@mat3ra/wode 2025.10.2-2 → 2025.11.3-0

package/assets/subworkflows/espresso/electronic_density_mesh.yml

@@ -1,19 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Electronic Density Mesh
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_scf
-      name: pw_scf
-    type: executionBuilder
-  - config:
-      execName: pp.x
-      flavorName: pp_density
-      name: pp_density
-    type: executionBuilder

package/assets/subworkflows/espresso/esm.yml

@@ -1,14 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Effective Screening Medium (ESM)
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_esm
-      name: pw_esm
-    type: executionBuilder

package/assets/subworkflows/espresso/esm_relax.yml

@@ -1,14 +0,0 @@
-application:
-  name: espresso
-  version: "6.3"
-method:
-  name: PseudopotentialMethod
-model:
-  name: DFTModel
-name: Effective Screening Medium (ESM) Relax
-units:
-  - config:
-      execName: pw.x
-      flavorName: pw_esm_relax
-      name: pw_esm_relax
-    type: executionBuilder

package/assets/subworkflows/espresso/espresso_extract_kpoints.yml

@@ -1,16 +0,0 @@
-# Note: this subworkflow is assumed to be run after a pw_scf unit
-# and is this NOT self-sufficient!
-name: Extract KPOINTS
-application:
-  name: python
-  version: 3.10.13
-method:
-  name: UnknownMethod
-model:
-  name: UnknownModel
-units:
-  - config:
-      name: Extract kpoints
-      execName: python
-      flavorName: espresso_extract_kpoints
-    type: executionBuilder

package/assets/subworkflows/espresso/espresso_xml_get_qpt_irr.yml

@@ -1,12 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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

@@ -1,22 +0,0 @@
-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

@@ -1,22 +0,0 @@
-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

@@ -1,21 +0,0 @@
-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

@@ -1,86 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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

@@ -1,14 +0,0 @@
-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

@@ -1,14 +0,0 @@
-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

@@ -1,29 +0,0 @@
-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

@@ -1,29 +0,0 @@
-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

@@ -1,34 +0,0 @@
-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

@@ -1,29 +0,0 @@
-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

@@ -1,14 +0,0 @@
-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

@@ -1,14 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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

@@ -1,19 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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

@@ -1,35 +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:
-# 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

@@ -1,18 +0,0 @@
-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

@@ -1,19 +0,0 @@
-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

@@ -1,17 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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