From 6e0a506cd2a0318f4ad7897826fca2f04bcda334 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Mon, 6 Nov 2023 22:11:35 +0000
Subject: [PATCH 01/11] reordered task numbers

---
 .../1_surface_dose_from_gamma_source.ipynb                        | 0
 .../2_surface_dose_from_gamma_source_study.ipynb                  | 0
 .../3_cell_dose_from_neutron.py                                   | 0
 .../4_cell_dose_from_photon.py                                    | 0
 .../5_mesh_dose_from_neutrons.py                                  | 0
 .../README.md                                                     | 0
 .../compare_dose_simulation_with_back_of_envelope.py              | 0
 .../.ipynb                                                        | 0
 .../0_simple_transmutation_reaction_rate_simulation.py            | 0
 .../1_example_transmutation_isotope_build_up.ipynb                | 0
 .../2_example_tally_change_with_burnup.ipynb                      | 0
 .../3_full_pulse_schedule.py                                      | 0
 .../README.md                                                     | 0
 .../1_cell_based_shut_down_dose_rate_example.py}                  | 0
 .../1_time_filter_tally.py                                        | 0
 .../2_time_filter_tally_with_reflective_sphere.py                 | 0
 .../3_time_and_energy_filter_tally.py                             | 0
 .../1_find_volume_of_cell.ipynb                                   | 0
 .../1_make_CAD_shapes_from_points.ipynb                           | 0
 .../2_make_CAD_components_from_parameters.ipynb                   | 0
 .../3_make_CAD_reactors.ipynb                                     | 0
 .../README.md                                                     | 0
 .../1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb                 | 0
 .../2_making_components_for_a_2d_mesh_tally_vtk.ipynb             | 0
 .../3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb | 0
 .../README.md                                                     | 0
 .../1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb | 0
 .../README.md                                                     | 0
 28 files changed, 0 insertions(+), 0 deletions(-)
 rename tasks/{task_09_CSG_dose_tallies => task_09_CSG_instantaneous_dose_tallies}/1_surface_dose_from_gamma_source.ipynb (100%)
 rename tasks/{task_09_CSG_dose_tallies => task_09_CSG_instantaneous_dose_tallies}/2_surface_dose_from_gamma_source_study.ipynb (100%)
 rename tasks/{task_09_CSG_dose_tallies => task_09_CSG_instantaneous_dose_tallies}/3_cell_dose_from_neutron.py (100%)
 rename tasks/{task_09_CSG_dose_tallies => task_09_CSG_instantaneous_dose_tallies}/4_cell_dose_from_photon.py (100%)
 rename tasks/{task_09_CSG_dose_tallies => task_09_CSG_instantaneous_dose_tallies}/5_mesh_dose_from_neutrons.py (100%)
 rename tasks/{task_09_CSG_dose_tallies => task_09_CSG_instantaneous_dose_tallies}/README.md (100%)
 rename tasks/{task_09_CSG_dose_tallies => task_09_CSG_instantaneous_dose_tallies}/compare_dose_simulation_with_back_of_envelope.py (100%)
 rename tasks/{task_14_activation_transmutation_depletion => task_10_activation_transmutation_depletion}/.ipynb (100%)
 rename tasks/{task_14_activation_transmutation_depletion => task_10_activation_transmutation_depletion}/0_simple_transmutation_reaction_rate_simulation.py (100%)
 rename tasks/{task_14_activation_transmutation_depletion => task_10_activation_transmutation_depletion}/1_example_transmutation_isotope_build_up.ipynb (100%)
 rename tasks/{task_14_activation_transmutation_depletion => task_10_activation_transmutation_depletion}/2_example_tally_change_with_burnup.ipynb (100%)
 rename tasks/{task_14_activation_transmutation_depletion => task_10_activation_transmutation_depletion}/3_full_pulse_schedule.py (100%)
 rename tasks/{task_14_activation_transmutation_depletion => task_10_activation_transmutation_depletion}/README.md (100%)
 rename tasks/{task_09_CSG_dose_tallies/shut_down_dose_rate_example.py => task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py} (100%)
 rename tasks/{task_15_detectors_examples => task_11_detectors_examples}/1_time_filter_tally.py (100%)
 rename tasks/{task_15_detectors_examples => task_11_detectors_examples}/2_time_filter_tally_with_reflective_sphere.py (100%)
 rename tasks/{task_15_detectors_examples => task_11_detectors_examples}/3_time_and_energy_filter_tally.py (100%)
 rename tasks/{task_16_stochastic_volume_calculation => task_12_stochastic_volume_calculation}/1_find_volume_of_cell.ipynb (100%)
 rename tasks/{task_10_making_CAD_geometry => task_14_making_CAD_geometry}/1_make_CAD_shapes_from_points.ipynb (100%)
 rename tasks/{task_10_making_CAD_geometry => task_14_making_CAD_geometry}/2_make_CAD_components_from_parameters.ipynb (100%)
 rename tasks/{task_10_making_CAD_geometry => task_14_making_CAD_geometry}/3_make_CAD_reactors.ipynb (100%)
 rename tasks/{task_10_making_CAD_geometry => task_14_making_CAD_geometry}/README.md (100%)
 rename tasks/{task_12_CAD_mesh_fast_flux => task_15_CAD_mesh_fast_flux}/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb (100%)
 rename tasks/{task_12_CAD_mesh_fast_flux => task_15_CAD_mesh_fast_flux}/2_making_components_for_a_2d_mesh_tally_vtk.ipynb (100%)
 rename tasks/{task_12_CAD_mesh_fast_flux => task_15_CAD_mesh_fast_flux}/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb (100%)
 rename tasks/{task_12_CAD_mesh_fast_flux => task_15_CAD_mesh_fast_flux}/README.md (100%)
 rename tasks/{task_11_CAD_cell_tally_heat => task_16_CAD_cell_tally_heat}/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb (100%)
 rename tasks/{task_11_CAD_cell_tally_heat => task_16_CAD_cell_tally_heat}/README.md (100%)

