diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index a1b92801..882ad707 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -24,12 +24,12 @@ jobs: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} path: actions - - - name: Run Yaml linter - uses: ./actions/yaml/lint - with: - python-version: 3.10.13 - targets: ./assets +# TODO: re-add when we have Python code to lint +# - name: Run Py linter +# uses: ./actions/py/lint +# with: +# python-version: 3.10.13 +# targets: ./assets run-js-tests: runs-on: ubuntu-latest @@ -77,4 +77,3 @@ jobs: with: npm-token: ${{ secrets.NPM_TOKEN }} github-token: ${{ secrets.BOT_GITHUB_TOKEN }} - diff --git a/assets/subworkflows/deepmd/deepmd.yml b/assets/subworkflows/deepmd/deepmd.yml deleted file mode 100644 index 0f9572f2..00000000 --- a/assets/subworkflows/deepmd/deepmd.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/deepmd/espresso_cp_md.yml b/assets/subworkflows/deepmd/espresso_cp_md.yml deleted file mode 100644 index 46449ae0..00000000 --- a/assets/subworkflows/deepmd/espresso_cp_md.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/average_electrostatic_potential_find_minima.yml b/assets/subworkflows/espresso/average_electrostatic_potential_find_minima.yml deleted file mode 100644 index a3d13e66..00000000 --- a/assets/subworkflows/espresso/average_electrostatic_potential_find_minima.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/average_electrostatic_potential_via_band_structure.yml b/assets/subworkflows/espresso/average_electrostatic_potential_via_band_structure.yml deleted file mode 100644 index d6ec54e6..00000000 --- a/assets/subworkflows/espresso/average_electrostatic_potential_via_band_structure.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/band_gap.yml b/assets/subworkflows/espresso/band_gap.yml deleted file mode 100644 index 32c6c42b..00000000 --- a/assets/subworkflows/espresso/band_gap.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/band_gap_hse_dos.yml b/assets/subworkflows/espresso/band_gap_hse_dos.yml deleted file mode 100644 index ae0d57ae..00000000 --- a/assets/subworkflows/espresso/band_gap_hse_dos.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/band_structure.yml b/assets/subworkflows/espresso/band_structure.yml deleted file mode 100644 index 2f861c57..00000000 --- a/assets/subworkflows/espresso/band_structure.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/band_structure_dos.yml b/assets/subworkflows/espresso/band_structure_dos.yml deleted file mode 100644 index 130cccf0..00000000 --- a/assets/subworkflows/espresso/band_structure_dos.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/band_structure_hse.yml b/assets/subworkflows/espresso/band_structure_hse.yml deleted file mode 100644 index 6713d0e1..00000000 --- a/assets/subworkflows/espresso/band_structure_hse.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/band_structure_magn.yml b/assets/subworkflows/espresso/band_structure_magn.yml deleted file mode 100644 index 5c927290..00000000 --- a/assets/subworkflows/espresso/band_structure_magn.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/band_structure_soc.yml b/assets/subworkflows/espresso/band_structure_soc.yml deleted file mode 100644 index 1ff6f9f9..00000000 --- a/assets/subworkflows/espresso/band_structure_soc.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/dielectric_tensor.yml b/assets/subworkflows/espresso/dielectric_tensor.yml deleted file mode 100644 index deb53545..00000000 --- a/assets/subworkflows/espresso/dielectric_tensor.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/dos.yml b/assets/subworkflows/espresso/dos.yml deleted file mode 100644 index cc82f101..00000000 --- a/assets/subworkflows/espresso/dos.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/electronic_density_mesh.yml b/assets/subworkflows/espresso/electronic_density_mesh.yml deleted file mode 100644 index 02625f17..00000000 --- a/assets/subworkflows/espresso/electronic_density_mesh.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/esm.yml b/assets/subworkflows/espresso/esm.yml deleted file mode 100644 index 1ff351a5..00000000 --- a/assets/subworkflows/espresso/esm.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/esm_relax.yml b/assets/subworkflows/espresso/esm_relax.yml deleted file mode 100644 index 2b345204..00000000 --- a/assets/subworkflows/espresso/esm_relax.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/espresso_extract_kpoints.yml b/assets/subworkflows/espresso/espresso_extract_kpoints.yml deleted file mode 100644 index a61a6b90..00000000 --- a/assets/subworkflows/espresso/espresso_extract_kpoints.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/espresso_xml_get_qpt_irr.yml b/assets/subworkflows/espresso/espresso_xml_get_qpt_irr.yml deleted file mode 100644 index 2b1772b7..00000000 --- a/assets/subworkflows/espresso/espresso_xml_get_qpt_irr.yml +++ /dev/null @@ -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: [] diff --git a/assets/subworkflows/espresso/fixed_cell_relaxation.yml b/assets/subworkflows/espresso/fixed_cell_relaxation.yml deleted file mode 100644 index 0fc20c89..00000000 --- a/assets/subworkflows/espresso/fixed_cell_relaxation.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/gw_band_structure_band_gap_full_frequency.yml b/assets/subworkflows/espresso/gw_band_structure_band_gap_full_frequency.yml deleted file mode 100644 index af48af6d..00000000 --- a/assets/subworkflows/espresso/gw_band_structure_band_gap_full_frequency.