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Restructure/detailed balance foundation #2770

Merged
merged 147 commits into from
Oct 14, 2024
Merged

Restructure/detailed balance foundation #2770

merged 147 commits into from
Oct 14, 2024

Commits on Apr 30, 2024

  1. change numberdensity to input

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    wkerzendorf committed Apr 30, 2024
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Commits on May 4, 2024

  1. fixed number density

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    wkerzendorf committed May 4, 2024
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Commits on May 5, 2024

  1. some fixes

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    wkerzendorf committed May 5, 2024
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Commits on May 6, 2024

  1. removing density

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    wkerzendorf committed May 6, 2024
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  2. remove atomic and isotope mass

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    wkerzendorf committed May 6, 2024
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  3. add isotopic_number_density

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    wkerzendorf committed May 6, 2024
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  4. Merge remote-tracking branch 'upstream/master' into restructure/plasm… 

    …a_prepare
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    wkerzendorf committed May 6, 2024
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  5. add opacities package

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    wkerzendorf committed May 6, 2024
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Commits on May 7, 2024

  1. Update imports in property_collections.py, base.py, test_numba_interf… 

    …ace.py, transport_montecarlo_numba_interface.py, conftest.py, formal_integral.py, base.py, and macro_atom.py
    @wkerzendorf
    wkerzendorf committed May 7, 2024
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  2. Add calculate_transition_probabilities function to util.py in macro_a… 

    …tom package
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    wkerzendorf committed May 7, 2024
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Commits on May 9, 2024

  1. Add calculate_transition_probabilities function to util.py in macro_a… 

    …tom package
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    wkerzendorf committed May 9, 2024
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  2. Remove unused imports and update plasma properties

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    wkerzendorf committed May 9, 2024
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  3. add __init__ to macroatom

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    wkerzendorf committed May 9, 2024
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Commits on May 10, 2024

  1. blackify tardis

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    wkerzendorf committed May 10, 2024
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  2. blackified

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    wkerzendorf committed May 10, 2024
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  3. chore: Update imports and remove unused code

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    wkerzendorf committed May 10, 2024
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  4. chore: Add PlanckRadiationField and DilutePlanckRadiationField classes

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    wkerzendorf committed May 10, 2024
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  5. chore: Update imports and remove unused code

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    wkerzendorf committed May 10, 2024
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Commits on May 13, 2024

  1. removed density

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    wkerzendorf committed May 13, 2024
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Commits on May 20, 2024

  1. Merge remote-tracking branch 'upstream/master' into restructure/plasm… 

    …a_prepare
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    wkerzendorf committed May 20, 2024
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Commits on May 23, 2024

  1. Merge branch 'restructure/plasma_prepare' into restructure/plasma_opa… 

    …cities
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    wkerzendorf committed May 23, 2024
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Commits on Jun 6, 2024

  1. ruff output

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    wkerzendorf committed Jun 6, 2024
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  2. cleanup and adding object mode

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    wkerzendorf committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. starting to make radiation_field a thing

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  2. Merge remote-tracking branch 'upstream/master' into restructure/plasm… 

    …a_opacities
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    wkerzendorf committed Jun 7, 2024
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Commits on Jun 9, 2024

  1. switched over to old tau_sobolev calculation

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  2. renamed function to indicate numba use

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    wkerzendorf committed Jun 9, 2024
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  3. Merge branch 'restructure/plasma_opacities' into restructure/plasma_r… 

    …adiation_field
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    wkerzendorf committed Jun 9, 2024
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Commits on Jun 10, 2024

  1. address comments

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    wkerzendorf committed Jun 10, 2024
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  2. Merge branch 'restructure/plasma_opacities' into restructure/plasma_r… 

    …adiation_field
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    wkerzendorf committed Jun 10, 2024
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Commits on Jun 11, 2024

  1. added dilute planckian radiation field

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    wkerzendorf committed Jun 11, 2024
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Commits on Jun 13, 2024

