@mat3ra/wode 2025.10.2-2 → 2025.11.3-0

package/dist/subworkflows/create.js

@@ -51,11 +51,13 @@ function createModel({
  * @summary Create method from subworkflow data
  * @param config {Object} method configuration
  * @param methodFactoryCls {any}
+ * @param applicationConfig {Object} application configuration
  * @returns {{method, setSearchText}}
  */
 function createMethod({
   config,
-  methodFactoryCls
+  methodFactoryCls,
+  applicationConfig = {}
 }) {
   const {
     name,
@@ -63,8 +65,10 @@ function createMethod({
     config: methodConfig = {}
   } = config;
   const defaultConfig = _getConfigFromModelOrMethodName(name, "Method");
+  const defaultConfigForApp = new _standata.ApplicationMethodStandata().getDefaultMethodConfigForApplication(applicationConfig);
   const method = methodFactoryCls.create({
     ...defaultConfig,
+    ...defaultConfigForApp,
     ...methodConfig
   });
   return {
@@ -102,7 +106,8 @@ function createTopLevel({
     setSearchText
   } = createMethod({
     config: methodConfig,
-    methodFactoryCls
+    methodFactoryCls,
+    applicationConfig: appConfig
   });
   return {
     application,
@@ -238,12 +243,11 @@ function createSubworkflow({
       application
     });
   }
+  let subworkflow = subworkflowCls.fromArguments(application, model, method, name, units, config);
   const {
     functions = {},
-    attributes = {},
-    ...cfg
+    attributes = {}
   } = config;
-  let subworkflow = subworkflowCls.fromArguments(application, model, method, name, units, cfg);
   subworkflow = (0, _utils.applyConfig)({
     obj: subworkflow,
     config: {

package/dist/subworkflows/subworkflow.js

@@ -23,11 +23,11 @@ function _toPrimitive(t, r) { if ("object" != typeof t || !t) return t; var e =
 
 class BaseSubworkflow extends (0, _mixwith.mix)(_entity.NamedDefaultableRepetitionImportantSettingsInMemoryEntity).with(_convergence.ConvergenceMixin, _entity.ContextAndRenderFieldsMixin) {}
 class Subworkflow extends BaseSubworkflow {
-  constructor(config) {
+  constructor(config, _Application = _ade.Application, _ModelFactory = _mode.ModelFactory, _UnitFactory = _units.UnitFactory) {
     super(config);
-    this._Application = _ade.Application;
-    this._ModelFactory = _mode.ModelFactory;
-    this._UnitFactory = _units.UnitFactory;
+    this._Application = _Application;
+    this._ModelFactory = _ModelFactory;
+    this._UnitFactory = _UnitFactory;
     this.initialize();
   }
   initialize() {
@@ -72,9 +72,15 @@ class Subworkflow extends BaseSubworkflow {
    * @summary Used to generate initial application tree, therefore omit setting application.
    */
   static fromArguments(application, model, method, name, units = [], config = {}, Cls = Subworkflow) {
+    const nameForIdGeneration = config.attributes?.name || name;
+    const {
+      functions,
+      attributes,
+      ...cleanConfig
+    } = config;
     return new Cls({
-      ...config,
-      _id: Cls.generateSubworkflowId(name),
+      ...cleanConfig,
+      _id: Cls.generateSubworkflowId(nameForIdGeneration),
       name,
       application: application.toJSON(),
       properties: _lodash.default.sortedUniq(_lodash.default.flatten(units.filter(x => x.resultNames).map(x => x.resultNames))),

package/dist/workflows/relaxation.js

@@ -11,6 +11,7 @@ const RelaxationLogicMixin = superclass => class extends superclass {
     if (!appName) return undefined;
     const subworkflowStandata = new _standata.SubworkflowStandata();
     const relaxationSubworkflow = subworkflowStandata.getRelaxationSubworkflowByApplication(appName);
+    if (!relaxationSubworkflow) return undefined;
     return new this._Subworkflow(relaxationSubworkflow);
   }
   isRelaxationSubworkflow(subworkflow) {

