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New docu for reactions
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‎doc/interface/reaction/index.rst‎

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Reaction models
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===============
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This section describes the configuration of reaction models for different phases in CADET unit operations.
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The corresponding group that contains the reaction models for each phase reads:
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- For bulk phase: ``/input/model/unit_XXX/reaction_bulk``
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- For solid phase: ``/input/model/unit_XXX/reaction_solid``
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- For particle phase: ``/input/model/unit_XXX/reaction_particle_YYY``
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- For cross phase: ``/input/model/unit_XXX/reaction_cross_phase_YYY``
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Where ``XXX`` denotes the index of the unit operation and ``YYY`` denotes the index of the particle type.
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Configuration Steps
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-------------------
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Before defining the reaction model parameters, it is necessary to specify how many reaction models are used in each phase.
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1. **Set the number of reactions**: This is done by setting ``/NREACT`` to the number of reaction models used in the phase.
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For example:
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- ``/input/model/unit_000/reaction_bulk/NREACT = 2`` indicates that 2 reaction models are used in the bulk phase
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- ``/input/model/unit_000/reaction_solid/NREACT = 1`` indicates that 1 reaction model is used in the solid phase
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2. **Define reaction model parameters**: After setting ``NREACT``, the parameters for each individual reaction model are specified.
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The group that contains the parameters of each reaction model reads:
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``/input/model/unit_XXX/reaction_phase/reaction_model_ZZZ``.
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Where ``XXX`` denotes the index of the unit operation, ``phase`` is either ``bulk``, ``solid``, ``particle_YYY``,
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or ``cross_phase_YYY``, and ``ZZZ`` denotes the index of the reaction model (starting from ``000``).
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**Example**: If ``NREACT = 2`` for the bulk phase, then the parameters would be found in:
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- ``/input/model/unit_000/reaction_bulk/reaction_model_000`` (first reaction model)
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- ``/input/model/unit_000/reaction_bulk/reaction_model_001`` (second reaction model)
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The reaction model parameters are specified in the following sections:
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**Single-Phase Reaction Models** (for bulk, solid, and particle phases):
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.. toctree::
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:maxdepth: 2
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mass_action_law
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michaelis_menten_kinetics
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**Cross-Phase Reaction Models** (only for cross-phase reactions):
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.. toctree::
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:maxdepth: 2
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mass_action_law_cross_phase
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.. note::
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Cross-phase reaction models can **only** be used in the cross-phase configuration (``reaction_cross_phase_YYY``).
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They cannot be used in bulk, solid, or particle phase configurations.
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For reactions within a single phase, use the standard reaction models listed above.
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Externally dependent reaction models
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------------------------------------
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Note that parameter sensitivities with respect to column radius, column length, particle core radius, and particle radius may be wrong when using externally dependent reaction models.
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This is caused by not taking into account the derivative of the external profile with respect to column position.
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.. _multiple-particle-types_reactions:
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Multiple particle types
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-----------------------
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The group that contains the parameters of a reaction model in unit operation with index ``XXX`` reads ``/input/model/unit_XXX/reaction_particle``.
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This is valid for models with a single particle type.
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If a model has multiple particle types, it may have a different reaction model in each type.
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The parameters are then placed in the group ``/input/model/unit_XXX/reaction_particle_YYY`` instead, where ``YYY`` denotes the index of the particle type.
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Note that, in any case, ``/input/model/unit_XXX/reaction_particle_000`` contains the parameters of the first (and possibly sole) particle type.
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This group also takes precedence over a possibly existing ``/input/model/unit_XXX/adsorption_particle`` group.

