Gamma sampling documentation #2859

CePowers · 2024-10-15T13:05:13Z

📝 Description

Type: 📝 documentation

I created a new file for the gamma ray documentation about packet sampling. I also added a new citation to the tardis.bib file that is used in the packet sampling file.

📌 Resources

Examples, notebooks, and links to useful references.

🚦 Testing

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Testing pipeline
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☑️ 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

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tardis-bot · 2024-10-15T13:07:12Z

*beep* *bop*
Hi human,
I ran ruff on the latest commit (6c73d4d).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

11	W191	[ ] Indentation contains tabs
3	E999	[ ] SyntaxError: Expected a statement
1	W292	[*] No newline at end of file

Complete output(might be large):

docs/physics/tardisgamma/index.rst:1:1: E999 SyntaxError: Expected an expression
docs/physics/tardisgamma/packetsampling.rst:1:8: E999 SyntaxError: Simple statements must be separated by newlines or semicolons
docs/tardis.bib:1:1: E999 SyntaxError: Expected a statement
docs/tardis.bib:308:1: W191 Indentation contains tabs
docs/tardis.bib:309:1: W191 Indentation contains tabs
docs/tardis.bib:310:1: W191 Indentation contains tabs
docs/tardis.bib:311:1: W191 Indentation contains tabs
docs/tardis.bib:312:1: W191 Indentation contains tabs
docs/tardis.bib:313:1: W191 Indentation contains tabs
docs/tardis.bib:314:1: W191 Indentation contains tabs
docs/tardis.bib:315:1: W191 Indentation contains tabs
docs/tardis.bib:316:1: W191 Indentation contains tabs
docs/tardis.bib:317:1: W191 Indentation contains tabs
docs/tardis.bib:318:1: W191 Indentation contains tabs
docs/tardis.bib:367:2: W292 [*] No newline at end of file
Found 15 errors.
[*] 1 fixable with the `--fix` option.

codecov · 2024-10-15T13:17:09Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 69.60%. Comparing base (5f11626) to head (6c73d4d).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2859      +/-   ##
==========================================
- Coverage   69.95%   69.60%   -0.36%     
==========================================
  Files         216      216              
  Lines       16077    16077              
==========================================
- Hits        11247    11190      -57     
- Misses       4830     4887      +57

☔ View full report in Codecov by Sentry.
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tardis-bot · 2024-10-15T13:25:43Z

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

tardis-bot · 2024-10-15T14:01:57Z

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (81ec6e8) and the latest commit (644cf55).
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 [6ae9446d] <master>   | After [644cf55f]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 2.96±0.3μs                   | 3.65±0.2μs          | ~1.23   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 2.94±0.4μs                   | 3.50±0.2μs          | ~1.19   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 470±200ns                    | 551±100ns           | ~1.17   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 492±200ns                    | 561±200ns           | ~1.14   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 24.2±6μs                     | 22.0±5μs            | ~0.91   | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 2.24±0.9μs                   | 1.92±1μs            | ~0.86   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 4.12±0.3ms                   | 3.51±0ms            | ~0.85   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 561±100ns                    | 612±200ns           | 1.09    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 40.9±20μs                    | 43.8±20μs           | 1.07    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 754±0.6ns                    | 796±1ns             | 1.06    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 206±0.05ns                   | 215±0.5ns           | 1.04    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 7.17±1μs                     | 7.36±2μs            | 1.03    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 1.21±0μs                     | 1.24±0μs            | 1.02    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 1.33±0.4μs                   | 1.35±0.4μs          | 1.02    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 5.95±1μs                     | 6.06±0.7μs          | 1.02    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 39.5±0.02s                   | 39.8±0.03s          | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 66.1±0.2ms                   | 66.9±0.3ms          | 1.01    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 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                                 |
|          | 1.69±0.01ms                  | 1.70±0.01ms         | 1.00    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 2.42±0.4ms                   | 2.43±0.4ms          | 1.00    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 53.0±20μs                    | 51.5±20μs           | 0.97    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 31.6±0.04μs                  | 30.8±0.02μs         | 0.97    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 2.70±0.01ms                  | 2.59±0.01ms         | 0.96    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |

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

jvshields · 2024-10-28T14:25:53Z

docs/physics/tardisgamma/packetsampling.rst

+
+
+We use the `radioactivedecay <https://radioactivedecay.github.io>` python package to calculate the number of decays in each channel for each shell and at every timestep for each isotope.
+The composition is also updated after each timestep following :cite:`2024arXiv240308769G`.


