diff --git a/doc/interface/reaction/index.rst b/doc/interface/reaction/index.rst index a1b6e14a7..e5f3addea 100644 --- a/doc/interface/reaction/index.rst +++ b/doc/interface/reaction/index.rst @@ -3,12 +3,65 @@ Reaction models =============== +Reactions can take place on different phases in the model. The interface specification depends on the phase where and between the reaction takes place. + +A reaction can be located in: + +- **Column**: The reaction group is defined under the corresponding transport phase i.e. ``unit_XXX/liquid_reaction_YYY``. +- **Particle**: The reaction group is defined under the corresponding particle phase i.e. ``particle_type_XXX/liquid_reaction_YYY`` or ``particle_type_XXX/solid_reaction_YYY``. + +Furthermore, we differ between reactions which take place in either a single phase or between two phases. + +Single Phase Reactions +---------------- +Single phase reactions take place either in the liquid phase, the solid phase. + +The number of reaction models is specified at the unit or particle level using the following parameters: + + - ``NREAC_LIQUID`` for liquid phase reactions i.e. ``unit_XXX/NREAC_LIQUID`` or ``particle_type_XXX/NREAC_LIQUID``., + - ``NREAC_SOLID`` for solid phase reactions i.e. ``unit_XXX/NREAC_SOLID`` or ``particle_type_XXX/NREAC_SOLID``. + +The input group for parameter of single reactions is given by ``phase_reaction_YYY`` where ``phase`` is one of ``liquid`` or ``solid`` and ``YYY`` is a 0-based index for the reaction group. + +**Single-Phase Reaction Models**: + .. toctree:: :maxdepth: 2 mass_action_law michaelis_menten_kinetics + +Cross Phase Reactions +--------------------- +Cross phase reactions take place between a liquid phase and a solid phase. + +To specify the number of reaction models, use the parameter at the column or particle level: + - ``NREAC_CROSS_PHASE`` for cross-phase reactions i.e. ``unit_XXX/NREAC_CROSS_PHASE`` or ``particle_type_XXX/NREAC_CROSS_PHASE``. + +The input group for cross-phase reactions is given by ``cross_phase_reaction_YYY`` where ``YYY`` is a 0-based index for the reaction group. + +**Cross-Phase Reaction Models**: + +.. toctree:: + :maxdepth: 1 + + mass_action_law_cross_phase + +.. note:: + - Cross-phase reaction models can **only** be used in the cross-phase formulation + - For the LRM model, cross-phase reactions are not supported in the particle phase. + +Step by Step Guide to Define Reactions +-------------------------------------- + +1. Choose the appropriate reaction model based on the kinetics of your system (e.g., Mass Action Law, Michaelis-Menten). +2. Choose a phase for your reaction (liquid, solid or cross phase) and define the input group accordingly (i.e., ``liquid_reaction_000, solid_reaction_000, cross_phase_reaction_000``). +3. Choose how many reaction model types you want to define for the selected phase and set up the corresponding parameter in the configuration file (e.g., ``NREAC_LIQUID``, ``NREAC_SOLID``, ``NREAC_CROSS_PHASE``). + **Note** here that the input group depends on whether the reaction is defined in a particle phase or not. +4. Define the reaction parameters according to the chosen model's specifications. Refer to the specific reaction model documentation for details on required parameters. + + Externally dependent reaction models ------------------------------------ @@ -30,17 +83,3 @@ However, if only one index is passed in ``EXTFUN``, this external source is used 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. This is caused by not taking into account the derivative of the external profile with respect to column position. - - -.. _multiple-particle-types_reactions: - -Multiple particle types ------------------------ - -The group that contains the parameters of a reaction model in unit operation with index ``XXX`` reads ``/input/model/unit_XXX/reaction_particle``. -This is valid for models with a single particle type. -If a model has multiple particle types, it may have a different reaction model in each type. -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. - -Note that, in any case, ``/input/model/unit_XXX/reaction_particle_000`` contains the parameters of the first (and possibly sole) particle type. -This group also takes precedence over a possibly existing ``/input/model/unit_XXX/adsorption_particle`` group. diff --git a/doc/interface/reaction/mass_action_law.rst b/doc/interface/reaction/mass_action_law.rst index 8951a9e28..c422ead45 100644 --- a/doc/interface/reaction/mass_action_law.rst +++ b/doc/interface/reaction/mass_action_law.rst @@ -3,158 +3,85 @@ Mass Action Law ~~~~~~~~~~~~~~~ -**Group /input/model/unit_XXX/reaction - REACTION_MODEL = MASS_ACTION_LAW** +**Group /input/model/unit_XXX(/particle_type_YYY)/phase_reaction_ZZZ/ - TYPE = MASS_ACTION_LAW** For information on model equations, refer to :ref:`mass_action_law_model`. -``MAL_KFWD_BULK`` +Notes +----- - Forward rate constants for bulk volume reactions (available for external functions) - - ================ ========================= =================================== - **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` - ================ ========================= =================================== - -``MAL_KBWD_BULK`` +- ``reaction_phase_ZZZ`` refers to one of the phase-specific raction groups listed in :ref:`FFReaction`, e.g., ``reaction_bulk_ZZZ``, ``reaction_solid_ZZZ``, or ``reaction_particle_ZZZ`` (for particle type ``YYY``). +- Some dimensions below depend on the hosting phase of this model instance: + - Bulk phase or particle liquid phase: ``NVAR = NCOMP`` + - Particle solid phase: ``NVAR = NTOTALBOUND`` (total number of bound states across all components) - Backward rate constants for bulk volume reactions (available for external functions) - - ================ ========================= =================================== - **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` - ================ ========================= =================================== - -``MAL_KFWD_LIQUID`` +``MAL_KFWD`` - Forward rate constants for particle liquid phase reactions (available for external functions) + Forward rate constants for reactions in this phase (available for external functions) ================ ========================= =================================== **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` ================ ========================= =================================== -``MAL_KBWD_LIQUID`` +``MAL_KBWD`` - Backward rate constants for particle liquid phase reactions (available for external functions) + Backward rate constants for reactions in this phase (available for external functions) ================ ========================= =================================== **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` ================ ========================= =================================== - -``MAL_KFWD_SOLID`` - Forward rate constants for particle solid phase reactions (available for external functions) - - ================ ========================= =================================== - **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` - ================ ========================= =================================== - -``MAL_KBWD_SOLID`` +``MAL_STOICHIOMETRY`` - Backward rate constants for particle solid phase reactions (available for external functions) - - ================ ========================= =================================== - **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` - ================ ========================= =================================== - -``MAL_STOICHIOMETRY_BULK`` - - Stoichiometric matrix of bulk volume reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage + Stoichiometric matrix as :math:`\texttt{NVAR} \times \texttt{NREACT}` matrix in row-major storage (phase-dependent ``NVAR``, see Notes) ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + **Type:** double **Length:** :math:`\texttt{NVAR} \cdot \texttt{NREACT}` ================ ======================================================== - -``MAL_EXPONENTS_BULK_FWD`` - 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) - - ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` - ================ ======================================================== - -``MAL_EXPONENTS_BULK_BWD`` +``MAL_EXPONENTS_FWD`` - 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) + Forward exponent matrix as :math:`\texttt{NVAR} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY}` by default) ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + **Type:** double **Length:** :math:`\texttt{NVAR} \cdot \texttt{NREACT}` ================ ======================================================== - -``MAL_STOICHIOMETRY_LIQUID`` - Stoichiometric matrix of particle liquid phase reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage - - ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` - ================ ======================================================== - -``MAL_EXPONENTS_LIQUID_FWD`` +``MAL_EXPONENTS_BWD`` - 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) + Backward exponent matrix as :math:`\texttt{NVAR} \times \texttt{NREACT}` matrix in row-major storage (optional, calculated from :math:`\texttt{MAL_STOICHIOMETRY}` by default) ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + **Type:** double **Length:** :math:`\texttt{NVAR} \cdot \texttt{NREACT}` ================ ======================================================== - -``MAL_EXPONENTS_LIQUID_BWD`` - 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) - - ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` - ================ ======================================================== - -``MAL_EXPONENTS_LIQUID_FWD_MODSOLID`` +CADET Python Interface Example +------------------------------ +This example shows the configuration of one mass-action-law reaction system. +The system has two components A and B, where A reactions to B. +In addition to that the model includes: +- A forward reaction rate constant of 1.0 +- A backward reaction rate constant of 1.0 - 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) - - ================ ============================================================ - **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` - ================ ============================================================ - -``MAL_EXPONENTS_LIQUID_BWD_MODSOLID`` +.. code-block:: - 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) - - ================ ============================================================ - **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` - ================ ============================================================ - -``MAL_STOICHIOMETRY_SOLID`` +# Reaction in a bulk liquid