@mat3ra/wode 2025.10.1-0

package/assets/subworkflows/espresso/espresso_xml_get_qpt_irr.yml

@@ -0,0 +1,12 @@
+application:
+  name: python
+  version: 3.10.13
+dynamicSubworkflow:
+  name: getQpointIrrep
+  subfolder: espresso
+method:
+  name: UnknownMethod
+model:
+  name: UnknownModel
+name: espresso-xml-get-qpt-irr
+units: []

package/assets/subworkflows/espresso/fixed_cell_relaxation.yml

@@ -0,0 +1,16 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Fixed-cell Relaxation
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_relax
+      name: pw_relax
+    functions:
+      head: true
+    type: executionBuilder

package/assets/subworkflows/espresso/gw_band_structure_band_gap_full_frequency.yml

@@ -0,0 +1,22 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+  setSearchText: .*dojo-oncv.*
+model:
+  name: DFTModel
+name: Full Frequency GW Band Structure + Band Gap
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    functions:
+      head: true
+    type: executionBuilder
+  - config:
+      execName: gw.x
+      flavorName: gw_bands_full_frequency
+      name: gw_bands_full_frequency
+    type: executionBuilder

package/assets/subworkflows/espresso/gw_band_structure_band_gap_plasmon_pole.yml

@@ -0,0 +1,22 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+  setSearchText: .*dojo-oncv.*
+model:
+  name: DFTModel
+name: Plasmon-Pole GW Band Structure + Band Gap
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    functions:
+      head: true
+    type: executionBuilder
+  - config:
+      execName: gw.x
+      flavorName: gw_bands_plasmon_pole
+      name: gw_bands_plasmon_pole
+    type: executionBuilder

package/assets/subworkflows/espresso/hubbard_u_hp.yml

@@ -0,0 +1,21 @@
+name: Hubbard U
+application:
+  name: espresso
+  version: "7.2"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf_dft_u
+      name: pw_scf_dft_u
+    functions:
+      head: true
+    type: executionBuilder
+  - config:
+      execName: hp.x
+      flavorName: hp
+      name: hp
+    type: executionBuilder

package/assets/subworkflows/espresso/kpoint_convergence.yml

@@ -0,0 +1,86 @@
+name: K-point Convergence
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+units:
+  - config:
+      name: Init tolerance
+      flowchartId: init-tolerance
+      operand: TOL
+      value: 1.0e-5
+    type: assignment
+  - config:
+      name: Init increment
+      flowchartId: init-increment
+      operand: INC
+      value: 1
+    type: assignment
+  - config:
+      name: Init result
+      flowchartId: init-result
+      operand: PREV_RESULT
+      value: 0
+    type: assignment
+  - config:
+      name: Init parameter
+      flowchartId: init-parameter
+      operand: PARAMETER
+      value: 1
+    type: assignment
+  - config:
+      name: pw_scf_kpt_conv
+      flowchartId: pwscf-kpoint-convergence
+      execName: pw.x
+      flavorName: pw_scf_kpt_conv
+    type: executionBuilder
+  - config:
+      name: store result
+      flowchartId: store-result
+      operand: RESULT
+      value: total_energy
+      input:
+        - name: total_energy
+          scope: pwscf-kpoint-convergence
+    type: assignment
+  - config:
+      name: check convergence
+      flowchartId: check-convergence
+      statement: "abs((PREV_RESULT-RESULT)/RESULT) < TOL"
+      maxOccurrences: 50
+      then: convergence-is-reached
+      else: update-result
+    type: condition
+  - config:
+      name: update result
+      flowchartId: update-result
+      operand: PREV_RESULT
+      value: RESULT
+      input:
+        - name: RESULT
+          scope: global
+    type: assignment
+  - config:
+      name: increment parameter
+      flowchartId: increment-parameter
+      operand: PREV_RESULT
+      value: PARAMETER+INC
+      input:
+        - name: INC
+          scope: global
+        - name: PARAMETER
+          scope: global
+      next: pwscf-kpoint-convergence
+    type: assignment
+  - config:
+      name: exit
+      flowchartId: convergence-is-reached
+      operand: PARAMETER
+      value: PARAMETER
+      input:
+        - name: PARAMETER
+          scope: global
+    type: assignment

