@mat3ra/mode 2025.11.10-0 → 2025.11.22-0

package/dist/js/models/dft.js

@@ -33,9 +33,11 @@ class DFTModel extends model_1.Model {
         const [slug] = this.treeBranchForSubType.functionals || [];
         return (0, tree_1.treeSlugToNamedObject)(slug);
     }
+    // eslint-disable-next-line class-methods-use-this
     get defaultRefiners() {
         return [];
     }
+    // eslint-disable-next-line class-methods-use-this
     get defaultModifiers() {
         return [];
     }
@@ -69,11 +71,17 @@ class DFTModel extends model_1.Model {
     }
     toJSON() {
         const pickSlugFromObject = (item) => underscore_1.default.pick(item, "slug");
+        const baseJson = super.toJSON();
+        const keysToExclude = ["type", "subtype", "functional", "refiners", "modifiers", "method"];
+        const restJson = Object.fromEntries(Object.entries(baseJson).filter(([key]) => !keysToExclude.includes(key)));
         return {
-            ...super.toJSON(),
+            type: this.type,
+            subtype: this.subtype,
+            method: this.Method.toJSONWithCleanData(),
             functional: pickSlugFromObject(this.functional),
             refiners: this.refiners,
             modifiers: this.modifiers,
+            ...restJson,
         };
     }
     get allFunctionals() {

package/dist/js/tree.d.ts

@@ -1,5 +1,67 @@
 import { ApplicationSchemaBase, SlugifiedEntry } from "@mat3ra/esse/dist/js/types";
 import type { ModelTree } from "./types";
+export declare const MODEL_TREE: {
+    dft: {
+        gga: {
+            refiners: string[];
+            modifiers: string[];
+            methods: {
+                pseudopotential: string[];
+                localorbital: string[];
+                unknown: string[];
+            };
+            functionals: string[];
+        };
+        lda: {
+            refiners: string[];
+            modifiers: string[];
+            methods: {
+                pseudopotential: string[];
+                localorbital: string[];
+                unknown: string[];
+            };
+            functionals: string[];
+        };
+        hybrid: {
+            methods: {
+                pseudopotential: string[];
+                localorbital: string[];
+                unknown: string[];
+            };
+            functionals: string[];
+        };
+        other: {
+            methods: {
+                pseudopotential: string[];
+                localorbital: string[];
+                unknown: string[];
+            };
+            functionals: string[];
+        };
+    };
+    ml: {
+        re: {
+            methods: {
+                linear: string[];
+                kernel_ridge: string[];
+            };
+        };
+    };
+    unknown: {
+        unknown: {
+            methods: {
+                unknown: string[];
+            };
+        };
+    };
+}, MODEL_NAMES: {
+    dft: string;
+    lda: string;
+    gga: string;
+    hybrid: string;
+    ml: string;
+    re: string;
+};
 export declare const METHODS: {
     readonly pseudopotential: "pseudopotential";
     readonly localorbital: "localorbital";
@@ -8,8 +70,6 @@ export declare const METHODS: {
 export declare const getPseudopotentialTypesFromTree: () => string[];
 export declare const getDFTFunctionalsFromTree: () => string[];
 export declare const getDFTFunctionalsByApproximation: (approximation: string) => string[] | undefined;
-export declare const MODEL_TREE: ModelTree;
-export declare const MODEL_NAMES: Record<string, string>;
 export declare const treeSlugToNamedObject: (modelSlug: string) => SlugifiedEntry;
 export declare const getTreeByApplicationNameAndVersion: ({ name, }: Pick<ApplicationSchemaBase, "name" | "version">) => ModelTree;
 export declare const getDefaultModelTypeForApplication: (application: ApplicationSchemaBase) => string;