  1. refactor: Convert species lists to proper format in assemble_plasma f… 

    …unction
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    wkerzendorf committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. moved radiation field into plasma. Resulting in some renames

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Commits on Jun 19, 2024

  1. Merge remote-tracking branch 'upstream/master' into restructure/plasm… 

    …a_radiation_field
    @wkerzendorf
    wkerzendorf committed Jun 19, 2024
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  2. some fixes

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    wkerzendorf committed Jun 19, 2024
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  3. black montecarlo

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    wkerzendorf committed Jun 19, 2024
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  4. Merge remote-tracking branch 'upstream/master' into restructure/plasm… 

    …a_opacities
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    wkerzendorf committed Jun 19, 2024
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  5. Merge branch 'restructure/plasma_opacities' into restructure/plasma_r… 

    …adiation_field
    @wkerzendorf
    wkerzendorf committed Jun 19, 2024
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  6. chore: Initialize atom data and simulation state in initialization.py

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    wkerzendorf committed Jun 19, 2024
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  7. updating the documentation

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    wkerzendorf committed Jun 19, 2024
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Commits on Jun 20, 2024

  1. feat: Add EstimatedRadiationFieldProperties class for Monte Carlo est… 

    …imators
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Commits on Jun 21, 2024

  1. trying to get rid of j_blues in plasma with MC restructure

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    wkerzendorf committed Jun 21, 2024
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Commits on Jun 22, 2024

  1. completely restructure j_blues. Estimators and all.

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    wkerzendorf committed Jun 22, 2024
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  2. cleanup for the restructure

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    wkerzendorf committed Jun 22, 2024
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Commits on Jul 23, 2024

  1. Merge remote-tracking branch 'upstream/master' into restructure/plasm… 

    …a_radiation_field
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  2. remove parse_input.py

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    wkerzendorf committed Jul 23, 2024
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  3. chore: Refactor radiation field configuration parsing and state creation 

    Refactor the `parse_radiation_field_configuration.py` module to improve code organization and readability. Update the import statements to reflect the changes in the module structure. Replace the deprecated `DiluteBlackBodyRadiationFieldState` class with the new `DilutePlanckianRadiationField` class from the `tardis.plasma.radiation_field` module. This change ensures consistency and compatibility with the latest codebase.

Also, update the `tardis/simulation/base.py` module to import the `DilutePlanckianRadiationField` class from the `tardis.plasma.radiation_field` module. This change ensures that the correct class is used for creating the radiation field in the simulation.
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  4. revert astropy_helpers

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    wkerzendorf committed Jul 23, 2024
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  5. remove astropy_helpers

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  6. removed test.txt

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    wkerzendorf committed Jul 23, 2024
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  7. blackified code

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    wkerzendorf committed Jul 23, 2024
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  8. Merge branch 'restructure/plasma_radiation_field' into restructure/si… 

    …mulation_from_config_cleanup
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  9. Merge branch 'restructure/simulation_from_config_cleanup' into restru… 

    …cture/base_estimator_cleanup
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  10. cleanup simulation from merges

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    wkerzendorf committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. fix

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    wkerzendorf committed Jul 24, 2024
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  2. remove unused Input

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    wkerzendorf committed Jul 24, 2024
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  3. added description

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  4. Merge branch 'restructure/plasma_radiation_field' into restructure/si… 

    …mulation_from_config_cleanup
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    wkerzendorf committed Jul 24, 2024
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  5. blackiefied codebase

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  6. Merge branch 'restructure/simulation_from_config_cleanup' into restru… 

    …cture/base_estimator_cleanup
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  7. cleanup of branch

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  8. blackify code

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  9. Merge branch 'restructure/plasma_radiation_field' into restructure/si… 

    …mulation_from_config_cleanup
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  10. chore: Refactor atom data parsing and simulation state initialization

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  11. Merge branch 'restructure/simulation_from_config_cleanup' into restru… 

    …cture/base_estimator_cleanup
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  12. restructure logger

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  13. Merge branch 'restructure/simulation_from_config_cleanup' into restru… 