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/gw_band_structure_band_gap_plasmon_pole.yml b/assets/subworkflows/espresso/gw_band_structure_band_gap_plasmon_pole.yml deleted file mode 100644 index 9c6835fc..00000000 --- a/assets/subworkflows/espresso/gw_band_structure_band_gap_plasmon_pole.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/hubbard_u_hp.yml b/assets/subworkflows/espresso/hubbard_u_hp.yml deleted file mode 100644 index b9cd9007..00000000 --- a/assets/subworkflows/espresso/hubbard_u_hp.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/kpoint_convergence.yml b/assets/subworkflows/espresso/kpoint_convergence.yml deleted file mode 100644 index f2faa94d..00000000 --- a/assets/subworkflows/espresso/kpoint_convergence.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/neb.yml b/assets/subworkflows/espresso/neb.yml deleted file mode 100644 index 749668e8..00000000 --- a/assets/subworkflows/espresso/neb.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/ph_init_qpoints.yml b/assets/subworkflows/espresso/ph_init_qpoints.yml deleted file mode 100644 index 88be83ed..00000000 --- a/assets/subworkflows/espresso/ph_init_qpoints.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/ph_single_irr_qpt.yml b/assets/subworkflows/espresso/ph_single_irr_qpt.yml deleted file mode 100644 index 04f67e6e..00000000 --- a/assets/subworkflows/espresso/ph_single_irr_qpt.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/phonon_dispersions.yml b/assets/subworkflows/espresso/phonon_dispersions.yml deleted file mode 100644 index a28e5df9..00000000 --- a/assets/subworkflows/espresso/phonon_dispersions.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/phonon_dos.yml b/assets/subworkflows/espresso/phonon_dos.yml deleted file mode 100644 index a381c6b2..00000000 --- a/assets/subworkflows/espresso/phonon_dos.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/phonon_dos_dispersion.yml b/assets/subworkflows/espresso/phonon_dos_dispersion.yml deleted file mode 100644 index 5965d8f3..00000000 --- a/assets/subworkflows/espresso/phonon_dos_dispersion.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/phonon_reduce.yml b/assets/subworkflows/espresso/phonon_reduce.yml deleted file mode 100644 index ef2efac0..00000000 --- a/assets/subworkflows/espresso/phonon_reduce.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/post_processor.yml b/assets/subworkflows/espresso/post_processor.yml deleted file mode 100644 index 0038efd1..00000000 --- a/assets/subworkflows/espresso/post_processor.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/pre_processor.yml b/assets/subworkflows/espresso/pre_processor.yml deleted file mode 100644 index 679a5d66..00000000 --- a/assets/subworkflows/espresso/pre_processor.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/pw_scf.yml b/assets/subworkflows/espresso/pw_scf.yml deleted file mode 100644 index 7edc6162..00000000 --- a/assets/subworkflows/espresso/pw_scf.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/recalculate_bands.yml b/assets/subworkflows/espresso/recalculate_bands.yml deleted file mode 100644 index c59faa41..00000000 --- a/assets/subworkflows/espresso/recalculate_bands.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/surface_energy.yml b/assets/subworkflows/espresso/surface_energy.yml deleted file mode 100644 index 38b21eaf..00000000 --- a/assets/subworkflows/espresso/surface_energy.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/total_energy.yml b/assets/subworkflows/espresso/total_energy.yml deleted file mode 100644 index 3b9eeb9c..00000000 --- a/assets/subworkflows/espresso/total_energy.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/valence_band_offset_calc_from_previous_esp_vbm.yml b/assets/subworkflows/espresso/valence_band_offset_calc_from_previous_esp_vbm.yml deleted file mode 100644 index ce6fc145..00000000 --- a/assets/subworkflows/espresso/valence_band_offset_calc_from_previous_esp_vbm.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/variable_cell_relaxation.yml b/assets/subworkflows/espresso/variable_cell_relaxation.yml deleted file mode 100644 index 828978e8..00000000 --- a/assets/subworkflows/espresso/variable_cell_relaxation.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/espresso/zero_point_energy.yml b/assets/subworkflows/espresso/zero_point_energy.yml deleted file mode 100644 index 9f70ab86..00000000 --- a/assets/subworkflows/espresso/zero_point_energy.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/jupyterLab/jupyter_notebook.yml b/assets/subworkflows/jupyterLab/jupyter_notebook.yml deleted file mode 100644 index e602a901..00000000 --- a/assets/subworkflows/jupyterLab/jupyter_notebook.