_toc.yml

format: jb-book
root: docs/index
parts:
  - caption: Installation options
    chapters:
    - file: docs/install_pip
    - file: docs/install_conda
    - file: docs/install_mamba
    - file: docs/install_docker
    - file: docs/install_extras
    - file: docs/install_cloud_binder
    - file: docs/install_cloud_codespaces
  - caption: Cross Sections
    chapters:
    - file: tasks/task_01_cross_sections/README
    - file: tasks/task_01_cross_sections/1_isotope_xs_plot
    - file: tasks/task_01_cross_sections/2_element_xs_plot
    - file: tasks/task_01_cross_sections/3_material_xs_plot
    - file: tasks/task_01_cross_sections/4_material_mean_free_path
    - file: tasks/task_01_cross_sections/4_Doppler_broadening
  - caption: Materials
    chapters:
    - file: tasks/task_02_making_materials/README
    - file: tasks/task_02_making_materials/1_example_materials_from_isotopes
    - file: tasks/task_02_making_materials/2_example_materials_from_elements
    - file: tasks/task_02_making_materials/3_example_materials_from_material_maker
    - file: tasks/task_02_making_materials/4_example_materials_parameter_study
    - file: tasks/task_02_making_materials/5_example_materials_mixed
  - caption: Making CSG Geometry
    chapters:
    - file: tasks/task_03_making_CSG_geometry/README
    - file: tasks/task_03_making_CSG_geometry/1_simple_csg_geometry
    - file: tasks/task_03_making_CSG_geometry/2_intermediate_csg_geometry
    - file: tasks/task_03_making_CSG_geometry/3_viewing_the_geometry_as_vtk
  - caption: Making source terms
    chapters:
    - file: tasks/task_04_make_sources/README
    - file: tasks/task_04_make_sources/1_point_source_plots
    - file: tasks/task_04_make_sources/2_ring_source
    - file: tasks/task_04_make_sources/3_plasma_source_plots
    - file: tasks/task_04_make_sources/4_neutron_tracks
    - file: tasks/task_04_make_sources/5_gamma_source_example
    - file: tasks/task_04_make_sources/6_unstructured_mesh_spatial_source
    - file: tasks/task_04_make_sources/7_structured_mesh_source
  - caption: CSG cell TBR tally
    chapters:
    - file: tasks/task_05_CSG_cell_tally_TBR/README
    - file: tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production
    - file: tasks/task_05_CSG_cell_tally_TBR/2_example_tritium_production_study
    # TODO need converting to notebooks
    # - file: tasks/task_05_CSG_cell_tally_TBR/3_example_tritium_production_study_with_openmc_lib
  - caption: CSG cell DPA tally
    chapters:
    - file: tasks/task_06_CSG_cell_tally_DPA/README
    - file: tasks/task_06_CSG_cell_tally_DPA/1_find_dpa
  - caption: CSG cell spectra tally
    chapters:
    - file: tasks/task_07_CSG_cell_tally_spectra/README
    - file: tasks/task_07_CSG_cell_tally_spectra/1_example_neutron_flux_and_units
    - file: tasks/task_07_CSG_cell_tally_spectra/2_example_neutron_spectra_on_cell
    - file: tasks/task_07_CSG_cell_tally_spectra/3_example_neutron_spectra_on_surface
    - file: tasks/task_07_CSG_cell_tally_spectra/4_example_photon_spectra
    - file: tasks/task_07_CSG_cell_tally_spectra/5_neutron_energy_loss_plot
  - caption: CSG cell mesh tally
    chapters:
    - file: tasks/task_08_CSG_mesh_tally/README
    - file: tasks/task_08_CSG_mesh_tally/1_example_2d_regular_mesh_tallies
    - file: tasks/task_08_CSG_mesh_tally/2_example_3d_regular_mesh_tallies
    - file: tasks/task_08_CSG_mesh_tally/3_example_cylinder_mesh_tallies
  - caption: CSG cell instantaneous dose tally
    chapters:
    - file: tasks/task_09_CSG_instantaneous_dose_tallies/README
    - file: tasks/task_09_CSG_instantaneous_dose_tallies/1_surface_dose_from_gamma_source
    - file: tasks/task_09_CSG_instantaneous_dose_tallies/2_surface_dose_from_gamma_source_study
    - file: tasks/task_09_CSG_instantaneous_dose_tallies/5_mesh_dose_from_neutrons
    # TODO need converting to notebooks
    # - file: tasks/task_09_CSG_instantaneous_dose_tallies/3_cell_dose_from_neutron