phase:: - Stoichiometric matrix of particle solid phase reactions as :math:`\texttt{NTOTALBND} \times \texttt{NREACT}` matrix in row-major storage - - ================ ============================================================ - **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` - ================ ============================================================ - -``MAL_EXPONENTS_SOLID_FWD`` + input.model.unit_000.NREAC_LIQUID = 1 + input.model.unit_000.reaction_liquid_000.type = MASS_ACTION_LAW + input.model.unit_000.reaction_liquid_000.MAL_KFWD = [1.0] + input.model.unit_000.reaction_liquid_000.MAL_KBWD = [1.0] + input.model.unit_000.reaction_liquid_000.MAL_STOICHIOMETRY = [-1.0, 1.0] # A -> B - 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) - - ================ ============================================================ - **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` - ================ ============================================================ - -``MAL_EXPONENTS_SOLID_BWD`` +# Reaction in a particle liquid phase:: - 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) - - ================ ============================================================ - **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` - ================ ============================================================ - -``MAL_EXPONENTS_SOLID_FWD_MODLIQUID`` + input.model.unit_000.particle_type_000.NREAC_PORE = 1 + input.model.unit_000.particle_type_000.reaction_liquid_000.type = MASS_ACTION_LAW + input.model.unit_000.particle_type_000.reaction_liquid_000.MAL_KFWD = [1.0] + input.model.unit_000.particle_type_000.reaction_liquid_000.MAL_KBWD = [1.0] + input.model.unit_000.particle_type_000.reaction_liquid_000.MAL_STOICHIOMETRY = [-1.0, 1.0] # A -> B - 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) - - ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` - ================ ======================================================== - -``MAL_EXPONENTS_SOLID_BWD_MODLIQUID`` +See also +-------- - 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) - - ================ ======================================================== - **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` - ================ ======================================================== +- Cross-phase variant: :ref:`mass_action_law_cross_phase_config` (supports liquid/solid modifiers and bulk coupling) diff --git a/doc/interface/reaction/mass_action_law_cross_phase.rst b/doc/interface/reaction/mass_action_law_cross_phase.rst new file mode 100644 index 000000000..07d02c027 --- /dev/null +++ b/doc/interface/reaction/mass_action_law_cross_phase.rst @@ -0,0 +1,149 @@ +.. _mass_action_law_cross_phase_config: + +Mass Action Law Cross Phase +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +**Group /input/model/unit_XXX(/particle_type_YYY)/phase_reaction_ZZZ/ - REACTION_MODEL = MASS_ACTION_LAW_CROSS_PHASE** + +For information on model equations, refer to :ref:`mass_action_law_model_cross_phase`. + + +``MAL_KFWD_LIQUID`` + + Forward rate constants for particle liquid phase reactions (available for external functions) + + ================ ========================= =================================== + **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` + ================ ========================= =================================== + +``MAL_KBWD_LIQUID`` + + Backward rate constants for particle liquid phase reactions (available for external functions) + + ================ ========================= =================================== + **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` + ================ ========================= =================================== + +``MAL_KFWD_SOLID`` + + Forward rate constants for particle solid phase reactions (available for external functions) + + ================ ========================= =================================== + **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` + ================ ========================= =================================== + +``MAL_KBWD_SOLID`` + + Backward rate constants for particle solid phase reactions (available for external functions) + + ================ ========================= =================================== + **Type:** double **Range:** :math:`\geq 0` **Length:** :math:`\texttt{NREACT}` + ================ ========================= =================================== + +``MAL_STOICHIOMETRY_LIQUID`` + + Stoichiometric matrix of particle liquid phase reactions as :math:`\texttt{NCOMP} \times \texttt{NREACT}` matrix in row-major storage + + ================ ======================================================== + **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + ================ ======================================================== + +``MAL_EXPONENTS_LIQUID_FWD`` + + 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) + + ================ ======================================================== + **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + ================ ======================================================== + +``MAL_EXPONENTS_LIQUID_BWD`` + + 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) + + ================ ======================================================== + **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + ================ ======================================================== + +``MAL_EXPONENTS_LIQUID_FWD_MODSOLID`` + + 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) + + ================ ============================================================ + **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` + ================ ============================================================ + +``MAL_EXPONENTS_LIQUID_BWD_MODSOLID`` + + 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) + + ================ ============================================================ + **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` + ================ ============================================================ + +``MAL_STOICHIOMETRY_SOLID`` + + Stoichiometric matrix of particle solid phase reactions as :math:`\texttt{NTOTALBND} \times \texttt{NREACT}` matrix in row-major storage + + ================ ============================================================ + **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` + ================ ============================================================ + +``MAL_EXPONENTS_SOLID_FWD`` + + 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) + + ================ ============================================================ + **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` + ================ ============================================================ + +``MAL_EXPONENTS_SOLID_BWD`` + + 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) + + ================ ============================================================ + **Type:** double **Length:** :math:`\texttt{NTOTALBND} \cdot \texttt{NREACT}` + ================ ============================================================ + +``MAL_EXPONENTS_SOLID_FWD_MODLIQUID`` + + 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) + + ================ ======================================================== + **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + ================ ======================================================== + +``MAL_EXPONENTS_SOLID_BWD_MODLIQUID`` + + 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) + + ================ ======================================================== + **Type:** double **Length:** :math:`\texttt{NCOMP} \cdot \texttt{NREACT}` + ================ ======================================================== + +Examples +-------- + +Cross-phase reaction that consumes one bulk and one liquid component and produces a solid state (one reaction):: + + input.model.unit_000.reaction_cross_phase_000.NREAC_CROSS_PHASE = 1 + input.model.unit_000.reaction_cross_phase_000.type = MASS_ACTION_LAW_CROSS_PHASE + input.model.unit_000.reaction_cross_phase_000.reaction_model_000.MAL_KFWD_LIQUID = [1.0] + input.model.unit_000.reaction_cross_phase_000.reaction_model_000.MAL_KFWD_SOLID = [1.0] + input.model.unit_000.reaction_cross_phase_000.reaction_model_000.MAL_STOICHIOMETRY_LIQUID = [... length NCOMP*1 ...] + input.model.unit_000.reaction_cross_phase_000.reaction_model_000.MAL_STOICHIOMETRY_SOLID = [... length NTOTALBND*1 ...] + +Cross-Phase reaction in a particle:: + + input.model.unit_000.particle_type_000.reaction_cross_phase_000.NREAC_CROSS_PHASE = 1 + input.model.unit_000.particle_type_000.reaction_cross_phase_000.type = MASS_ACTION_LAW_CROSS_PHASE + input.model.unit_000.particle_type_000.reaction_cross_phase_000.reaction_model_000.MAL_KFWD_LIQUID = [1.0] + input.model.unit_000.particle_type_000.reaction_cross_phase_000.reaction_model_000.MAL_KFWD_SOLID = [1.0] + input.model.unit_000.particle_type_000.reaction_cross_phase_000.reaction_model_000.MAL_STOICHIOMETRY_LIQUID = [... length NCOMP*1 ...] + input.model.unit_000.particle_type_000.reaction_cross_phase_000.reaction_model_000.MAL_STOICHIOMETRY_SOLID = [... length NTOTALBND*1 ...] + + + +See also +-------- + +- Single-phase variant: :ref:`mass_action_law_config` diff --git a/doc/interface/reaction/michaelis_menten_kinetics.rst b/doc/interface/reaction/michaelis_menten_kinetics.rst index 3c858fe67..8e1a86324 100644 --- a/doc/interface/reaction/michaelis_menten_kinetics.rst +++ b/doc/interface/reaction/michaelis_menten_kinetics.rst @@ -3,10 +3,19 @@ Michaelis Menten kinetics ~~~~~~~~~~~~~~~~~~~~~~~~~ -**Group /input/model/unit_XXX/reaction - REACTION_MODEL = MICHAELIS_MENTEN** +**Group /input/model/unit_XXX(/particle_type_YYY)/phase_reaction_ZZZ/ - TYPE = MICHAELIS_MENTEN** For information on model equations, refer to :ref:`michaelis_menten_kinetics_model`. +Notes +----- + +- ``reaction_phase_ZZZ`` refers to one of the phase-specific raction groups listed in :ref:`FFReaction`, e.g., ``reaction_bulk_ZZZ``, ``reaction_solid_ZZZ``, or ``reaction_particle_ZZZ`` (for particle type ``YYY``). +- Some dimensions below depend on the hosting phase of this model instance: + - Bulk phase or particle liquid phase: ``NVAR = NCOMP`` + - Particle solid phase: ``NVAR = NTOTALBOUND`` (total number of bound states across all components) + + ``MM_STOICHIOMETRY_BULK`` Stoichiometric matrix :math:`S`. @@ -18,7 +27,7 @@ For information on model equations, refer to :ref:`michaelis_menten_kinetics_mod **Unit:** None ================ ============================= ======================================================== - **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NCOMP}` + **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NVAR}` ================ ============================= ======================================================== ``MM_VMAX`` @@ -53,7 +62,7 @@ For information on model equations, refer to :ref:`michaelis_menten_kinetics_mod **Unit:** :math:`mol^{-1}~m^{-3}` ================ ============================= ============================================================================= - **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NCOMP} \cdot \texttt{NCOMP}` + **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NVAR} \cdot \texttt{NVAR}` ================ ============================= ============================================================================= ``MM_KI_UC`` @@ -65,12 +74,12 @@ For information on model equations, refer to :ref:`michaelis_menten_kinetics_mod **Unit:** :math:`mol^{-1}~m^{-3}` ================ ============================= ============================================================================= - **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NCOMP} \cdot \texttt{NCOMP}` + **Type:** double **Range:** :math:`\mathbb{R}` **Length:** :math:`\texttt{NREACT} \cdot \texttt{NVAR} \cdot \texttt{NVAR}` ================ ============================= ============================================================================= -Example configuration -^^^^^^^^^^^^^^^^^^^^^ -This example shows the configuration of one Michaelis-Menten reaction system in CADET-Python. +CADET Python Interface Example +------------------------------ +This example shows the configuration of one Michaelis-Menten reaction system in bulk liquid phase. The system has two components A and B, where A is the substrate and B is the product. In addition to that the model includes: @@ -81,15 +90,16 @@ In addition to that the model includes: .. code-block:: Python3 #Configure the reaction system - model.root.input.model.unit_001.reaction_model = 'MICHAELIS_MENTEN' + input.model.unit_000.NREAC_LIQUID = 1 + input.model.unit_000.reaction_liquid_000.type = 'MICHAELIS_MENTEN' # Km values 2D array [reaction][components] - model.root.input.model.unit_001.reaction_bulk.mm_km = [ + input.model.unit_000.reaction_liquid_000.mm_km = [ [KM_a, 0.0] # A is substrate ] # Competitive inhibition constants - 3D array [reaction][components][components] - model.root.input.model.unit_001.reaction_bulk.mm_ki_c = [ + input.model.unit_000.reaction_liquid_000.mm_ki_c = [ [ [0.0, KI_b_a], # Inhibition konstant for A (Product inhibtion B inhibits A) [0.0, 0.0], # Inhibition konstant for B (not active) @@ -97,7 +107,7 @@ In addition to that the model includes: ] # Uncompetitive inhibition constants - 3D array [reaction][components][components] - model.root.input.model.unit_001.reaction_bulk.mm_ki_uc = [ + input.model.unit_000.reaction_liquid_000.mm_ki_uc = [ [ [0.0, 0.0], # Inhibition konstant for A (not active) [0.0, 0.0], # Inhibition konstant for B (not active) @@ -105,10 +115,10 @@ In addition to that the model includes: ] # Vmax values 1D array [reaction] - model.root.input.model.unit_001.reaction_bulk.mm_vmax = [vmax] + input.model.unit_000.reaction_liquid_000.mm_vmax = [vmax] # Stoichiometry matrix 2D array [components][reaction] - model.root.input.model.unit_001.reaction_bulk.mm_stoichiometry_bulk = [ + input.model.unit_000.reaction_liquid_000.mm_stoichiometry = [ [-1], [1] # A -> B ] diff --git a/doc/modelling/reaction/index.rst b/doc/modelling/reaction/index.rst index 58b8991b8..805e275f9 100644 --- a/doc/modelling/reaction/index.rst +++ b/doc/modelling/reaction/index.rst @@ -4,13 +4,35 @@ Reaction models =============== -Reaction models describe the (net) fluxes :math:`f_{\mathrm{react}}` of a +Reaction models describe the (net) fluxes :math:`f_{\mathrm{react}}(c)` of a reaction mechanism. -CADET features multiple reaction types: + +In this kind of mechanism, the fluxes are typically defined as a function of the concentration of the components involved in the reaction and the reaction parameters. + +In CADET, reaction models are defined for each phase of a unit operation separately, i.e., for the liquid phase and solid phase. +For more information on the interface specification, see :ref:`FFReaction`. + +CADET features the following reaction model types: - :ref:`mass_action_law_model` - :ref:`michaelis_menten_kinetics_model` +It is possible to combine reaction models within the same phase. + +Cross phase reaction models +--------------------------- + +If a reaction is defined between a liquid phase and solid phases, the net fluxes of the reaction are defined +as a function of the concentrations in the respective phases and is called a cross phase reaction. + +CADET features the following cross phase reaction types: + + - :ref:`mass_action_law_model_cross_phase` + +Further details on the interface specification are provided in :ref:`the corresponding section `. + +Application examples +-------------------- Historically, a chromatography system is modeled as a reaction system without considering any transport phenomenon. We also introduce some reaction-based models that can be solved in CADET: diff --git a/doc/modelling/reaction/mass_action_law_model.rst b/doc/modelling/reaction/mass_action_law_model.rst new file mode 100644 index 000000000..27f018077 --- /dev/null +++ b/doc/modelling/reaction/mass_action_law_model.rst @@ -0,0 +1,80 @@ +.. _mass_action_law_model: + +Mass Action Law +--------------- + +The mass action law reaction model is suitable for most reactions. +Note that the concentrations are directly used for calculating the fluxes. +Hence, the model only holds for dilute solutions under the assumption of a well-stirred reaction vessel. +These assumptions can be weakened by passing to the generalized mass action law, which uses chemical activities instead of concentrations. + +The mass action law states that the speed of a reaction is proportional to the product of the concentrations of their reactants. + +The indices used in the equations have the following meaning: + +- :math:`i` is the component index, ranging from :math:`0` to :math:`N_{\mathrm{comp}}-1` +- :math:`j` is the reaction index, ranging from :math:`0` to :math:`N_{\mathrm{react}}-1` +- :math:`\ell` is the component index used in products and sums, ranging from :math:`0` to :math:`N_{\mathrm{comp}}-1` + +The net flux for component :math:`i` is given by + +.. math:: + + \begin{aligned} + f_{\mathrm{react},i}\left(c\right) &= \sum_{j=0}^{N_{\mathrm{react}}-1} s_{i,j} \varphi_j\left(c\right), \\ + \varphi_j(c) &= k_{\mathrm{fwd},j} \prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c_{\ell}\right)^{e_{\mathrm{fwd},\ell,j}} - k_{\mathrm{bwd},j} \prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c_{\ell}\right)^{e_{\mathrm{bwd},\ell,j}}, + \end{aligned} + +where :math:`S = (s_{i,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` is the stoichiometric matrix, :math:`\varphi_j(c)` is the net flux of reaction :math:`j`, and :math:`k_{\mathrm{fwd},j}` and :math:`k_{\mathrm{bwd},j}` are the rate constants. +The matrices :math:`E_{\mathrm{fwd}} = (e_{\mathrm{fwd},\ell,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` and :math:`E_{\mathrm{bwd}} = (e_{\mathrm{bwd},\ell,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` are usually derived by the order of the reaction, that is, + +.. math:: + :label: MRMassActionLawExpMatDefault + + \begin{aligned} + e_{\mathrm{fwd},\ell,j} &= \max(0, -s_{\ell,j}), \\ + e_{\mathrm{bwd},\ell,j} &= \max(0, s_{\ell,j}). + \end{aligned} + +However, these defaults can be changed by providing those matrices. + +This model applies to reactions occurring within a single phase (liquid, particle liquid, or solid phase) only. + +For reactions involving multiple phases, see :ref:`mass_action_law_model_cross_phase`. + + +Correlation of forward- and backward rate constants +--------------------------------------------------- + +Note that forward rate constant :math:`k_{\mathrm{fwd},i}` and backward +rate constant :math:`k_{\mathrm{bwd},i}` of reaction :math:`i` are +linearly correlated due to the form of the equilibrium constant +:math:`k_{\mathrm{eq},i}`: + +.. math:: + + \begin{aligned} + k_{\mathrm{fwd},i} = k_{\mathrm{eq},i} k_{\mathrm{bwd},i}. + \end{aligned} + +This correlation can potentially degrade performance of some optimization algorithms. +The parameters can be decoupled by reparameterization: + +.. math:: + + \begin{aligned} + r_{\mathrm{net},i} &= k_{\mathrm{fwd},i} f_{\mathrm{fwd},i} - k_{\mathrm{bwd},i} f_{\mathrm{bwd},i}\\ + &= k_{\mathrm{bwd},i} \left[ k_{\mathrm{eq},i} f_{\mathrm{fwd},i} - f_{\mathrm{bwd},i} \right] \\ + &= k_{\mathrm{fwd},i} \left[ f_{\mathrm{fwd},i} - \frac{1}{k_{\mathrm{eq},i}} f_{\mathrm{bwd},i} \right]. + \end{aligned} + +This can be achieved by a (nonlinear) parameter transform + +.. math:: + + \begin{aligned} + F\left( k_{\mathrm{eq},i}, k_{\mathrm{bwd},i} \right) &= \begin{pmatrix} k_{\mathrm{eq},i} k_{\mathrm{bwd},i} \\ k_{\mathrm{bwd},i} \end{pmatrix} \\ + \text{ with Jacobian } J_F\left( k_{\mathrm{eq},i}, k_{\mathrm{bwd},i} \right) &= \begin{pmatrix} k_{\mathrm{bwd},i} & k_{\mathrm{eq},i} \\ 0 & 1 \end{pmatrix}. + \end{aligned} + +For more information on model parameters required to define in CADET file format, see :ref:`_mass_action_law_config`. diff --git a/doc/modelling/reaction/mass_action_law.rst b/doc/modelling/reaction/mass_action_law_model_cross_phase.rst similarity index 58% rename from doc/modelling/reaction/mass_action_law.rst rename to doc/modelling/reaction/mass_action_law_model_cross_phase.rst index 5b21664bf..d4b921056 100644 --- a/doc/modelling/reaction/mass_action_law.rst +++ b/doc/modelling/reaction/mass_action_law_model_cross_phase.rst @@ -1,28 +1,38 @@ -.. _mass_action_law_model: +.. _mass_action_law_model_cross_phase: -Mass action law ---------------- +Mass Action Law Cross Phase +--------------------------- -The mass action law reaction model is suitable for most reactions. +The mass action law cross phase reaction model describes reactions that occur between different phases (liquid and solid phases). +This model extends the basic mass action law to handle interactions between phases, such as reactions between liquid phase components and bound states in the solid phase. Note that the concentrations are directly used for calculating the fluxes. Hence, the model only holds for dilute solutions under the assumption of a well-stirred reaction vessel. These assumptions can be weakened by passing to the generalized mass action law, which uses chemical activities instead of concentrations. The mass action law states that the speed of a reaction is proportional to the product of the concentrations of their reactants. -The net flux for component :math:`i` is given by +For