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/nwchem/total_energy.yml b/assets/subworkflows/nwchem/total_energy.yml deleted file mode 100644 index 1b16eb4c..00000000 --- a/assets/subworkflows/nwchem/total_energy.yml +++ /dev/null @@ -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 diff --git a/assets/subworkflows/python/ml/classification_tail.yml b/assets/subworkflows/python/ml/classification_tail.yml deleted file mode 100644 index 3fd1dd74..00000000 --- a/assets/subworkflows/python/ml/classification_tail.yml +++ /dev/null @@ -1,56 +0,0 @@ -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 diff --git a/assets/subworkflows/python/ml/clustering_tail.yml b/assets/subworkflows/python/ml/clustering_tail.yml deleted file mode 100644 index 09984658..00000000 --- a/assets/subworkflows/python/ml/clustering_tail.yml +++ /dev/null @@ -1,62 +0,0 @@ -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 diff --git a/assets/subworkflows/python/ml/regression_tail.yml b/assets/subworkflows/python/ml/regression_tail.yml deleted file mode 100644 index 252ff4bf..00000000 --- a/assets/subworkflows/python/ml/regression_tail.yml +++ /dev/null @@ -1,56 +0,0 @@ -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:multilayer_perceptron:sklearn - name: Model Train and Predict - type: executionBuilder - - attributes: - postProcessors: - - name: remove_virtual_environment - results: - - basename: my_parity_plot.png - filetype: image - name: file_content - tags: - - remove-all-results - config: - execName: python - flavorName: pyml:post_processing:parity_plot:matplotlib - name: Parity Plot - type: executionBuilder diff --git a/assets/subworkflows/python/ml/train_head.yml b/assets/subworkflows/python/ml/train_head.yml deleted file mode 100644 index 1faaa12f..00000000 --- a/assets/subworkflows/python/ml/train_head.yml +++ /dev/null @@ -1,61 +0,0 @@ -application: - name: python - version: 3.10.13 -method: - name: UnknownMethod -model: - name: UnknownModel -name: Set Up the Job -units: - - config: - flowchartId: head-set-predict-status - name: Set Workflow Mode - operand: IS_WORKFLOW_RUNNING_TO_PREDICT - tags: - - pyml:workflow-type-setter - value: "False" - type: assignment - - config: - enableRender: true - flowchartId: head-fetch-training-data - input: - - basename: "{{DATASET_BASENAME}}" - objectData: - CONTAINER: "" - NAME: "{{DATASET_FILEPATH}}" - PROVIDER: "" - REGION: "" - name: Fetch Dataset - source: object_storage - type: io - - config: - else: end-of-ml-train-head - flowchartId: head-branch-on-predict-status - input: - - name: IS_WORKFLOW_RUNNING_TO_PREDICT - scope: global - name: Train or Predict? - statement: IS_WORKFLOW_RUNNING_TO_PREDICT - then: head-fetch-trained-model - type: condition - - config: - enableRender: true - flowchartId: head-fetch-trained-model - input: - - basename: "" - objectData: - CONTAINER: "" - NAME: "" - PROVIDER: "" - REGION: "" - name: Fetch Trained Model as file - source: object_storage - tags: - - set-io-unit-filenames - type: io - - config: - flowchartId: end-of-ml-train-head - name: End Setup - operand: IS_SETUP_COMPLETE - value: "True" - type: assignment diff --git a/assets/subworkflows/python/python_script.yml b/assets/subworkflows/python/python_script.yml deleted file mode 100644 index 8c764d4f..00000000 --- a/assets/subworkflows/python/python_script.yml +++ /dev/null @@ -1,14 +0,0 @@ -application: - name: python - version: 3.10.13 -method: - name: UnknownMethod -model: - name: UnknownModel -name: Python Script -units: - - config: - execName: python - flavorName: hello_world - name: python - type: executionBuilder diff --git a/assets/subworkflows/shell/batch_espresso_pwscf.yml b/assets/subworkflows/shell/batch_espresso_pwscf.yml deleted file mode 100644 index dd6a36bc..00000000 --- a/assets/subworkflows/shell/batch_espresso_pwscf.yml +++ /dev/null @@ -1,14 +0,0 @@ -application: - name: shell - version: 5.1.8 -method: - name: UnknownMethod -model: - name: UnknownModel -name: Shell Batch Job (Espresso PWSCF) -units: - - config: - execName: sh - flavorName: job_espresso_pw_scf - name: shell - type: executionBuilder diff --git a/assets/subworkflows/shell/hello_world.yml b/assets/subworkflows/shell/hello_world.yml deleted file mode 100644 index 02cedb3b..00000000 --- a/assets/subworkflows/shell/hello_world.yml +++ /dev/null @@ -1,14 +0,0 @@ -application: - name: shell - version: 5.1.8 -method: - name: UnknownMethod -model: - name: UnknownModel -name: Shell Hello World -units: - - config: - execName: sh - flavorName: hello_world - name: shell - type: executionBuilder diff --git a/assets/subworkflows/vasp/band_gap.yml b/assets/subworkflows/vasp/band_gap.yml deleted file mode 100644 index e69ba946..00000000 --- a/assets/subworkflows/vasp/band_gap.yml +++ /dev/null @@ -1,21 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Band Gap -units: - - config: - execName: vasp - flavorName: vasp - name: vasp - functions: - head: true - type: executionBuilder - - config: - execName: vasp - flavorName: vasp_nscf - name: vasp_nscf - type: executionBuilder diff --git a/assets/subworkflows/vasp/band_structure.yml b/assets/subworkflows/vasp/band_structure.yml deleted file mode 100644 index e4211159..00000000 --- a/assets/subworkflows/vasp/band_structure.yml +++ /dev/null @@ -1,21 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Band Structure -units: - - config: - execName: vasp - flavorName: vasp - name: vasp - functions: - head: true - type: executionBuilder - - config: - execName: vasp - flavorName: vasp_bands - name: vasp_bands - type: executionBuilder diff --git a/assets/subworkflows/vasp/band_structure_dos.yml b/assets/subworkflows/vasp/band_structure_dos.yml deleted file mode 100644 index 90b7ea5f..00000000 --- a/assets/subworkflows/vasp/band_structure_dos.yml +++ /dev/null @@ -1,23 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Band Structure + Density of States -units: - - config: - execName: vasp - flavorName: vasp - name: vasp - functions: - addResults: - - density_of_states - head: true - type: executionBuilder - - config: - execName: vasp - flavorName: vasp_bands - name: vasp_bands - type: executionBuilder diff --git a/assets/subworkflows/vasp/dos.yml b/assets/subworkflows/vasp/dos.yml deleted file mode 100644 index f8101aff..00000000 --- a/assets/subworkflows/vasp/dos.yml +++ /dev/null @@ -1,18 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Density of States -units: - - config: - execName: vasp - flavorName: vasp - name: vasp - functions: - addResults: - - density_of_states - head: true - type: executionBuilder diff --git a/assets/subworkflows/vasp/fixed_cell_relaxation.yml b/assets/subworkflows/vasp/fixed_cell_relaxation.yml deleted file mode 100644 index 9406dace..00000000 --- a/assets/subworkflows/vasp/fixed_cell_relaxation.yml +++ /dev/null @@ -1,16 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Fixed-cell Relaxation -units: - - config: - execName: vasp - flavorName: vasp_relax - name: vasp_relax - functions: - head: true - type: executionBuilder diff --git a/assets/subworkflows/vasp/initial_final_total_energies.yml b/assets/subworkflows/vasp/initial_final_total_energies.yml deleted file mode 100644 index 32e39746..00000000 --- a/assets/subworkflows/vasp/initial_final_total_energies.yml +++ /dev/null @@ -1,25 +0,0 @@ -application: - name: vasp - version: 5.4.4 -config: - isMultiMaterial: true - functions: - setDefaultCompute: null -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Initial/Final Total Energies -units: - - config: - execName: vasp - flavorName: vasp_neb_initial - name: vasp_neb_initial - functions: - head: true - type: executionBuilder - - config: - execName: vasp - flavorName: vasp_neb_final - name: vasp_neb_final - type: executionBuilder diff --git a/assets/subworkflows/vasp/kpoint_convergence.yml b/assets/subworkflows/vasp/kpoint_convergence.yml deleted file mode 100644 index a4827e0c..00000000 --- a/assets/subworkflows/vasp/kpoint_convergence.yml +++ /dev/null @@ -1,89 +0,0 @@ -name: K-point Convergence -application: - name: vasp - version: 5.4.4 -model: - name: DFTModel -method: - config: - type: pseudopotential - subtype: paw - name: PseudopotentialMethod -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: vasp_kpt_conv - flowchartId: vasp-kpoint-convergence - execName: vasp - flavorName: vasp_kpt_conv - type: executionBuilder - - config: - name: store result - flowchartId: store-result - operand: RESULT - value: total_energy - input: - - name: total_energy - scope: vasp-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: vasp-kpoint-convergence - type: assignment - - config: - name: exit - flowchartId: convergence-is-reached - operand: PARAMETER - value: PARAMETER - input: - - name: PARAMETER - scope: global - type: assignment diff --git a/assets/subworkflows/vasp/neb_subworkflow.yml b/assets/subworkflows/vasp/neb_subworkflow.yml deleted file mode 100644 index c22d6c57..00000000 --- a/assets/subworkflows/vasp/neb_subworkflow.yml +++ /dev/null @@ -1,16 +0,0 @@ -application: - name: vasp - version: 5.4.4 -config: - isMultiMaterial: true -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Nudged Elastic Band (NEB) -units: - - config: - execName: vasp - flavorName: vasp_neb - name: vasp_neb - type: executionBuilder diff --git a/assets/subworkflows/vasp/prepare_images.yml b/assets/subworkflows/vasp/prepare_images.yml deleted file mode 100644 index 918a9cee..00000000 --- a/assets/subworkflows/vasp/prepare_images.yml +++ /dev/null @@ -1,16 +0,0 @@ -application: - name: shell - version: 5.1.8 -config: - isMultiMaterial: true -method: - name: Method -model: - name: Model -name: Prepare Directories -units: - - config: - execName: sh - flavorName: bash_vasp_prepare_neb_images - name: prepare-neb-images - type: executionBuilder diff --git a/assets/subworkflows/vasp/recalculate_bands.yml b/assets/subworkflows/vasp/recalculate_bands.yml deleted file mode 100644 index a0f9d304..00000000 --- a/assets/subworkflows/vasp/recalculate_bands.yml +++ /dev/null @@ -1,16 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Recalculate Bands -units: - - config: - execName: vasp - flavorName: vasp_bands - name: vasp_bands - functions: - head: true - type: executionBuilder diff --git a/assets/subworkflows/vasp/surface_energy.yml b/assets/subworkflows/vasp/surface_energy.yml deleted file mode 100644 index 2ffc3320..00000000 --- a/assets/subworkflows/vasp/surface_energy.yml +++ /dev/null @@ -1,18 +0,0 @@ -application: - name: vasp - version: 5.4.4 -dynamicSubworkflow: - name: surfaceEnergy -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Surface Energy -units: - - config: - execName: vasp - flavorName: vasp_symprec - name: vasp_symprec - functions: - head: true - type: executionBuilder diff --git a/assets/subworkflows/vasp/total_energy.yml b/assets/subworkflows/vasp/total_energy.yml deleted file mode 100644 index 01dbde44..00000000 --- a/assets/subworkflows/vasp/total_energy.yml +++ /dev/null @@ -1,16 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Total Energy -units: - - config: - execName: vasp - flavorName: vasp - name: vasp - functions: - head: true - type: executionBuilder diff --git a/assets/subworkflows/vasp/variable_cell_relaxation.yml b/assets/subworkflows/vasp/variable_cell_relaxation.yml