diff --git a/tasks/task_09_CSG_dose_tallies/1_surface_dose_from_gamma_source.ipynb b/tasks/task_09_CSG_instantaneous_dose_tallies/1_surface_dose_from_gamma_source.ipynb
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/1_surface_dose_from_gamma_source.ipynb
rename to tasks/task_09_CSG_instantaneous_dose_tallies/1_surface_dose_from_gamma_source.ipynb
diff --git a/tasks/task_09_CSG_dose_tallies/2_surface_dose_from_gamma_source_study.ipynb b/tasks/task_09_CSG_instantaneous_dose_tallies/2_surface_dose_from_gamma_source_study.ipynb
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/2_surface_dose_from_gamma_source_study.ipynb
rename to tasks/task_09_CSG_instantaneous_dose_tallies/2_surface_dose_from_gamma_source_study.ipynb
diff --git a/tasks/task_09_CSG_dose_tallies/3_cell_dose_from_neutron.py b/tasks/task_09_CSG_instantaneous_dose_tallies/3_cell_dose_from_neutron.py
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/3_cell_dose_from_neutron.py
rename to tasks/task_09_CSG_instantaneous_dose_tallies/3_cell_dose_from_neutron.py
diff --git a/tasks/task_09_CSG_dose_tallies/4_cell_dose_from_photon.py b/tasks/task_09_CSG_instantaneous_dose_tallies/4_cell_dose_from_photon.py
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/4_cell_dose_from_photon.py
rename to tasks/task_09_CSG_instantaneous_dose_tallies/4_cell_dose_from_photon.py
diff --git a/tasks/task_09_CSG_dose_tallies/5_mesh_dose_from_neutrons.py b/tasks/task_09_CSG_instantaneous_dose_tallies/5_mesh_dose_from_neutrons.py
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/5_mesh_dose_from_neutrons.py
rename to tasks/task_09_CSG_instantaneous_dose_tallies/5_mesh_dose_from_neutrons.py
diff --git a/tasks/task_09_CSG_dose_tallies/README.md b/tasks/task_09_CSG_instantaneous_dose_tallies/README.md
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/README.md
rename to tasks/task_09_CSG_instantaneous_dose_tallies/README.md
diff --git a/tasks/task_09_CSG_dose_tallies/compare_dose_simulation_with_back_of_envelope.py b/tasks/task_09_CSG_instantaneous_dose_tallies/compare_dose_simulation_with_back_of_envelope.py
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/compare_dose_simulation_with_back_of_envelope.py
rename to tasks/task_09_CSG_instantaneous_dose_tallies/compare_dose_simulation_with_back_of_envelope.py
diff --git a/tasks/task_14_activation_transmutation_depletion/.ipynb b/tasks/task_10_activation_transmutation_depletion/.ipynb
similarity index 100%
rename from tasks/task_14_activation_transmutation_depletion/.ipynb
rename to tasks/task_10_activation_transmutation_depletion/.ipynb
diff --git a/tasks/task_14_activation_transmutation_depletion/0_simple_transmutation_reaction_rate_simulation.py b/tasks/task_10_activation_transmutation_depletion/0_simple_transmutation_reaction_rate_simulation.py
similarity index 100%
rename from tasks/task_14_activation_transmutation_depletion/0_simple_transmutation_reaction_rate_simulation.py
rename to tasks/task_10_activation_transmutation_depletion/0_simple_transmutation_reaction_rate_simulation.py
diff --git a/tasks/task_14_activation_transmutation_depletion/1_example_transmutation_isotope_build_up.ipynb b/tasks/task_10_activation_transmutation_depletion/1_example_transmutation_isotope_build_up.ipynb
similarity index 100%
rename from tasks/task_14_activation_transmutation_depletion/1_example_transmutation_isotope_build_up.ipynb
rename to tasks/task_10_activation_transmutation_depletion/1_example_transmutation_isotope_build_up.ipynb
diff --git a/tasks/task_14_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb b/tasks/task_10_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb
similarity index 100%
rename from tasks/task_14_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb
rename to tasks/task_10_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb
diff --git a/tasks/task_14_activation_transmutation_depletion/3_full_pulse_schedule.py b/tasks/task_10_activation_transmutation_depletion/3_full_pulse_schedule.py
similarity index 100%
rename from tasks/task_14_activation_transmutation_depletion/3_full_pulse_schedule.py
rename to tasks/task_10_activation_transmutation_depletion/3_full_pulse_schedule.py
diff --git a/tasks/task_14_activation_transmutation_depletion/README.md b/tasks/task_10_activation_transmutation_depletion/README.md
similarity index 100%
rename from tasks/task_14_activation_transmutation_depletion/README.md
rename to tasks/task_10_activation_transmutation_depletion/README.md
diff --git a/tasks/task_09_CSG_dose_tallies/shut_down_dose_rate_example.py b/tasks/task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py
similarity index 100%
rename from tasks/task_09_CSG_dose_tallies/shut_down_dose_rate_example.py
rename to tasks/task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py
diff --git a/tasks/task_15_detectors_examples/1_time_filter_tally.py b/tasks/task_11_detectors_examples/1_time_filter_tally.py
similarity index 100%
rename from tasks/task_15_detectors_examples/1_time_filter_tally.py
rename to tasks/task_11_detectors_examples/1_time_filter_tally.py
diff --git a/tasks/task_15_detectors_examples/2_time_filter_tally_with_reflective_sphere.py b/tasks/task_11_detectors_examples/2_time_filter_tally_with_reflective_sphere.py
similarity index 100%
rename from tasks/task_15_detectors_examples/2_time_filter_tally_with_reflective_sphere.py
rename to tasks/task_11_detectors_examples/2_time_filter_tally_with_reflective_sphere.py
diff --git a/tasks/task_15_detectors_examples/3_time_and_energy_filter_tally.py b/tasks/task_11_detectors_examples/3_time_and_energy_filter_tally.py
similarity index 100%
rename from tasks/task_15_detectors_examples/3_time_and_energy_filter_tally.py
rename to tasks/task_11_detectors_examples/3_time_and_energy_filter_tally.py
diff --git a/tasks/task_16_stochastic_volume_calculation/1_find_volume_of_cell.ipynb b/tasks/task_12_stochastic_volume_calculation/1_find_volume_of_cell.ipynb
similarity index 100%
rename from tasks/task_16_stochastic_volume_calculation/1_find_volume_of_cell.ipynb
rename to tasks/task_12_stochastic_volume_calculation/1_find_volume_of_cell.ipynb
diff --git a/tasks/task_10_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb b/tasks/task_14_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb
similarity index 100%
rename from tasks/task_10_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb
rename to tasks/task_14_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb
diff --git a/tasks/task_10_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb b/tasks/task_14_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb
similarity index 100%
rename from tasks/task_10_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb
rename to tasks/task_14_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb
diff --git a/tasks/task_10_making_CAD_geometry/3_make_CAD_reactors.ipynb b/tasks/task_14_making_CAD_geometry/3_make_CAD_reactors.ipynb
similarity index 100%
rename from tasks/task_10_making_CAD_geometry/3_make_CAD_reactors.ipynb
rename to tasks/task_14_making_CAD_geometry/3_make_CAD_reactors.ipynb
diff --git a/tasks/task_10_making_CAD_geometry/README.md b/tasks/task_14_making_CAD_geometry/README.md
similarity index 100%
rename from tasks/task_10_making_CAD_geometry/README.md
rename to tasks/task_14_making_CAD_geometry/README.md
diff --git a/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb b/tasks/task_15_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb
similarity index 100%
rename from tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb
rename to tasks/task_15_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb
diff --git a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb b/tasks/task_15_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb
similarity index 100%
rename from tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb
rename to tasks/task_15_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb
diff --git a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_15_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
similarity index 100%
rename from tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
rename to tasks/task_15_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
diff --git a/tasks/task_12_CAD_mesh_fast_flux/README.md b/tasks/task_15_CAD_mesh_fast_flux/README.md
similarity index 100%
rename from tasks/task_12_CAD_mesh_fast_flux/README.md
rename to tasks/task_15_CAD_mesh_fast_flux/README.md
diff --git a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb b/tasks/task_16_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb
similarity index 100%
rename from tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb
rename to tasks/task_16_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb
diff --git a/tasks/task_11_CAD_cell_tally_heat/README.md b/tasks/task_16_CAD_cell_tally_heat/README.md
similarity index 100%
rename from tasks/task_11_CAD_cell_tally_heat/README.md
rename to tasks/task_16_CAD_cell_tally_heat/README.md