Not sure if this citation is working correctly in the built docs.

jvshields · 2024-10-28T14:28:42Z

docs/physics/tardisgamma/packetsampling.rst

+===============
+
+
+In the simulation, we use spherical symmetry where the ejecta is divided into multiple spherical shells. To find the mass of each shell we multiply the mass fractions of each of the elements and isotopes with the density. We can set the timespace for the simulation


Is it worth mentioning spherical symmetry? I don't think spherical symmetry is specific to the gamma-ray part of the code. Perhaps just add a hyperlink to https://tardis-sn.github.io/tardis/physics/setup/model.html#Shell-Structure if you want to mention it.

I thought it was relevant to mention at least how the ejecta is broken down into shells because it goes into how we find the mass of each shell. I added the hyperlink but if it still doesn't make sense to mention it, I can remove that part.

jvshields · 2024-10-28T14:29:46Z

docs/physics/tardisgamma/packetsampling.rst

+
+
+In the simulation, we use spherical symmetry where the ejecta is divided into multiple spherical shells. To find the mass of each shell we multiply the mass fractions of each of the elements and isotopes with the density. We can set the timespace for the simulation
+to be between t\ :sub:`start`\  and t\ :sub:`end`\  using either a linear or a logarithmic scale.


I think this warrants more description. At least a short description of why you'd want to use one or the other timescales.

CePowers added 6 commits October 14, 2024 21:54

Created file for packet sampling

dab93af

Fixed some spacing.

913c9c7

Added packet sampling file to the index

132c177

Added Guttman et al 2024 to the bibliography

37d3edb

Added citation

3891667

Fixed typos

9e08aca

Changed citation type to article.

670646d

CePowers added 3 commits October 15, 2024 11:09

Changed citaion for Guttman et al 2024

a7dc2f8

Fixed citation to match updated reference.

c02ffc1

Added link to radioactive decay python package

644cf55

andrewfullard added the documentation label Oct 21, 2024

Knights-Templars marked this pull request as draft October 28, 2024 14:24

jvshields reviewed Oct 28, 2024

View reviewed changes

CePowers added 4 commits October 29, 2024 09:34

Merge branch 'master' into gamma_sampling

6a80b78

Added link to the documentation page about the model shell structure.

b6e41c7

Changed name of Guttman et al 2024 in bib file

46f7710

Changed citation to match .bib file

6c73d4d

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Gamma sampling documentation #2859

Gamma sampling documentation #2859

CePowers commented Oct 15, 2024

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jvshields Oct 28, 2024

jvshields Oct 28, 2024

CePowers Oct 29, 2024

jvshields Oct 28, 2024



		We use the `radioactivedecay <https://radioactivedecay.github.io>` python package to calculate the number of decays in each channel for each shell and at every timestep for each isotope.
		The composition is also updated after each timestep following :cite:`2024arXiv240308769G`.

		===============


		In the simulation, we use spherical symmetry where the ejecta is divided into multiple spherical shells. To find the mass of each shell we multiply the mass fractions of each of the elements and isotopes with the density. We can set the timespace for the simulation



		In the simulation, we use spherical symmetry where the ejecta is divided into multiple spherical shells. To find the mass of each shell we multiply the mass fractions of each of the elements and isotopes with the density. We can set the timespace for the simulation
		to be between t\ :sub:`start`\ and t\ :sub:`end`\ using either a linear or a logarithmic scale.

Gamma sampling documentation #2859

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CePowers commented Oct 15, 2024

📝 Description

📌 Resources

🚦 Testing

☑️ Checklist

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