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Preamble to InterfaceKinetics refactoring #1184

Merged
merged 25 commits into from
Feb 6, 2022
Merged

Preamble to InterfaceKinetics refactoring #1184

merged 25 commits into from
Feb 6, 2022

Commits on Feb 4, 2022

  1. [SCons] Add option to disable legacy reactions

    @ischoegl
    ischoegl committed Feb 4, 2022
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  2. [CI] Add runner probing 'no_legacy_reactions' option

    @ischoegl
    ischoegl committed Feb 4, 2022
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  3. [Kinetics] Fix compilation errors with 'no_legacy_reactions'=y

    @ischoegl
    ischoegl committed Feb 4, 2022
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  4. [Kinetics] Make ArrheniusBase independent from ReactionRate

    @ischoegl
    ischoegl committed Feb 4, 2022
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  5. [Kinetics] (Re)-implement updateFromStruct 

    Co-authored-by: Ray Speth <[email protected]>
    @ischoegl @speth
    ischoegl and speth committed Feb 4, 2022
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  6. [Kinetics] Rename MultiBulkRate to MultiRate

    @ischoegl
    ischoegl committed Feb 4, 2022
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  7. [Kinetics] Add ReactionRate::setContext

    @ischoegl
    ischoegl committed Feb 4, 2022
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  8. [Python] Consolidate constructors and properties in reaction.pyx

    @ischoegl
    ischoegl committed Feb 4, 2022
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  9. Remove remmants of BlowersMasel2

    @ischoegl
    ischoegl committed Feb 4, 2022
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  10. Use ArrheniusBase for low and high FalloffRate rates

    @ischoegl
    ischoegl committed Feb 4, 2022
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  11. Mark ArrheniusBase as the successor of Arrhenius(2)

    @ischoegl
    ischoegl committed Feb 4, 2022
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  12. Streamline nomenclature for activation_energy (Blowers-Masel) 

    The recently introduced Blowers-Masel rate parameterization introduces
alternative definitions of activationEnergy (C++) and activation_energy
(Python). Renaming the alternative definitions with a prefix 'effective'
allows for more efficient inheritance structures.
    @ischoegl
    ischoegl committed Feb 4, 2022
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  13. [Kinetics] Consolidate getRateParameters versions

    @ischoegl
    ischoegl committed Feb 4, 2022
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  14. [Kinetics] Isolate serialization of legacy rates

    @ischoegl
    ischoegl committed Feb 4, 2022
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  15. Switch PlogRate to use ArrheniusBase and limit use of 'Arrhenius'

    @ischoegl
    ischoegl committed Feb 4, 2022
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  16. Mark remaining legacy objects with '2' suffix

    @ischoegl
    ischoegl committed Feb 4, 2022
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  17. [Kinetics] Add deprecation messages to legacy files

    @ischoegl
    ischoegl committed Feb 4, 2022
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  18. Remove suffix '3' from ChebyshevRate(3) 

    ChebyshevRate3 was introduced to avoid a conflict with the pre-existing
class 'ChebyshevRate'. Since its introduction, the conflict was removed.
This commit restores the original name to this class.
    @ischoegl
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  19. [Kinetics] Calculate Blowers-Masel deltaH internally

    @ischoegl
    ischoegl committed Feb 4, 2022
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  20. [Kinetics] Re-introduce updateFromStruct instances 

    Co-authored-by: Ray Speth <[email protected]>
    @ischoegl @speth
    ischoegl and speth committed Feb 4, 2022
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  21. [Kinetics] Remove remaining 'bulk' references and add todo comments

    @ischoegl
    ischoegl committed Feb 4, 2022
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Commits on Feb 5, 2022

  1. Various code and docstring improvements

    @ischoegl
    ischoegl committed Feb 5, 2022
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  2. Add ArrheniusTypeRate to Sphinx documentation

    @ischoegl
    ischoegl committed Feb 5, 2022
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Commits on Feb 6, 2022

  1. Fix typo in 'SConstruct'

    @ischoegl
    ischoegl committed Feb 6, 2022
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  2. Minor updates 

    - Add todo item for deprecation of Arrhenius2 constructor
- Add missing override declarations in BlowersMaselRate
    @ischoegl
    ischoegl committed Feb 6, 2022
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