package/assets/subworkflows/espresso/neb.yml

@@ -0,0 +1,16 @@
+application:
+  name: espresso
+  version: "6.3"
+config:
+  isMultiMaterial: true
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Nudged Elastic Band (NEB)
+units:
+  - config:
+      execName: neb.x
+      flavorName: neb
+      name: neb
+    type: executionBuilder

package/assets/subworkflows/espresso/ph_init_qpoints.yml

@@ -0,0 +1,14 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: ph-init-qpoints
+units:
+  - config:
+      execName: ph.x
+      flavorName: ph_init_qpoints
+      name: ph_init_qpoints
+    type: executionBuilder

package/assets/subworkflows/espresso/ph_single_irr_qpt.yml

@@ -0,0 +1,14 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: ph-single-irr-qpt
+units:
+  - config:
+      execName: ph.x
+      flavorName: ph_single_irr_qpt
+      name: ph_single_irr_qpt
+    type: executionBuilder

package/assets/subworkflows/espresso/phonon_dispersions.yml

@@ -0,0 +1,29 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Phonon Dispersions
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    type: executionBuilder
+  - config:
+      execName: ph.x
+      flavorName: ph_grid
+      name: ph_grid
+    type: executionBuilder
+  - config:
+      execName: q2r.x
+      flavorName: q2r
+      name: q2r
+    type: executionBuilder
+  - config:
+      execName: matdyn.x
+      flavorName: matdyn_path
+      name: matdyn_path
+    type: executionBuilder

package/assets/subworkflows/espresso/phonon_dos.yml

@@ -0,0 +1,29 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Phonon Density of States
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    type: executionBuilder
+  - config:
+      execName: ph.x
+      flavorName: ph_grid
+      name: ph_grid
+    type: executionBuilder
+  - config:
+      execName: q2r.x
+      flavorName: q2r
+      name: q2r
+    type: executionBuilder
+  - config:
+      execName: matdyn.x
+      flavorName: matdyn_grid
+      name: matdyn_grid
+    type: executionBuilder

package/assets/subworkflows/espresso/phonon_dos_dispersion.yml

@@ -0,0 +1,34 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Phonon Density of States + Dispersions
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    type: executionBuilder
+  - config:
+      execName: ph.x
+      flavorName: ph_grid
+      name: ph_grid
+    type: executionBuilder
+  - config:
+      execName: q2r.x
+      flavorName: q2r
+      name: q2r
+    type: executionBuilder
+  - config:
+      execName: matdyn.x
+      flavorName: matdyn_grid
+      name: matdyn_grid
+    type: executionBuilder
+  - config:
+      execName: matdyn.x
+      flavorName: matdyn_path
+      name: matdyn_path
+    type: executionBuilder

package/assets/subworkflows/espresso/phonon_reduce.yml

@@ -0,0 +1,29 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: reduce
+units:
+  - config:
+      execName: ph.x
+      flavorName: ph_grid_restart
+      name: ph_grid_restart
+    type: executionBuilder
+  - config:
+      execName: q2r.x
+      flavorName: q2r
+      name: q2r
+    type: executionBuilder
+  - config:
+      execName: matdyn.x
+      flavorName: matdyn_grid
+      name: matdyn_grid
+    type: executionBuilder
+  - config:
+      execName: matdyn.x
+      flavorName: matdyn_path
+      name: matdyn_path
+    type: executionBuilder

package/assets/subworkflows/espresso/post_processor.yml

@@ -0,0 +1,14 @@
+application:
+  name: shell
+  version: 5.1.8
+method:
+  name: UnknownMethod
+model:
+  name: UnknownModel
+name: post-processor
+units:
+  - config:
+      execName: sh
+      flavorName: espresso_collect_dynmat
+      name: shell
+    type: executionBuilder