single-phase reactions within a single phase only, see :ref:`mass_action_law_model`. -.. math:: +Cross-Phase Reactions +~~~~~~~~~~~~~~~~~~~~~ - \begin{aligned} - f_{\mathrm{react},i}^l\left(c^l\right) &= \sum_{j=0}^{N_{\mathrm{react}}-1} s_{i,j}^l \varphi^l_j\left(c^l\right), \\ - \varphi^l_j(c^l) &= k^l_{\mathrm{fwd},j} \prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^l_{\ell}\right)^{e^l_{\mathrm{fwd},\ell,j}} - k^l_{\mathrm{bwd},j} \prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^l_{\ell}\right)^{e^l_{\mathrm{bwd},\ell,j}}, - \end{aligned} +In situations where both liquid and solid phase are present (e.g., in a bead), reactions can occur between phases, where one phase may act as a modifier in the net flux equation of the other phase. + +In the following :math:`l` denotes the liquid phase and :math:`s` the solid phase. +Depending on the unit operation, the liquid phase can be considered as the bulk :math:`b` or particle :math:`p` phase. -where :math:`S^l = (s^l_{i,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` is the stoichiometric matrix, :math:`\varphi^l_j(c)` is the net flux of reaction :math:`j`, and :math:`k^l_{\mathrm{fwd},j}` and :math:`k^l_{\mathrm{bwd},j}` are the rate constants. -The matrices :math:`E^l_{\mathrm{fwd}} = (e^l_{\mathrm{fwd},\ell,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` and :math:`E^l_{\mathrm{bwd}} = (e^l_{\mathrm{bwd},\ell,j}) \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` are usually derived by the order of the reaction, that is, +The indices used in the equations have the following meaning: + +- :math:`j` is the reaction index, ranging from :math:`0` to :math:`N_{\mathrm{react}}-1` +- :math:`\ell` is the component index for liquid phase components, ranging from :math:`0` to :math:`N_{\mathrm{comp}}-1` +- :math:`m` is the bound state index for solid phase components, ranging from :math:`0` to :math:`\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1` + +Liquid Phase Reactions Modified by Solid Phase +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The exponent matrices are usually derived by the order of the reaction, that is, .. math:: - :label: MRMassActionLawExpMatDefault + :label: MRMassActionLawExpMatDefaultCrossPhase \begin{aligned} e^l_{\mathrm{fwd},\ell,j} &= \max(0, -s^l_{\ell,j}), \\ @@ -31,26 +41,28 @@ The matrices :math:`E^l_{\mathrm{fwd}} = (e^l_{\mathrm{fwd},\ell,j}) \in \mathbb However, these defaults can be changed by providing those matrices. -In situations where both liquid and solid phase are present (e.g., in a bead), the respective other phase may act as a modifier in the net flux equation. For example, consider reactions in the liquid phase of a particle given by .. math:: \begin{aligned} - f_{\mathrm{react},i}^p\left(c^p, c^s\right) &= \sum_{j=0}^{N_{\mathrm{react}}-1} s_{i,j}^p \varphi^p_j\left(c^p, c^s\right),\end{aligned} + f_{\mathrm{react},i}^l\left(c^l, c^s\right) &= \sum_{j=0}^{N_{\mathrm{react}}-1} s_{i,j}^l \varphi^l_j\left(c^l, c^s\right),\end{aligned} where .. math:: \begin{split} - \varphi^p_j(c^p, c^s) = k^p_{\mathrm{fwd},j} &\left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^p_{\ell}\right)^{e^p_{\mathrm{fwd},\ell,j}}\right] \left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{ps}_{\mathrm{fwd},m,j}}\right] \\ - - k^p_{\mathrm{bwd},j} &\left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^p_{\ell}\right)^{e^p_{\mathrm{bwd},\ell,j}}\right] \left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{ps}_{\mathrm{bwd},m,j}}\right]. + \varphi^l_j(c^l, c^s) = k^l_{\mathrm{fwd},j} &\left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^l_{\ell}\right)^{e^l_{\mathrm{fwd},\ell,j}}\right] \left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{ls}_{\mathrm{fwd},m,j}}\right] \\ + - k^l_{\mathrm{bwd},j} &\left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^l_{\ell}\right)^{e^l_{\mathrm{bwd},\ell,j}}\right] \left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{ls}_{\mathrm{bwd},m,j}}\right]. \end{split} The forward and backward rates of the liquid phase particle reactions can be modified by a power of every bound state in the solid phase of the particle. -The exponents of these powers are given by the matrices :math:`E^{ps}_{\mathrm{fwd}} = (e^{ps}_{\mathrm{fwd},m,j})` and :math:`E^{ps}_{\mathrm{bwd}} = (e^{ps}_{\mathrm{bwd},m,j})`, which are both of size :math:`(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}`. -Whereas the exponent matrices :math:`E^{p}_{\mathrm{fwd}}, E^{p}_{\mathrm{bwd}} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{p} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefault`, the exponent matrices :math:`E^{ps}_{\mathrm{fwd}}, E^{ps}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`. +The exponents of these powers are given by the matrices :math:`E^{ls}_{\mathrm{fwd}} = (e^{ls}_{\mathrm{fwd},m,j})` and :math:`E^{ls}_{\mathrm{bwd}} = (e^{ls}_{\mathrm{bwd},m,j})`, which are both of size :math:`(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}`. +Whereas the exponent matrices :math:`E^{p}_{\mathrm{fwd}}, E^{p}_{\mathrm{bwd}} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{p} \in \mathbb{R}^{N_{\mathrm{comp}} \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefaultCrossPhase`, the exponent matrices :math:`E^{ls}_{\mathrm{fwd}}, E^{ls}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`. + +Solid Phase Reactions Modified by Liquid Phase +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Vice versa, the rates of solid phase reactions can be modified by liquid phase concentrations. The corresponding exponent matrices :math:`E^{sp}_{\mathrm{fwd}} = (e^{sp}_{\mathrm{fwd},\ell,j})` and :math:`E^{sp}_{\mathrm{bwd}} = (e^{sp}_{\mathrm{bwd},\ell,j})` are both of size :math:`N_{\mathrm{comp}} \times N_{\mathrm{react}}`. @@ -58,7 +70,7 @@ The corresponding exponent matrices :math:`E^{sp}_{\mathrm{fwd}} = (e^{sp}_{\mat .. math:: \begin{aligned} - f_{\mathrm{react},i}^s\left(c^s, c^p\right) &= \sum_{j=0}^{N_{\mathrm{react}}-1} s_{i,j}^s \varphi^s_j\left(c^s, c^p\right), + f_{\mathrm{react},i}^s\left(c^s, c^l\right) &= \sum_{j=0}^{N_{\mathrm{react}}-1} s_{i,j}^s \varphi^s_j\left(c^s, c^l\right), \end{aligned} where @@ -66,11 +78,11 @@ where .. math:: \begin{split} - \varphi^s_j(c^s, c^p) = k^s_{\mathrm{fwd},j} &\left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{s}_{\mathrm{fwd},m,j}}\right] \left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^p_{\ell}\right)^{e^{sp}_{\mathrm{fwd},\ell,j}}\right] \\ - - k^p_{\mathrm{bwd},j} &\left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{s}_{\mathrm{bwd},m,j}}\right] \left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^p_{\ell}\right)^{e^{sp}_{\mathrm{bwd},\ell,j}}\right]. + \varphi^s_j(c^s, c^l) = k^s_{\mathrm{fwd},j} &\left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{s}_{\mathrm{fwd},m,j}}\right] \left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^l_{\ell}\right)^{e^{sp}_{\mathrm{fwd},\ell,j}}\right] \\ + - k^l_{\mathrm{bwd},j} &\left[\prod_{m=0}^{\sum_{i=0}^{N_{\mathrm{comp}}-1} N_{\mathrm{bnd},i}-1} \left(c^s_{m}\right)^{e^{s}_{\mathrm{bwd},m,j}}\right] \left[\prod_{\ell=0}^{N_{\mathrm{comp}}-1} \left(c^l_{\ell}\right)^{e^{sp}_{\mathrm{bwd},\ell,j}}\right]. \end{split} -Whereas the exponent matrices :math:`E^{s}_{\mathrm{fwd}}, E^{s}_{\mathrm{bwd}} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{s} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefault`, the exponent matrices :math:`E^{sp}_{\mathrm{fwd}}, E^{sp}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`. +Whereas the exponent matrices :math:`E^{s}_{\mathrm{fwd}}, E^{s}_{\mathrm{bwd}} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}` are initialized based on the stoichiometric matrix :math:`S^{s} \in \mathbb{R}^{(\sum_i N_{\mathrm{bnd},i}) \times N_{\mathrm{react}}}`, see Eq. :eq:`MRMassActionLawExpMatDefaultCrossPhase`, the exponent matrices :math:`E^{sp}_{\mathrm{fwd}}, E^{sp}_{\mathrm{bwd}}` of the modifier terms default to :math:`0`. Correlation of forward- and backward rate constants @@ -107,4 +119,4 @@ This can be achieved by a (nonlinear) parameter transform \text{ with Jacobian } J_F\left( k_{\mathrm{eq},i}, k_{\mathrm{bwd},i} \right) &= \begin{pmatrix} k_{\mathrm{bwd},i} & k_{\mathrm{eq},i} \\ 0 & 1 \end{pmatrix}. \end{aligned} -For more information on model parameters required to define in CADET file format, see :ref:`mass_action_law_config`. +For more information on model parameters required to define in CADET file format, see :ref:`_mass_action_law_cross_phase_config`. diff --git a/src/libcadet/CMakeLists.txt b/src/libcadet/CMakeLists.txt index 1a1cec957..7d0362753 100644 --- a/src/libcadet/CMakeLists.txt +++ b/src/libcadet/CMakeLists.txt @@ -116,6 +116,7 @@ set(LIBCADET_EXCHANGEMODEL_SOURCES set(LIBCADET_REACTIONMODEL_SOURCES ${CMAKE_SOURCE_DIR}/src/libcadet/model/reaction/DummyReaction.cpp ${CMAKE_SOURCE_DIR}/src/libcadet/model/reaction/MassActionLawReaction.cpp + ${CMAKE_SOURCE_DIR}/src/libcadet/model/reaction/MassActionLawReactionCrossPhase.cpp ${CMAKE_SOURCE_DIR}/src/libcadet/model/reaction/MichaelisMentenReaction.cpp ${CMAKE_SOURCE_DIR}/src/libcadet/model/reaction/CrystallizationReaction.cpp diff --git a/src/libcadet/ReactionModelFactory.cpp b/src/libcadet/ReactionModelFactory.cpp index 598662c47..d0b06d2e5 100644 --- a/src/libcadet/ReactionModelFactory.cpp +++ b/src/libcadet/ReactionModelFactory.cpp @@ -20,6 +20,7 @@ namespace cadet namespace reaction { void registerMassActionLawReaction(std::unordered_map>& reactions); + void registerMassActionLawReactionCrossPhase(std::unordered_map>& reactions); void registerDummyReaction(std::unordered_map>& reactions); void registerMichaelisMentenReaction(std::unordered_map>& reactions); @@ -32,6 +33,7 @@ namespace cadet // Register all reaction models here model::reaction::registerDummyReaction(_dynamicModels); model::reaction::registerMassActionLawReaction(_dynamicModels); + model::reaction::registerMassActionLawReactionCrossPhase(_dynamicModels); model::reaction::registerMichaelisMentenReaction(_dynamicModels); model::reaction::registerCrystallizationReaction(_dynamicModels); diff --git a/src/libcadet/linalg/BandedEigenSparseRowIterator.hpp b/src/libcadet/linalg/BandedEigenSparseRowIterator.hpp index c14d5e25b..f802be581 100644 --- a/src/libcadet/linalg/BandedEigenSparseRowIterator.hpp +++ b/src/libcadet/linalg/BandedEigenSparseRowIterator.hpp @@ -92,13 +92,18 @@ class BandedEigenSparseRowIterator */ inline void addArray(double const* row, int startDiag, int length, double factor) { - // shift to column index to start with - int idx = startDiag - _row; - - for (int i = 0; i < length; i++) { - _values[idx + i] = factor * row[i]; + for (int i = 0; i < length; ++i) + { + int col = _row + startDiag + i; + for (int j = 0; j < _numNonZero; ++j) + { + if (_colIdx[j] == col) + { + _values[j] += factor * row[i]; + break; + } + } } - } /** @@ -123,8 +128,22 @@ class BandedEigenSparseRowIterator { cadet_assert((col >= 0) && (col < _size)); - // Try to find the element - // TODO: Use binary search + // Binary search + int left = 0, right = _numNonZero - 1; + while (left <= right) + { + int mid = (left + right) / 2; + if (_colIdx[mid] == col) return _values[mid]; + if (_colIdx[mid] < col) left = mid + 1; + else right = mid - 1; + } + + // if element not found + _matrix->coeffRef(_row, col) = 0.0; + + updateOnRowChange(); + + // Fallback for (int i = 0; i < _numNonZero; ++i) { if (_colIdx[i] == col) @@ -140,12 +159,14 @@ class BandedEigenSparseRowIterator { cadet_assert((col >= 0) && (col < _matrix->rows())); - // Try to find the element - // TODO: Use binary search - for (int i = 0; i < _numNonZero; ++i) + // Binary search + int left = 0, right = _numNonZero - 1; + while (left <= right) { - if (_colIdx[i] == col) - return _values[i]; + int mid = (left + right) / 2; + if (_colIdx[mid] == col) return _values[mid]; + if (_colIdx[mid] < col) left = mid + 1; + else right = mid - 1; } // We don't have it diff --git a/src/libcadet/model/ColumnModel1D-InitialConditions.cpp b/src/libcadet/model/ColumnModel1D-InitialConditions.cpp index 3dea7e70f..47b2ac0cd 100644 --- a/src/libcadet/model/ColumnModel1D-InitialConditions.cpp +++ b/src/libcadet/model/ColumnModel1D-InitialConditions.cpp @@ -613,7 +613,8 @@ void ColumnModel1D::consistentInitialState(const SimulationTime& simTime, double } // reset jacobian pattern - setJacobianPattern(_globalJacDisc, _disc.curSection, _dynReactionBulk); + bool hasBulkReaction = _reaction.hasReactions(); + setJacobianPattern(_globalJacDisc, _disc.curSection, hasBulkReaction); } CADET_PARFOR_END; } diff --git a/src/libcadet/model/ColumnModel1D.cpp b/src/libcadet/model/ColumnModel1D.cpp index a30b49392..b4e186eaa 100644 --- a/src/libcadet/model/ColumnModel1D.cpp +++ b/src/libcadet/model/ColumnModel1D.cpp @@ -39,6 +39,7 @@ #include #include + #include "ParallelSupport.hpp" #ifdef CADET_PARALLELIZE #include @@ -56,7 +57,7 @@ constexpr double SurfVolRatioSlab = 1.0; ColumnModel1D::ColumnModel1D(UnitOpIdx unitOpIdx) : UnitOperationBase(unitOpIdx), - _globalJac(), _globalJacDisc(), _jacInlet(), _dynReactionBulk(nullptr), + _globalJac(), _globalJacDisc(), _jacInlet(), _analyticJac(true), _jacobianAdDirs(0), _factorizeJacobian(false), _tempState(nullptr), _initC(0), _initCp(0), _initCs(0), _initState(0), _initStateDot(0) { @@ -74,8 +75,7 @@ ColumnModel1D::~ColumnModel1D() CADET_NOEXCEPT _binding.clear(); // binding models are deleted in the respective particle model _dynReaction.clear(); // particle reaction models are deleted in the respective particle model - delete _dynReactionBulk; - + _reaction.clearDynamicReactionModels(); delete _linearSolver; } @@ -313,28 +313,34 @@ bool ColumnModel1D::configureModelDiscretization(IParameterProvider& paramProvid // ==== Construct and configure dynamic reaction model bool reactionConfSuccess = true; + _reaction.clearDynamicReactionModels(); - _dynReactionBulk = nullptr; - if (paramProvider.exists("REACTION_MODEL")) + // Bulk liquid phase reactions + if (paramProvider.exists("NREAC_LIQUID")) { - const std::string dynReactName = paramProvider.getString("REACTION_MODEL"); - _dynReactionBulk = helper.createDynamicReactionModel(dynReactName); - if (!_dynReactionBulk) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactName); - - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction_bulk", _dynReactionBulk->usesParamProviderInDiscretizationConfig()); - reactionConfSuccess = _dynReactionBulk->configureModelDiscretization(paramProvider, _disc.nComp, nullptr, nullptr); + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + else + { + _reaction.empty(); } // ==== Construct and configure binding and particle reaction -> done in particle model, only pointers are copied here. _binding = std::vector(_disc.nParType, nullptr); - _dynReaction = std::vector(_disc.nParType, nullptr); + _reacParticle.resize(_disc.nParType, nullptr); for (unsigned int parType = 0; parType < _disc.nParType; ++parType) { _binding[parType] = _particles[parType]->getBinding(); - - _dynReaction[parType] = _particles[parType]->getReaction(); + _reacParticle[parType] = _particles[parType]->getReaction(); // Check if binding and reaction particle type dependence is the same for all particle types if (parType > 0) @@ -344,17 +350,10 @@ bool ColumnModel1D::configureModelDiscretization(IParameterProvider& paramProvid if (_singleBinding != !_particles[parType]->bindingParDep()) throw InvalidParameterException("Binding particle type dependence must be the same for all particle types, check field BINDING_PARTYPE_DEPENDENT"); } - - if (_dynReaction[parType]) - { - if (_singleDynReaction != !_particles[parType]->reactionParDep()) - throw InvalidParameterException("Reaction particle type dependence must be the same for all particle types, check field REACTION_PARTYPE_DEPENDENT"); - } } else // if no particle reaction or binding exists in first particle type, default to single mode { _singleBinding = _binding[parType] ? !_particles[parType]->bindingParDep() : true; - _singleDynReaction = _dynReaction[parType] ? !_particles[parType]->reactionParDep() : true; } } @@ -480,16 +479,17 @@ bool ColumnModel1D::configure(IParameterProvider& paramProvider) particleConfSuccess = particleConfSuccess && _particles[parType]->configure(_unitOpIdx, paramProvider, _parameters, _disc.nParType, _disc.nBoundBeforeType, _disc.strideBound[_disc.nParType]); } - // Reconfigure reaction model + // Reconfigure bulk liquid reaction model bool dynReactionConfSuccess = true; - if (_dynReactionBulk && _dynReactionBulk->requiresConfiguration()) - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction_bulk", _dynReactionBulk->requiresConfiguration()); - dynReactionConfSuccess = _dynReactionBulk->configure(paramProvider, _unitOpIdx, ParTypeIndep); - } + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; // jaobian pattern set after binding and particle surface diffusion are configured - setJacobianPattern(_globalJac, 0, _dynReactionBulk); + bool hasBulkReaction = false; + if (_reaction.getDynReactionVector("liquid")[0] != nullptr) + hasBulkReaction = true; + + setJacobianPattern(_globalJac, 0, hasBulkReaction); _globalJacDisc = _globalJac; // the solver repetitively solves the linear system with a static pattern of the jacobian (set above). // The goal of analyzePattern() is to reorder the nonzero elements of the matrix, such that the factorization step creates less fill-in @@ -507,13 +507,13 @@ unsigned int ColumnModel1D::threadLocalMemorySize() const CADET_NOEXCEPT { if (_binding[i] && _binding[i]->requiresWorkspace()) lms.fitBlock(_binding[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); - - if (_dynReaction[i] && _dynReaction[i]->requiresWorkspace()) - lms.fitBlock(_dynReaction[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); + // Particle reaction + _reacParticle[i]->setWorkspaceRequirements("cross_phase", _disc.nParType, _disc.nComp, _disc.strideBound, lms); + _reacParticle[i]->setWorkspaceRequirements("liquid", _disc.nParType, _disc.nComp, _disc.strideBound, lms); + _reacParticle[i]->setWorkspaceRequirements("solid", _disc.nParType, _disc.nComp, _disc.strideBound, lms); } - - if (_dynReactionBulk && _dynReactionBulk->requiresWorkspace()) - lms.fitBlock(_dynReactionBulk->workspaceSize(_disc.nComp, 0, nullptr)); + // Bulk reaction + _reaction.setWorkspaceRequirements("liquid", _disc.nComp, 0, lms); const unsigned int maxStrideBound = *std::max_element(_disc.strideBound, _disc.strideBound + _disc.nParType); lms.add(_disc.nComp + maxStrideBound); @@ -576,7 +576,8 @@ void ColumnModel1D::notifyDiscontinuousSectionTransition(double t, unsigned int Indexer idxr(_disc); // todo: only reset jacobian pattern if it changes, i.e. once in configuration and then only for changes in SurfDiff+kinetic binding. - setJacobianPattern(_globalJac, 0, _dynReactionBulk); + bool hasReaction = _reaction.getDynReactionVector("liquid")[0]; + setJacobianPattern(_globalJac, 0, hasReaction); _globalJacDisc = _globalJac; _convDispOp.notifyDiscontinuousSectionTransition(t, secIdx, _jacInlet); @@ -988,7 +989,16 @@ int ColumnModel1D::residualImpl(double t, unsigned int secIdx, StateType const* const unsigned int parType = (pblk - 1) / _disc.nPoints; const unsigned int colNode = (pblk - 1) % _disc.nPoints; - linalg::BandedEigenSparseRowIterator jacIt(_globalJac, idxr.offsetCp(ParticleTypeIndex{ parType }, ParticleIndex{ colNode })); + linalg::BandedEigenSparseRowIterator jacIt; + + if (wantJac) + { + jacIt = linalg::BandedEigenSparseRowIterator( + _globalJac, + idxr.offsetCp(ParticleTypeIndex{ parType }, ParticleIndex{ colNode }) + ); + } + model::columnPackingParameters packing { _parTypeVolFrac[parType + _disc.nParType * colNode], @@ -996,6 +1006,7 @@ int ColumnModel1D::residualImpl(double t, unsigned int secIdx, StateType const* ColumnPosition{ _convDispOp.relativeCoordinate(colNode), 0.0, 0.0 } }; + _particles[parType]->residual(t, secIdx, y + idxr.offsetCp(ParticleTypeIndex{ parType }, ParticleIndex{ colNode }), y + idxr.offsetC() + colNode * idxr.strideColNode(), @@ -1027,47 +1038,55 @@ int ColumnModel1D::residualBulk(double t, unsigned int secIdx, StateType const* if (wantRes) _convDispOp.residual(*this, t, secIdx, yBase, yDotBase, resBase, typename cadet::ParamSens::enabled()); - if (!_dynReactionBulk || (_dynReactionBulk->numReactionsLiquid() == 0)) + if (_reaction.getDynReactionVector("liquid").size() == 0) return 0; Indexer idxr(_disc); LinearBufferAllocator tlmAlloc = threadLocalMem.get(); + StateType const* y = yBase + idxr.offsetC(); - // Dynamic reactions - if (_dynReactionBulk) { - - StateType const* y = yBase + idxr.offsetC(); - - if (wantJac && !wantRes) // only compute Jacobian + if (wantJac && !wantRes) // only compute Jacobian + { + for (unsigned int col = 0; col < _disc.nPoints; ++col, y += idxr.strideColNode()) { - for (unsigned int col = 0; col < _disc.nPoints; ++col, y += idxr.strideColNode()) + const ColumnPosition colPos{ _convDispOp.relativeCoordinate(col), 0.0, 0.0 }; + linalg::BandedEigenSparseRowIterator jac(_globalJac, idxr.offsetC() + col * idxr.strideColNode()); + + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) { - const ColumnPosition colPos{ _convDispOp.relativeCoordinate(col), 0.0, 0.0 }; + if (!