Macroatom restructure

[Rodot-]

📝 Restructures the MacroAtom to make it more independent from the plasma

Type: 🚀 feature

The properties of the macro atom used for montecarlo/opacity purposes should be decoupled from the plasma, this PR attempts to restructure the macro atom workflow.

🚦 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

[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (2df54e5) and the latest commit (537562c).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

| Change   | Before [2df54e5d] <master>   | After [537562c1]    |   Ratio | Benchmark (Parameter)                                                                                                |
|----------|------------------------------|---------------------|---------|----------------------------------------------------------------------------------------------------------------------|
| -        | 1.62±0.04μs                  | 1.21±0μs            |    0.75 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |

All benchmarks:

Benchmarks that have improved:

| Change   | Before [2df54e5d] <master>   | After [537562c1]    |   Ratio | Benchmark (Parameter)                                                                                                |
|----------|------------------------------|---------------------|---------|----------------------------------------------------------------------------------------------------------------------|
| -        | 1.62±0.04μs                  | 1.21±0μs            |    0.75 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |

Benchmarks that have stayed the same:

| Change   | Before [2df54e5d] <master>   | After [537562c1]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 501±100ns                    | 621±200ns           | ~1.24   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 44.1±20μs                    | 52.7±20μs           | ~1.20   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 45.7±20μs                    | 51.5±30μs           | ~1.13   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 3.05±0.6μs                   | 3.41±0.6μs          | ~1.12   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 561±200ns                    | 621±200ns           | ~1.11   | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 2.81±0.8μs                   | 3.02±0.6μs          | 1.07    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 6.37±2μs                     | 6.83±1μs            | 1.07    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 3.45±0ms                     | 3.65±0.04ms         | 1.06    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 18.8±4μs                     | 19.8±4μs            | 1.05    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 530±200ns                    | 551±200ns           | 1.04    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 1.44±0.4μs                   | 1.50±0.3μs          | 1.04    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 202±0.07ns                   | 206±0.1ns           | 1.02    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 2.51±0.4ms                   | 2.56±0.4ms          | 1.02    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 1.66±0ms                     | 1.68±0.01ms         | 1.01    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 2.07±0m                      | 2.07±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 63.2±0.2ms                   | 63.4±0.04ms         | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 39.3±0.05s                   | 38.9±0.02s          | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 1.06±0m                      | 1.04±0m             | 0.99    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 2.25±1μs                     | 2.23±2μs            | 0.99    | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 31.1±0.08μs                  | 30.4±0.02μs         | 0.98    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 7.97±2μs                     | 7.67±2μs            | 0.96    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 2.79±0.01ms                  | 2.60±0ms            | 0.93    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |
|          | 770±0.3ns                    | 719±0.5ns           | 0.93    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |

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

[andrewfullard]

Suggests we perhaps need some slice handling by the solver? Or something similar. Not directly relevant to this PR.

[andrewfullard]

I think this shows us that we don't need all the atomic data to be passed around all the time.

[Rodot-]

Definitely not, some kind of MacroAtomData structure could be useful

[wkerzendorf]

that is part of the opacity state - I presume?

[Rodot-]

what do you mean?