deleted file mode 100644 index decf2c12..00000000 --- a/assets/subworkflows/vasp/variable_cell_relaxation.yml +++ /dev/null @@ -1,18 +0,0 @@ -application: - name: vasp - version: 5.4.4 -config: - systemName: vasp-variable-cell-relaxation -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Variable-cell Relaxation -units: - - config: - execName: vasp - flavorName: vasp_vc_relax - name: vasp_vc_relax - functions: - head: true - type: executionBuilder diff --git a/assets/subworkflows/vasp/zero_point_energy.yml b/assets/subworkflows/vasp/zero_point_energy.yml deleted file mode 100644 index 41ddfa31..00000000 --- a/assets/subworkflows/vasp/zero_point_energy.yml +++ /dev/null @@ -1,16 +0,0 @@ -application: - name: vasp - version: 5.4.4 -method: - name: PseudopotentialMethod -model: - name: DFTModel -name: Zero Point Energy -units: - - config: - execName: vasp - flavorName: vasp_zpe - name: vasp_zpe - functions: - head: true - type: executionBuilder diff --git a/assets/workflows/deepmd/deepmd_md.yml b/assets/workflows/deepmd/deepmd_md.yml deleted file mode 100644 index e26d66b3..00000000 --- a/assets/workflows/deepmd/deepmd_md.yml +++ /dev/null @@ -1,6 +0,0 @@ -name: Molecular Dynamics - DeePMD -units: -- name: espresso_cp_md - type: subworkflow -- name: deepmd - type: subworkflow diff --git a/assets/workflows/espresso/band_gap.yml b/assets/workflows/espresso/band_gap.yml deleted file mode 100644 index 8ca140c3..00000000 --- a/assets/workflows/espresso/band_gap.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Band Gap -units: -- name: band_gap - type: subworkflow diff --git a/assets/workflows/espresso/band_gap_dos_hse.yml b/assets/workflows/espresso/band_gap_dos_hse.yml deleted file mode 100644 index a9d55113..00000000 --- a/assets/workflows/espresso/band_gap_dos_hse.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Band Gap + DoS - HSE -units: -- name: band_gap_hse_dos - type: subworkflow diff --git a/assets/workflows/espresso/band_structure.yml b/assets/workflows/espresso/band_structure.yml deleted file mode 100644 index 68ccd126..00000000 --- a/assets/workflows/espresso/band_structure.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Band Structure -units: -- name: band_structure - type: subworkflow diff --git a/assets/workflows/espresso/band_structure_dos.yml b/assets/workflows/espresso/band_structure_dos.yml deleted file mode 100644 index d077de9e..00000000 --- a/assets/workflows/espresso/band_structure_dos.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Band Structure + Density of States -units: -- name: band_structure_dos - type: subworkflow diff --git a/assets/workflows/espresso/band_structure_hse.yml b/assets/workflows/espresso/band_structure_hse.yml deleted file mode 100644 index 5b6888d0..00000000 --- a/assets/workflows/espresso/band_structure_hse.yml +++ /dev/null @@ -1,14 +0,0 @@ -name: Band Structure - HSE -units: -- name: pw_scf - type: subworkflow - config: - attributes: - name: Preliminary SCF Calculation -- name: espresso_extract_kpoints - type: subworkflow -- name: band_structure_hse - type: subworkflow - config: - attributes: - name: Main HSE Run diff --git a/assets/workflows/espresso/band_structure_magn.yml b/assets/workflows/espresso/band_structure_magn.yml deleted file mode 100644 index ffac8042..00000000 --- a/assets/workflows/espresso/band_structure_magn.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: Bandstructure with spin magnetism - QE -units: -- name: band_structure_magn - type: subworkflow - config: - attributes: - name: Bandstructure with spin magnetism diff --git a/assets/workflows/espresso/band_structure_soc.yml b/assets/workflows/espresso/band_structure_soc.yml deleted file mode 100644 index 5010b211..00000000 --- a/assets/workflows/espresso/band_structure_soc.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: Bandstructure with SOC - QE -units: -- name: band_structure_soc - type: subworkflow - config: - attributes: - name: Bandstructure with SOC diff --git a/assets/workflows/espresso/dielectric_tensor.yml b/assets/workflows/espresso/dielectric_tensor.yml deleted file mode 100644 index 75b7d0b9..00000000 --- a/assets/workflows/espresso/dielectric_tensor.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Dielectric Function -units: -- name: dielectric_tensor - type: subworkflow diff --git a/assets/workflows/espresso/dos.yml b/assets/workflows/espresso/dos.yml deleted file mode 100644 index 495082cd..00000000 --- a/assets/workflows/espresso/dos.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Density of States -units: -- name: dos - type: subworkflow diff --git a/assets/workflows/espresso/electronic_density_mesh.yml b/assets/workflows/espresso/electronic_density_mesh.yml deleted file mode 100644 index 291859bb..00000000 --- a/assets/workflows/espresso/electronic_density_mesh.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Electronic Density Mesh -units: -- name: electronic_density_mesh - type: subworkflow diff --git a/assets/workflows/espresso/esm.yml b/assets/workflows/espresso/esm.yml deleted file mode 100644 index e6813b60..00000000 --- a/assets/workflows/espresso/esm.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Effective Screening Medium (ESM) -units: -- name: esm - type: subworkflow diff --git a/assets/workflows/espresso/esm_relax.yml b/assets/workflows/espresso/esm_relax.yml deleted file mode 100644 index 137a7f0c..00000000 --- a/assets/workflows/espresso/esm_relax.