@mat3ra/wode 2025.10.1-0

package/assets/workflows/espresso/phonon_map.yml

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+name: Phonon Map
+units:
+- name: phononMap
+  type: workflow
+  units:
+  - name: pw_scf
+    type: subworkflow
+  - name: ph_init_qpoints
+    type: subworkflow
+  - name: espresso_xml_get_qpt_irr
+    type: subworkflow
+- config:
+    functions:
+      setDefaultCompute: null
+    input:
+      name: Q_POINTS
+    mapUnit: true
+  name: phonon_map_workflow
+  type: workflow
+  units:
+  - name: pre_processor
+    type: subworkflow
+  - name: ph_single_irr_qpt
+    type: subworkflow
+  - name: post_processor
+    type: subworkflow
+- name: phonon_reduce
+  type: subworkflow

package/assets/workflows/espresso/recalculate_bands.yml

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+name: Recalculate Bands
+units:
+- name: recalculate_bands
+  type: subworkflow

package/assets/workflows/espresso/surface_energy.yml

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+name: Surface Energy
+units:
+- name: surface_energy
+  type: subworkflow

package/assets/workflows/espresso/total_energy.yml

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+name: Total Energy
+units:
+- name: total_energy
+  type: subworkflow

package/assets/workflows/espresso/valence_band_offset.yml

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+# Valence band offset for an interface via the potential lineup method.
+# Designed to work with a 2D heterostructure, e.g. MoS2 on WS2.
+# The workflow assumes 3 structures being present:
+#   - Interface - e.g. MoS2/WS2 heterostructure
+#   - Interface Left - e.g. MoS2
+#   - Interface Right - e.g. WS2
+# and repeats bandstructure + electrostatic potential calculation (subworkflow) for them.
+# Then, calculates the band offset based on the data extracted.
+#
+# Relevant references:
+#   - http://dx.doi.org/10.1103/PhysRevLett.61.734
+#   - http://dx.doi.org/10.1103/physrevb.44.5572
+#   - http://dx.doi.org/10.1088/0953-8984/19/21/213203
+#
+# See also our tutorial:
+# https://docs.mat3ra.com/tutorials/dft/electronic/valence-band-offset/
+
+name: Valence Band Offset (2D)
+units:
+  # interface-related subworkflows
+  - name: average_electrostatic_potential_via_band_structure
+    type: subworkflow
+    config:
+      attributes:
+        name: BS + Avg ESP (Interface)
+    unitConfigs:
+      - index: 0
+        type: assignment
+        config:
+          attributes:
+            name: Set Material Index (Interface)
+            value: "0"
+  - name: average_electrostatic_potential_find_minima
+    type: subworkflow
+    config:
+      attributes:
+        name: Find ESP Values (Interface)
+    unitConfigs:
+      - index: 1
+        type: assignment
+        config:
+          attributes:
+            operand: AVG_ESP_INTERFACE
+
+  # interface-left-related subworkflows
+  - name: average_electrostatic_potential_via_band_structure
+    type: subworkflow
+    config:
+      attributes:
+        name: BS + Avg ESP (interface left)
+    unitConfigs:
+      - index: 0
+        type: assignment
+        config:
+          attributes:
+            name: Set Material Index (Interface left)
+            value: "1"
+      - index: 2
+        type: executionBuilder
+        config:
+          attributes:
+            flowchartId: pw-bands-calculate-band-gap-left
+      - index: 3
+        type: assignment
+        config:
+          attributes:
+            input:
+              - name: band_gaps
+                scope: pw-bands-calculate-band-gap-left
+      - index: 4
+        type: assignment
+        config:
+          attributes:
+            operand: VBM_LEFT
+      - index: 7
+        type: executionBuilder
+        config:
+          attributes:
+            flowchartId: average-electrostatic-potential-left
+      - index: 8
+        type: assignment
+        config:
+          attributes:
+            input:
+              - name: average_potential_profile
+                scope: average-electrostatic-potential-left
+  - name: average_electrostatic_potential_find_minima
+    type: subworkflow
+    config:
+      attributes:
+        name: Find ESP Value (Interface left)
+    unitConfigs:
+      - index: 0
+        type: executionBuilder
+        config:
+          attributes:
+            flowchartId: python-find-extrema-left
+      - index: 1
+        type: assignment
+        config:
+          attributes:
+            operand: AVG_ESP_LEFT
+            input:
+              - name: STDOUT
+                scope: python-find-extrema-left
+
+  # interface-right-related subworkflows
+  - name: average_electrostatic_potential_via_band_structure
+    type: subworkflow
+    config:
+      attributes:
+        name: BS + Avg ESP (interface right)
+    unitConfigs:
+      - index: 0
+        type: assignment
+        config:
+          attributes:
+            name: Set Material Index (Interface right)
+            value: "2"
+      - index: 2
+        type: executionBuilder
+        config:
+          attributes:
+            flowchartId: pw-bands-calculate-band-gap-right
+      - index: 3
+        type: assignment
+        config:
+          attributes:
+            input:
+              - name: band_gaps
+                scope: pw-bands-calculate-band-gap-right
+      - index: 4
+        type: assignment
+        config:
+          attributes:
+            operand: VBM_RIGHT
+      - index: 7
+        type: executionBuilder
+        config:
+          attributes:
+            flowchartId: average-electrostatic-potential-right
+      - index: 8
+        type: assignment
+        config:
+          attributes:
+            input:
+              - name: average_potential_profile
+                scope: average-electrostatic-potential-right
+  - name: average_electrostatic_potential_find_minima
+    type: subworkflow
+    config:
+      attributes:
+        name: Find ESP Value (Interface right)
+    unitConfigs:
+      - index: 0
+        type: executionBuilder
+        config:
+          attributes:
+            flowchartId: python-find-extrema-right
+      - index: 1
+        type: assignment
+        config:
+          attributes:
+            operand: AVG_ESP_RIGHT
+            input:
+              - name: STDOUT
+                scope: python-find-extrema-right
+
+  # final subworkflow to calculate valence band offset
+  - name: valence_band_offset_calc_from_previous_esp_vbm
+    type: subworkflow