‎doc/interface/reaction/mass_action_law.rst‎

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Mass Action Law
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~~~~~~~~~~~~~~~
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**Group /input/model/unit_XXX/reaction - REACTION_MODEL = MASS_ACTION_LAW**
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**Group /input/model/unit_XXX/reaction_phase/reaction_model_YYY - REACTION_MODEL = MASS_ACTION_LAW**
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For information on model equations, refer to :ref:`mass_action_law_model`.
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``MAL_KFWD_BULK``
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``MAL_KFWD``
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Forward rate constants for bulk volume reactions (available for external functions)
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================ ========================= ===================================
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**Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}`
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================ ========================= ===================================
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``MAL_KBWD_BULK``
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``MAL_KBWD``
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Backward rate constants for bulk volume reactions (available for external functions)
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================ ========================= ===================================
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**Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}`
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================ ========================= ===================================
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``MAL_KFWD_LIQUID``
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Forward rate constants for particle liquid phase reactions (available for external functions)
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================ ========================= ===================================
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**Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}`
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================ ========================= ===================================
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``MAL_KBWD_LIQUID``
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Backward rate constants for particle liquid phase reactions (available for external functions)
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================ ========================= ===================================
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**Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}`
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================ ========================= ===================================
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``MAL_KFWD_SOLID``
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Forward rate constants for particle solid phase reactions (available for external functions)
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================ ========================= ===================================
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**Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}`
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================ ========================= ===================================
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``MAL_KBWD_SOLID``
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Backward rate constants for particle solid phase reactions (available for external functions)
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**Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}`
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================ ========================= ===================================
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``MAL_STOICHIOMETRY_BULK``
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``MAL_STOICHIOMETRY``
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Stoichiometric matrix of bulk volume reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage
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================ ========================================================
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`
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================ ========================================================
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``MAL_EXPONENTS_BULK_FWD``
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Forward exponent matrix of bulk volume reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_BULK}` by default)
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================ ========================================================
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`
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``MAL_EXPONENTS_BULK_BWD``
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``MAL_EXPONENTS_FWD``
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Backward exponent matrix of bulk volume reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_BULK}` by default)
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`
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``MAL_STOICHIOMETRY_LIQUID``
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Stoichiometric matrix of particle liquid phase reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage
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================ ========================================================
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`
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================ ========================================================
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``MAL_EXPONENTS_LIQUID_FWD``
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Forward exponent matrix of particle liquid phase reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_LIQUID}` by default)
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`
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``MAL_EXPONENTS_LIQUID_BWD``
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Backward exponent matrix of particle liquid phase reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_LIQUID}` by default)
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Forward exponent matrix of bulk volume reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_BULK}` by default)
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`
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``MAL_EXPONENTS_LIQUID_FWD_MODSOLID``
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Forward solid phase modifier exponent matrix of particle liquid phase reactions as :math:`\texttt{NTOTALBND} \times \texttt{NREACT}` matrix in row-major storage (optional, defaults to all 0)
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**Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}`
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================ ============================================================
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``MAL_EXPONENTS_LIQUID_BWD_MODSOLID``
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Backward solid phase modifier exponent matrix of particle liquid phase reactions as :math:`\texttt{NTOTALBND} \times \texttt{NREACT}` matrix in row-major storage (optional, defaults to all 0)
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**Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}`
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``MAL_STOICHIOMETRY_SOLID``
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Stoichiometric matrix of particle solid phase reactions as :math:`\texttt{NTOTALBND} \times \texttt{NREACT}` matrix in row-major storage
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**Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}`
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``MAL_EXPONENTS_SOLID_FWD``
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Forward exponent matrix of particle solid phase reactions as :math:`\texttt{NTOTALBND} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_SOLID}` by default)
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**Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}`
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``MAL_EXPONENTS_SOLID_BWD``
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Backward exponent matrix of particle solid phase reactions as :math:`\texttt{NTOTALBND} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_SOLID}` by default)
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**Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}`
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``MAL_EXPONENTS_SOLID_FWD_MODLIQUID``
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``MAL_EXPONENTS_BWD``
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Forward liquid phase modifier exponent matrix of particle solid phase reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, defaults to all 0)
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`
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``MAL_EXPONENTS_SOLID_BWD_MODLIQUID``
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Backward liquid phase modifier exponent matrix of particle solid phase reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, defaults to all 0)
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Backward exponent matrix of bulk volume reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY_BULK}` by default)
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**Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}`

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