package/assets/subworkflows/espresso/pre_processor.yml

@@ -0,0 +1,14 @@
+application:
+  name: shell
+  version: 5.1.8
+method:
+  name: UnknownMethod
+model:
+  name: UnknownModel
+name: pre-processor
+units:
+  - config:
+      execName: sh
+      flavorName: espresso_link_outdir_save
+      name: shell
+    type: executionBuilder

package/assets/subworkflows/espresso/pw_scf.yml

@@ -0,0 +1,16 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: pw-scf
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    functions:
+      head: true
+    type: executionBuilder

package/assets/subworkflows/espresso/recalculate_bands.yml

@@ -0,0 +1,19 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Recalculate Bands
+units:
+  - 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/surface_energy.yml

@@ -0,0 +1,16 @@
+application:
+  name: espresso
+  version: "6.3"
+dynamicSubworkflow:
+  name: surfaceEnergy
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Surface Energy
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    type: executionBuilder

package/assets/subworkflows/espresso/total_energy.yml

@@ -0,0 +1,16 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Total Energy
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    functions:
+      head: true
+    type: executionBuilder

package/assets/subworkflows/espresso/valence_band_offset_calc_from_previous_esp_vbm.yml

@@ -0,0 +1,35 @@
+# 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:
+# VBM_LEFT, VBM_RIGHT, AVG_ESP_LEFT, AVG_ESP_RIGHT, AVG_ESP_INTERFACE
+application:
+  name: python
+  version: 3.10.13
+method:
+  name: UnknownMethod
+model:
+  name: UnknownModel
+name: Calculate VBO
+units:
+  - config:
+      name: Difference of valence band maxima
+      operand: VBM_DIFF
+      value: "VBM_LEFT - VBM_RIGHT"
+    type: assignment
+  - config:
+      name: Difference of macroscopically averaged ESP in bulk
+      operand: AVG_ESP_DIFF
+      value: "AVG_ESP_LEFT[0] - AVG_ESP_RIGHT[0]"
+    type: assignment
+  - config:
+      name: Lineup of macroscopically averaged ESP in interface
+      operand: ESP_LINEUP
+      value: "np.abs(AVG_ESP_INTERFACE[0] - AVG_ESP_INTERFACE[1])"
+    type: assignment
+  - config:
+      name: Valence Band Offset
+      operand: VALENCE_BAND_OFFSET
+      value: "abs(VBM_DIFF - AVG_ESP_DIFF + (np.sign(AVG_ESP_DIFF) * ESP_LINEUP))"
+      results:
+        - name: valence_band_offset
+    type: assignment

package/assets/subworkflows/espresso/variable_cell_relaxation.yml

@@ -0,0 +1,18 @@
+application:
+  name: espresso
+  version: "6.3"
+config:
+  systemName: espresso-variable-cell-relaxation
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Variable-cell Relaxation
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_vc-relax
+      name: pw_vc-relax
+    functions:
+      head: true
+    type: executionBuilder

package/assets/subworkflows/espresso/zero_point_energy.yml

@@ -0,0 +1,19 @@
+application:
+  name: espresso
+  version: "6.3"
+method:
+  name: PseudopotentialMethod
+model:
+  name: DFTModel
+name: Zero Point Energy
+units:
+  - config:
+      execName: pw.x
+      flavorName: pw_scf
+      name: pw_scf
+    type: executionBuilder
+  - config:
+      execName: ph.x
+      flavorName: ph_gamma
+      name: ph_zpe
+    type: executionBuilder

package/assets/subworkflows/jupyterLab/jupyter_notebook.yml

@@ -0,0 +1,17 @@
+application:
+  name: jupyterLab
+  version: 4.3.0
+method:
+  name: UnknownMethod
+model:
+  name: UnknownModel
+name: Jupyter Notebook
+units:
+  - attributes:
+      preProcessors:
+        - name: record_python_environment
+    config:
+      execName: jupyter
+      flavorName: notebook
+      name: notebook
+    type: executionBuilder