package/assets/workflows/espresso/variable_cell_relaxation.yml

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+name: Variable-cell Relaxation
+units:
+- name: variable_cell_relaxation
+  type: subworkflow

package/assets/workflows/espresso/zero_point_energy.yml

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+name: Zero Point Energy
+units:
+- name: zero_point_energy
+  type: subworkflow

package/assets/workflows/jupyterLab/jupyter_notebook.yml

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+name: Jupyter Notebook
+units:
+- name: jupyter_notebook
+  type: subworkflow

package/assets/workflows/nwchem/total_energy.yml

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+name: Total Energy
+units:
+- name: total_energy
+  type: subworkflow

package/assets/workflows/python/ml/classification_workflow.yml

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+config:
+  attributes:
+    isUsingDataset: true
+name: Python ML Train Classification
+units:
+- name: train_head
+  type: subworkflow
+- name: classification_tail
+  type: subworkflow

package/assets/workflows/python/ml/clustering_workflow.yml

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+config:
+  attributes:
+    isUsingDataset: true
+name: Python ML Train Clustering
+units:
+- name: train_head
+  type: subworkflow
+- name: classification_tail
+  type: subworkflow

package/assets/workflows/python/ml/regression_workflow.yml

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+config:
+  attributes:
+    isUsingDataset: true
+name: Python ML Train Regression
+units:
+- name: train_head
+  type: subworkflow
+- name: regression_tail
+  type: subworkflow

package/assets/workflows/python/python_script.yml

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+name: Python Script
+units:
+- name: python_script
+  type: subworkflow

package/assets/workflows/shell/batch_espresso_pwscf.yml

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+name: Shell Batch Job (Espresso PWSCF)
+units:
+- name: batch_espresso_pwscf
+  type: subworkflow

package/assets/workflows/shell/hello_world.yml

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+name: Shell Script
+units:
+- name: hello_world
+  type: subworkflow

package/assets/workflows/vasp/band_gap.yml

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+name: Band Gap
+units:
+- name: band_gap
+  type: subworkflow

package/assets/workflows/vasp/band_structure.yml

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+name: Band Structure
+units:
+- name: band_structure
+  type: subworkflow

package/assets/workflows/vasp/band_structure_dos.yml

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+name: Band Structure + Density of States
+units:
+- name: band_structure_dos
+  type: subworkflow