From 983217a85a329fc3f571d33fe1da3d66de11f634 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Mon, 6 Nov 2023 23:11:58 +0000
Subject: [PATCH 02/11] more task renaming

---
 .../1_cell_based_shut_down_dose_rate_example.py                  | 1 -
 .../1_time_filter_tally.py                                       | 0
 .../2_time_filter_tally_with_reflective_sphere.py                | 0
 .../3_time_and_energy_filter_tally.py                            | 0
 .../1_find_volume_of_cell.ipynb                                  | 0
 .../1_shielded_room_survival_biasing.ipynb                       | 0
 .../2_shielded_room_single_ww.ipynb                              | 0
 .../3_sphere_iterative_per_run_ww.ipynb                          | 0
 .../4_sphere_iterative_per_batch_ww.ipynb                        | 0
 .../README.md                                                    | 0
 .../1_make_CAD_shapes_from_points.ipynb                          | 0
 .../2_make_CAD_components_from_parameters.ipynb                  | 0
 .../3_make_CAD_reactors.ipynb                                    | 0
 .../README.md                                                    | 0
 .../1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb                | 0
 .../2_making_components_for_a_2d_mesh_tally_vtk.ipynb            | 0
 ...3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb | 0
 .../README.md                                                    | 0
 ...1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb | 0
 .../README.md                                                    | 0
 20 files changed, 1 deletion(-)
 rename tasks/{task_11_detectors_examples => task_12_detectors_examples}/1_time_filter_tally.py (100%)
 rename tasks/{task_11_detectors_examples => task_12_detectors_examples}/2_time_filter_tally_with_reflective_sphere.py (100%)
 rename tasks/{task_11_detectors_examples => task_12_detectors_examples}/3_time_and_energy_filter_tally.py (100%)
 rename tasks/{task_12_stochastic_volume_calculation => task_13_stochastic_volume_calculation}/1_find_volume_of_cell.ipynb (100%)
 rename tasks/{task_13_variance_reduction => task_14_variance_reduction}/1_shielded_room_survival_biasing.ipynb (100%)
 rename tasks/{task_13_variance_reduction => task_14_variance_reduction}/2_shielded_room_single_ww.ipynb (100%)
 rename tasks/{task_13_variance_reduction => task_14_variance_reduction}/3_sphere_iterative_per_run_ww.ipynb (100%)
 rename tasks/{task_13_variance_reduction => task_14_variance_reduction}/4_sphere_iterative_per_batch_ww.ipynb (100%)
 rename tasks/{task_13_variance_reduction => task_14_variance_reduction}/README.md (100%)
 rename tasks/{task_14_making_CAD_geometry => task_15_making_CAD_geometry}/1_make_CAD_shapes_from_points.ipynb (100%)
 rename tasks/{task_14_making_CAD_geometry => task_15_making_CAD_geometry}/2_make_CAD_components_from_parameters.ipynb (100%)
 rename tasks/{task_14_making_CAD_geometry => task_15_making_CAD_geometry}/3_make_CAD_reactors.ipynb (100%)
 rename tasks/{task_14_making_CAD_geometry => task_15_making_CAD_geometry}/README.md (100%)
 rename tasks/{task_15_CAD_mesh_fast_flux => task_16_CAD_mesh_fast_flux}/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb (100%)
 rename tasks/{task_15_CAD_mesh_fast_flux => task_16_CAD_mesh_fast_flux}/2_making_components_for_a_2d_mesh_tally_vtk.ipynb (100%)
 rename tasks/{task_15_CAD_mesh_fast_flux => task_16_CAD_mesh_fast_flux}/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb (100%)
 rename tasks/{task_15_CAD_mesh_fast_flux => task_16_CAD_mesh_fast_flux}/README.md (100%)
 rename tasks/{task_16_CAD_cell_tally_heat => task_17_CAD_cell_tally_heat}/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb (100%)
 rename tasks/{task_16_CAD_cell_tally_heat => task_17_CAD_cell_tally_heat}/README.md (100%)