package/dist/js/tree.js

@@ -3,83 +3,33 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getDefaultModelTypeForApplication = exports.getTreeByApplicationNameAndVersion = exports.treeSlugToNamedObject = exports.MODEL_NAMES = exports.MODEL_TREE = exports.getDFTFunctionalsByApproximation = exports.getDFTFunctionalsFromTree = exports.getPseudopotentialTypesFromTree = exports.METHODS = void 0;
-const utils_1 = require("@mat3ra/code/dist/js/utils");
+exports.getDefaultModelTypeForApplication = exports.getTreeByApplicationNameAndVersion = exports.treeSlugToNamedObject = exports.getDFTFunctionalsByApproximation = exports.getDFTFunctionalsFromTree = exports.getPseudopotentialTypesFromTree = exports.METHODS = exports.MODEL_NAMES = exports.MODEL_TREE = void 0;
+const modelsTreeConfigByApplication_json_1 = __importDefault(require("@mat3ra/standata/dist/js/runtime_data/models/modelsTreeConfigByApplication.json"));
+const modelTree_json_1 = __importDefault(require("@mat3ra/standata/dist/js/runtime_data/models/modelTree.json"));
 const lodash_1 = __importDefault(require("lodash"));
-const underscore_1 = __importDefault(require("underscore"));
-// TODO: migrate to use manifest instead
+exports.MODEL_TREE = modelTree_json_1.default.MODEL_TREE, exports.MODEL_NAMES = modelTree_json_1.default.MODEL_NAMES;
 exports.METHODS = {
     pseudopotential: "pseudopotential",
     localorbital: "localorbital",
     unknown: "unknown",
 };
-const methods = {
-    [exports.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.
-    [exports.METHODS.localorbital]: ["pople"],
-    [exports.METHODS.unknown]: ["unknown"],
+const getPseudopotentialTypesFromTree = () => {
+    var _a;
+    const dftTree = exports.MODEL_TREE.dft;
+    const firstBranch = Object.values(dftTree)[0];
+    return ((_a = firstBranch === null || firstBranch === void 0 ? void 0 : firstBranch.methods) === null || _a === void 0 ? void 0 : _a.pseudopotential) || [];
 };
-const getPseudopotentialTypesFromTree = () => methods[exports.METHODS.pseudopotential];
 exports.getPseudopotentialTypesFromTree = getPseudopotentialTypesFromTree;
-// DFT-specific
-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 = () => {
+    return Object.keys(exports.MODEL_TREE.dft);
 };
-const getDFTFunctionalsFromTree = () => Object.keys(DFTModelTree);
 exports.getDFTFunctionalsFromTree = getDFTFunctionalsFromTree;
 const getDFTFunctionalsByApproximation = (approximation) => {
-    const branch = DFTModelTree[approximation];
-    return branch && branch.functionals;
+    const dftTree = exports.MODEL_TREE.dft;
+    const branch = dftTree[approximation];
+    return branch === null || branch === void 0 ? void 0 : branch.functionals;
 };
 exports.getDFTFunctionalsByApproximation = getDFTFunctionalsByApproximation;
-// GENERAL
-exports.MODEL_TREE = {
-    dft: DFTModelTree,
-    ml: {
-        re: {
-            methods: {
-                linear: ["least_squares", "ridge"],
-                kernel_ridge: ["least_squares"],
-            },
-        },
-    },
-    unknown: {
-        unknown: {
-            methods: {
-                unknown: ["unknown"],
-            },
-        },
-    },
-};
-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,
@@ -87,52 +37,10 @@ const treeSlugToNamedObject = (modelSlug) => {
     };
 };
 exports.treeSlugToNamedObject = treeSlugToNamedObject;
-const VASP_MODELS_TREE = (0, utils_1.deepClone)(underscore_1.default.pick(exports.MODEL_TREE, "dft"));
-const ESPRESSO_MODELS_TREE = (0, utils_1.deepClone)(underscore_1.default.pick(exports.MODEL_TREE, "dft"));
-const NWCHEM_MODELS_TREE = (0, utils_1.deepClone)(underscore_1.default.pick(exports.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_1.default.pick(exports.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, }) => {
     // TODO: add logic to filter by version when necessary
-    const cfgs = MODELS_TREE_CONFIGS_BY_APPLICATION_NAME_VERSION.filter((cfg) => cfg.name === name).map((cfg) => cfg.tree);
-    return Object.assign({}, ...cfgs);
+    // @ts-ignore
+    return modelsTreeConfigByApplication_json_1.default[name] || {};
 };
 exports.getTreeByApplicationNameAndVersion = getTreeByApplicationNameAndVersion;
 const getDefaultModelTypeForApplication = (application) => {

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/mode",
-    "version": "2025.11.10-0",
+    "version": "2025.11.22-0",
     "description": "MOdel and method DEfinitions",
     "scripts": {
         "test": "nyc --reporter=text mocha --recursive --bail",
@@ -54,7 +54,7 @@
     "devDependencies": {
         "@exabyte-io/eslint-config": "2025.5.13-0",
         "@mat3ra/esse": "2025.10.8-0",
-        "@mat3ra/standata": "2025.10.2-0",
+        "@mat3ra/standata": "2025.11.12-0",
         "@mat3ra/code": "2025.10.8-0",
         "@mat3ra/tsconfig": "2024.6.3-0",
         "@types/chai": "^4.3.11",

package/src/js/models/dft.ts

@@ -33,10 +33,12 @@ export class DFTModel extends Model {
         return treeSlugToNamedObject(slug);
     }
 
+    // eslint-disable-next-line class-methods-use-this
     get defaultRefiners(): SlugifiedEntry[] {
         return [];
     }
 