package/assets/workflows/vasp/dos.yml

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+name: Density of States
+units:
+- name: dos
+  type: subworkflow

package/assets/workflows/vasp/fixed_cell_relaxation.yml

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+name: Fixed-cell Relaxation
+units:
+- name: fixed_cell_relaxation
+  type: subworkflow

package/assets/workflows/vasp/kpoint_convergence.yml

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+name: K-point Convergence
+units:
+- name: kpoint_convergence
+  type: subworkflow

package/assets/workflows/vasp/neb.yml

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+name: Nudged Elastic Band (NEB)
+units:
+- name: initial_final_total_energies
+  type: subworkflow
+- name: prepare_images
+  type: subworkflow
+- name: neb_subworkflow
+  type: subworkflow

package/assets/workflows/vasp/recalculate_bands.yml

@@ -0,0 +1,4 @@
+name: Recalculate Bands
+units:
+- name: recalculate_bands
+  type: subworkflow

package/assets/workflows/vasp/surface_energy.yml

@@ -0,0 +1,4 @@
+name: Surface Energy
+units:
+- name: surface_energy
+  type: subworkflow

package/assets/workflows/vasp/total_energy.yml

@@ -0,0 +1,4 @@
+name: Total Energy
+units:
+- name: total_energy
+  type: subworkflow

package/assets/workflows/vasp/variable_cell_relaxation.yml

@@ -0,0 +1,4 @@
+name: Variable-cell Relaxation
+units:
+- name: variable_cell_relaxation
+  type: subworkflow

package/assets/workflows/vasp/zero_point_energy.yml

@@ -0,0 +1,4 @@
+name: Zero Point Energy
+units:
+- name: zero_point_energy
+  type: subworkflow

package/build_workflows.js

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+const fs = require("fs");
+const path = require("path");
+const yaml = require("js-yaml");
+
+const allApplications = [
+    "espresso",
+    "jupyterLab",
+    "nwchem",
+    "python",
+    "python/ml",
+    "shell",
+    "vasp",
+    "deepmd",
+];
+
+const allWorkflows = { workflows: {}, subworkflows: {} };
+
+const JSONstringifyOrder = (obj, space) => {
+    const allKeys = new Set();
+    // eslint-disable-next-line no-sequences
+    JSON.stringify(obj, (key, value) => (allKeys.add(key), value));
+    return JSON.stringify(obj, Array.from(allKeys).sort(), space);
+};
+
+const loadFile = (name, dir, file, type) => {
+    const entryPath = path.resolve(dir, file);
+    if (!fs.statSync(entryPath).isFile()) {
+        console.log(`Skipping ${entryPath} as it is not a file.`);
+        return;
+    }
+    const obj = fs.readFileSync(path.resolve(dir, file), "utf8");
+    const key = file.split(".")[0];
+    allWorkflows[type][name][key] = yaml.load(obj);
+};
+
+allApplications.forEach((name) => {
+    allWorkflows.workflows[name] = {};
+    allWorkflows.subworkflows[name] = {};
+    const wfDir = path.resolve(__dirname, "assets", "workflows", name);
+    const swDir = path.resolve(__dirname, "assets", "subworkflows", name);
+    try {
+        const wfFiles = fs.readdirSync(wfDir);
+        const swFiles = fs.readdirSync(swDir);
+        console.log(
+            `Building ${name}: ${wfFiles.length} workflow(s) and ${swFiles.length} subworkflow(s)`,
+        );
+        wfFiles.forEach((file) => loadFile(name, wfDir, file, "workflows"));
+        swFiles.forEach((file) => loadFile(name, swDir, file, "subworkflows"));
+    } catch (e) {
+        console.log(e);
+    }
+});
+
+const write_path = "workflows.js";
+// write to src for unit test coverage simplicity
+fs.writeFileSync(
+    `./src/workflows/${write_path}`,
+    "module.exports = {workflowData: " + JSONstringifyOrder(allWorkflows) + "}",
+    "utf8",
+);
+fs.writeFileSync(
+    `./dist/workflows/${write_path}`,
+    "module.exports = {workflowData: " + JSONstringifyOrder(allWorkflows) + "}",
+    "utf8",
+);