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Effective Screening Medium (ESM) Relax -units: -- name: esm_relax - type: subworkflow diff --git a/assets/workflows/espresso/fixed_cell_relaxation.yml b/assets/workflows/espresso/fixed_cell_relaxation.yml deleted file mode 100644 index b7331462..00000000 --- a/assets/workflows/espresso/fixed_cell_relaxation.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Fixed-cell Relaxation -units: -- name: fixed_cell_relaxation - type: subworkflow diff --git a/assets/workflows/espresso/gw_band_structure_band_gap_full_frequency.yml b/assets/workflows/espresso/gw_band_structure_band_gap_full_frequency.yml deleted file mode 100644 index f69008a7..00000000 --- a/assets/workflows/espresso/gw_band_structure_band_gap_full_frequency.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Full Frequency GW Band Structure + Band Gap -units: -- name: gw_band_structure_band_gap_full_frequency - type: subworkflow diff --git a/assets/workflows/espresso/gw_band_structure_band_gap_plasmon_pole.yml b/assets/workflows/espresso/gw_band_structure_band_gap_plasmon_pole.yml deleted file mode 100644 index 54892450..00000000 --- a/assets/workflows/espresso/gw_band_structure_band_gap_plasmon_pole.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Plasmon-Pole GW Band Structure + Band Gap -units: -- name: gw_band_structure_band_gap_plasmon_pole - type: subworkflow diff --git a/assets/workflows/espresso/hubbard_u_hp.yml b/assets/workflows/espresso/hubbard_u_hp.yml deleted file mode 100644 index 194061c2..00000000 --- a/assets/workflows/espresso/hubbard_u_hp.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: Hubbard U - HP -units: -- name: hubbard_u_hp - type: subworkflow - config: - attributes: - name: Hubbard U Calculation diff --git a/assets/workflows/espresso/kpoint_convergence.yml b/assets/workflows/espresso/kpoint_convergence.yml deleted file mode 100644 index 9857dc84..00000000 --- a/assets/workflows/espresso/kpoint_convergence.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: K-point Convergence -units: -- name: kpoint_convergence - type: subworkflow diff --git a/assets/workflows/espresso/neb.yml b/assets/workflows/espresso/neb.yml deleted file mode 100644 index 03256cb0..00000000 --- a/assets/workflows/espresso/neb.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Nudged Elastic Band (NEB) -units: -- name: neb - type: subworkflow diff --git a/assets/workflows/espresso/phonon_dispersions.yml b/assets/workflows/espresso/phonon_dispersions.yml deleted file mode 100644 index e5314509..00000000 --- a/assets/workflows/espresso/phonon_dispersions.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Phonon Dispersions -units: -- name: phonon_dispersions - type: subworkflow diff --git a/assets/workflows/espresso/phonon_dos.yml b/assets/workflows/espresso/phonon_dos.yml deleted file mode 100644 index 89601048..00000000 --- a/assets/workflows/espresso/phonon_dos.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Phonon Density of States -units: -- name: phonon_dos - type: subworkflow diff --git a/assets/workflows/espresso/phonon_dos_dispersion.yml b/assets/workflows/espresso/phonon_dos_dispersion.yml deleted file mode 100644 index 379ac6cd..00000000 --- a/assets/workflows/espresso/phonon_dos_dispersion.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Phonon Density of States + Dispersions -units: -- name: phonon_dos_dispersion - type: subworkflow diff --git a/assets/workflows/espresso/phonon_map.yml b/assets/workflows/espresso/phonon_map.yml deleted file mode 100644 index 516409b6..00000000 --- a/assets/workflows/espresso/phonon_map.yml +++ /dev/null @@ -1,28 +0,0 @@ -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 diff --git a/assets/workflows/espresso/recalculate_bands.yml b/assets/workflows/espresso/recalculate_bands.yml deleted file mode 100644 index 12d0d2c0..00000000 --- a/assets/workflows/espresso/recalculate_bands.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Recalculate Bands -units: -- name: recalculate_bands - type: subworkflow diff --git a/assets/workflows/espresso/surface_energy.yml b/assets/workflows/espresso/surface_energy.yml deleted file mode 100644 index 1ccb718f..00000000 --- a/assets/workflows/espresso/surface_energy.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Surface Energy -units: -- name: surface_energy - type: subworkflow diff --git a/assets/workflows/espresso/total_energy.yml b/assets/workflows/espresso/total_energy.yml deleted file mode 100644 index d543a4bd..00000000 --- a/assets/workflows/espresso/total_energy.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Total Energy -units: -- name: total_energy - type: subworkflow diff --git a/assets/workflows/espresso/valence_band_offset.yml b/assets/workflows/espresso/valence_band_offset.yml deleted file mode 100644 index c9a64809..00000000 --- a/assets/workflows/espresso/valence_band_offset.yml +++ /dev/null @@ -1,171 +0,0 @@ -# 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 diff --git a/assets/workflows/espresso/variable_cell_relaxation.yml b/assets/workflows/espresso/variable_cell_relaxation.yml deleted file mode 100644 index 3294d8ca..00000000 --- a/assets/workflows/espresso/variable_cell_relaxation.