diff --git a/tasks/task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py b/tasks/task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py
index 15103a09..fe766dfa 100644
--- a/tasks/task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py
+++ b/tasks/task_11_CSG_shut_down_dose_tallies/1_cell_based_shut_down_dose_rate_example.py
@@ -168,7 +168,6 @@
     # decay gamma source from the stable material at that time
     # also there are no decay products in this first timestep for this model
 
-
         photon_sources_for_timestep = []
         print(f"making photon source for timestep {i_cool}")
 
diff --git a/tasks/task_11_detectors_examples/1_time_filter_tally.py b/tasks/task_12_detectors_examples/1_time_filter_tally.py
similarity index 100%
rename from tasks/task_11_detectors_examples/1_time_filter_tally.py
rename to tasks/task_12_detectors_examples/1_time_filter_tally.py
diff --git a/tasks/task_11_detectors_examples/2_time_filter_tally_with_reflective_sphere.py b/tasks/task_12_detectors_examples/2_time_filter_tally_with_reflective_sphere.py
similarity index 100%
rename from tasks/task_11_detectors_examples/2_time_filter_tally_with_reflective_sphere.py
rename to tasks/task_12_detectors_examples/2_time_filter_tally_with_reflective_sphere.py
diff --git a/tasks/task_11_detectors_examples/3_time_and_energy_filter_tally.py b/tasks/task_12_detectors_examples/3_time_and_energy_filter_tally.py
similarity index 100%
rename from tasks/task_11_detectors_examples/3_time_and_energy_filter_tally.py
rename to tasks/task_12_detectors_examples/3_time_and_energy_filter_tally.py
diff --git a/tasks/task_12_stochastic_volume_calculation/1_find_volume_of_cell.ipynb b/tasks/task_13_stochastic_volume_calculation/1_find_volume_of_cell.ipynb
similarity index 100%
rename from tasks/task_12_stochastic_volume_calculation/1_find_volume_of_cell.ipynb
rename to tasks/task_13_stochastic_volume_calculation/1_find_volume_of_cell.ipynb
diff --git a/tasks/task_13_variance_reduction/1_shielded_room_survival_biasing.ipynb b/tasks/task_14_variance_reduction/1_shielded_room_survival_biasing.ipynb
similarity index 100%
rename from tasks/task_13_variance_reduction/1_shielded_room_survival_biasing.ipynb
rename to tasks/task_14_variance_reduction/1_shielded_room_survival_biasing.ipynb
diff --git a/tasks/task_13_variance_reduction/2_shielded_room_single_ww.ipynb b/tasks/task_14_variance_reduction/2_shielded_room_single_ww.ipynb
similarity index 100%
rename from tasks/task_13_variance_reduction/2_shielded_room_single_ww.ipynb
rename to tasks/task_14_variance_reduction/2_shielded_room_single_ww.ipynb
diff --git a/tasks/task_13_variance_reduction/3_sphere_iterative_per_run_ww.ipynb b/tasks/task_14_variance_reduction/3_sphere_iterative_per_run_ww.ipynb
similarity index 100%
rename from tasks/task_13_variance_reduction/3_sphere_iterative_per_run_ww.ipynb
rename to tasks/task_14_variance_reduction/3_sphere_iterative_per_run_ww.ipynb
diff --git a/tasks/task_13_variance_reduction/4_sphere_iterative_per_batch_ww.ipynb b/tasks/task_14_variance_reduction/4_sphere_iterative_per_batch_ww.ipynb
similarity index 100%
rename from tasks/task_13_variance_reduction/4_sphere_iterative_per_batch_ww.ipynb
rename to tasks/task_14_variance_reduction/4_sphere_iterative_per_batch_ww.ipynb
diff --git a/tasks/task_13_variance_reduction/README.md b/tasks/task_14_variance_reduction/README.md
similarity index 100%
rename from tasks/task_13_variance_reduction/README.md
rename to tasks/task_14_variance_reduction/README.md
diff --git a/tasks/task_14_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb b/tasks/task_15_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb
similarity index 100%
rename from tasks/task_14_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb
rename to tasks/task_15_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb
diff --git a/tasks/task_14_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb b/tasks/task_15_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb
similarity index 100%
rename from tasks/task_14_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb
rename to tasks/task_15_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb
diff --git a/tasks/task_14_making_CAD_geometry/3_make_CAD_reactors.ipynb b/tasks/task_15_making_CAD_geometry/3_make_CAD_reactors.ipynb
similarity index 100%
rename from tasks/task_14_making_CAD_geometry/3_make_CAD_reactors.ipynb
rename to tasks/task_15_making_CAD_geometry/3_make_CAD_reactors.ipynb
diff --git a/tasks/task_14_making_CAD_geometry/README.md b/tasks/task_15_making_CAD_geometry/README.md
similarity index 100%
rename from tasks/task_14_making_CAD_geometry/README.md
rename to tasks/task_15_making_CAD_geometry/README.md
diff --git a/tasks/task_15_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb b/tasks/task_16_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb
similarity index 100%
rename from tasks/task_15_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb
rename to tasks/task_16_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb
diff --git a/tasks/task_15_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb b/tasks/task_16_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb
similarity index 100%
rename from tasks/task_15_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb
rename to tasks/task_16_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb
diff --git a/tasks/task_15_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
similarity index 100%
rename from tasks/task_15_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
rename to tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
diff --git a/tasks/task_15_CAD_mesh_fast_flux/README.md b/tasks/task_16_CAD_mesh_fast_flux/README.md
similarity index 100%
rename from tasks/task_15_CAD_mesh_fast_flux/README.md
rename to tasks/task_16_CAD_mesh_fast_flux/README.md
diff --git a/tasks/task_16_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb b/tasks/task_17_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb
similarity index 100%
rename from tasks/task_16_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb
rename to tasks/task_17_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb
diff --git a/tasks/task_16_CAD_cell_tally_heat/README.md b/tasks/task_17_CAD_cell_tally_heat/README.md
similarity index 100%
rename from tasks/task_16_CAD_cell_tally_heat/README.md
rename to tasks/task_17_CAD_cell_tally_heat/README.md