package/dist/workflows/workflow.js

@@ -29,13 +29,13 @@ const {
 } = _mode.tree;
 class BaseWorkflow extends (0, _mixwith.mix)(_entity.NamedDefaultableRepetitionContextAndRenderInMemoryEntity).with(_ide.ComputedEntityMixin, _relaxation.RelaxationLogicMixin) {}
 class Workflow extends BaseWorkflow {
-  constructor(config) {
+  constructor(config, _Subworkflow = _subworkflow.Subworkflow, _UnitFactory = _factory.UnitFactory, _Workflow = Workflow, _MapUnit = _units.MapUnit) {
     if (!config._id) config._id = Workflow.generateWorkflowId(config.name);
     super(config);
-    this._Subworkflow = _subworkflow.Subworkflow;
-    this._UnitFactory = _factory.UnitFactory;
-    this._Workflow = Workflow;
-    this._MapUnit = _units.MapUnit;
+    this._Subworkflow = _Subworkflow;
+    this._UnitFactory = _UnitFactory;
+    this._Workflow = _Workflow;
+    this._MapUnit = _MapUnit;
     if (!config.skipInitialize) this.initialize();
   }
   initialize() {

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/wode",
-    "version": "2025.10.2-2",
+    "version": "2025.11.3-0",
     "description": "WOrkflow DEfinitions",
     "scripts": {
         "test": "nyc --reporter=text mocha --recursive --bail --require @babel/register/lib --require tests/setup.js tests",
@@ -56,7 +56,7 @@
         "@mat3ra/code": "2025.7.15-0",
         "@mat3ra/esse": "2025.7.15-0",
         "@mat3ra/made": "2025.7.15-0",
-        "@mat3ra/standata": "2025.10.2-0",
+        "@mat3ra/standata": "git+https://github.com/Exabyte-io/standata.git#f53b8da6ff0421b8397d606a6d8b0127dc68c64c",
         "chai": "^4.3.4",
         "eslint": "7.32.0",
         "eslint-config-airbnb": "19.0.2",

package/src/subworkflows/create.js

@@ -5,7 +5,7 @@ import {
     MethodFactory,
     ModelFactory,
 } from "@mat3ra/mode";
-import { workflowSubforkflowMapByApplication } from "@mat3ra/standata";
+import { ApplicationMethodStandata, workflowSubforkflowMapByApplication } from "@mat3ra/standata";
 import _ from "lodash";
 
 import { UnitFactory } from "../units";
@@ -40,12 +40,19 @@ function createModel({ config, modelFactoryCls }) {
  * @summary Create method from subworkflow data
  * @param config {Object} method configuration
  * @param methodFactoryCls {any}
+ * @param applicationConfig {Object} application configuration
  * @returns {{method, setSearchText}}
  */
-function createMethod({ config, methodFactoryCls }) {
+function createMethod({ config, methodFactoryCls, applicationConfig = {} }) {
     const { name, setSearchText = null, config: methodConfig = {} } = config;
     const defaultConfig = _getConfigFromModelOrMethodName(name, "Method");
-    const method = methodFactoryCls.create({ ...defaultConfig, ...methodConfig });
+    const defaultConfigForApp =
+        new ApplicationMethodStandata().getDefaultMethodConfigForApplication(applicationConfig);
+    const method = methodFactoryCls.create({
+        ...defaultConfig,
+        ...defaultConfigForApp,
+        ...methodConfig,
+    });
     return { method, setSearchText };
 }
 
@@ -61,7 +68,11 @@ function createTopLevel({ subworkflowData, modelFactoryCls, methodFactoryCls, Ap
     const { application: appConfig, model: modelConfig, method: methodConfig } = subworkflowData;
     const application = AppRegistry.createApplication(appConfig);
     const model = createModel({ config: modelConfig, modelFactoryCls });
-    const { method, setSearchText } = createMethod({ config: methodConfig, methodFactoryCls });
+    const { method, setSearchText } = createMethod({
+        config: methodConfig,
+        methodFactoryCls,
+        applicationConfig: appConfig,
+    });
     return {
         application,
         model,
@@ -168,8 +179,8 @@ function createSubworkflow({
         });
     }
 