+    // eslint-disable-next-line class-methods-use-this
     get defaultModifiers(): SlugifiedEntry[] {
         return [];
     }
@@ -82,11 +84,19 @@ export class DFTModel extends Model {
 
     toJSON(): Record<string, unknown> {
         const pickSlugFromObject = (item: SlugifiedEntry) => _.pick(item, "slug");
+        const baseJson = super.toJSON();
+        const keysToExclude = ["type", "subtype", "functional", "refiners", "modifiers", "method"];
+        const restJson = Object.fromEntries(
+            Object.entries(baseJson).filter(([key]) => !keysToExclude.includes(key)),
+        );
         return {
-            ...super.toJSON(),
+            type: this.type,
+            subtype: this.subtype,
+            method: this.Method.toJSONWithCleanData(),
             functional: pickSlugFromObject(this.functional),
             refiners: this.refiners,
             modifiers: this.modifiers,
+            ...restJson,
         };
     }
 

package/src/js/tree.ts

@@ -1,11 +1,11 @@
-import { deepClone } from "@mat3ra/code/dist/js/utils";
 import { ApplicationSchemaBase, SlugifiedEntry } from "@mat3ra/esse/dist/js/types";
+import MODELS_TREE_CONFIG_BY_APPLICATION from "@mat3ra/standata/dist/js/runtime_data/models/modelsTreeConfigByApplication.json";
+import MODEL_TREE_DATA from "@mat3ra/standata/dist/js/runtime_data/models/modelTree.json";
 import lodash from "lodash";
-import _ from "underscore";
 
 import type { ModelTree } from "./types";
 
-// TODO: migrate to use manifest instead
+export const { MODEL_TREE, MODEL_NAMES } = MODEL_TREE_DATA;
 
 export const METHODS = {
     pseudopotential: "pseudopotential",
@@ -13,78 +13,20 @@ export const METHODS = {
     unknown: "unknown",
 } as const;
 
-const methods: Record<string, string[]> = {
-    [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"],
+export const getPseudopotentialTypesFromTree = (): string[] => {
+    const dftTree = MODEL_TREE.dft as Record<string, any>;
+    const firstBranch = Object.values(dftTree)[0];
+    return firstBranch?.methods?.pseudopotential || [];
 };
 
-export const getPseudopotentialTypesFromTree = (): string[] => methods[METHODS.pseudopotential];
-
-// DFT-specific
-
-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"],
-    },
+export const getDFTFunctionalsFromTree = (): string[] => {
+    return Object.keys(MODEL_TREE.dft);
 };
 
-export const getDFTFunctionalsFromTree = (): string[] => Object.keys(DFTModelTree);
-
 export const getDFTFunctionalsByApproximation = (approximation: string): string[] | undefined => {
-    const branch = DFTModelTree[approximation as keyof typeof DFTModelTree];
-    return branch && branch.functionals;
-};
-
-// GENERAL
-
-export const MODEL_TREE: ModelTree = {
-    dft: DFTModelTree,
-    ml: {
-        re: {
-            methods: {
-                linear: ["least_squares", "ridge"],
-                kernel_ridge: ["least_squares"],
-            },
-        },
-    },
-    unknown: {
-        unknown: {
-            methods: {
-                unknown: ["unknown"],
-            },
-        },
-    },
-};
-
-export const MODEL_NAMES: Record<string, string> = {
-    dft: "density functional theory",
-    lda: "local density approximation",
-    gga: "generalized gradient approximation",
-    hybrid: "hybrid functional",
-    ml: "machine learning",
-    re: "regression",
+    const dftTree = MODEL_TREE.dft as Record<string, any>;
+    const branch = dftTree[approximation];
+    return branch?.functionals;
 };
 
 export const treeSlugToNamedObject = (modelSlug: string): SlugifiedEntry => {
@@ -94,73 +36,12 @@ export const treeSlugToNamedObject = (modelSlug: string): SlugifiedEntry => {
     };
 };
 
-// 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);
-
-type DftOnlyTree = { dft: typeof DFTModelTree };
-
-const VASP_MODELS_TREE = deepClone(_.pick(MODEL_TREE, "dft")) as DftOnlyTree;
-const ESPRESSO_MODELS_TREE = deepClone(_.pick(MODEL_TREE, "dft")) as DftOnlyTree;
-const NWCHEM_MODELS_TREE = deepClone(_.pick(MODEL_TREE, "dft")) as DftOnlyTree;
-
-(["gga", "lda"] as const).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 = _.pick(MODEL_TREE, "unknown") as ModelTree;
-// const ML_MODELS_TREE = _.pick(MODEL_TREE, "ml");
-
-const MODELS_TREE_CONFIGS_BY_APPLICATION_NAME_VERSION: Array<{
-    name: string;
-    tree: ModelTree;
-}> = [
-    {
-        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,
-    },
-];
-
 export const getTreeByApplicationNameAndVersion = ({
     name,
 }: Pick<ApplicationSchemaBase, "name" | "version">): ModelTree => {
     // TODO: add logic to filter by version when necessary
-    const cfgs = MODELS_TREE_CONFIGS_BY_APPLICATION_NAME_VERSION.filter(
-        (cfg) => cfg.name === name,
-    ).map((cfg) => cfg.tree);
-    return Object.assign({}, ...cfgs);
+    // @ts-ignore
+    return MODELS_TREE_CONFIG_BY_APPLICATION[name] || {};
 };
 
 export const getDefaultModelTypeForApplication = (application: ApplicationSchemaBase): string => {