@mat3ra/mode 2025.10.2-0 → 2025.11.5-0

package/dist/tree.js

@@ -1,165 +0,0 @@
-"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/src/data/method_list.js

@@ -1,2 +0,0 @@
-/* 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 Pseudopotential","path":"/qm/wf/none/psp/us"},{"categories":{"tier1":"qm","tier2":"wf","type":"pw"},"tags":["plane wave"],"name":"Wave function: Plane wave","path":"/qm/wf/none/pw/none"}],"name":"Plane-wave Ultra-soft Pseudopotential (Conjugate Gradient Diagonalization, Gaussian Smearing)","path":"/qm/wf/none/smearing/gaussian::/opt/diff/ordern/cg/none::/qm/wf/none/psp/us::/qm/wf/none/pw/none"},{"units":[{"categories":{"subtype":"methfessel-paxton","tier1":"qm","tier2":"wf","type":"smearing"},"tags":["occupation number"],"name":"Methfessel-Paxton Smearing","path":"/qm/wf/none/smearing/methfessel-paxton"},{"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 Pseudopotential","path":"/qm/wf/none/psp/us"},{"categories":{"tier1":"qm","tier2":"wf","type":"pw"},"tags":["plane wave"],"name":"Wave function: Plane wave","path":"/qm/wf/none/pw/none"}],"name":"Plane-wave Ultra-soft Pseudopotential (Conjugate Gradient Diagonalization, Methfessel-paxton Smearing)","path":"/qm/wf/none/smearing/methfessel-paxton::/opt/diff/ordern/cg/none::/qm/wf/none/psp/us::/qm/wf/none/pw/none"},{"units":[{"categories":{"subtype":"linear","tier1":"qm","tier2":"wf","type":"tetrahedron"},"tags":["occupation number"],"name":"Linear Tetrahedron Method","path":"/qm/wf/none/tetrahedron/linear"},{"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 Pseudopotential","path":"/qm/wf/none/psp/us"},{"categories":{"tier1":"qm","tier2":"wf","type":"pw"},"tags":["plane wave"],"name":"Wave function: Plane wave","path":"/qm/wf/none/pw/none"}],"name":"Plane-wave Ultra-soft Pseudopotential (Conjugate Gradient Diagonalization, Linear Tetrahedron Method)","path":"/qm/wf/none/tetrahedron/linear::/opt/diff/ordern/cg/none::/qm/wf/none/psp/us::/qm/wf/none/pw/none"},{"units":[{"categories":{"subtype":"gaussian","tier1":"qm","tier2":"wf","type":"smearing"},"tags":["occupation number"],"name":"Gaussian Smearing","path":"/qm/wf/none/smearing/gaussian"},{"categories":{"tier1":"linalg","tier2":"diag","type":"davidson"},"tags":["diagonalization"],"name":"Davidson Diagonalization","path":"/linalg/diag/none/davidson/none"},{"categories":{"subtype":"us","tier1":"qm","tier2":"wf","type":"psp"},"tags":["pseudopotential"],"name":"Ultra-soft Pseudopotential","path":"/qm/wf/none/psp/us"},{"categories":{"tier1":"qm","tier2":"wf","type":"pw"},"tags":["plane wave"],"name":"Wave function: Plane wave","path":"/qm/wf/none/pw/none"}],"name":"Plane-wave Ultra-soft Pseudopotential (Davidson Diagonalization, Gaussian Smearing)","path":"/qm/wf/none/smearing/gaussian::/linalg/diag/none/davidson/none::/qm/wf/none/psp/us::/qm/wf/none/pw/none"},{"units":[{"categories":{"subtype":"methfessel-paxton","tier1":"qm","tier2":"wf","type":"smearing"},"tags":["occupation number"],"name":"Methfessel-Paxton Smearing","path":"/qm/wf/none/smearing/methfessel-paxton"},{"categories":{"tier1":"linalg","tier2":"diag","type":"davidson"},"tags":["diagonalization"],"name":"Davidson Diagonalization","path":"/linalg/diag/none/davidson/none"},{"categories":{"subtype":"us","tier1":"qm","tier2":"wf","type":"psp"},"tags":["pseudopotential"],"name":"Ultra-soft Pseudopotential","path":"/qm/wf/none/psp/us"},{"categories":{"tier1":"qm","tier2":"wf","type":"pw"},"tags":["plane wave"],"name":"Wave function: Plane wave","path":"/qm/wf/none/pw/none"}],"name":"Plane-wave Ultra-soft 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package/src/data/model_list.js

