Ionization rates #2897
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Ionization rates #2897
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*beep* *bop* 16 W291 [*] Trailing whitespace
11 E999 [ ] SyntaxError: Expected ',', found ':'
11 F401 [ ] `tardis.plasma.equilibrium.rates.collision_strengths.UpsilonCMFGENSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
9 W293 [*] Blank line contains whitespace
6 G004 [ ] Logging statement uses f-string
5 E902 [ ] No such file or directory (os error 2)
4 RET505 [ ] Unnecessary `else` after `return` statement
3 I001 [*] Import block is un-sorted or un-formatted
2 PTH117 [ ] `os.path.isabs()` should be replaced by `Path.is_absolute()`
2 W292 [*] No newline at end of file
2 W605 [*] Invalid escape sequence: `\A`
1 ANN204 [ ] Missing return type annotation for special method `__getitem__`
1 RET506 [ ] Unnecessary `else` after `raise` statement
1 D202 [*] No blank lines allowed after function docstring (found 1)
1 D406 [*] Section name should end with a newline ("Returns")
1 D407 [*] Missing dashed underline after section ("Returns")
1 F541 [*] f-string without any placeholders
Complete output(might be large): .github/workflows/benchmarks.yml:3:4: E999 SyntaxError: Expected an expression
.github/workflows/benchmarks.yml:20:5: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:86:49: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:116:81: W291 [*] Trailing whitespace
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.github/workflows/benchmarks.yml:204:1: W293 [*] Blank line contains whitespace
.github/workflows/benchmarks.yml:223:22: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:224:170: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:226:84: W291 [*] Trailing whitespace
.github/workflows/benchmarks.yml:243:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:7:4: E999 SyntaxError: Expected an expression
.github/workflows/release.yml:94:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:97:1: W293 [*] Blank line contains whitespace
.github/workflows/release.yml:104:1: W293 [*] Blank line contains whitespace
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.github/workflows/release.yml:144:23: W292 [*] No newline at end of file
.github/workflows/tests.yml:7:4: E999 SyntaxError: Expected an expression
.mailmap:1:38: E999 SyntaxError: Expected an expression
.mailmap:290:39: W292 [*] No newline at end of file
CHANGELOG.md:4:15: E999 SyntaxError: Expected ',', found ':'
CITATION.cff:3:1: E999 SyntaxError: Invalid annotated assignment target
README.rst:1:1: E999 SyntaxError: Expected a statement
docs/contributing/development/benchmarks.rst:1:1: E999 SyntaxError: Expected a statement
docs/contributing/development/running_tests.rst:1:1: E999 SyntaxError: Expected a statement
docs/contributing/development/running_tests.rst:37:42: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:60:112: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:61:124: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:65:92: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:66:107: W291 [*] Trailing whitespace
docs/contributing/development/running_tests.rst:76:62: W291 [*] Trailing whitespace
docs/io/output/how_to_rpacket_tracking.ipynb:cell 12:1:62: W291 [*] Trailing whitespace
docs/physics/setup/model.ipynb:cell 2:2:1: I001 [*] Import block is un-sorted or un-formatted
docs/physics/setup/model.ipynb:cell 25:19:12: F541 [*] f-string without any placeholders
docs/quickstart.ipynb:cell 12:1:39: W291 [*] Trailing whitespace
docs/quickstart.ipynb:cell 12:5:35: W291 [*] Trailing whitespace
docs/quickstart.ipynb:cell 16:10:26: W605 [*] Invalid escape sequence: `\A`
docs/quickstart.ipynb:cell 16:11:40: W605 [*] Invalid escape sequence: `\A`
docs/resources/credits.rst:1:1: E999 SyntaxError: Expected a statement
docs/workflows/v_inner_solver_workflow.ipynb:1:1: E902 No such file or directory (os error 2)
tardis/io/configuration/config_reader.py:53:29: G004 Logging statement uses f-string
tardis/io/configuration/config_reader.py:117:9: RET505 Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:141:13: RET505 Unnecessary `else` after `return` statement
tardis/io/configuration/config_reader.py:218:29: G004 Logging statement uses f-string
tardis/io/configuration/schemas/montecarlo_definitions.yml:1:13: E999 SyntaxError: Expected an expression
tardis/io/model/parse_geometry_configuration.py:50:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/io/model/parse_radiation_field_configuration.py:118:13: G004 Logging statement uses f-string
tardis/model/base.py:340:12: PTH117 `os.path.isabs()` should be replaced by `Path.is_absolute()`
tardis/model/base.py:375:21: G004 Logging statement uses f-string
tardis/opacities/macro_atom/macroatom_state.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/opacities/opacity_state.py:210:9: ANN204 Missing return type annotation for special method `__getitem__`
tardis/opacities/opacity_state.py:216:9: D407 [*] Missing dashed underline after section ("Returns")
tardis/opacities/opacity_state.py:216:9: D406 [*] Section name should end with a newline ("Returns")
tardis/opacities/opacity_state.py:251:5: D202 [*] No blank lines allowed after function docstring (found 1)
tardis/opacities/tests/__init__.py:1:1: E902 No such file or directory (os error 2)
tardis/plasma/equilibrium/rates/__init__.py:2:5: F401 `tardis.plasma.equilibrium.rates.collision_strengths.UpsilonCMFGENSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:3:5: F401 `tardis.plasma.equilibrium.rates.collision_strengths.UpsilonRegemorterSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:6:5: F401 `tardis.plasma.equilibrium.rates.collisional_ionization_rates.CollisionalIonizationRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:9:5: F401 `tardis.plasma.equilibrium.rates.collisional_ionization_strengths.CollisionalIonizationSeaton` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:12:5: F401 `tardis.plasma.equilibrium.rates.collisional_rates.ThermalCollisionalRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:15:5: F401 `tardis.plasma.equilibrium.rates.photoionization_rates.AnalyticPhotoionizationRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:16:5: F401 `tardis.plasma.equilibrium.rates.photoionization_rates.EstimatedPhotoionizationRateSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:19:5: F401 `tardis.plasma.equilibrium.rates.photoionization_strengths.AnalyticPhotoionizationCoeffSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:20:5: F401 `tardis.plasma.equilibrium.rates.photoionization_strengths.EstimatedPhotoionizationCoeffSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:21:5: F401 `tardis.plasma.equilibrium.rates.photoionization_strengths.SpontaneousRecombinationCoeffSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/plasma/equilibrium/rates/__init__.py:24:5: F401 `tardis.plasma.equilibrium.rates.radiative_rates.RadiativeRatesSolver` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
