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Macroatom restructure #2786

Merged
merged 89 commits into from
Aug 13, 2024
Merged

Macroatom restructure #2786

merged 89 commits into from
Aug 13, 2024

Commits on Aug 1, 2024

  1. created file for opacity solver

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  2. Added opacity states for the continuum and macroatom

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  3. Updated the opacity state and macroatom state to work with legacy plasma

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  4. Added numba initialize from opacity state, added methods to solve opa… 

    …city state with the solver
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  5. moved line2macro_level_upper to the macroatom state

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  6. renamed a macroatom variable, added solver to montecarlo solver

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  7. ran black

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  8. corrected an import

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  9. corrected an import

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  10. ran black

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  11. Added line_interaction_type to the to_numba function, should be reqor… 

    …ked in the future
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  12. fixed initialization of opacity state

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  13. Updated handling of continuum vs noncontinuum macroblock references

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  14. Fixed a typo

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  15. refactored the state objects to put them in the correct folders

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  16. another typo

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  17. added basic docstrings to the continuum state

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  18. Added docstrings to macroatom state

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  19. Updated docstrings onithe opacity_state file

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  20. Added docstrings to the solver

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  21. Updated Docstring Style

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Commits on Aug 2, 2024

  1. Merge branch 'master' of github.com:tardis-sn/tardis into opacity_sta… 

    …te_restructure
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  2. ran black

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  3. changed Opacity solver to take kwargs

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  4. ran black

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  5. Added class attributes to Opacity Solver

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  6. Changed names of the opacity state and numba equivalent

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  7. Merge branch 'master' into opacity_state_restructure

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  8. Added test for the opacity solver

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  9. added conftest to the opacities module

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  10. fixed up tests for the opacity_solver

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  11. ran black

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  12. Added new test for the numba opacity state

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  13. ran black, updated name of the test

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  14. Make a function to calculate markov chain indices

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  15. Extracted more functions

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Commits on Aug 6, 2024

  1. Merged with master

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Commits on Aug 7, 2024

  1. Moved more calculations over to functions (maybe this should be a sep… 

    …arate graph?) and implimented a basic MacroAtomSolver
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  2. Forgot an extra arg to the macroatom state

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  3. fixed up continuum vs non-continuum initialization and handling of co… 

    …ntinuum_interaction_species when no continuum_interaction
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  4. broke about the base transition probabilities properties into functions

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  5. Added the default transition probabilities to the solver

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  6. See previous commit, added a comment

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  7. Improved code flow for continuum vs non-continuum

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  8. See previous commit

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  9. See previous commit

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  10. removed non-continuum interaction species from non-continuum solver path

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  11. broke up the solver to have a common method for both continuum and no… 

    …n-continuum
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  12. Made a separate solver for the macroatom when working with the contin… 

    …uum:
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  13. cleaned up default solver a bit

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  14. ditto

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  15. ran black, added personal comments

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  16. first attempt to work basic macroatom solver into the opacity solver

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  17. Fixed calculate_deactivation_channel_probs missing argument 'B'

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  18. Fixed calculate_deactivation_channel_probs missing argument 'B'

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  19. Fixed accessign the macro_atom_data from the plasma

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  20. Fixed typo

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  21. Small fix to make tests pass, need to revisit later

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  22. Small fix to make tests pass, need to revisit later

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  23. Small fix to make tests pass, need to revisit later

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  24. Small fix to make tests pass, need to revisit later

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  25. Small fix to make tests pass, need to revisit later

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  26. Small fix to make tests pass, need to revisit later

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  27. Added switch to swap our the macroatom solver when using the continuum

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  28. Made a passthrough when continuum processes are enabled in case we do… 

    …n't want to worry about that part of the restructure
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Commits on Aug 8, 2024

  1. Removed switch to auto-build continuum macrostate using legacy mode

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  2. Fixed initialization in default macroatom solver

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  3. grab continuum interaction species from the legacy plasma

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  4. Added in the rest of the transition probability properties to the con… 

    …tinuum macro atom solver. Manually hard-coded and should be changed
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  5. Removed old method of doing this

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  6. switch back to using legacy solve for continuum in case we don't want… 

    … to work on that solver
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  7. Moved the MacroAtomContinuumSolver to a new file (deleted from this P… 

    …R) and restrctured code accordingly
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  8. moved 'calculate_' functions derived from transition_probabilities.py… 

    … to a new file (deleted in this PR, will be posted in another)
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  9. Moved MacroAtomState Solving out of the plasma state from_legacy_plasma

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  10. Added docstrings to MacroAtomSolver

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  11. Added docstrings to macro_atom base.py

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  12. Fixed up docstrings in macroatom_sovler

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  13. Added check to verify macroatom_state is None when line_interaction_t… 

    …ype is scatter
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  14. removed some comments, fixed up OpacitySolver initialization

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  15. Moved handling of the opacity solver over to the simulation base

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  16. Fixed typo

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  17. Grabbed the line interaction type from the right place (makes me thin… 

    …k we should just to a to_numba method here or not require it)
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Commits on Aug 9, 2024

  1. Changed 'non_markov_transition...' to 'transtiition...'

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  2. decoupled macro_atom from the opacity solver

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  3. Fixed typo

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  4. Updated the to_numba tests

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Commits on Aug 12, 2024

  1. UPdated docstrings/removed unused imports

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  2. Merge branch 'master' of github.com:tardis-sn/tardis into macroatom_r… 

    …estructure
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  3. Merge branch 'master' into macroatom_restructure

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