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 (e4ddc1e).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

5	E902	[ ] stream did not contain valid UTF-8
1	I001	[*] Import block is un-sorted or un-formatted
1	E999	[ ] SyntaxError: Expected an expression
1	W291	[*] Trailing 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.ipynb:cell 6:1:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/tardisgamma/opacities.ipynb:cell 8:10:31: W291 [*] Trailing whitespace
Found 8 errors.
[*] 2 fixable with the `--fix` option.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.17%. Comparing base (13c9a31) to head (e4ddc1e).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2876      +/-   ##
==========================================
- Coverage   69.52%   69.17%   -0.35%     
==========================================
  Files         228      228              
  Lines       16429    16429              
==========================================
- Hits        11422    11365      -57     
- Misses       5007     5064      +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 (13c9a31) and the latest commit (e4ddc1e).
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 [13c9a314] <master>   | After [e4ddc1ef]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 3.56±0.01ms                  | 5.01±0.6ms          | ~1.41   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 47.3±40μs                    | 62.8±30μs           | ~1.33   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 511±200ns                    | 611±100ns           | ~1.20   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 24.1±6μs                     | 27.1±8μs            | ~1.12   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 641±100ns                    | 571±200ns           | ~0.89   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 1.93±0.7μs                   | 1.71±0.2μs          | ~0.89   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 4.12±1μs                     | 3.23±0.6μs          | ~0.78   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 40.6±20μs                    | 44.1±20μs           | 1.09    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 37.3±0.05μs                  | 39.6±0.06μs         | 1.06    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 203±0.1ns                    | 209±0.01ns          | 1.03    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 7.15±2μs                     | 7.40±2μs            | 1.03    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 541±100ns                    | 551±200ns           | 1.02    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 2.59±0.01ms                  | 2.64±0ms            | 1.02    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 2.98±0.7μs                   | 3.03±0.3μs          | 1.02    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 2.52±0.4ms                   | 2.56±0.5ms          | 1.01    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 38.3±0s                      | 38.3±0.07s          | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 1.04±0m                      | 1.04±0m             | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 2.08±0m                      | 2.08±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 1.19±0μs                     | 1.19±0μs            | 1.00    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 63.0±0.09ms                  | 63.1±0.2ms          | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 1.68±0ms                     | 1.66±0ms            | 0.99    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 760±0.6ns                    | 739±0.5ns           | 0.97    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 6.22±0.6μs                   | 5.88±0.8μs          | 0.95    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 2.12±1μs                     | 1.97±2μs            | 0.93    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |

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.

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

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[jvshields]

Line #13.    plt.ylabel("Opacity (cm^-1)")

To make this look right, you want to do plt.ylabel(f"Opacity (cm$^{-1}$))

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