dft-d3&functional=pbe"},{"parameters":{"dispersionCorrection":"dft-d3","functional":"pbe"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"gga"},"tags":["density functional theory"],"name":"DFT GGA 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(SOC)","path":"/pb/qm/abin/gw/evgw?spinOrbitCoupling=true&functional=pbe&require=pb%2Fqm%2Fdft%2Fksdft%2Fgga%3Ffunctional%3Dpbe%26spinOrbitCoupling%3Dtrue"},{"parameters":{"spinOrbitCoupling":true,"functional":"pbesol","require":"pb/qm/dft/ksdft/gga?functional=pbe&spinOrbitCoupling=true"},"categories":{"subtype":"evgw","tier1":"pb","tier2":"qm","tier3":"abin","type":"gw"},"name":"evGW@pbesol (SOC)","path":"/pb/qm/abin/gw/evgw?spinOrbitCoupling=true&functional=pbesol&require=pb%2Fqm%2Fdft%2Fksdft%2Fgga%3Ffunctional%3Dpbe%26spinOrbitCoupling%3Dtrue"},{"parameters":{"spinOrbitCoupling":true,"dispersionCorrection":"dft-d3","functional":"hse06"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid HSE-D3 (SOC)","path":"/pb/qm/dft/ksdft/hybrid?spinOrbitCoupling=true&dispersionCorrection=dft-d3&functional=hse06"},{"parameters":{"spinPolarization":"collinear","dispersionCorrection":"dft-d3","functional":"hse06"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid HSE-D3 (collinear)","path":"/pb/qm/dft/ksdft/hybrid?spinPolarization=collinear&dispersionCorrection=dft-d3&functional=hse06"},{"parameters":{"dispersionCorrection":"dft-d3","functional":"hse06"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid HSE-D3","path":"/pb/qm/dft/ksdft/hybrid?dispersionCorrection=dft-d3&functional=hse06"},{"parameters":{"spinOrbitCoupling":true,"functional":"hse06"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid HSE 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(SOC)","path":"/pb/qm/dft/ksdft/hybrid?spinOrbitCoupling=true&dispersionCorrection=dft-d3&functional=b3lyp"},{"parameters":{"spinPolarization":"collinear","dispersionCorrection":"dft-d3","functional":"b3lyp"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid B3LYP-D3 (collinear)","path":"/pb/qm/dft/ksdft/hybrid?spinPolarization=collinear&dispersionCorrection=dft-d3&functional=b3lyp"},{"parameters":{"dispersionCorrection":"dft-d3","functional":"b3lyp"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid B3LYP-D3","path":"/pb/qm/dft/ksdft/hybrid?dispersionCorrection=dft-d3&functional=b3lyp"},{"parameters":{"spinOrbitCoupling":true,"functional":"b3lyp"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid B3LYP 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package/src/data/model_method_map.js

@@ -0,0 +1,2 @@
+/* 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/src/default_methods.js

@@ -0,0 +1,38 @@
+import lodash from "lodash";
+
+import { MODEL_NAMES, MODEL_TREE } from "./tree";
+
+export const PseudopotentialMethodConfig = {
+    type: "pseudopotential",
+    subtype: "us",
+};
+
+export const LocalOrbitalMethodConfig = {
+    type: "localorbital",
+    subtype: "pople",
+};
+
+export const UnknownMethodConfig = {
+    type: "unknown",
+    subtype: "unknown",
+};
+
+export function allowedTypes(model) {
+    return lodash
+        .keys(lodash.get(MODEL_TREE, `${model.type}.${model.subtype}.methods`, []))
+        .map((x) => {
+            return {
+                slug: x,
+                name: lodash.get(MODEL_NAMES, x, x),
+            };
+        });
+}
+
+export function allowedSubtypes(model, type) {
+    return lodash.get(MODEL_TREE, `${model.type}.${model.subtype}.methods.${type}`, []).map((x) => {
+        return {
+            slug: x,
+            name: lodash.get(MODEL_NAMES, x, x),
+        };
+    });
+}

package/src/default_models.js

@@ -0,0 +1,9 @@
+export const DFTModelConfig = {
+    type: "dft",
+    subtype: "gga",
+};
+
+export const UnknownModelConfig = {
+    type: "unknown",
+    subtype: "unknown",
+};

package/src/index.js

@@ -0,0 +1,32 @@
+import { MethodStandata, ModelStandata } from "@mat3ra/standata";
+
+import * as default_methods from "./default_methods";
+import * as default_models from "./default_models";
+import { Method } from "./method";
+import { MethodFactory } from "./methods/factory";
+import { PseudopotentialMethod } from "./methods/pseudopotential";
+import { Model } from "./model";
+import { DFTModel } from "./models/dft";
+import { ModelFactory } from "./models/factory";
+// TODO : can replace these with subpackages in exports in package.json
+import * as tree from "./tree";
+
+const methodStandata = new MethodStandata();
+const modelStandata = new ModelStandata();
+
+const categorizedMethodList = methodStandata.getAll();
+const categorizedModelList = modelStandata.getAll();
+
+export {
+    Method,
+    Model,
+    MethodFactory,
+    ModelFactory,
+    PseudopotentialMethod,
+    DFTModel,
+    tree,
+    default_models,
+    default_methods,
+    categorizedModelList,
+    categorizedMethodList,
+};

package/src/method.js

@@ -0,0 +1,77 @@
+import { InMemoryEntity } from "@mat3ra/code/dist/js/entity";
+import { deepClone } from "@mat3ra/code/dist/js/utils";
+import lodash from "lodash";
+
+import { PseudopotentialMethodConfig } from "./default_methods";
+
+export class Method extends 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 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.isEmpty(lodash.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 deepClone(json);
+    }
+}

package/src/methods/factory.js

@@ -0,0 +1,17 @@
+import { Method } from "../method";
+import { PseudopotentialMethod } from "./pseudopotential";
+
+export class MethodFactory {
+    static Method = Method;
+
+    static PseudopotentialMethod = PseudopotentialMethod;
+
+    static create(config) {
+        switch (config.type) {
+            case "pseudopotential":
+                return new this.PseudopotentialMethod(config);
+            default:
+                return new this.Method(config);
+        }
+    }
+}