MDOcean/calkit.yaml at main · symbiotic-engineering/MDOcean · GitHub

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name: mdocean
title: MDOcean
description: Multidisciplinary Design Optimization (MDO) to optimize an
  ocean wave energy converter (WEC).
environments:
  tex:
    kind: docker
    image: texlive/texlive:latest-full
    description: TeXlive via Docker.
  pubs:
    kind: conda
    path: pubs/environment.yaml
    python: '3.14'
  mermaid:
    kind: docker
    image: minlag/mermaid-cli:latest
    description: Mermaid CLI via Docker.
    wdir: /data
    command_mode: entrypoint
  # pdf2svg:
  #   kind: docker
  #   path: pubs/defense/latex-standalone/Dockerfile
  #   description: pdf2svg via Docker.
  #   image: pdf2svg
  quarto:
    kind: docker
    image: ghcr.io/quarto-dev/quarto:latest
    description: Quarto via Docker.
    wdir: /data
  playwright:
    kind: docker
    path: pubs/defense/quarto/Dockerfile
    description: Playwright via Docker.
    image: playwright
  bibtex-conda:
    path: dev/latex/environment.yml
    kind: conda
dependencies:
  - docker
  - matlab
env_vars:
  QT_QPA_PLATFORM: offscreen
parameters:
  mermaid_name:
    - taxonomy
    - mod_freq_domain_ctrl_synthesis
    - mod_freq_domain_ctrl_evaluation
    - mod_freq_domain_ctrl_combined
  latex_standalone_name:
    - circuit_intrinsic
    - circuit_pto
    - circuit_kinematics
    - control_method_venn_diagram
    - meem_dims
# subprojects:
#   - path: mdocean/simulation/modules/OpenFLASH
pipeline:
  stages:
    mermaid-make-pdfs:
      kind: command
      environment: mermaid
      command: -i mdocean/plots/non_matlab_figs/{name}.mmd -o
        mdocean/plots/non_matlab_figs/pdf/{name}.pdf -f
      iterate_over:
        - arg_name: name
          values:
            - parameter: mermaid_name
      inputs:
        - mdocean/plots/non_matlab_figs/{name}.mmd
      outputs:
        - mdocean/plots/non_matlab_figs/pdf/{name}.pdf
    mermaid-make-pngs:
      kind: command
      environment: mermaid
      command: -i mdocean/plots/non_matlab_figs/{name}.mmd -o
        mdocean/plots/non_matlab_figs/img/{name}.png
      iterate_over:
        - arg_name: name
          values:
            - parameter: mermaid_name
      inputs:
        - mdocean/plots/non_matlab_figs/{name}.mmd
      outputs:
        - path: mdocean/plots/non_matlab_figs/img/{name}.png
    make-drag-integral:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); make_drag_integral
      inputs:
        - ./mdocean/inputs/make_drag_integral.m
        - ./mdocean/simulation/modules/dynamics/make_drag_integral_LUT.m
        - ./mdocean/simulation/modules/dynamics/compute_drag_integral.m
      outputs:
        - ./mdocean/inputs/drag_integral.mat
    make-var-bounds:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); b = var_bounds();
        save('./mdocean/inputs/var_bounds.mat','b');
      inputs:
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/util/remove_underscores.m
      outputs:
        - ./mdocean/inputs/var_bounds.mat
    make-calkit-stages:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); analysis_to_calkit;
      inputs:
        - mdocean/analysis/
        - mdocean/inputs/
        - mdocean/optimization/multiobjective/
        - mdocean/optimization/sensitivities/
        - mdocean/optimization/compare_run.m
        - mdocean/optimization/find_nominal_inputs.m
        - mdocean/optimization/gradient_optim.m
        - mdocean/optimization/max_avg_power.m
        - mdocean/optimization/run_solver.m
        - mdocean/plots/util/
        - mdocean/plots/matlab_figs/
        - mdocean/plots/all_figures.m
        - mdocean/plots/check_figures.m
        - mdocean/plots/fig_tab_pub_mapping.m
        - mdocean/plots/get_fig_tab_names.m
        - mdocean/plots/move_results_to_pubs.m
        - mdocean/simulation/
      outputs:
        - path: calkit_stages.yaml
          storage: git
    analysis-AllFigCompare:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=AllFigCompare;
        obj.run_analysis();
      inputs:
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@AllFigCompare/AllFigCompare.m
        - ./mdocean/analysis/@AllFigCompare/analysis_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
      outputs:
        - results/AllFigCompare/intermed.mat
    postpro-AllFigCompare:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=AllFigCompare;
        obj.run_all_from_load();
      inputs:
        - from_stage_outputs: analysis-AllFigCompare
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@AllFigCompare/AllFigCompare.m
        - ./mdocean/analysis/@AllFigCompare/post_process_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
        - results/AllFigCompare/intermed.mat
      outputs:
        - results/AllFigCompare/runtime_bar_chart.pdf
        - results/AllFigCompare/runtime_bar_chart.fig
        - results/AllFigCompare/end.mat
        - path: results/AllFigCompare/end.json
          storage: git
    analysis-Comparison:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=Comparison; obj.run_analysis();
      inputs:
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@Comparison/Comparison.m
        - ./mdocean/analysis/@Comparison/analysis_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/compare_run.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/optimization/gradient_optim.m