_reaction.getDynReactionVector("liquid")[i]) + continue; - linalg::BandedEigenSparseRowIterator jac(_globalJac, idxr.offsetC() + col * idxr.strideColNode()); - // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - _dynReactionBulk->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(y), -1.0, jac, tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _disc.nComp, reinterpret_cast(y), -1.0, jac, tlmAlloc); } - - return 0; } - ResidualType* res = resBase + idxr.offsetC(); + return 0; + } + + ResidualType* res = resBase + idxr.offsetC(); - for (unsigned int col = 0; col < _disc.nPoints; ++col, y += idxr.strideColNode(), res += idxr.strideColNode()) + for (unsigned int col = 0; col < _disc.nPoints; ++col, y += idxr.strideColNode(), res += idxr.strideColNode()) + { + const ColumnPosition colPos{ _convDispOp.relativeCoordinate(col), 0.0, 0.0}; + linalg::BandedEigenSparseRowIterator jac(_globalJac, idxr.offsetC() + col * idxr.strideColNode()); + + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) { - const ColumnPosition colPos{ _convDispOp.relativeCoordinate(col), 0.0, 0.0}; - _dynReactionBulk->residualLiquidAdd(t, secIdx, colPos, y, res, -1.0, tlmAlloc); + if (!_reaction.getDynReactionVector("liquid")[i]) + continue; + + _reaction.getDynReactionVector("liquid")[i]->residualFluxAdd(t, secIdx, colPos, _disc.nComp, y, res, -1.0, tlmAlloc); if (wantJac) { - linalg::BandedEigenSparseRowIterator jac(_globalJac, idxr.offsetC() + col * idxr.strideColNode()); // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - _dynReactionBulk->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(y), -1.0, jac, tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _disc.nComp, reinterpret_cast(y), -1.0, jac, tlmAlloc); } } } + return 0; } @@ -1083,7 +1102,7 @@ parts::cell::CellParameters ColumnModel1D::makeCellResidualParams(unsigned int p _particles[parType]->getPorosity(), _particles[parType]->getPoreAccessFactor(), _binding[parType], - (_dynReaction[parType] && (_dynReaction[parType]->numReactionsCombined() > 0)) ? _dynReaction[parType] : nullptr + (_reacParticle[parType]) ? _reacParticle[parType] : nullptr }; } @@ -1320,7 +1339,7 @@ bool ColumnModel1D::setParameter(const ParameterId& pId, double value) if (_convDispOp.setParameter(pId, value)) return true; - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1351,7 +1370,7 @@ bool ColumnModel1D::setParameter(const ParameterId& pId, int value) if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1382,7 +1401,7 @@ bool ColumnModel1D::setParameter(const ParameterId& pId, bool value) if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1437,7 +1456,7 @@ void ColumnModel1D::setSensitiveParameterValue(const ParameterId& pId, double va if (_convDispOp.setSensitiveParameterValue(_sensParams, pId, value)) return; - if (model::setSensitiveParameterValue(pId, value, _sensParams, std::vector{ _dynReactionBulk }, true)) + if (model::setSensitiveParameterValue(pId, value, _sensParams, _reaction.getDynReactionVector("liquid"), false)) return; } @@ -1508,7 +1527,7 @@ bool ColumnModel1D::setSensitiveParameter(const ParameterId& pId, unsigned int a return true; } - if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, std::vector { _dynReactionBulk }, true)) + if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, _reaction.getDynReactionVector("liquid"), false)) { LOG(Debug) << "Found parameter " << pId << " in DynamicBulkReactionModel: Dir " << adDirection << " is set to " << adValue; return true; diff --git a/src/libcadet/model/ColumnModel1D.hpp b/src/libcadet/model/ColumnModel1D.hpp index 7eec7f094..0c55107fe 100644 --- a/src/libcadet/model/ColumnModel1D.hpp +++ b/src/libcadet/model/ColumnModel1D.hpp @@ -20,6 +20,7 @@ #include "model/UnitOperationBase.hpp" #include "model/particle/ParticleModel.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "cadet/StrongTypes.hpp" #include "cadet/SolutionExporter.hpp" #include "model/parts/ConvectionDispersionOperatorDG.hpp" @@ -296,7 +297,8 @@ class ColumnModel1D : public UnitOperationBase std::vector _particles; //!< Particle dispersion operator parts::AxialConvectionDispersionOperatorBaseDG _convDispOp; //!< Convection dispersion operator base for interstitial volume transport - IDynamicReactionModel* _dynReactionBulk; //!< Dynamic reactions in the bulk volume + ReactionSystem _reaction; //!< Reaction system for bulk phase + std::vector _reacParticle; //!< Reaction systems for particle phases cadet::linalg::EigenSolverBase* _linearSolver; //!< Linear solver diff --git a/src/libcadet/model/ColumnModel2D-InitialConditions.cpp b/src/libcadet/model/ColumnModel2D-InitialConditions.cpp index f8755fb4a..c977c43de 100644 --- a/src/libcadet/model/ColumnModel2D-InitialConditions.cpp +++ b/src/libcadet/model/ColumnModel2D-InitialConditions.cpp @@ -630,7 +630,7 @@ void ColumnModel2D::consistentInitialState(const SimulationTime& simTime, double _particles[parType]->getPorosity(), _particles[parType]->getPoreAccessFactor(), _binding[parType], - (_dynReaction[parType] && (_dynReaction[parType]->numReactionsCombined() > 0)) ? _dynReaction[parType] : nullptr + _reacParticle[parType] }; const int localOffsetToParticle = idxr.offsetCp(ParticleTypeIndex{ parType }, ParticleIndex{ static_cast(pblk) }); @@ -839,7 +839,8 @@ void ColumnModel2D::consistentInitialState(const SimulationTime& simTime, double } // reset jacobian pattern //@todo can this be avoided? - setJacobianPattern(_globalJacDisc, simTime.secIdx, _dynReactionBulk); + bool hasBulkReactions = _reaction.hasReactions(); + setJacobianPattern(_globalJacDisc, simTime.secIdx, hasBulkReactions); } /** diff --git a/src/libcadet/model/ColumnModel2D.cpp b/src/libcadet/model/ColumnModel2D.cpp index d0f9fab92..3f248bb77 100644 --- a/src/libcadet/model/ColumnModel2D.cpp +++ b/src/libcadet/model/ColumnModel2D.cpp @@ -317,7 +317,7 @@ namespace model { ColumnModel2D::ColumnModel2D(UnitOpIdx unitOpIdx) : UnitOperationBase(unitOpIdx), - _dynReactionBulk(nullptr), _jacInlet(), _analyticJac(true), _jacobianAdDirs(0), _factorizeJacobian(false), _tempState(nullptr), + _jacInlet(), _analyticJac(true), _jacobianAdDirs(0), _factorizeJacobian(false), _tempState(nullptr), _initC(0), _singleRadiusInitC(true), _initCp(0), _singleRadiusInitCp(true), _initCs(0), _singleRadiusInitCs(true), _initState(0), _initStateDot(0) { } @@ -334,13 +334,13 @@ ColumnModel2D::~ColumnModel2D() CADET_NOEXCEPT _binding.clear(); // binding models are deleted in the respective particle model _dynReaction.clear(); // particle reaction models are deleted in the respective particle model - delete _dynReactionBulk; delete[] _disc.parTypeOffset; delete[] _disc.nBound; delete[] _disc.boundOffset; delete[] _disc.strideBound; delete[] _disc.nBoundBeforeType; + _reaction.clearDynamicReactionModels(); delete _linearSolver; } @@ -512,27 +512,32 @@ bool ColumnModel2D::configureModelDiscretization(IParameterProvider& paramProvid // ==== Construct and configure dynamic reaction model bool reactionConfSuccess = true; - _dynReactionBulk = nullptr; - if (paramProvider.exists("REACTION_MODEL")) + _reaction.clearDynamicReactionModels(); + // bulk liquid reactions + if (paramProvider.exists("NREAC_LIQUID")) { - const std::string dynReactName = paramProvider.getString("REACTION_MODEL"); - _dynReactionBulk = helper.createDynamicReactionModel(dynReactName); - if (!_dynReactionBulk) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactName); - - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction_bulk", _dynReactionBulk->usesParamProviderInDiscretizationConfig()); - reactionConfSuccess = _dynReactionBulk->configureModelDiscretization(paramProvider, _disc.nComp, nullptr, nullptr); + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + else + { + _reaction.empty(); } // ==== Construct and configure binding and particle reaction -> done in particle model, only pointers are copied here. _binding = std::vector(_disc.nParType, nullptr); - _dynReaction = std::vector(_disc.nParType, nullptr); - + _reacParticle = std::vector(_disc.nParType, nullptr); for (unsigned int parType = 0; parType < _disc.nParType; ++parType) { _binding[parType] = _particles[parType]->getBinding(); - - _dynReaction[parType] = _particles[parType]->getReaction(); + _reacParticle[parType] = _particles[parType]->getReaction(); // Check if binding and reaction particle type dependence is the same for all particle types if (parType > 0) @@ -542,17 +547,10 @@ bool ColumnModel2D::configureModelDiscretization(IParameterProvider& paramProvid if (_singleBinding != !_particles[parType]->bindingParDep()) throw InvalidParameterException("Binding particle type dependence must be the same for all particle types, check field BINDING_PARTYPE_DEPENDENT"); } - - if (_dynReaction[parType]) - { - if (_singleDynReaction != !_particles[parType]->reactionParDep()) - throw InvalidParameterException("Reaction particle type dependence must be the same for all particle types, check field REACTION_PARTYPE_DEPENDENT"); - } } else // if no particle reaction or binding exists in first particle type, default to single mode { _singleBinding = _binding[parType] ? !_particles[parType]->bindingParDep() : true; - _singleDynReaction = _dynReaction[parType] ? !_particles[parType]->reactionParDep() : true; } } @@ -701,13 +699,16 @@ bool ColumnModel2D::configure(IParameterProvider& paramProvider) // Reconfigure reaction model bool dynReactionConfSuccess = true; - if (_dynReactionBulk && _dynReactionBulk->requiresConfiguration()) - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction_bulk", _dynReactionBulk->requiresConfiguration()); - dynReactionConfSuccess = _dynReactionBulk->configure(paramProvider, _unitOpIdx, ParTypeIndep); - } + // Reconfigure reaction model + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; - setJacobianPattern(_globalJac, 0, _dynReactionBulk); + // jaobian pattern set after binding and particle surface diffusion are configured + bool hasBulkReaction = false; + if (_reaction.getDynReactionVector("liquid")[0] != nullptr) + hasBulkReaction = true; + + setJacobianPattern(_globalJac, 0, hasBulkReaction); _globalJacDisc = _globalJac; // the solver repetitively solves the linear system with a static pattern of the jacobian (set above). @@ -728,13 +729,13 @@ unsigned int ColumnModel2D::threadLocalMemorySize() const CADET_NOEXCEPT { if (_binding[i] && _binding[i]->requiresWorkspace()) lms.fitBlock(_binding[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); - - if (_dynReaction[i] && _dynReaction[i]->requiresWorkspace()) - lms.fitBlock(_dynReaction[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); + // Particle reactions + _reacParticle[i]->setWorkspaceRequirements("cross_phase", _disc.nParType, _disc.nComp, _disc.strideBound, lms); + _reacParticle[i]->setWorkspaceRequirements("liquid", _disc.nParType, _disc.nComp, _disc.strideBound, lms); + _reacParticle[i]->setWorkspaceRequirements("solid", _disc.nParType, _disc.nComp, _disc.strideBound, lms); } - - if (_dynReactionBulk && _dynReactionBulk->requiresWorkspace()) - lms.fitBlock(_dynReactionBulk->workspaceSize(_disc.nComp, 0, nullptr)); + // Bulk liquid reactions + _reaction.setWorkspaceRequirements("liquid", _disc.nComp, 0, lms); const unsigned int maxStrideBound = *std::max_element(_disc.strideBound, _disc.strideBound + _disc.nParType); lms.add(_disc.nComp + maxStrideBound); @@ -1156,7 +1157,7 @@ int ColumnModel2D::residualBulk(double t, unsigned int secIdx, StateType const* if (wantRes) _convDispOp.residual(*this, t, secIdx, yBase, yDotBase, resBase, wantJac, typename ParamSens::enabled()); - if (!