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Variable-cell Relaxation -units: -- name: variable_cell_relaxation - type: subworkflow diff --git a/assets/workflows/espresso/zero_point_energy.yml b/assets/workflows/espresso/zero_point_energy.yml deleted file mode 100644 index 187c107a..00000000 --- a/assets/workflows/espresso/zero_point_energy.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Zero Point Energy -units: -- name: zero_point_energy - type: subworkflow diff --git a/assets/workflows/jupyterLab/jupyter_notebook.yml b/assets/workflows/jupyterLab/jupyter_notebook.yml deleted file mode 100644 index 0c592b48..00000000 --- a/assets/workflows/jupyterLab/jupyter_notebook.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Jupyter Notebook -units: -- name: jupyter_notebook - type: subworkflow diff --git a/assets/workflows/nwchem/total_energy.yml b/assets/workflows/nwchem/total_energy.yml deleted file mode 100644 index d543a4bd..00000000 --- a/assets/workflows/nwchem/total_energy.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Total Energy -units: -- name: total_energy - type: subworkflow diff --git a/assets/workflows/python/ml/classification_workflow.yml b/assets/workflows/python/ml/classification_workflow.yml deleted file mode 100644 index 08d85cd8..00000000 --- a/assets/workflows/python/ml/classification_workflow.yml +++ /dev/null @@ -1,9 +0,0 @@ -config: - attributes: - isUsingDataset: true -name: Python ML Train Classification -units: -- name: train_head - type: subworkflow -- name: classification_tail - type: subworkflow diff --git a/assets/workflows/python/ml/clustering_workflow.yml b/assets/workflows/python/ml/clustering_workflow.yml deleted file mode 100644 index d9b2dd36..00000000 --- a/assets/workflows/python/ml/clustering_workflow.yml +++ /dev/null @@ -1,9 +0,0 @@ -config: - attributes: - isUsingDataset: true -name: Python ML Train Clustering -units: -- name: train_head - type: subworkflow -- name: classification_tail - type: subworkflow diff --git a/assets/workflows/python/ml/regression_workflow.yml b/assets/workflows/python/ml/regression_workflow.yml deleted file mode 100644 index 805d8eaf..00000000 --- a/assets/workflows/python/ml/regression_workflow.yml +++ /dev/null @@ -1,9 +0,0 @@ -config: - attributes: - isUsingDataset: true -name: Python ML Train Regression -units: -- name: train_head - type: subworkflow -- name: regression_tail - type: subworkflow diff --git a/assets/workflows/python/python_script.yml b/assets/workflows/python/python_script.yml deleted file mode 100644 index 17bba021..00000000 --- a/assets/workflows/python/python_script.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Python Script -units: -- name: python_script - type: subworkflow diff --git a/assets/workflows/shell/batch_espresso_pwscf.yml b/assets/workflows/shell/batch_espresso_pwscf.yml deleted file mode 100644 index 95bea989..00000000 --- a/assets/workflows/shell/batch_espresso_pwscf.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Shell Batch Job (Espresso PWSCF) -units: -- name: batch_espresso_pwscf - type: subworkflow diff --git a/assets/workflows/shell/hello_world.yml b/assets/workflows/shell/hello_world.yml deleted file mode 100644 index 0becd9b6..00000000 --- a/assets/workflows/shell/hello_world.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Shell Script -units: -- name: hello_world - type: subworkflow diff --git a/assets/workflows/vasp/band_gap.yml b/assets/workflows/vasp/band_gap.yml deleted file mode 100644 index 8ca140c3..00000000 --- a/assets/workflows/vasp/band_gap.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Band Gap -units: -- name: band_gap - type: subworkflow diff --git a/assets/workflows/vasp/band_structure.yml b/assets/workflows/vasp/band_structure.yml deleted file mode 100644 index 68ccd126..00000000 --- a/assets/workflows/vasp/band_structure.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Band Structure -units: -- name: band_structure - type: subworkflow diff --git a/assets/workflows/vasp/band_structure_dos.yml b/assets/workflows/vasp/band_structure_dos.yml deleted file mode 100644 index d077de9e..00000000 --- a/assets/workflows/vasp/band_structure_dos.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Band Structure + Density of States -units: -- name: band_structure_dos - type: subworkflow diff --git a/assets/workflows/vasp/dos.yml b/assets/workflows/vasp/dos.yml deleted file mode 100644 index 495082cd..00000000 --- a/assets/workflows/vasp/dos.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Density of States -units: -- name: dos - type: subworkflow diff --git a/assets/workflows/vasp/fixed_cell_relaxation.yml b/assets/workflows/vasp/fixed_cell_relaxation.yml deleted file mode 100644 index b7331462..00000000 --- a/assets/workflows/vasp/fixed_cell_relaxation.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Fixed-cell Relaxation -units: -- name: fixed_cell_relaxation - type: subworkflow diff --git a/assets/workflows/vasp/kpoint_convergence.yml b/assets/workflows/vasp/kpoint_convergence.yml deleted file mode 100644 index 9857dc84..00000000 --- a/assets/workflows/vasp/kpoint_convergence.