-    const { functions = {}, attributes = {}, ...cfg } = config;
-    let subworkflow = subworkflowCls.fromArguments(application, model, method, name, units, cfg);
+    let subworkflow = subworkflowCls.fromArguments(application, model, method, name, units, config);
+    const { functions = {}, attributes = {} } = config;
     subworkflow = applyConfig({ obj: subworkflow, config: { functions, attributes } });
     if (setSearchText) subworkflow.model.method.setSearchText(setSearchText);
     return subworkflow;

package/src/subworkflows/subworkflow.js

@@ -24,11 +24,16 @@ class BaseSubworkflow extends mix(NamedDefaultableRepetitionImportantSettingsInM
 export class Subworkflow extends BaseSubworkflow {
     static usePredefinedIds = false;
 
-    constructor(config) {
+    constructor(
+        config,
+        _Application = Application,
+        _ModelFactory = ModelFactory,
+        _UnitFactory = UnitFactory,
+    ) {
         super(config);
-        this._Application = Application;
-        this._ModelFactory = ModelFactory;
-        this._UnitFactory = UnitFactory;
+        this._Application = _Application;
+        this._ModelFactory = _ModelFactory;
+        this._UnitFactory = _UnitFactory;
         this.initialize();
     }
 
@@ -86,9 +91,12 @@ export class Subworkflow extends BaseSubworkflow {
         config = {},
         Cls = Subworkflow,
     ) {
+        const nameForIdGeneration = config.attributes?.name || name;
+        const { functions, attributes, ...cleanConfig } = config;
+
         return new Cls({
-            ...config,
-            _id: Cls.generateSubworkflowId(name),
+            ...cleanConfig,
+            _id: Cls.generateSubworkflowId(nameForIdGeneration),
             name,
             application: application.toJSON(),
             properties: lodash.sortedUniq(

package/src/workflows/relaxation.js

@@ -8,6 +8,7 @@ export const RelaxationLogicMixin = (superclass) =>
             const subworkflowStandata = new SubworkflowStandata();
             const relaxationSubworkflow =
                 subworkflowStandata.getRelaxationSubworkflowByApplication(appName);
+            if (!relaxationSubworkflow) return undefined;
             return new this._Subworkflow(relaxationSubworkflow);
         }
 

package/src/workflows/workflow.js

@@ -31,14 +31,19 @@ export class Workflow extends BaseWorkflow {
 
     static usePredefinedIds = false;
 
-    constructor(config) {
+    constructor(
+        config,
+        _Subworkflow = Subworkflow,
+        _UnitFactory = UnitFactory,
+        _Workflow = Workflow,
+        _MapUnit = MapUnit,
+    ) {
         if (!config._id) config._id = Workflow.generateWorkflowId(config.name);
-
         super(config);
-        this._Subworkflow = Subworkflow;
-        this._UnitFactory = UnitFactory;
-        this._Workflow = Workflow;
-        this._MapUnit = MapUnit;
+        this._Subworkflow = _Subworkflow;
+        this._UnitFactory = _UnitFactory;
+        this._Workflow = _Workflow;
+        this._MapUnit = _MapUnit;
         if (!config.skipInitialize) this.initialize();
     }
 

package/assets/subworkflows/deepmd/deepmd.yml

@@ -1,31 +0,0 @@
-application:
-  name: deepmd
-  version: "2.0.2"
-method:
-  name: UnknownMethod
-model:
-  name: UnknownModel
-name: DeePMD
-units:
-  - config:
-      execName: python
-      flavorName: espresso_cp_to_deepmd
-      name: espresso_cp_to_deepmd
-    functions:
-      head: true
-    type: executionBuilder
-  - config:
-      execName: dp
-      flavorName: dp_train_se_e2_r
-      name: dp_train_se_e2_r
-    type: executionBuilder
-  - config:
-      execName: python
-      flavorName: espresso_to_lammps_structure
-      name: espresso_to_lammps_structure
-    type: executionBuilder
-  - config:
-      execName: lmp
-      flavorName: lammps_md
-      name: lammps_md
-    type: executionBuilder

package/assets/subworkflows/deepmd/espresso_cp_md.yml

@@ -1,16 +0,0 @@
-application:
-  name: espresso
-  version: "7.2"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: CP-MD
-units:
-  - config:
-      execName: cp.x
-      flavorName: cp
-      name: cp
-    functions:
-      head: true
-    type: executionBuilder

package/assets/subworkflows/espresso/average_electrostatic_potential_find_minima.yml