From d6050f1d08fe8aa6bb8b22af7c53b88232efdba6 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 8 Nov 2023 22:52:29 +0000
Subject: [PATCH 03/11] sorted table of tasks

---
 README.md | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index a7bfe907..790910bb 100644
--- a/README.md
+++ b/README.md
@@ -38,14 +38,24 @@ The video below gives a brief explainer of what to expect in the workshop and so
 | [Task 6 - DPA](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_06_CSG_cell_tally_DPA) | Displacements Per Atom, Cell tallies, Simulations, Volume calculations | [link](https://youtu.be/VLn59FSc4GA) | [![Task 6](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml) |
 | [Task 7 - Neutron and photon spectra](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_07_CSG_cell_tally_spectra) | Neutron Spectra, Photon Spectra, Cell tallies, Energy group structures, Flux, Current | [link](https://youtu.be/qHqAuqMLYPA) | [![Task 7](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml) |
 | [Task 8 - Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_08_CSG_mesh_tally) | Mesh tallies, Structured meshes | [link](https://youtu.be/KYIsDjip1nQ) |[![Task 8](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml)|
-| [Task 9 - Dose](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_09_CSG_dose_tallies) | Instantaneous Dose, Cell tallies, Dose coefficients |  |[![Task 9](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml)|
-| [Task 10 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) |[![Task 10](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml)|
-| [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating |  |[![Task 11](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml)|
-| [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux |  |[![Task 12](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml)|
-| [Task 13 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_13_variance_reduction) | Variance reduction, weight windows |  |[![Task 13](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml)|
-| [Task 14 - Activation transmutation depletion](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_activation_transmutation_depletion) | Isotope build up and tally variation as a function of time |  |[![Task 14](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml)|
-| [Task 15 - Detector examples](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_detector_examples) | Time filter detector response time of flight |  |[![Task 15](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml)|
-| [Task 16 - stochastic volume calculation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_stochastic_volume_calculation) | stochastic volume material atoms in cell |  |[![Task 16](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml)|
+
+| [Task 9 - Instantaneous Dose](https://github.com/fusion-energy/neutronics-workshop/tree/reshuffle/tasks/task_09_CSG_instantaneous_dose_tallies) | Instantaneous Dose, Cell tallies, Dose coefficients |  |[![Task 9](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml)|
+
+| [Task 10 - Activation transmutation depletion](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_activation_transmutation_depletion) | Isotope build up and tally variation as a function of time |  |[![Task 10](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml)|
+
+| [Task 11 - CSG shut down Dose](https://github.com/fusion-energy/neutronics-workshop/tree/reshuffle/tasks/task_11_CSG_shut_down_dose_tallies) | Shut down Dose, Cell tallies, Dose coefficients |  |[![Task 11](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml)|
+
+| [Task 12 - Detector examples](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_detector_examples) | Time filter detector response time of flight |  |[![Task 12](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml)|
+
+| [Task 13 - stochastic volume calculation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_stochastic_volume_calculation) | stochastic volume material atoms in cell |  |[![Task 13](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml)|
+
+| [Task 14 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_13_variance_reduction) | Variance reduction, weight windows |  |[![Task 13](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml)|
+
+| [Task 15 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) |[![Task 15](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml)|
+
+| [Task 16 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating |  |[![Task 16](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml)|
+
+| [Task 17 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_17_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux |  |[![Task 17](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml)|
 