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: K-point Convergence -units: -- name: kpoint_convergence - type: subworkflow diff --git a/assets/workflows/vasp/neb.yml b/assets/workflows/vasp/neb.yml deleted file mode 100644 index c47e73a4..00000000 --- a/assets/workflows/vasp/neb.yml +++ /dev/null @@ -1,8 +0,0 @@ -name: Nudged Elastic Band (NEB) -units: -- name: initial_final_total_energies - type: subworkflow -- name: prepare_images - type: subworkflow -- name: neb_subworkflow - type: subworkflow diff --git a/assets/workflows/vasp/recalculate_bands.yml b/assets/workflows/vasp/recalculate_bands.yml deleted file mode 100644 index 12d0d2c0..00000000 --- a/assets/workflows/vasp/recalculate_bands.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Recalculate Bands -units: -- name: recalculate_bands - type: subworkflow diff --git a/assets/workflows/vasp/surface_energy.yml b/assets/workflows/vasp/surface_energy.yml deleted file mode 100644 index 1ccb718f..00000000 --- a/assets/workflows/vasp/surface_energy.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Surface Energy -units: -- name: surface_energy - type: subworkflow diff --git a/assets/workflows/vasp/total_energy.yml b/assets/workflows/vasp/total_energy.yml deleted file mode 100644 index d543a4bd..00000000 --- a/assets/workflows/vasp/total_energy.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Total Energy -units: -- name: total_energy - type: subworkflow diff --git a/assets/workflows/vasp/variable_cell_relaxation.yml b/assets/workflows/vasp/variable_cell_relaxation.yml deleted file mode 100644 index 3294d8ca..00000000 --- a/assets/workflows/vasp/variable_cell_relaxation.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Variable-cell Relaxation -units: -- name: variable_cell_relaxation - type: subworkflow diff --git a/assets/workflows/vasp/zero_point_energy.yml b/assets/workflows/vasp/zero_point_energy.yml deleted file mode 100644 index 187c107a..00000000 --- a/assets/workflows/vasp/zero_point_energy.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: Zero Point Energy -units: -- name: zero_point_energy - type: subworkflow diff --git a/package-lock.json b/package-lock.json index 3d18d799..8c1498d7 100644 --- a/package-lock.json +++ b/package-lock.json @@ -35,7 +35,7 @@ "@mat3ra/esse": "2025.7.15-0", "@mat3ra/made": "2025.7.15-0", "@mat3ra/mode": "^2025.10.2-0", - "@mat3ra/standata": "2025.10.2-0", + "@mat3ra/standata": "git+https://github.com/Exabyte-io/standata.git#f53b8da6ff0421b8397d606a6d8b0127dc68c64c", "@mat3ra/utils": "2025.9.20-0", "chai": "^4.3.4", "eslint": "7.32.0", @@ -3235,10 +3235,11 @@ } }, "node_modules/@mat3ra/standata": { - "version": "2025.10.2-0", - "resolved": "https://registry.npmjs.org/@mat3ra/standata/-/standata-2025.10.2-0.tgz", - "integrity": "sha512-cwGDL+FB7F091L6lNOLzs83M8GPWQpNA2BAlc+SYd4p5SCIF8zwF3J+rvFgqdK5reU59xsJ258daOz/cCA8Rqg==", + "version": "0.0.0", + "resolved": "git+ssh://git@github.com/Exabyte-io/standata.git#f53b8da6ff0421b8397d606a6d8b0127dc68c64c", + "integrity": "sha512-GYbV5G0ZVSUKaCq/CGAnH498F4nThcM2SLqMZUO8NxXU8SmFXP18H42Fw/4VrsGxte1Ich5vH4gchNzXEp+CnA==", "dev": true, + "license": "Apache-2.0", "dependencies": { "@babel/cli": "7.16.0", "@babel/core": "7.24.1", diff --git a/package.json b/package.json index 2b047ac1..a413853f 100644 --- a/package.json +++ b/package.json @@ -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", diff --git a/src/subworkflows/create.js b/src/subworkflows/create.js index 095e42ee..161457af 100644 --- a/src/subworkflows/create.js +++ b/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; diff --git a/src/subworkflows/subworkflow.js b/src/subworkflows/subworkflow.js index 57ee4f33..67ba7ae9 100644 --- a/src/subworkflows/subworkflow.js +++ b/src/subworkflows/subworkflow.js @@ -91,9 +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( diff --git a/src/workflows/relaxation.js b/src/workflows/relaxation.js index 10fc5371..36df6876 100644 --- a/src/workflows/relaxation.js +++ b/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); } diff --git a/src/workflows/workflow.js b/src/workflows/workflow.js index b33c7e6f..d2355c5d 100644 --- a/src/workflows/workflow.js +++ b/src/workflows/workflow.js @@ -39,9 +39,7 @@ export class Workflow extends BaseWorkflow { _MapUnit = MapUnit, ) { if (!config._id) config._id = Workflow.generateWorkflowId(config.name); - super(config); - this._Subworkflow = _Subworkflow; this._UnitFactory = _UnitFactory; this._Workflow = _Workflow; diff --git a/tests/workflow.test.js b/tests/workflow.test.js index 1b6c07b1..f4f145d0 100644 --- a/tests/workflow.test.js +++ b/tests/workflow.test.js @@ -5,8 +5,8 @@ import { builders, createWorkflows, Subworkflow, UnitFactory, Workflow } from ". import { createWorkflow } from "../src/workflows/create"; // Expected predefined IDs constants - update these after running test to see actual values -const EXPECTED_WORKFLOW_ID = "6e937035-b03b-5b2c-a2ba-28f1f49d4a3d"; -const EXPECTED_SUBWORKFLOW_ID = "a27b9ca8-5618-528e-8f40-37c27883984f"; +const EXPECTED_WORKFLOW_ID = "512cb2cc-5cca-52c7-9dd9-1d2b57196188"; +const EXPECTED_SUBWORKFLOW_ID = "82673aa1-c4d7-5b2c-b216-7579760fdfaf"; const EXPECTED_UNIT_ID = "9fc7a088-5533-5f70-bb33-f676ec65f565"; describe("workflows", () => { @@ -103,8 +103,7 @@ describe("workflows", () => { }); describe("workflow property", () => { - // TODO: unskip when all WFs are added to Standata - it.skip("isMultiMaterial is read correctly", () => { + it("isMultiMaterial is read correctly", () => { // Nudged Elastic Band is multi-material const mmWorkflow = createWorkflow({ appName: "espresso",