    …cture/base_estimator_cleanup
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  14. working on continuum radfield properties

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    wkerzendorf committed Jul 24, 2024
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  15. Refactor continuum processes module structure

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    wkerzendorf committed Jul 24, 2024
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  16. Refactor opacities module structure

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Commits on Jul 25, 2024

  1. cleanup from restructure

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  2. Merge remote-tracking branch 'upstream/master' into restructure/base_… 

    …estimator_cleanup
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    wkerzendorf committed Jul 25, 2024
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  3. cleanup

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  4. clean up

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  5. more cleanup

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  6. Merge remote-tracking branch 'upstream/master' into restructure/base_… 

    …estimator_cleanup
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  7. cleanup standard_plasmas.py

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Commits on Jul 26, 2024

  1. working nlte ionizations

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  2. Merge remote-tracking branch 'upstream/master' into restructure/base_… 

    …estimator_cleanup
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    wkerzendorf committed Jul 26, 2024
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  3. start of assemble plasma cleanup

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  4. cleanup standard_plasmas.py

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  5. updated tests

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  6. some more cleanup

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  7. fix benchmarks

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  8. cleanup assembly

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    wkerzendorf committed Jul 26, 2024
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  9. cleanup assembly

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  10. Merge remote-tracking branch 'upstream/master' into restructure/base_… 

    …estimator_cleanup
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  11. working on the restructure

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  12. Merge remote-tracking branch 'upstream/master' into restructure/base_… 

    …estimator_cleanup
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    wkerzendorf committed Jul 26, 2024
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Commits on Jul 27, 2024

  1. slowly fixing the assembly module

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  2. blackify

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  3. reverse the import pygraphviz

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    wkerzendorf committed Jul 27, 2024
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  4. fix docstrings

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    wkerzendorf committed Jul 27, 2024
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  5. fixed all plasma

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    wkerzendorf committed Jul 27, 2024
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  6. slow fixes

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    wkerzendorf committed Jul 27, 2024
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  7. Refactor recomb_rate_coeff.py and test_continuum_property_solver.py

    @wkerzendorf
    wkerzendorf committed Jul 27, 2024
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  8. fixing assembly

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    wkerzendorf committed Jul 27, 2024
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  9. restructure the read in

    @wkerzendorf
    wkerzendorf committed Jul 27, 2024
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  10. fixup plasma assemble to be clean

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    wkerzendorf committed Jul 27, 2024
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  11. fix shell info widget

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    wkerzendorf committed Jul 27, 2024
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Commits on Jul 28, 2024

  1. fix the widgets

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    wkerzendorf committed Jul 28, 2024
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  2. fixing hopefully last bugs

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    wkerzendorf committed Jul 28, 2024
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  3. slowly fix up assembly

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    wkerzendorf committed Jul 28, 2024
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Commits on Jul 29, 2024

  1. working on getting the notebook running

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    wkerzendorf committed Jul 29, 2024
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  2. Refactor code to address comments

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    wkerzendorf committed Jul 29, 2024
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  3. Merge branch 'restructure/base_estimator_cleanup' into restructure/as… 

    …semble_plasma_cleanup
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    wkerzendorf committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. feat: Add RadiativeRatesSolver class for detailed balance rates calcu… 

    …lation
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    wkerzendorf committed Jul 30, 2024
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  2. feat: Add solve method to RadiativeRatesSolver class

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    wkerzendorf committed Jul 30, 2024
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  3. add rates ipynb

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    wkerzendorf committed Jul 30, 2024
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  4. remove abundance

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    wkerzendorf committed Jul 30, 2024
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  5. feat: Refactor code to improve readability and maintainability

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    wkerzendorf committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. first commit of the rates solver working

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    wkerzendorf committed Jul 31, 2024
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  2. fix up detailed balance foundation

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    wkerzendorf committed Jul 31, 2024
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  3. Merge remote-tracking branch 'upstream/master' into restructure/assem… 