package/dist/context/context.js

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+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = void 0;
+var _BoundaryConditionsFormDataProvider = require("./providers/BoundaryConditionsFormDataProvider");
+var _QENEBContextProvider = _interopRequireDefault(require("./providers/by_application/espresso/QENEBContextProvider"));
+var _QEPWXContextProvider = _interopRequireDefault(require("./providers/by_application/espresso/QEPWXContextProvider"));
+var _NWChemTotalEnergyContextProvider = _interopRequireDefault(require("./providers/by_application/nwchem/NWChemTotalEnergyContextProvider"));
+var _VASPContextProvider = _interopRequireDefault(require("./providers/by_application/vasp/VASPContextProvider"));
+var _VASPNEBContextProvider = _interopRequireDefault(require("./providers/by_application/vasp/VASPNEBContextProvider"));
+var _CollinearMagnetizationContextProvider = require("./providers/CollinearMagnetizationContextProvider");
+var _HubbardContextProviderLegacy = require("./providers/HubbardContextProviderLegacy");
+var _HubbardJContextProvider = require("./providers/HubbardJContextProvider");
+var _HubbardUContextProvider = require("./providers/HubbardUContextProvider");
+var _HubbardVContextProvider = require("./providers/HubbardVContextProvider");
+var _IonDynamicsContextProvider = require("./providers/IonDynamicsContextProvider");
+var _MLSettingsContextProvider = require("./providers/MLSettingsContextProvider");
+var _MLTrainTestSplitContextProvider = require("./providers/MLTrainTestSplitContextProvider");
+var _NEBFormDataProvider = require("./providers/NEBFormDataProvider");
+var _NonCollinearMagnetizationContextProvider = require("./providers/NonCollinearMagnetizationContextProvider");
+var _PlanewaveCutoffsContextProvider = require("./providers/PlanewaveCutoffsContextProvider");
+var _PointsGridFormDataProvider = require("./providers/PointsGridFormDataProvider");
+var _PointsPathFormDataProvider = require("./providers/PointsPathFormDataProvider");
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
+var _default = exports.default = {
+  BoundaryConditionsFormDataProvider: _BoundaryConditionsFormDataProvider.BoundaryConditionsFormDataProvider,
+  MLSettingsContextProvider: _MLSettingsContextProvider.MLSettingsContextProvider,
+  MLTrainTestSplitContextProvider: _MLTrainTestSplitContextProvider.MLTrainTestSplitContextProvider,
+  NEBFormDataProvider: _NEBFormDataProvider.NEBFormDataProvider,
+  PlanewaveCutoffsContextProvider: _PlanewaveCutoffsContextProvider.PlanewaveCutoffsContextProvider,
+  PointsGridFormDataProvider: _PointsGridFormDataProvider.PointsGridFormDataProvider,
+  PointsPathFormDataProvider: _PointsPathFormDataProvider.PointsPathFormDataProvider,
+  ExplicitPointsPathFormDataProvider: _PointsPathFormDataProvider.ExplicitPointsPathFormDataProvider,
+  ExplicitPointsPath2PIBAFormDataProvider: _PointsPathFormDataProvider.ExplicitPointsPath2PIBAFormDataProvider,
+  HubbardJContextProvider: _HubbardJContextProvider.HubbardJContextProvider,
+  HubbardUContextProvider: _HubbardUContextProvider.HubbardUContextProvider,
+  HubbardVContextProvider: _HubbardVContextProvider.HubbardVContextProvider,
+  HubbardContextProviderLegacy: _HubbardContextProviderLegacy.HubbardContextProviderLegacy,
+  IonDynamicsContextProvider: _IonDynamicsContextProvider.IonDynamicsContextProvider,
+  CollinearMagnetizationContextProvider: _CollinearMagnetizationContextProvider.CollinearMagnetizationContextProvider,
+  NonCollinearMagnetizationContextProvider: _NonCollinearMagnetizationContextProvider.NonCollinearMagnetizationContextProvider,
+  VASPContextProvider: _VASPContextProvider.default,
+  VASPNEBContextProvider: _VASPNEBContextProvider.default,
+  QEPWXContextProvider: _QEPWXContextProvider.default,
+  QENEBContextProvider: _QENEBContextProvider.default,
+  NWChemTotalEnergyContextProvider: _NWChemTotalEnergyContextProvider.default
+};