    # - file: tasks/task_09_CSG_instantaneous_dose_tallies/4_cell_dose_from_photon
    # - file: tasks/task_09_CSG_instantaneous_dose_tallies/compare_dose_simulation_with_back_of_envelope
  - caption: Activation Transmutation Depletion
    chapters:
    - file: tasks/task_10_activation_transmutation_depletion/README
      # TODO convert to notebooks
      # task_10_activation_transmutation_depletion/0_simple_transmutation_reaction_rate_simulation.py
    - file: tasks/task_10_activation_transmutation_depletion/1_example_transmutation_isotope_build_up
    - file: tasks/task_10_activation_transmutation_depletion/2_example_tally_change_with_burnup
    - file: tasks/task_10_activation_transmutation_depletion/3_full_pulse_schedule
  - caption: CSG shutdown dose tallies
    chapters:
    - file: tasks/task_11_CSG_shut_down_dose_tallies/README
    - file: tasks/task_11_CSG_shut_down_dose_tallies/4_D1S_regularmesh_shutdown_dose_rate
    - file: tasks/task_11_CSG_shut_down_dose_tallies/5_D1S_regularmesh_shutdown_dose_rate_different_source_terms
      # TODO convert to notebooks
      # task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py
      # task_11_CSG_shut_down_dose_tallies/2_faster_mulitiple_puse_shut_down_dose_rate_example.py
  # - caption: Detectors Examples
  #   chapters:
  #   - file: tasks/task_12_detectors_examples/README
      # TODO convert to notebooks
    # - file: task_12_detectors_examples/1_time_filter_tally.py
    # - file: task_12_detectors_examples/2_time_filter_tally_with_reflective_sphere.py
    # - file: task_12_detectors_examples/3_time_and_energy_filter_tally.py
  - caption: Volume Calculations
    chapters:
      - file: tasks/task_13_volume_calculations/README
      - file: tasks/task_13_volume_calculations/1_find_volume_of_csg_cell
      - file: tasks/task_13_volume_calculations/2_find_volume_of_dagmc_cell
  - caption: Variance Reduction
    chapters:
      - file: tasks/task_14_variance_reduction/README
      - file: tasks/task_14_variance_reduction/1_shielded_room_survival_biasing
      - file: tasks/task_14_variance_reduction/2_shielded_room_single_ww
      - file: tasks/task_14_variance_reduction/3_sphere_iterative_per_run_ww
      - file: tasks/task_14_variance_reduction/4_sphere_iterative_per_batch_ww
      - file: tasks/task_14_variance_reduction/5_shielded_room_fw_cadis
  - caption: Making CAD geometry
    chapters:
      - file: tasks/task_15_making_CAD_geometry/README
      - file: tasks/task_15_making_CAD_geometry/1_making_cad_with_cadquery
      - file: tasks/task_15_making_CAD_geometry/2_making_cad_with_paramak
  - caption: Converting CAD Geometry
    chapters:
    - file: tasks/task_16_converting_CAD_geometry_to_DAGMC/README
    - file: tasks/task_16_converting_CAD_geometry_to_DAGMC/1_converting_cad_files
    - file: tasks/task_16_converting_CAD_geometry_to_DAGMC/2_converting_cad_in_memory
  - caption: Using DAGMC models in OpenMC
    chapters:
    - file: tasks/task_17_using_DAGMC_models_in_openmc/README
    - file: tasks/task_17_using_DAGMC_models_in_openmc/1_cad_model_simulation_minimal
    - file: tasks/task_17_using_DAGMC_models_in_openmc/2_cad_model_simulation_with_boundary_types
    - file: tasks/task_17_using_DAGMC_models_in_openmc/3_cad_model_simulation_with_hybrid_csg
  - caption: CAD mesh fast flux simulation
    chapters:
    - file: tasks/task_18_CAD_mesh_fast_flux/README
    - file: tasks/task_18_CAD_mesh_fast_flux/1_simulate_fast_neutron_flux_on_cad
  - caption: CAD shutdown dose tallies
    chapters:
    - file: tasks/task_20_CAD_shut_down_dose_rate/README
    - file: tasks/task_20_CAD_shut_down_dose_rate/1_unstructured_mesh_R2S_shutdown_dose_rate
    - file: tasks/task_20_CAD_shut_down_dose_rate/2_unstructured_mesh_R2S_shutdown_dose_rate_several_materials
  - caption: Design study
    chapters:
    - file: tasks/task_21_design_task/README
    - file: tasks/task_21_design_task/1_optimal_design