    …ble_plasma_cleanup
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    wkerzendorf committed Jul 31, 2024
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  4. Merge branch 'restructure/assemble_plasma_cleanup' into restructure/d… 

    …etailed_balance_foundation
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    wkerzendorf committed Jul 31, 2024
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Commits on Aug 6, 2024

  1. further work on including the rates

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    wkerzendorf committed Aug 6, 2024
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  2. including the new rates structure

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    wkerzendorf committed Aug 6, 2024
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  3. getting the rates ready

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    wkerzendorf committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. feat: Refactor collision_rates module to improve code organization an… 

    …d readability
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    wkerzendorf committed Aug 7, 2024
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  2. further work on collisional strengths

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    wkerzendorf committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. further work on the collisional cross sections

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    wkerzendorf committed Aug 8, 2024
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  2. further work o nthe collisional rates

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    wkerzendorf committed Aug 8, 2024
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  3. feat: Add ThermalCollisionalRateSolver class for calculating thermal … 

    …collisional rates
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    wkerzendorf committed Aug 8, 2024
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Commits on Aug 12, 2024

  1. further fixes

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    wkerzendorf committed Aug 12, 2024
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  2. further testing

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    wkerzendorf committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. Merge remote-tracking branch 'upstream/master' into restructure/detai… 

    …led_balance_foundation
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    wkerzendorf committed Aug 13, 2024
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  2. refactor: Refactor collisional rates calculation in ThermalCollisiona… 

    …lRateSolver
    @wkerzendorf
    wkerzendorf committed Aug 13, 2024
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  3. finished collisional_rates

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    wkerzendorf committed Aug 13, 2024
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Commits on Sep 24, 2024

  1. Fixes collisional rates test so it can run (still fails)

    @andrewfullard
    andrewfullard committed Sep 24, 2024
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  2. Correct de-excitation rate calculation

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    andrewfullard committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. Merge branch 'master' into pr/wkerzendorf/2770

    @andrewfullard
    andrewfullard committed Sep 25, 2024
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Commits on Sep 30, 2024

  1. Merge branch 'master' into pr/wkerzendorf/2770

    @andrewfullard
    andrewfullard committed Sep 30, 2024
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  2. Add Chianti upsilon solver

    @andrewfullard
    andrewfullard committed Sep 30, 2024
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  3. Docstrings and better variable names

    @andrewfullard
    andrewfullard committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Fix rename error

    @andrewfullard
    andrewfullard committed Oct 1, 2024
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  2. Comparison notebook between Chianti, CMFGEN et al.

    @andrewfullard
    andrewfullard committed Oct 1, 2024
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  3. Add reference data and config, save notebook with plots

    @andrewfullard
    andrewfullard committed Oct 1, 2024
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  4. Chianti test beginnings

    @andrewfullard
    andrewfullard committed Oct 1, 2024
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Commits on Oct 7, 2024

  1. Working tests

    @andrewfullard
    andrewfullard committed Oct 7, 2024
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  2. Up to date comparison notebook

    @andrewfullard
    andrewfullard committed Oct 7, 2024
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  3. Remove irrelevant change

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    andrewfullard committed Oct 7, 2024
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  4. Corrected changes to the plasma solver factory

    @andrewfullard
    andrewfullard committed Oct 7, 2024
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  5. Merge branch 'master' into pr/wkerzendorf/2770

    @andrewfullard
    andrewfullard committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. Partially fixes tests

    @andrewfullard
    andrewfullard committed Oct 8, 2024
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  2. Slightly dirty fix for electron densities not refreshing properly

    @andrewfullard
    andrewfullard committed Oct 8, 2024
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Commits on Oct 9, 2024

  1. Fix NLTE tests by passing electron densities as an option input to th… 

    …e population solvers
    @andrewfullard
    andrewfullard committed Oct 9, 2024
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Commits on Oct 14, 2024

  1. Ruff formatting

    @andrewfullard
    andrewfullard committed Oct 14, 2024
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