 <!-- # Run in the cloud (low CPU count)
 

From 25b7db41ccacfec30c4c912bc9de26d534be135a Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 8 Nov 2023 22:58:54 +0000
Subject: [PATCH 04/11] tidy task table

---
 README.md       | 11 +----------
 tasks/README.md | 19 -------------------
 2 files changed, 1 insertion(+), 29 deletions(-)
 delete mode 100644 tasks/README.md

diff --git a/README.md b/README.md
index 790910bb..eb572f25 100644
--- a/README.md
+++ b/README.md
@@ -38,23 +38,14 @@ The video below gives a brief explainer of what to expect in the workshop and so
 | [Task 6 - DPA](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_06_CSG_cell_tally_DPA) | Displacements Per Atom, Cell tallies, Simulations, Volume calculations | [link](https://youtu.be/VLn59FSc4GA) | [![Task 6](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_6.yml) |
 | [Task 7 - Neutron and photon spectra](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_07_CSG_cell_tally_spectra) | Neutron Spectra, Photon Spectra, Cell tallies, Energy group structures, Flux, Current | [link](https://youtu.be/qHqAuqMLYPA) | [![Task 7](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_7.yml) |
 | [Task 8 - Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_08_CSG_mesh_tally) | Mesh tallies, Structured meshes | [link](https://youtu.be/KYIsDjip1nQ) |[![Task 8](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_8.yml)|
-
 | [Task 9 - Instantaneous Dose](https://github.com/fusion-energy/neutronics-workshop/tree/reshuffle/tasks/task_09_CSG_instantaneous_dose_tallies) | Instantaneous Dose, Cell tallies, Dose coefficients |  |[![Task 9](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_9.yml)|
-
 | [Task 10 - Activation transmutation depletion](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_activation_transmutation_depletion) | Isotope build up and tally variation as a function of time |  |[![Task 10](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_10.yml)|
-
 | [Task 11 - CSG shut down Dose](https://github.com/fusion-energy/neutronics-workshop/tree/reshuffle/tasks/task_11_CSG_shut_down_dose_tallies) | Shut down Dose, Cell tallies, Dose coefficients |  |[![Task 11](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_11.yml)|
-
 | [Task 12 - Detector examples](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_detector_examples) | Time filter detector response time of flight |  |[![Task 12](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_12.yml)|
-
 | [Task 13 - stochastic volume calculation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_stochastic_volume_calculation) | stochastic volume material atoms in cell |  |[![Task 13](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml)|
-
-| [Task 14 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_13_variance_reduction) | Variance reduction, weight windows |  |[![Task 13](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_13.yml)|
-
+| [Task 14 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_14_variance_reduction) | Variance reduction, weight windows |  |[![Task 14](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_14.yml)|
 | [Task 15 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) |[![Task 15](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_15.yml)|
-
 | [Task 16 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating |  |[![Task 16](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_16.yml)|
-
 | [Task 17 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_17_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux |  |[![Task 17](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml/badge.svg?branch=main)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_task_17.yml)|
 
 <!-- # Run in the cloud (low CPU count)
diff --git a/tasks/README.md b/tasks/README.md
deleted file mode 100644
index 0014e5a8..00000000
--- a/tasks/README.md
+++ /dev/null
@@ -1,19 +0,0 @@
-
-| Tasks | Keywords | Video(s) |
-|-|-|-|
-| [Task 1 - Cross sections](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_01_cross_sections) | Nuclear data, cross-sections, MT numbers, Doppler | [link1](https://youtu.be/eBZ2lY_2v7I)  [link2](https://youtu.be/ELZNeIdSuMY) [link3](https://youtu.be/ec5BLLL6Q_g) [link4](https://youtu.be/mkl1mVnTO6g) |
-| [Task 2 - Materials](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_02_making_materials) | Materials, Neutronics Material Maker, Mixed materials | [link](https://youtu.be/-NGnY-1TWCA) |
-| [Task 3 - CSG geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_03_making_CSG_geometry) | CSG geometry, Geometry visualisation | [link](https://youtu.be/Ovr7oYukYRw) |
-| [Task 4 - Sources](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_04_make_sources) | Neutron point sources, Gamma sources, Plasma sources, Neutron track visualisation | [link](https://youtu.be/j9dT1Viqcu4) |
-| [Task 5 - TBR](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_05_CSG_cell_tally_TBR) | Tritium Breeding Ratio, Cell tallies, Simulations | [link](https://youtu.be/Vc7Qy7QW4o8) |
-| [Task 6 - DPA](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_06_CSG_cell_tally_DPA) | Displacements Per Atom, Cell tallies, Simulations, Volume calculations | [link](https://youtu.be/VLn59FSc4GA) |
-| [Task 7 - Neutron and photon spectra](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_07_CSG_cell_tally_spectra) | Neutron Spectra, Photon Spectra, Cell tallies, Energy group structures, Flux, Current | [link](https://youtu.be/qHqAuqMLYPA) |
-| [Task 8 - Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_08_CSG_mesh_tally) | Mesh tallies, Structured meshes | [link](https://youtu.be/KYIsDjip1nQ) |
-| [Task 9 - Dose](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_09_CSG_surface_tally_dose) | Dose, Cell tallies, Dose coefficients |  |
-| [Task 10 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) |
-| [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating |  |
-| [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux |  |
-| [Task 13 - Variance reduction](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_variance_reduction) | Variance reduction with weight windows |  |
-| [Task 14 - Activation and transmutation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_activation_transmutation) | Actionation of material, evolution of materials, tallies as a function of time, burn up, transmutation and isotope creation |  |
-| [Task 15 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies |  |
-| [Task 16 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_parameter_study_optimisation) | Data science machine learning approaches |  |