package/assets/subworkflows/nwchem/total_energy.yml

@@ -0,0 +1,16 @@
+application:
+  name: nwchem
+  version: 7.0.2
+method:
+  name: LocalOrbitalMethod
+model:
+  name: DFTModel
+name: Total Energy
+units:
+  - config:
+      execName: nwchem
+      flavorName: nwchem_total_energy
+      name: nwchem_total_energy
+    functions:
+      head: true
+    type: executionBuilder

package/assets/subworkflows/python/ml/classification_tail.yml

@@ -0,0 +1,56 @@
+application:
+  name: python
+  version: 3.10.13
+method:
+  name: UnknownMethod
+model:
+  name: UnknownModel
+name: Machine Learning
+units:
+  - attributes:
+      enableRender: true
+    config:
+      execName: python
+      flavorName: pyml:setup_variables_packages
+      name: Setup Variables and Packages
+    type: executionBuilder
+  - config:
+      execName: python
+      flavorName: pyml:data_input:read_csv:pandas
+      name: Data Input
+    type: executionBuilder
+  - config:
+      execName: python
+      flavorName: pyml:data_input:train_test_split:sklearn
+      name: Train Test Split
+    type: executionBuilder
+  - config:
+      execName: python
+      flavorName: pyml:pre_processing:standardization:sklearn
+      name: Data Standardize
+    type: executionBuilder
+  - attributes:
+      results:
+        - name: workflow:pyml_predict
+      tags:
+        - remove-all-results
+        - creates-predictions-csv-during-predict-phase
+    config:
+      execName: python
+      flavorName: pyml:model:random_forest_classification:sklearn
+      name: Model Train and Predict
+    type: executionBuilder
+  - attributes:
+      postProcessors:
+        - name: remove_virtual_environment
+      results:
+        - basename: my_roc_plot.png
+          filetype: image
+          name: file_content
+      tags:
+        - remove-all-results
+    config:
+      execName: python
+      flavorName: pyml:post_processing:roc_curve:sklearn
+      name: ROC Curve Plot
+    type: executionBuilder

package/assets/subworkflows/python/ml/clustering_tail.yml

@@ -0,0 +1,62 @@
+application:
+  name: python
+  version: 3.10.13
+method:
+  name: UnknownMethod
+model:
+  name: UnknownModel
+name: Machine Learning
+units:
+  - attributes:
+      enableRender: true
+    config:
+      execName: python
+      flavorName: pyml:setup_variables_packages
+      name: Setup Variables and Packages
+    type: executionBuilder
+  - config:
+      execName: python
+      flavorName: pyml:data_input:read_csv:pandas
+      name: Data Input
+    type: executionBuilder
+  - config:
+      execName: python
+      flavorName: pyml:data_input:train_test_split:sklearn
+      name: Train Test Split
+    type: executionBuilder
+  - config:
+      execName: python
+      flavorName: pyml:pre_processing:standardization:sklearn
+      name: Data Standardize
+    type: executionBuilder
+  - attributes:
+      results:
+        - name: workflow:pyml_predict
+      tags:
+        - remove-all-results
+        - creates-predictions-csv-during-predict-phase
+    config:
+      execName: python
+      flavorName: pyml:model:k_means_clustering:sklearn
+      name: Model Train and Predict
+    type: executionBuilder
+  - attributes:
+      postProcessors:
+        - name: remove_virtual_environment
+      results:
+        - basename: train_test_split.png
+          filetype: image
+          name: file_content
+        - basename: train_clusters.png
+          filetype: image
+          name: file_content
+        - basename: test_clusters.png
+          filetype: image
+          name: file_content
+      tags:
+        - remove-all-results
+    config:
+      execName: python
+      flavorName: pyml:post_processing:pca_2d_clusters:matplotlib
+      name: 2D PCA Clusters Plot
+    type: executionBuilder