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feature/rapid equilibrium reactions #324

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AntoniaBerger
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@AntoniaBerger AntoniaBerger commented Nov 18, 2024

Fixes #20.
This PR will add the feature to set reactions in a rapid equilibrium.

Workflow:

  • Add a function that calculates the mass matrix with respect to conserved moieties.
  • Think about whether we need a new class or if we should implement rapid equilibrium for each reaction model.
  • Link the residual with the conserved moieties mass matrix.
  • How to handle different phases
  • Add error messages.
    • How many reactions are in rapid equilibrium?
    • What's the dimensionality of the stoichiometric matrix?
  • Run tests and make sure my changes don't break existing functionality.
  • Add test, that ensures the functionality of the new feature.
  • Update the documentation.

More information about the algorithm are available under the forum post about reactions in rapid equilibrium

@jbreue16
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if you write the keyword to close the issue right in front of the corresponding issue, it will automatically be closed when the PR is merged. I.e. writing "fixes" instead of "resolves therefore" in the PR description .. maybe "resolves" also works

@AntoniaBerger AntoniaBerger changed the title Feature/rapid equilibrium reactions feature/rapid equilibrium reactions Nov 19, 2024
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Implement reactions in quasi-equilibrium
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