_dynReactionBulk || (_dynReactionBulk->numReactionsLiquid() == 0)) + if (_reaction.getDynReactionVector("liquid").size() == 0) return 0; // Get offsets @@ -1173,15 +1174,20 @@ int ColumnModel2D::residualBulk(double t, unsigned int secIdx, StateType const* const double z = _convDispOp.relativeAxialCoordinate(axNode);; const ColumnPosition colPos{ z, r, 0.0 }; - _dynReactionBulk->residualLiquidAdd(t, secIdx, colPos, y, res, -1.0, tlmAlloc); + + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) + { + if (!_reaction.getDynReactionVector("liquid")[i]) + continue; + _reaction.getDynReactionVector("liquid")[i]->residualFluxAdd(t, secIdx, colPos, _disc.nComp, y, res, -1.0, tlmAlloc); if (wantJac) { const int rowIdx = axNode * idxr.strideColAxialNode() + radNode * idxr.strideColRadialNode(); linalg::BandedEigenSparseRowIterator jac(_globalJac, rowIdx); - // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - _dynReactionBulk->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(y), -1.0, jac, tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _disc.nComp, reinterpret_cast(y), -1.0, jac, tlmAlloc); + } } } } @@ -1413,7 +1419,7 @@ bool ColumnModel2D::setParameter(const ParameterId& pId, double value) if (_convDispOp.setParameter(pId, value)) return true; - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1446,7 +1452,7 @@ bool ColumnModel2D::setParameter(const ParameterId& pId, int value) if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1477,7 +1483,7 @@ bool ColumnModel2D::setParameter(const ParameterId& pId, bool value) if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1517,7 +1523,7 @@ void ColumnModel2D::setSensitiveParameterValue(const ParameterId& pId, double va if (_convDispOp.setSensitiveParameterValue(_sensParams, pId, value)) return; - if (model::setSensitiveParameterValue(pId, value, _sensParams, std::vector{ _dynReactionBulk }, true)) + if (model::setSensitiveParameterValue(pId, value, _sensParams, _reaction.getDynReactionVector("liquid"), false)) return; } @@ -1576,7 +1582,7 @@ bool ColumnModel2D::setSensitiveParameter(const ParameterId& pId, unsigned int a return true; } - if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, std::vector { _dynReactionBulk }, true)) + if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, _reaction.getDynReactionVector("liquid"),false)) { LOG(Debug) << "Found parameter " << pId << " in DynamicBulkReactionModel: Dir " << adDirection << " is set to " << adValue; return true; diff --git a/src/libcadet/model/ColumnModel2D.hpp b/src/libcadet/model/ColumnModel2D.hpp index 70104a47a..99dfb0478 100644 --- a/src/libcadet/model/ColumnModel2D.hpp +++ b/src/libcadet/model/ColumnModel2D.hpp @@ -303,7 +303,8 @@ class ColumnModel2D : public UnitOperationBase std::vector _particles; //!< Particle dispersion operator parts::TwoDimensionalConvectionDispersionOperatorDG _convDispOp; //!< Convection dispersion operator for interstitial volume transport - IDynamicReactionModel* _dynReactionBulk; //!< Dynamic reactions in the bulk volume + ReactionSystem _reaction; //!< Reaction system for bulk phase + std::vector _reacParticle; //!< Reaction systems for particle phases cadet::linalg::EigenSolverBase* _linearSolver; //!< Linear solver diff --git a/src/libcadet/model/GeneralRateModel.cpp b/src/libcadet/model/GeneralRateModel.cpp index 91c93e50f..dd589b9ec 100644 --- a/src/libcadet/model/GeneralRateModel.cpp +++ b/src/libcadet/model/GeneralRateModel.cpp @@ -66,7 +66,7 @@ int schurComplementMultiplierGRM(void* userData, double const* x, double* z) template GeneralRateModel::GeneralRateModel(UnitOpIdx unitOpIdx) : UnitOperationBase(unitOpIdx), - _hasSurfaceDiffusion(0, false), _dynReactionBulk(nullptr), + _hasSurfaceDiffusion(0, false), _jacP(nullptr), _jacPdisc(nullptr), _jacPF(nullptr), _jacFP(nullptr), _jacInlet(), _hasParDepSurfDiffusion(false), _analyticJac(true), _jacobianAdDirs(0), _factorizeJacobian(false), _tempState(nullptr), _initC(0), _initCp(0), _initCs(0), _initState(0), _initStateDot(0) @@ -84,7 +84,8 @@ GeneralRateModel::~GeneralRateModel() CADET_NOEXCEPT delete[] _jacP; delete[] _jacPdisc; - delete _dynReactionBulk; + _reaction.empty(); + _dynReaction.clear(); clearParDepSurfDiffusion(); } @@ -202,7 +203,6 @@ bool GeneralRateModel::configureModelDiscretization(IParameter _binding = std::vector(_disc.nParType, nullptr); bool bindingConfSuccess = true; clearDynamicReactionModels(); - _dynReaction = std::vector(_disc.nParType, nullptr); bool reactionConfSuccess = true; for (int parType = 0; parType < _disc.nParType; parType++) @@ -262,25 +262,9 @@ bool GeneralRateModel::configureModelDiscretization(IParameter bindingConfSuccess = _binding[parType]->configureModelDiscretization(paramProvider, _disc.nComp, _disc.nBound + parType * _disc.nComp, _disc.boundOffset + parType * _disc.nComp) && bindingConfSuccess; } + _reacParticle.resize(_disc.nParType); // ==== Construct and configure dynamic particle reaction model - if (paramProvider.exists("REACTION_MODEL")) - { - const std::string dynReactModelName = paramProvider.getString("REACTION_MODEL"); - _dynReaction[parType] = helper.createDynamicReactionModel(dynReactModelName); - - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction[parType]->usesParamProviderInDiscretizationConfig()); - - if (paramProvider.exists("REACTION_PARTYPE_DEPENDENT")) - _singleBinding = !paramProvider.getInt("REACTION_PARTYPE_DEPENDENT"); - else - _singleBinding = _disc.nParType == 1; - - if (!_dynReaction[parType]) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactModelName); - - reactionConfSuccess = reactionConfSuccess && _dynReaction[parType]->configureModelDiscretization(paramProvider, _disc.nComp, _disc.nBound + parType * _disc.nComp, _disc.boundOffset + parType * _disc.nComp) && reactionConfSuccess; - } // Set particle geometry if (paramProvider.exists("PAR_GEOM")) @@ -299,6 +283,82 @@ bool GeneralRateModel::configureModelDiscretization(IParameter paramProvider.popScope(); } + _reaction.clearDynamicReactionModels(); + _reacParticle.clear(); + _reacParticle.resize(_disc.nParType); + + if (_disc.nParType > 0) + { + for (unsigned int par = 0; par < _disc.nParType; par++) + { + + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); + paramProvider.pushScope(particleScope); // particle_type_xxx + + ReactionSystem parReaction; + + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + int nReactions = paramProvider.getInt("NREAC_CROSS_PHASE"); + + reactionConfSuccess = _reacParticle[par].configureDiscretization("cross_phase", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + if (paramProvider.exists("NREAC_LIQUID")) + { + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("pore", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + if (paramProvider.exists("NREAC_SOLID")) + { + int nReactions = paramProvider.getInt("NREAC_SOLID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("solid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + paramProvider.popScope(); // particle_type_xxx + + } + + } + if (paramProvider.exists("NREAC_LIQUID")) + { + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + else + { + _reaction.empty(); + } + // Precompute offsets of particle type DOFs _disc.parTypeOffset = new unsigned int[_disc.nParType + 1]; _disc.nParCellsBeforeType = new unsigned int[_disc.nParType + 1]; @@ -449,23 +509,6 @@ bool GeneralRateModel::configureModelDiscretization(IParameter // ==== Construct and configure dynamic bulk reaction model - _dynReactionBulk = nullptr; - if (paramProvider.exists("REACTION_MODEL")) - { - const std::string dynReactName = paramProvider.getString("REACTION_MODEL"); - _dynReactionBulk = helper.createDynamicReactionModel(dynReactName); - if (!_dynReactionBulk) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactName); - - if (_dynReactionBulk->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope("reaction_bulk"); - - reactionConfSuccess = reactionConfSuccess && _dynReactionBulk->configureModelDiscretization(paramProvider, _disc.nComp, nullptr, nullptr); - - if (_dynReactionBulk->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); - } - // Allocate memory _tempState = new double[numDofs()]; @@ -833,36 +876,24 @@ bool GeneralRateModel::configure(IParameterProvider& paramProv // Reconfigure reaction model bool dynReactionConfSuccess = true; - if (_dynReactionBulk && _dynReactionBulk->requiresConfiguration()) - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction_bulk", _dynReactionBulk->requiresConfiguration()); - dynReactionConfSuccess = _dynReactionBulk->configure(paramProvider, _unitOpIdx, ParTypeIndep); - } + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; - if (_singleDynReaction) - { - if (_dynReaction[0] && _dynReaction[0]->requiresConfiguration()) - { - paramProvider.pushScope("particle_type_000"); + for (unsigned int par = 0; par < _disc.nParType; par++) { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction[0]->requiresConfiguration()); - dynReactionConfSuccess = dynReactionConfSuccess && _dynReaction[0]->configure(paramProvider, _unitOpIdx, ParTypeIndep); - } - paramProvider.popScope(); - } - } - else - { - for (unsigned int type = 0; type < _disc.nParType; ++type) - { - if (!_dynReaction[type] || !