package/dist/context/mixins/ApplicationContextMixin.js

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+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.applicationContextMixin = applicationContextMixin;
+var _settings = require("../providers/settings");
+function applicationContextMixin(item) {
+  const properties = {
+    _application: undefined,
+    initApplicationContextMixin() {
+      this._application = this.config.context && this.config.context.application || _settings.globalSettings.Application.createDefault();
+    },
+    get application() {
+      return this._application;
+    }
+  };
+  Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
+}

package/dist/context/mixins/JobContextMixin.js

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+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.jobContextMixin = jobContextMixin;
+const defaultJob = {
+  workflow: {
+    subworkflows: [],
+    units: []
+  },
+  status: "pre-submission",
+  compute: {
+    queue: "D",
+    nodes: 1,
+    ppn: 1,
+    timeLimit: "3600"
+  },
+  _project: {
+    _id: ""
+  }
+};
+function jobContextMixin(item) {
+  const properties = {
+    isEdited: false,
+    _job: defaultJob,
+    get job() {
+      return this._job;
+    },
+    initJobContextMixin() {
+      const {
+        config
+      } = this;
+      this._job = config.context && config.context.job || defaultJob;
+      this.isEdited = false; // we always get the `defaultData` (recalculated from scratch, not persistent)
+    }
+  };
+  Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
+}

package/dist/context/mixins/MaterialContextMixin.js

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+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.materialContextMixin = materialContextMixin;
+var _settings = require("../providers/settings");
+function materialContextMixin(item) {
+  const properties = {
+    _material: undefined,
+    updateMaterialHash() {
+      if (this.isEditedIsSetToFalseOnMaterialUpdate) this.isEdited = false;
+      this.extraData = {
+        materialHash: this.material.hash
+      };
+    },
+    // Workaround: Material.createDefault() used to initiate workflow reducer and hence here too
+    //  does not have an id. Here we catch when such material is used and avoid resetting isEdited
+    get isMaterialCreatedDefault() {
+      return !this.material.id;
+    },
+    get isMaterialUpdated() {
+      return Boolean(this.extraData && this.extraData.materialHash !== this.material.hash);
+    },
+    get material() {
+      if (!this._material) {
+        throw new Error("Material is not set");
+      }
+      return this._material;
+    },
+    initMaterialContextMixin() {
+      this._material = this.config.context && this.config.context.material;
+      if (!this._material) {
+        this._material = _settings.globalSettings.Material.createDefault();
+      }
+      this.updateMaterialHash();
+    }
+  };
+  Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
+}

package/dist/context/mixins/MaterialsContextMixin.js

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+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.materialsContextMixin = materialsContextMixin;
+var _settings = require("../providers/settings");
+function materialsContextMixin(item) {
+  const properties = {
+    get materials() {
+      return this._materials;
+    },
+    initMaterialsContextMixin() {
+      const materials = this.config.context?.materials;
+      this._materials = materials && materials.length ? materials : [_settings.globalSettings.Material.createDefault()];
+    }
+  };
+  Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
+}

package/dist/context/mixins/MaterialsSetContextMixin.js

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+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.materialsSetContextMixin = materialsSetContextMixin;
+var _utils = require("@mat3ra/code/dist/js/entity/set/ordered/utils");
+function materialsSetContextMixin(item) {
+  const properties = {
+    _materialsSet: undefined,
+    get materialsSet() {
+      return this._materialsSet;
+    },
+    initMaterialsSetContextMixin() {
+      this._materialsSet = this.config.context?.materialsSet;
+    },
+    sortMaterialsByIndexInSet(materials = []) {
+      // DO NOT SORT IN PLACE AS IT CHANGES THE ORDER IN `this.materials` AND HAS SIDE EFFECTS (MaterialViewer).
+      return materials.concat().sort((a, b) => {
+        return (0, _utils.compareEntitiesInOrderedSetForSorting)(a, b, this.materialsSet._id, false);
+      });
+    }
+  };
+  Object.defineProperties(item, Object.getOwnPropertyDescriptors(properties));
+}