@@ -1,27 +0,0 @@
-# Note: this subworkflow is assumed to be used as part of the valence band offset workflow
-# and is this NOT self-sufficient!
-# Furthermore, this subworkflow expects the following variable(s) to exist in the global context:
-# array_from_context
-application:
-  name: python
-  version: 3.10.13
-method:
-  name: UnknownMethod
-model:
-  name: UnknownModel
-name: Find ESP Value
-units:
-  - config:
-      name: Find Extrema
-      execName: python
-      flavorName: generic:processing:find_extrema:scipy
-      flowchartId: python-find-extrema
-    type: executionBuilder
-  - config:
-      name: Set Average ESP Value
-      operand: AVG_ESP
-      value: "json.loads(STDOUT)['minima']"
-      input:
-        - name: STDOUT
-          scope: python-find-extrema
-    type: assignment

package/assets/subworkflows/espresso/average_electrostatic_potential_via_band_structure.yml

@@ -1,67 +0,0 @@
-config:
-  isMultiMaterial: true
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Band Structure + average ESP
-units:
-  - config:
-      name: Set Material Index
-      operand: MATERIAL_INDEX
-      value: 0
-    type: assignment
-  - config:
-      execName: pw.x
-      flavorName: pw_scf
-      name: pw_scf
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_bands
-      name: pw_bands
-      flowchartId: pw-bands-calculate-band-gap
-    type: executionBuilder
-    attributes:
-      results:
-        - name: band_gaps
-  - config:
-      name: Select indirect band gap
-      operand: BAND_GAP_INDIRECT
-      value: "[bandgap for bandgap in band_gaps['values'] if bandgap['type'] == 'indirect'][0]"
-      input:
-        - name: band_gaps
-          scope: pw-bands-calculate-band-gap
-    type: assignment
-  - config:
-      name: Set Valence Band Maximum
-      operand: VBM
-      value: "BAND_GAP_INDIRECT['eigenvalueValence']"
-    type: assignment
-  - config:
-      execName: bands.x
-      flavorName: bands
-      name: bands
-    type: executionBuilder
-  - config:
-      execName: pp.x
-      flavorName: pp_electrostatic_potential
-      name: Electrostatic Potential (ESP)
-    type: executionBuilder
-  - config:
-      execName: average.x
-      flavorName: average_potential
-      name: average ESP
-      flowchartId: average-electrostatic-potential
-    type: executionBuilder
-  - config:
-      name: Set Macroscopically Averaged ESP Data
-      operand: array_from_context
-      value: "average_potential_profile['yDataSeries'][1]"
-      input:
-        - name: average_potential_profile
-          scope: average-electrostatic-potential
-    type: assignment

package/assets/subworkflows/espresso/band_gap.yml

@@ -1,21 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Band Gap
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf
-      name: pw_scf
-    functions:
-      head: true
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_nscf
-      name: pw_nscf
-    type: executionBuilder

package/assets/subworkflows/espresso/band_gap_hse_dos.yml

@@ -1,30 +0,0 @@
-name: HSE Band Gap
-application:
-  name: espresso
-  version: "6.3"
-model:
-  name: DFTModel
-  config:
-    type: dft
-    subtype: hybrid
-    functional:
-      name: hse06
-      slug: hse06
-method:
-  name: PseudopotentialMethod
-  config:
-    type: pseudopotential
-    subtype: us
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf_hse
-      name: pw_scf_hse
-    functions:
-      head: true
-    type: executionBuilder
-  - config:
-      execName: projwfc.x
-      flavorName: projwfc
-      name: projwfc
-    type: executionBuilder

