Gammaray opacity documentation

[CePowers]

📝 Description

Type: 📝 documentation `

I started a new documentation file for the sources of opacity for gamma rays. I added information for Compton Scattering with plans to add other sources of opacity.

📌 Resources

Examples, notebooks, and links to useful references.

🚦 Testing

How did you test these changes?

• Testing pipeline
• Other method (describe)
• My changes can't be tested (explain why)

☑️ Checklist

• I requested two reviewers for this pull request
• I updated the documentation according to my changes
• I built the documentation by applying the build_docs label

Note: If you are not allowed to perform any of these actions, ping (@) a contributor.

[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (261871e).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

5	E902	[ ] stream did not contain valid UTF-8
3	W291	[*] Trailing whitespace
2	E999	[ ] SyntaxError: Expected an expression
1	E701	[ ] Multiple statements on one line (colon)
1	W292	[*] No newline at end of file
1	W293	[*] Blank line contains whitespace

Complete output(might be large):

docs/physics/tardisgamma/images/all_coeffs.png:1:1: E902 stream did not contain valid UTF-8
docs/physics/tardisgamma/images/coeff_fractions.png:1:1: E902 stream did not contain valid UTF-8
docs/physics/tardisgamma/images/compton_scattering_coefficient.png:1:1: E902 stream did not contain valid UTF-8
docs/physics/tardisgamma/images/pair_production_coefficient.png:1:1: E902 stream did not contain valid UTF-8
docs/physics/tardisgamma/images/photoabsorption_coefficient.png:1:1: E902 stream did not contain valid UTF-8
docs/physics/tardisgamma/index.rst:1:1: E999 SyntaxError: Expected an expression
docs/physics/tardisgamma/opacities.rst:1:1: E999 SyntaxError: Expected an expression
docs/physics/tardisgamma/opacities.rst:4:64: E701 Multiple statements on one line (colon)
docs/physics/tardisgamma/opacities.rst:4:118: W291 [*] Trailing whitespace
docs/physics/tardisgamma/opacities.rst:9:221: W291 [*] Trailing whitespace
docs/physics/tardisgamma/opacities.rst:25:310: W291 [*] Trailing whitespace
docs/physics/tardisgamma/opacities.rst:40:1: W293 [*] Blank line contains whitespace
docs/physics/tardisgamma/opacities.rst:81:39: W292 [*] No newline at end of file
Found 13 errors.
[*] 5 fixable with the `--fix` option.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.72%. Comparing base (fd4369f) to head (261871e).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2876      +/-   ##
==========================================
- Coverage   70.08%   69.72%   -0.36%     
==========================================
  Files         216      216              
  Lines       16034    16034              
==========================================
- Hits        11237    11180      -57     
- Misses       4797     4854      +57     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[tardis-bot]

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (b95388b) and the latest commit (b5c424d).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

All benchmarks:

Benchmarks that have stayed the same:

| Change   | Before [b95388b6] <master>   | After [b5c424d8]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 571±200ns                    | 682±100ns           | ~1.19   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 2.97±0.4μs                   | 3.44±0.3μs          | ~1.16   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 6.33±2μs                     | 7.28±2μs            | ~1.15   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 1.39±0.4μs                   | 1.54±0.5μs          | ~1.11   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 48.9±30μs                    | 44.3±40μs           | ~0.91   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 1.82±1μs                     | 1.98±1μs            | 1.09    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 21.2±5μs                     | 22.7±6μs            | 1.07    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 3.68±0.02ms                  | 3.87±0.01ms         | 1.05    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 5.88±1μs                     | 6.06±0.9μs          | 1.03    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 62.0±0.08ms                  | 62.9±0.3ms          | 1.02    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 41.6±20μs                    | 41.9±30μs           | 1.01    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 491±200ns                    | 491±100ns           | 1.00    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 2.54±0.01ms                  | 2.54±0.01ms         | 1.00    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 1.06±0m                      | 1.07±0m             | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 2.07±0m                      | 2.07±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 203±0.1ns                    | 203±0.2ns           | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 2.63±0.6ms                   | 2.62±0.5ms          | 1.00    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 39.7±0.03s                   | 39.5±0.05s          | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 1.21±0μs                     | 1.20±0μs            | 0.99    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 1.70±0.01ms                  | 1.69±0.01ms         | 0.99    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 592±200ns                    | 582±100ns           | 0.98    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 726±0.9ns                    | 711±0.7ns           | 0.98    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 32.6±0.02μs                  | 31.7±0.03μs         | 0.97    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 3.46±0.4μs                   | 3.21±0.6μs          | 0.93    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |

If you want to see the graph of the results, you can check it here

[andrewfullard]

Would like to see units on the y-axis of each plot

[jvshields]

Missing a period before this line.

[jvshields]

I think that this would be a lot more informative if all the different opacities were plotted together so you could more easily compare which opacity matters in which range. The text is fine and looks good, but I would definitely like to see the plots merged.

[andrewfullard]

The Total line being yellow is very difficult to read on white. I would also recommend using colourblind-safe colours for all lines.

[andrewfullard]

It would also be reasonable to limit the axes to cover the interesting region where all 3 opacities cross.

[andrewfullard]

I don't think the y-axis needs to be logarithmic here