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Small fixes and improvements / sparse coefficient matrices #1088

Merged
merged 28 commits into from
Sep 17, 2021

Commits on Sep 3, 2021

  1. [SCons] Update docstring

    'scons help' reports setting values in terms of 'yes' and 'no' rather than
    boolean flags that are otherwise used internally. This commit ensures that
    documentation for the newly added flag 'legacy-rate-constants' is
    consistent with this convention; accordingly, the setting is either enabled
    or disabled.
    ischoegl committed Sep 3, 2021
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  4. [Thermo] Fix compilation warning in MixtureFugacityTP.cpp

    Compilation with GNU g++ currently raises the following warning.
    
    warning: 'nSolnValues' may be used uninitialized in this function [-Wmaybe-uninitialized]
    
    The warning is resolved by providing an (invalid) initial value; the
    value is overwritten by a subsequent (pre-existing) if-else tree.
    ischoegl committed Sep 3, 2021
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  5. [Unittests] Resolve unused variable warning in test-surfSolver2

    Resolve GNU g++ warning:
    
    warning: unused variable 'p' [-Wunused-variable]
    ischoegl committed Sep 3, 2021
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Commits on Sep 5, 2021

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  2. [Kinetics] Update ChebyshevRate interface

    * Use consistent interface based on Array2D
    * Use column-major consistently in internal calculations
    * Deprecate Chebyshev::coeffs and Chebyshev::setup
    ischoegl committed Sep 5, 2021
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  3. [Kinetics] Remove unused functions from internal StoichManager.h classes

    Several internal methods defined for C1, C2, C3, and C_AnyN are unused;
    as there are no simple accessor methods defined in StoichManagerN,
    deprecation appears not to be required.
    ischoegl committed Sep 5, 2021
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  5. [Kinetics] Implement mechanism for Kinetics::finalizeSetup

    The 'Kinetics::finalizeSetup' method executes code after all reactions
    have been added. The new flag 'finalize' is added to 'Kinetics::addReaction'
    which determines whether 'finalizeSetup' is executed. While the default
    is 'true', imports within 'KineticsManager' use 'addReaction' with the
    flag set to 'false'.
    ischoegl committed Sep 5, 2021
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  6. [Kinetics] Merge irreversible and reversible product StoichManagerN

    as Kinetics::m_irrevProductManager is only used in conjunction with
    Kinetics::m_revProductManager, a new Kinetics::m_productManager provides
    for simpler code.
    ischoegl committed Sep 5, 2021
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  12. [Kinetics] Streamline Chebyshev interface

    Deprecate Tmin/Tmax, Pmin/Pmax as well as constructors to use
    std::pair<double,double> input/output
    ischoegl committed Sep 5, 2021
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  14. [Python] Make sparse API more efficient and deprecate *stoich methods

    Deprecate Kinetics.*_stoich_coeffs() method in favor of property:
    Behavior will change after Cantera 2.6; for new behavior, new properties
    Kinetics.*_stoich_coefficients are implemented
    ischoegl committed Sep 5, 2021
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  16. [Kinetics] Standardize Plog rates access

    This commit unifies parameter handling of Plog rate setters and
    getters to use std::multimap<...>.
    ischoegl committed Sep 5, 2021
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Commits on Sep 14, 2021

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Commits on Sep 15, 2021

  1. [Python] Switch sparse matrix output to CSC (from COO) format

    This change leverages the default internal storage format in Eigen (CSC)
    ischoegl committed Sep 15, 2021
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Commits on Sep 16, 2021

  1. Update formatting

    ischoegl committed Sep 16, 2021
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Commits on Sep 17, 2021

  1. [Kinetics] Improve nomenclature for final step of Kinetics setup

    Update nomenclature for previously introduced finalizeSetup method;
    new names are Kinetics::resizeReactions and StoichManagerN::resizeCoeffs
    ischoegl committed Sep 17, 2021
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