tardis/radiation_field/validate_radiation_field.py:1:1: E902 No such file or directory (os error 2)
tardis/spectrum/formal_integral.py:1:1: I001 [*] Import block is un-sorted or un-formatted
tardis/spectrum/formal_integral.py:358:13: RET506 Unnecessary `else` after `raise` statement
tardis/spectrum/formal_integral.py:698:5: RET505 Unnecessary `else` after `return` statement
tardis/spectrum/formal_integral.py:734:5: RET505 Unnecessary `else` after `return` statement
tardis/workflows/simple_tardis_workflow.py:230:17: G004 Logging statement uses f-string
tardis/workflows/simple_tardis_workflow.py:449:17: G004 Logging statement uses f-string
tardis/workflows/util.py:1:1: E902 No such file or directory (os error 2)
tardis/workflows/v_inner_solver.py:1:1: E902 No such file or directory (os error 2)
Found 77 errors.
[*] 36 fixable with the `--fix` option.
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2897 +/- ##
==========================================
- Coverage 70.39% 69.17% -1.22%
==========================================
Files 221 228 +7
Lines 16147 16427 +280
==========================================
- Hits 11366 11363 -3
- Misses 4781 5064 +283 ☔ View full report in Codecov by Sentry. |
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Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
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*beep* *bop* Hi, human. The Click here to see your results. |
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*beep* *bop* Significantly changed benchmarks: All benchmarks: Benchmarks that have stayed the same:
| Change | Before [5e2d0bb3] <master> | After [705c2baa] | Ratio | Benchmark (Parameter) |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
| | 22.1±5μs | 30.0±8μs | ~1.36 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
| | 551±200ns | 631±100ns | ~1.15 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation |
| | 41.5±30μs | 47.3±30μs | ~1.14 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission |
| | 3.09±0.3μs | 3.41±0.2μs | ~1.10 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell |
| | 6.55±0.9μs | 5.64±1μs | ~0.86 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket |
| | 2.68±0ms | 2.88±0.03ms | 1.07 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter') |
| | 2.28±1μs | 2.45±2μs | 1.07 | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators |
| | 39.0±0.1s | 40.6±0.01s | 1.04 | run_tardis.BenchmarkRunTardis.time_run_tardis |
| | 48.2±30μs | 50.3±60μs | 1.04 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter |
| | 3.98±0.05ms | 4.11±0.01ms | 1.03 | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom') |
| | 1.21±0μs | 1.22±0μs | 1.01 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary |
| | 1.06±0m | 1.05±0m | 0.99 | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking |
| | 2.11±0.01m | 2.09±0m | 0.99 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions |
| | 206±0.4ns | 204±0.03ns | 0.99 | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body |
| | 3.27±0.01μs | 3.25±0.5μs | 0.99 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket |
| | 7.36±2μs | 7.27±2μs | 0.99 | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley |
| | 40.5±0.03μs | 39.7±0.1μs | 0.98 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list |
| | 65.9±0.2ms | 64.6±0.3ms | 0.98 | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe |
| | 762±1ns | 737±0.8ns | 0.97 | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter |
| | 1.78±0.01ms | 1.72±0.01ms | 0.97 | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop |
| | 561±100ns | 531±200ns | 0.95 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation |
| | 2.84±0.4ms | 2.69±0.5ms | 0.95 | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop |
| | 601±200ns | 561±100ns | 0.93 | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation |
| | 1.69±0.6μs | 1.57±0.3μs | 0.93 | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line |
If you want to see the graph of the results, you can check it here |
jvshields
reviewed
Jan 22, 2025
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Line #21. home = str(Path('~').expanduser())
I assume this notebook won't be be part of the final PR because of these paths? I do think it would be nice to include a notebook with very similar content to this just demonstrating how somebody would build their own level populations the way you do here.
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I'm planning to keep it around for now as a first-pass of this kind of documentation. I don't want it only on my local copy.
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Line #1. spontaneous_recombination_rate_old = pd.read_csv("spontaneous_recomb.csv", index_col=[0, 1, 2])
Pretty sure I understand what this is coming from, but for the sake of reviewing this PR can you mention the differences between how it was being calculated before and now? Is it just the workflow prescription? At some point I was under the impression this is new calculations that we weren't doing before, so I'm not sure how we had recombination rates calculated with previous code.
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Added a comment on this. The previous data were recovered from a combination of the old plasma and the way Jack set up his continuum properties solver.
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I like this PR a lot and don't have comments for the code. Well documented generally and does a good job linking back to the reference equations. I have some questions about the notebook but am happy to approve this when you need the approval. |
jvshields
approved these changes
Jan 22, 2025
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📝 Description
Type: 🚀
featurePhoto- and collisional ionization rates in the new setup.
📌 Resources
Examples, notebooks, and links to useful references.
🚦 Testing
How did you test these changes?
☑️ Checklist
build_docslabel