From 018d471aa36b37fc014bc0b3423117fbe67a900c Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Wed, 8 Nov 2023 23:13:19 +0000
Subject: [PATCH 05/11] added .openmc_material

---
 ...r_a_2d_mesh_tally_and_matplotlib_png.ipynb | 26 ++++++++++++++-----
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
index e8201dfa..f17be799 100644
--- a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
+++ b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -14,6 +15,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -61,6 +63,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -78,6 +81,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -90,20 +94,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neutronics_material_maker import Material\n",
+    "\n",
+    "import neutronics_material_maker as nmm\n",
     "import openmc\n",
     "\n",
     "# Names of material tags can be found with the command line tool\n",
     "# mbsize -ll dagmc.h5m | grep 'NAME = mat:'\n",
     "\n",
     "# simplified material definitions have been used to keen this example minimal\n",
-    "mat_pf_coil_1 = Material.from_library(name='copper')\n",
+    "mat_pf_coil_1 = nmm.Material.from_library(name='copper').openmc_material\n",
     "\n",
-    "mat_pf_coil_2 = Material.from_library(name='copper')\n",
+    "mat_pf_coil_2 = nmm.Material.from_library(name='copper').openmc_material\n",
     "\n",
-    "mat_pf_coil_3 = Material.from_library(name='copper')\n",
+    "mat_pf_coil_3 = nmm.Material.from_library(name='copper').openmc_material\n",
     "\n",
-    "mat_pf_coil_4 = Material.from_library(name='copper')\n",
+    "mat_pf_coil_4 = nmm.Material.from_library(name='copper').openmc_material\n",
     "\n",
     "mat_pf_coil_case_1 = openmc.Material(name=\"pf_coil_case_1\")\n",
     "mat_pf_coil_case_1.add_element(\"Fe\", 1, \"ao\")\n",
@@ -153,9 +158,9 @@
     "mat_outboard_rear_blanket_wall.add_element(\"Fe\", 1, \"ao\")\n",
     "mat_outboard_rear_blanket_wall.set_density(\"g/cm3\", 7.7)\n",
     "\n",
-    "mat_inboard_tf_coils = Material.from_library(name='copper')\n",
+    "mat_inboard_tf_coils = nmm.Material.from_library(name='copper').openmc_material\n",
     "\n",
-    "mat_tf_coils = Material.from_library(name='copper')\n",
+    "mat_tf_coils = nmm.Material.from_library(name='copper').openmc_material\n",
     "\n",
     "\n",
     "materials = openmc.Materials(\n",
@@ -183,6 +188,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -234,6 +240,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -285,6 +292,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -317,6 +325,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -339,6 +348,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -374,6 +384,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -381,6 +392,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": []

From 21ada5e136ace5867f67ff2c8a7ac0fc3516e722 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 9 Nov 2023 13:11:40 +0000
Subject: [PATCH 06/11] changed material names

---
 ...r_a_2d_mesh_tally_and_matplotlib_png.ipynb | 26 +++++++++++++++----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
index f17be799..d01d90f4 100644
--- a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
+++ b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
@@ -80,6 +80,22 @@
     "my_reactor.export_dagmc_h5m(filename=\"dagmc.h5m\", min_mesh_size=5, max_mesh_size=20)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Names of material tags can be found with the command line tool"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!mbsize -ll dagmc.h5m | grep 'NAME = mat:'"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -98,8 +114,7 @@
     "import neutronics_material_maker as nmm\n",
     "import openmc\n",
     "\n",
-    "# Names of material tags can be found with the command line tool\n",
-    "# mbsize -ll dagmc.h5m | grep 'NAME = mat:'\n",
+    "\n",
     "\n",
     "# simplified material definitions have been used to keen this example minimal\n",
     "mat_pf_coil_1 = nmm.Material.from_library(name='copper').openmc_material\n",
@@ -159,9 +174,10 @@
     "mat_outboard_rear_blanket_wall.set_density(\"g/cm3\", 7.7)\n",
     "\n",
     "mat_inboard_tf_coils = nmm.Material.from_library(name='copper').openmc_material\n",
+    "mat_inboard_tf_coils.name = 'mat_inboard_tf_coils'\n",
     "\n",
     "mat_tf_coils = nmm.Material.from_library(name='copper').openmc_material\n",
-    "\n",
+    "mat_tf_coils.name = 'mat_tf_coils'\n",
     "\n",
     "materials = openmc.Materials(\n",
     "    [\n",
@@ -344,7 +360,7 @@
     ")\n",
     "\n",
     "# starts the simulation\n",
-    "my_model.run()"
+    "statepoint_filename = my_model.run()"
    ]
   },
   {
@@ -363,7 +379,7 @@
    "source": [
     "\n",
     "# open the results file\n",
-    "sp = openmc.StatePoint(\"statepoint.10.h5\")\n",
+    "sp = openmc.StatePoint(statepoint_filename)\n",
     "\n",
     "# access the tally using pandas dataframes\n",
     "heating_tally = sp.get_tally(name=\"heating\")\n",

From 1a24921a285c9bf8e2fc7652a2c2846c0c18be1a Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 9 Nov 2023 13:14:18 +0000
Subject: [PATCH 07/11] reducing chain level