        - ./mdocean/optimization/max_avg_power.m
        - ./mdocean/optimization/run_solver.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/matlab_figs/module_demos/visualize_geometry.m
        - ./mdocean/plots/matlab_figs/optim/optim_geomviz.m
        - ./mdocean/plots/matlab_figs/optim/optimplotx_custom.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/lin_ineq_constraints.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/run/run_and_catch_warnings.m
        - ./mdocean/simulation/sim_catch_warning.m
        - ./mdocean/simulation/simulation.m
      outputs:
        - results/Comparison/intermed.mat
    postpro-Comparison:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=Comparison;
        obj.run_all_from_load();
      inputs:
        - from_stage_outputs: analysis-Comparison
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@Comparison/Comparison.m
        - ./mdocean/analysis/@Comparison/post_process_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/matlab_figs/module_demos/visualize_geometry.m
        - ./mdocean/plots/matlab_figs/optim/compare.m
        - ./mdocean/plots/matlab_figs/sim_results/power_PDF.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/stacked_number_line.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
        - results/Comparison/intermed.mat
      outputs:
        - results/Comparison/overlaid_geometry.pdf
        - results/Comparison/overlaid_hydro_coeffs.pdf
        - results/Comparison/probability_CDF.pdf
        - results/Comparison/comparison_power_matrix.pdf
        - results/Comparison/stacked_optimal_design_vars.pdf
        - results/Comparison/stacked_optimal_outputs.pdf
        - results/Comparison/overlaid_geometry.fig
        - results/Comparison/overlaid_hydro_coeffs.fig
        - results/Comparison/probability_CDF.fig
        - results/Comparison/comparison_power_matrix.fig
        - results/Comparison/stacked_optimal_design_vars.fig
        - results/Comparison/stacked_optimal_outputs.fig
        - path: results/Comparison/optimal_design_vars.tex
          storage: git
        - path: results/Comparison/optimal_outputs.tex
          storage: git
        - results/Comparison/end.mat
        - path: results/Comparison/end.json
          storage: git
    analysis-Constraints:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=Constraints; obj.run_analysis();
      inputs:
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@Constraints/Constraints.m
        - ./mdocean/analysis/@Constraints/analysis_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
      outputs:
        - results/Constraints/intermed.mat
    postpro-Constraints:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=Constraints;
        obj.run_all_from_load();
      inputs:
        - from_stage_outputs: analysis-Constraints
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@Constraints/Constraints.m
        - ./mdocean/analysis/@Constraints/post_process_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
        - results/Constraints/intermed.mat
      outputs:
        - path: results/Constraints/constraints.tex
          storage: git
        - results/Constraints/end.mat
        - path: results/Constraints/end.json
          storage: git
    analysis-Cost:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=Cost; obj.run_analysis();
      inputs:
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@Cost/Cost.m
        - ./mdocean/analysis/@Cost/analysis_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
      outputs:
        - results/Cost/intermed.mat
    postpro-Cost:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=Cost; obj.run_all_from_load();
      inputs:
        - from_stage_outputs: analysis-Cost
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@Cost/Cost.m
        - ./mdocean/analysis/@Cost/post_process_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
        - results/Cost/intermed.mat
      outputs:
        - path: results/Cost/cost_parameters.tex
          storage: git
        - results/Cost/end.mat
        - path: results/Cost/end.json
          storage: git
    analysis-DampingPlateStructures:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=DampingPlateStructures;
        obj.run_analysis();
      inputs:
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@DampingPlateStructures/DampingPlateStructures.m
        - ./mdocean/analysis/@DampingPlateStructures/analysis_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/matlab_figs/structures/make_four_loads_plot.m
        - ./mdocean/plots/matlab_figs/structures/viz_damping_plate.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
      outputs:
        - results/DampingPlateStructures/intermed.mat
        - results/DampingPlateStructures/intermed_figs_1.fig
        - results/DampingPlateStructures/intermed_figs_2.fig
        - results/DampingPlateStructures/intermed_figs_3.fig
    postpro-DampingPlateStructures:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=DampingPlateStructures;
        obj.run_all_from_load();
      inputs:
        - from_stage_outputs: analysis-DampingPlateStructures
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@DampingPlateStructures/DampingPlateStructures.m
        - ./mdocean/analysis/@DampingPlateStructures/post_process_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
