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feat: Separate Mobile and Immobile Parts of Aggregate Species Concentrations #10

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@frankfeifan frankfeifan commented Jul 14, 2025

This PR aims to separate the mobile and immobile parts of each aggregate species in HPCReact. It is motivated by the fact that in some systems, the secondary species can be either mobile or immobile, so when doing reaction transport on the aggregate species concentrations, we should only transport the mobile part in the flux assembly while use the entire aggregate concentration in the accumulation assembly.

The main changes include:

  • A new flag array called m_mobileSecondarySpeciesFlag in both EquilibriumReactionsParameters and MixedReactionParameters to indicate the mobility of the secondary species: 1 if mobile and 0 if immobile.
  • A new function in massActions that separates the update for the total and mobile aggregate species concentration.
  • Call the new function in massActions in the mixed system update.

@frankfeifan frankfeifan self-assigned this Jul 14, 2025
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