---
 .../2_example_tally_change_with_burnup.ipynb                 | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tasks/task_10_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb b/tasks/task_10_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb
index 8872bab9..16f83e98 100644
--- a/tasks/task_10_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb
+++ b/tasks/task_10_activation_transmutation_depletion/2_example_tally_change_with_burnup.ipynb
@@ -113,7 +113,7 @@
     "This is the depltion specific part of the model setup.\n",
     "Here we:\n",
     "\n",
-    "    specify the chain file, this tells openmc the decay paths between isotopes including proabilities of different routes and half lives\n",
+    "    specify the chain file, this tells openmc the decay paths between isotopes including probabilities of different routes and half lives\n",
     "    \n",
     "    set the time steps and corresponding source rates "
    ]
@@ -135,7 +135,8 @@
     "operator = openmc.deplete.CoupledOperator(\n",
     "    model=model,\n",
     "    normalization_mode=\"source-rate\",  # set for fixed source simulation, otherwise defaults to fission simulation\n",
-    "    reduce_chain=True # reduced to only the isotopes present in depletable materials and their possible progeny\n",
+    "    reduce_chain=True, # reduced to only the isotopes present in depletable materials and their possible progeny\n",
+    "    reduce_chain_level=5\n",
     ")\n",
     "\n",
     "time_steps = [365*24*60*60] * 5 # 5 steps of 5 years in seconds\n",

From 800de4a543304d178746a90fa50208b7c7ced811 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Fri, 10 Nov 2023 08:14:06 +0000
Subject: [PATCH 08/11] [skip ci] started renaming materials

---
 ...ing_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
index f17be799..05bdeb12 100644
--- a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
+++ b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
@@ -159,9 +159,10 @@
     "mat_outboard_rear_blanket_wall.set_density(\"g/cm3\", 7.7)\n",
     "\n",
     "mat_inboard_tf_coils = nmm.Material.from_library(name='copper').openmc_material\n",
+    "mat_inboard_tf_coils.name = 'inboard_tf_coils'\n",
     "\n",
     "mat_tf_coils = nmm.Material.from_library(name='copper').openmc_material\n",
-    "\n",
+    "mat_tf_coils.name = 'tf_coil'\n",
     "\n",
     "materials = openmc.Materials(\n",
     "    [\n",
@@ -207,6 +208,9 @@
     "# makes use of the dagmc geometry\n",
     "dag_univ = openmc.DAGMCUniverse(\"dagmc.h5m\")\n",
     "\n",
+    "# prints all the material tags used in the dagmc geometry\n",
+    "print(dag_univ.material_names)\n",
+    "\n",
     "# creates an edge of universe boundary surface\n",
     "vac_surf = openmc.Sphere(r=10000, surface_id=9999, boundary_type=\"vacuum\")\n",
     "\n",

From c2946c1fb14a40fa33dd28405627b7a727a58deb Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Fri, 10 Nov 2023 10:06:37 +0000
Subject: [PATCH 09/11] changed material names to match dagmc

---
 ..._reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
index d2c05fbf..390a0adf 100644
--- a/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
+++ b/tasks/task_16_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb
@@ -174,7 +174,7 @@
     "mat_supports.add_element(\"Fe\", 1, \"ao\")\n",
     "mat_supports.set_density(\"g/cm3\", 7.7)\n",
     "\n",
-    "mat_outboard_rear_blanket_wall = openmc.Material(name=\"outboard_rear_blanket_wall\")\n",
+    "mat_outboard_rear_blanket_wall = openmc.Material(name=\"blanket_rear_wall\")\n",
     "mat_outboard_rear_blanket_wall.add_element(\"Fe\", 1, \"ao\")\n",
     "mat_outboard_rear_blanket_wall.set_density(\"g/cm3\", 7.7)\n",
     "\n",
@@ -385,7 +385,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "# open the results file\n",
     "sp = openmc.StatePoint(statepoint_filename)\n",
     "\n",
@@ -414,12 +413,6 @@
    "source": [
     "The vtk file should have appeared in the file explorer to the left. Right mouse click on the file to download it and then open with Paraview"
    ]
-  },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
   }
  ],
  "metadata": {

From 6206d80046ed91bc52fc9be463a1818c7a006e62 Mon Sep 17 00:00:00 2001
From: shimwell <mail@jshimwell.com>
Date: Fri, 10 Nov 2023 20:12:34 +0000
Subject: [PATCH 10/11] increased time out

---
 tests/test_task_16.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_task_16.py b/tests/test_task_16.py
index 1a5336d6..28143141 100644
--- a/tests/test_task_16.py
+++ b/tests/test_task_16.py
@@ -25,7 +25,7 @@ def _notebook_run(path):
     with open(path) as f:
         nb = nbformat.read(f, as_version=4)
         nb.metadata.get('kernelspec', {})['name'] = kernel_name
-        ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=1900) #, allow_errors=True
+        ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=4000) #, allow_errors=True
 
         try:
             ep.preprocess(nb, {'metadata': {'path': this_file_directory}})

From c58d0321165e4243136b624f72125a0153a9fdc7 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Nov 2023 20:54:52 +0000
Subject: [PATCH 11/11] Update test_task_14.py

---
 tests/test_task_14.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_task_14.py b/tests/test_task_14.py
index 3a6a2c91..039c5b68 100644
--- a/tests/test_task_14.py
+++ b/tests/test_task_14.py
@@ -25,7 +25,7 @@ def _notebook_run(path):
     with open(path) as f:
         nb = nbformat.read(f, as_version=4)
         nb.metadata.get('kernelspec', {})['name'] = kernel_name
-        ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=1900) #, allow_errors=True
+        ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=4000) #, allow_errors=True
 
         try:
             ep.preprocess(nb, {'metadata': {'path': this_file_directory}})