        - results/DampingPlateStructures/intermed.mat
      outputs:
        - results/DampingPlateStructures/damping_plate_aspect_ratio.pdf
        - results/DampingPlateStructures/damping_plate_deflection.pdf
        - results/DampingPlateStructures/damping_plate_moment.pdf
        - results/DampingPlateStructures/damping_plate_aspect_ratio.fig
        - results/DampingPlateStructures/damping_plate_deflection.fig
        - results/DampingPlateStructures/damping_plate_moment.fig
        - results/DampingPlateStructures/end.mat
        - path: results/DampingPlateStructures/end.json
          storage: git
    analysis-DescFcns:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=DescFcns; obj.run_analysis();
      inputs:
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@DescFcns/DescFcns.m
        - ./mdocean/analysis/@DescFcns/analysis_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/matlab_figs/module_demos/sin_desc_fcn_demo.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
      outputs:
        - results/DescFcns/intermed.mat
        - results/DescFcns/intermed_created_figs_1.fig
        - results/DescFcns/intermed_created_figs_3.fig
        - results/DescFcns/intermed_created_figs_2.fig
    postpro-DescFcns:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=DescFcns;
        obj.run_all_from_load();
      inputs:
        - from_stage_outputs: analysis-DescFcns
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@DescFcns/DescFcns.m
        - ./mdocean/analysis/@DescFcns/post_process_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs.m
        - ./mdocean/simulation/modules/hydro/get_hydro_coeffs_MEEM.m
        - ./mdocean/simulation/modules/hydro/get_m_k_h.m
        - ./mdocean/simulation/modules/hydro/group_velocity.m
        - ./mdocean/simulation/modules/hydro/run_MEEM.m
        - ./mdocean/simulation/modules/structures/concentrated_plate_nondim.m
        - ./mdocean/simulation/modules/structures/distributed_plate_nondim.m
        - ./mdocean/simulation/modules/structures/float_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_plate_stress.m
        - ./mdocean/simulation/modules/structures/get_stiffener_equivalent_properties.m
        - ./mdocean/simulation/modules/structures/structures.m
        - ./mdocean/simulation/simulation.m
        - results/DescFcns/intermed.mat
      outputs:
        - results/DescFcns/saturation_desc_fcn.pdf
        - results/DescFcns/saturation_desc_fcn_alpha.pdf
        - results/DescFcns/drag_desc_fcn.pdf
        - results/DescFcns/saturation_desc_fcn.fig
        - results/DescFcns/saturation_desc_fcn_alpha.fig
        - results/DescFcns/drag_desc_fcn.fig
        - results/DescFcns/end.mat
        - path: results/DescFcns/end.json
          storage: git
    analysis-DesignSpaceExploration:
      kind: matlab-command
      environment: _system
      command: add_mdocean_path(); obj=DesignSpaceExploration;
        obj.run_analysis();
      inputs:
        - ./mdocean/inputs/validation/RM3-CBS.xlsx
        - ./mdocean/analysis/@DesignSpaceExploration/DesignSpaceExploration.m
        - ./mdocean/analysis/@DesignSpaceExploration/analysis_fcn.m
        - ./mdocean/analysis/GenericAnalysis.m
        - ./mdocean/inputs/drag_integral.mat
        - ./mdocean/inputs/get_spar_exc.m
        - ./mdocean/inputs/parameters.m
        - ./mdocean/inputs/validation/WECSim/normalizeBEM.m
        - ./mdocean/inputs/validation/WECSim/readWAMIT.m
        - ./mdocean/inputs/var_bounds.m
        - ./mdocean/inputs/var_bounds.mat
        - ./mdocean/inputs/wave_conditions/trim_jpd.m
        - ./mdocean/optimization/find_nominal_inputs.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_ctrl_polar_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/make_slamming_plot.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_convergence.m
        - ./mdocean/plots/matlab_figs/dynamics_results/plot_drag_integral_debug.m
        - ./mdocean/plots/util/bluewhitered.m
        - ./mdocean/plots/util/check_fig_size.m
        - ./mdocean/plots/util/contourx.m
        - ./mdocean/plots/util/hatchfill2.m
        - ./mdocean/plots/util/improvePlot.m
        - ./mdocean/plots/util/imrange.m
        - ./mdocean/plots/util/remove_underscores.m
        - ./mdocean/plots/util/save_fig_with_diagnostic.m
        - ./mdocean/plots/util/signed_log.m
        - ./mdocean/plots/util/table2latex.m
        - ./mdocean/simulation/modules/dynamics/circle_intersect_optim.m
        - ./mdocean/simulation/modules/dynamics/constrained_opt_ctrl.m
        - ./mdocean/simulation/modules/dynamics/dynamics.m
        - ./mdocean/simulation/modules/dynamics/get_response_drag.m
        - ./mdocean/simulation/modules/dynamics/get_slamming_min_max.m
        - ./mdocean/simulation/modules/dynamics/multibody_impedance.m
        - ./mdocean/simulation/modules/dynamics/multibody_response.m
        - ./mdocean/simulation/modules/dynamics/spar_dynamics.m
        - ./mdocean/simulation/modules/econ/LCOE_from_capex_design_power.m
        - ./mdocean/simulation/modules/econ/econ.m
        - ./mdocean/simulation/modules/enviro.m
        - ./mdocean/simulation/modules/geometry.m
        - ./mdocean/simulation/modules/grid_CEM.m
        - ./mdocean/simulation/modules/hydro/dispersion.m
        - ./mdocean/simulation/modules/hydro/get_dynamic_coeffs.m