refactor: refactor hpcReact to generalize behavior and introduce solid species and surface complexation.

[CusiniM]

No description provided.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (fd1a3a7) to head (115dbf1).
Report is 1 commits behind head on main.

Additional details and impacted files

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  Coverage   100.00%   100.00%           
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  Files           17        22    +5     
  Lines          713       748   +35     
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+ Hits           713       748   +35     

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[Copilot]

Pull Request Overview

This PR refactors the reaction system framework by replacing the legacy “bulkGeneric” namespace with the more descriptive “reactionsSystems” namespace and generalizes reaction behavior. It also introduces solid species support and surface complexation via additional surface area parameters, with corresponding changes to parameters and unit test utilities.

• Refactored file organization and namespaces from bulkGeneric to reactionsSystems.
• Added new API elements (e.g. NUM_SURFACE_REACTIONS, equilibriumConstant handling) and updated function signatures (e.g. timeStepTest now takes a surfaceArea array).
• Updated documentation comments and unit tests across geochemistry and mass actions modules to reflect these changes.

Reviewed Changes

Copilot reviewed 32 out of 34 changed files in this pull request and generated no comments.

File	Description
src/reactions/reactionsSystems/Parameters.hpp	Added NUM_SURFACE_REACTIONS, new equilibrium constant member (with a misspelling)
src/reactions/reactionsSystems/MixedEquilibriumKineticReactions.*	Updated function signatures to include a surfaceArea parameter; adjusted documentation
src/reactions/reactionsSystems/KineticReactions_impl.hpp	Introduced computeReactionRatesQuotient_impl that now incorporates surfaceArea multipliers
Various geochemistry and unit test files	Updated includes and namespaces to reflect the new structure and added surface area support

Comments suppressed due to low confidence (3)

src/reactions/reactionsSystems/Parameters.hpp:80

• The member variable 'm_equilibiriumConstant' is misspelled; consider renaming it to 'm_equilibriumConstant' for clarity and consistency.

    m_rateConstantReverse( rateConstantReverse ),

src/reactions/reactionsSystems/MixedEquilibriumKineticReactions.hpp:60

• Update the documentation comment for the 'surfaceArea' parameter to clearly state its purpose, expected units, and behavior in the context of surface complexation.

   * @param logPrimarySpeciesConcentrations Log of primary species concentrations

src/reactions/unitTestUtilities/mixedReactionsTestUtilities.hpp:26

• Ensure that all calling sites and unit tests are updated to supply the new 'surfaceArea' parameter and that its dimensionality matches PARAMS_DATA::numKineticReactions().

                   REAL_TYPE const (&surfaceArea)[PARAMS_DATA::numKineticReactions()],