@@ -1,2 +0,0 @@
-/* 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/dft/ksdft/hybrid?spinOrbitCoupling=true&functional=b3lyp"},{"parameters":{"spinPolarization":"collinear","functional":"b3lyp"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid B3LYP (collinear)","path":"/pb/qm/dft/ksdft/hybrid?spinPolarization=collinear&functional=b3lyp"},{"parameters":{"functional":"b3lyp"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"hybrid"},"tags":["density functional theory"],"name":"DFT Hybrid B3LYP","path":"/pb/qm/dft/ksdft/hybrid?functional=b3lyp"},{"parameters":{"spinOrbitCoupling":true,"dispersionCorrection":"dft-d3","functional":"pz"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"lda"},"tags":["density functional theory"],"name":"DFT LDA PZ-D3 (SOC)","path":"/pb/qm/dft/ksdft/lda?spinOrbitCoupling=true&dispersionCorrection=dft-d3&functional=pz"},{"parameters":{"spinPolarization":"collinear","dispersionCorrection":"dft-d3","functional":"pz"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"lda"},"tags":["density functional theory"],"name":"DFT LDA PZ-D3 (collinear)","path":"/pb/qm/dft/ksdft/lda?spinPolarization=collinear&dispersionCorrection=dft-d3&functional=pz"},{"parameters":{"dispersionCorrection":"dft-d3","functional":"pz"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"lda"},"tags":["density functional theory"],"name":"DFT LDA PZ-D3","path":"/pb/qm/dft/ksdft/lda?dispersionCorrection=dft-d3&functional=pz"},{"parameters":{"hubbardType":"u","spinOrbitCoupling":true,"functional":"pz"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"lda"},"tags":["density functional theory"],"name":"DFT LDA PZ+U (SOC)","path":"/pb/qm/dft/ksdft/lda?hubbardType=u&spinOrbitCoupling=true&functional=pz"},{"parameters":{"spinOrbitCoupling":true,"functional":"pz"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"lda"},"tags":["density functional theory"],"name":"DFT LDA PZ (SOC)","path":"/pb/qm/dft/ksdft/lda?spinOrbitCoupling=true&functional=pz"},{"parameters":{"spinPolarization":"collinear","hubbardType":"u","functional":"pz"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"lda"},"tags":["density functional theory"],"name":"DFT LDA PZ+U (collinear)","path":"/pb/qm/dft/ksdft/lda?spinPolarization=collinear&hubbardType=u&functional=pz"},{"parameters":{"hubbardType":"u","functional":"pz"},"categories":{"tier1":"pb","tier2":"qm","tier3":"dft","type":"ksdft","subtype":"lda"},"tags":["density functional theory"],"name":"DFT LDA 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package/src/data/model_method_map.js

@@ -1,2 +0,0 @@
-/* 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

@@ -1,38 +0,0 @@
-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

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

package/src/method.js

@@ -1,77 +0,0 @@
-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/pseudopotential.js

@@ -1,99 +0,0 @@
-import { safeMakeArray } from "@mat3ra/code/dist/js/utils";
-import _ from "underscore";
-
-import { Method } from "../method";
-
-export class PseudopotentialMethod extends 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 = 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: _.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: _.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`
-            ]),
-        );
-    }
-}