package/assets/subworkflows/espresso/band_structure.yml

@@ -1,26 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Band Structure
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf
-      name: pw_scf
-    functions:
-      head: true
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_bands
-      name: pw_bands
-    type: executionBuilder
-  - config:
-      execName: bands.x
-      flavorName: bands
-      name: bands
-    type: executionBuilder

package/assets/subworkflows/espresso/band_structure_dos.yml

@@ -1,34 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Band Structure + Density of States
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf
-      name: pw_scf
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_bands
-      name: pw_bands
-    type: executionBuilder
-  - config:
-      execName: bands.x
-      flavorName: bands
-      name: bands
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_nscf
-      name: pw_nscf
-    type: executionBuilder
-  - config:
-      execName: projwfc.x
-      flavorName: projwfc
-      name: projwfc
-    type: executionBuilder

package/assets/subworkflows/espresso/band_structure_hse.yml

@@ -1,30 +0,0 @@
-# Note: this subworkflow is assumed to be part of the "Band Structure - HSE" workflow
-# and is this NOT self-sufficient!
-name: Band Structure - HSE
-application:
-  name: espresso
-  version: "6.3"
-model:
-  name: DFTModel
-  config:
-    type: dft
-    subtype: hybrid
-    functional:
-      name: hse06
-      slug: hse06
-method:
-  name: PseudopotentialMethod
-  config:
-    type: pseudopotential
-    subtype: us
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf_bands_hse
-      name: pw_scf_bands_hse
-    type: executionBuilder
-  - config:
-      execName: bands.x
-      flavorName: bands
-      name: bands
-    type: executionBuilder

package/assets/subworkflows/espresso/band_structure_magn.yml

@@ -1,31 +0,0 @@
-name: Spin magnetic bandstructure
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf_magn
-      name: pw_scf_magn
-    functions:
-      head: true
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_bands_magn
-      name: pw_bands_magn
-    type: executionBuilder
-  - config:
-      execName: bands.x
-      flavorName: bands_spin_up
-      name: bands_spin_up
-    type: executionBuilder
-  - config:
-      execName: bands.x
-      flavorName: bands_spin_dn
-      name: bands_spin_dn
-    type: executionBuilder

package/assets/subworkflows/espresso/band_structure_soc.yml

@@ -1,30 +0,0 @@
-name: Spin orbit coupling bandstructure
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-  setSearchText: nc-fr
-  config:
-    type: pseudopotential
-    subtype: nc-fr
-model:
-  name: DFTModel
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf_soc
-      name: pw_scf_soc
-    functions:
-      head: true
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_bands_soc
-      name: pw_bands_soc
-    type: executionBuilder
-  - config:
-      execName: bands.x
-      flavorName: bands
-      name: bands
-    type: executionBuilder

package/assets/subworkflows/espresso/dielectric_tensor.yml

@@ -1,35 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  config:
-    data: {}
-    subtype: nc
-    type: pseudopotential
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Compute Dielectric Function
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf
-      name: pw_scf
-    functions:
-      head: true
-    type: executionBuilder
-  - config:
-      name: Set No-Symmetry Flag
-      operand: NO_SYMMETRY_NO_INVERSION
-      value: True # yamllint disable-line rule:truthy
-    type: assignment
-  - config:
-      execName: pw.x
-      flavorName: pw_nscf
-      name: pw_nscf
-    type: executionBuilder
-  - config:
-      execName: epsilon.x
-      flavorName: dielectric_tensor
-      name: Compute dielectric function
-    type: executionBuilder

package/assets/subworkflows/espresso/dos.yml

@@ -1,24 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Density of States
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf
-      name: pw_scf
-    type: executionBuilder
-  - config:
-      execName: pw.x
-      flavorName: pw_nscf
-      name: pw_nscf
-    type: executionBuilder
-  - config:
-      execName: projwfc.x
-      flavorName: projwfc
-      name: projwfc
-    type: executionBuilder