_dynReaction[type]->requiresConfiguration()) - continue; + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); + + if (paramProvider.exists(particleScope)) + { + paramProvider.pushScope(particleScope); + if (paramProvider.exists("NREAC_CROSS_PHASE")) + dynReactionConfSuccess = _reacParticle[par].configure("cross_phase", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reacParticle[par].configure("pore", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_SOLID")) + dynReactionConfSuccess = _reacParticle[par].configure("solid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; - paramProvider.pushScope("particle_type_" + std::string(3 - std::to_string(type).length(), '0') + std::to_string(type)); - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction[type]->requiresConfiguration()); - dynReactionConfSuccess = dynReactionConfSuccess && _dynReaction[type]->configure(paramProvider, _unitOpIdx, type); - } paramProvider.popScope(); } } @@ -881,12 +912,14 @@ unsigned int GeneralRateModel::threadLocalMemorySize() const C if (_binding[i] && _binding[i]->requiresWorkspace()) lms.fitBlock(_binding[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); - if (_dynReaction[i] && _dynReaction[i]->requiresWorkspace()) - lms.fitBlock(_dynReaction[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); - } - - if (_dynReactionBulk && _dynReactionBulk->requiresWorkspace()) - lms.fitBlock(_dynReactionBulk->workspaceSize(_disc.nComp, 0, nullptr)); + // Reactions in particle + _reacParticle[i].setWorkspaceRequirements("cross_phase", 1, _disc.nComp, &_disc.strideBound[i], lms); + _reacParticle[i].setWorkspaceRequirements("pore", 1, _disc.nComp, &_disc.strideBound[i], lms); + _reacParticle[i].setWorkspaceRequirements("solid", 1, _disc.nComp, &_disc.strideBound[i], lms); + } + // Reactions in liquid bulk + _reaction.setWorkspaceRequirements("liquid", _disc.nComp, 0, lms); + const unsigned int maxStrideBound = *std::max_element(_disc.strideBound, _disc.strideBound + _disc.nParType); lms.add(_disc.nComp + maxStrideBound); @@ -1292,7 +1325,7 @@ int GeneralRateModel::residualBulk(double t, unsigned int secI else _convDispOp.jacobian(*this, t, secIdx, yBase, nullptr, nullptr); - if (!_dynReactionBulk || (_dynReactionBulk->numReactionsLiquid() == 0)) + if (!_reaction.getDynReactionVector("liquid")[0]) return 0; // Get offsets @@ -1304,13 +1337,20 @@ int GeneralRateModel::residualBulk(double t, unsigned int secI for (unsigned int col = 0; col < _disc.nCol; ++col, y += idxr.strideColCell(), res += idxr.strideColCell()) { const ColumnPosition colPos{ (0.5 + static_cast(col)) / static_cast(_disc.nCol), 0.0, 0.0 }; + + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) + { + if (!_reaction.getDynReactionVector("liquid")[i]) + continue; + if (wantRes) - _dynReactionBulk->residualLiquidAdd(t, secIdx, colPos, y, res, -1.0, tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->residualFluxAdd(t, secIdx, colPos, _disc.nComp, y, res, -1.0, tlmAlloc); if (wantJac) { // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - _dynReactionBulk->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(y), -1.0, _convDispOp.jacobian().row(col * idxr.strideColCell()), tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _disc.nComp, reinterpret_cast(y), -1.0, _convDispOp.jacobian().row(col * idxr.strideColCell()), tlmAlloc); + } } } @@ -2054,7 +2094,7 @@ parts::cell::CellParameters GeneralRateModel::makeCellResidual _parPorosity[parType], _poreAccessFactor.data() + _disc.nComp * parType, _binding[parType], - (_dynReaction[parType] && (_dynReaction[parType]->numReactionsCombined() > 0)) ? _dynReaction[parType] : nullptr + &_reacParticle[parType] }; } @@ -2873,7 +2913,7 @@ bool GeneralRateModel::setParameter(const ParameterId& pId, do if (_convDispOp.setParameter(pId, value)) return true; - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), true)) return true; } @@ -2897,7 +2937,7 @@ bool GeneralRateModel::setParameter(const ParameterId& pId, in if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), true)) return true; } @@ -2915,7 +2955,7 @@ bool GeneralRateModel::setParameter(const ParameterId& pId, bo if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), true)) return true; } @@ -2968,7 +3008,7 @@ void GeneralRateModel::setSensitiveParameterValue(const Parame if (_convDispOp.setSensitiveParameterValue(_sensParams, pId, value)) return; - if (model::setSensitiveParameterValue(pId, value, _sensParams, std::vector{ _dynReactionBulk }, true)) + if (model::setSensitiveParameterValue(pId, value, _sensParams, _reaction.getDynReactionVector("liquid"), false)) return; } @@ -3068,7 +3108,7 @@ bool GeneralRateModel::setSensitiveParameter(const ParameterId return true; } - if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, std::vector { _dynReactionBulk }, true)) + if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, _reaction.getDynReactionVector("liquid"), false)) { LOG(Debug) << "Found parameter " << pId << " in DynamicBulkReactionModel: Dir " << adDirection << " is set to " << adValue; return true; diff --git a/src/libcadet/model/GeneralRateModel.hpp b/src/libcadet/model/GeneralRateModel.hpp index 00e39fc76..01a4c9bc3 100644 --- a/src/libcadet/model/GeneralRateModel.hpp +++ b/src/libcadet/model/GeneralRateModel.hpp @@ -22,6 +22,7 @@ #include "cadet/StrongTypes.hpp" #include "cadet/SolutionExporter.hpp" #include "model/parts/ConvectionDispersionOperator.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "AutoDiff.hpp" #include "linalg/SparseMatrix.hpp" #include "linalg/BandMatrix.hpp" @@ -332,7 +333,9 @@ class GeneralRateModel : public UnitOperationBase // IExternalFunction* _extFun; //!< External function (owned by library user) ConvDispOperator _convDispOp; //!< Convection dispersion operator for interstitial volume transport - IDynamicReactionModel* _dynReactionBulk; //!< Dynamic reactions in the bulk volume + ReactionSystem _reaction; //!< Reaction system for bulk + std::vector _reacParticle; //!< Reaction systems for each particle type + linalg::BandMatrix* _jacP; //!< Particle jacobian diagonal blocks (all of them) linalg::FactorizableBandMatrix* _jacPdisc; //!< Particle jacobian diagonal blocks (all of them) with time derivatives from BDF method diff --git a/src/libcadet/model/GeneralRateModel2D-InitialConditions.cpp b/src/libcadet/model/GeneralRateModel2D-InitialConditions.cpp index 4b1d34658..0e3997bf1 100644 --- a/src/libcadet/model/GeneralRateModel2D-InitialConditions.cpp +++ b/src/libcadet/model/GeneralRateModel2D-InitialConditions.cpp @@ -645,7 +645,7 @@ void GeneralRateModel2D::consistentInitialState(const SimulationTime& simTime, d _parPorosity[type], _poreAccessFactor.data() + _disc.nComp * type, _binding[type], - (_dynReaction[type] && (_dynReaction[type]->numReactionsCombined() > 0)) ? _dynReaction[type] : nullptr + &_reacParticle[type] }; // This loop cannot be run in parallel without creating a Jacobian matrix for each thread which would increase memory usage diff --git a/src/libcadet/model/GeneralRateModel2D.cpp b/src/libcadet/model/GeneralRateModel2D.cpp index 7048f29a4..0824c5fd3 100644 --- a/src/libcadet/model/GeneralRateModel2D.cpp +++ b/src/libcadet/model/GeneralRateModel2D.cpp @@ -331,7 +331,7 @@ int schurComplementMultiplierGRM2D(void* userData, double const* x, double* z) GeneralRateModel2D::GeneralRateModel2D(UnitOpIdx unitOpIdx) : UnitOperationBase(unitOpIdx), - _dynReactionBulk(nullptr), _jacP(nullptr), _jacPdisc(nullptr), _jacPF(nullptr), _jacFP(nullptr), _jacInlet(), + _jacP(nullptr), _jacPdisc(nullptr), _jacPF(nullptr), _jacFP(nullptr), _jacInlet(), _analyticJac(true), _jacobianAdDirs(0), _factorizeJacobian(false), _tempState(nullptr), _initC(0), _singleRadiusInitC(true), _initCp(0), _singleRadiusInitCp(true), _initCs(0), _singleRadiusInitCs(true), _initState(0), _initStateDot(0) { @@ -341,8 +341,6 @@ GeneralRateModel2D::~GeneralRateModel2D() CADET_NOEXCEPT { delete[] _tempState; - delete _dynReactionBulk; - delete[] _jacPF; delete[] _jacFP; @@ -356,6 +354,9 @@ GeneralRateModel2D::~GeneralRateModel2D() CADET_NOEXCEPT delete[] _disc.boundOffset; delete[] _disc.strideBound; delete[] _disc.nBoundBeforeType; + + _reaction.clearDynamicReactionModels(); + _reacParticle.clear(); } unsigned int GeneralRateModel2D::numDofs() const CADET_NOEXCEPT @@ -416,7 +417,6 @@ bool GeneralRateModel2D::configureModelDiscretization(IParameterProvider& paramP _binding = std::vector(_disc.nParType, nullptr); bool bindingConfSuccess = true; clearDynamicReactionModels(); - _dynReaction = std::vector(_disc.nParType, nullptr); bool reactionConfSuccess = true; for (int parType = 0; parType < _disc.nParType; parType++) @@ -494,13 +494,6 @@ bool GeneralRateModel2D::configureModelDiscretization(IParameterProvider& paramP _singleBinding = !paramProvider.getInt("REACTION_PARTYPE_DEPENDENT"); else _singleBinding = _disc.nParType == 1; - - _dynReaction[parType] = helper.createDynamicReactionModel(dynReactModelName); - if (!_dynReaction[parType]) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactModelName); - - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction[parType]->usesParamProviderInDiscretizationConfig()); - reactionConfSuccess = reactionConfSuccess && _dynReaction[parType]->configureModelDiscretization(paramProvider, _disc.nComp, _disc.nBound + parType * _disc.nComp, _disc.boundOffset + parType * _disc.nComp) && reactionConfSuccess; } // Set particle geometry @@ -636,24 +629,89 @@ bool GeneralRateModel2D::configureModelDiscretization(IParameterProvider& paramP // ==== Construct and configure dynamic bulk reaction model - _dynReactionBulk = nullptr; - if (paramProvider.exists("REACTION_MODEL")) + _reaction.clearDynamicReactionModels(); + + _reacParticle.clear(); + _reacParticle.resize(_disc.nParType); + + + if (_disc.nParType > 0) { - const std::string dynReactName = paramProvider.getString("REACTION_MODEL"); - _dynReactionBulk = helper.createDynamicReactionModel(dynReactName); - if (!_dynReactionBulk) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactName); - if (_dynReactionBulk->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope("reaction_bulk"); + for (unsigned int par = 0; par < _disc.nParType; par++) + { - reactionConfSuccess = reactionConfSuccess && _dynReactionBulk->configureModelDiscretization(paramProvider, _disc.nComp, nullptr, nullptr); + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); + paramProvider.pushScope(particleScope); // particle_type_xxx + + ReactionSystem parReaction; + + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + int nReactions = paramProvider.getInt("NREAC_CROSS_PHASE"); + + reactionConfSuccess = _reacParticle[par].configureDiscretization("cross_phase", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + if (paramProvider.exists("NREAC_LIQUID")) + { + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + if (paramProvider.exists("NREAC_SOLID")) + { + int nReactions = paramProvider.getInt("NREAC_SOLID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("solid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + paramProvider.popScope(); // particle_type_xxx + + } - if (_dynReactionBulk->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); } - const bool transportSuccess = _convDispOp.configureModelDiscretization(paramProvider, helper, _disc.nComp, _disc.nCol, _disc.nRad, _dynReactionBulk); + bool hasBulkReaction = false; + if (paramProvider.exists("NREAC_LIQUID")) + { + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + hasBulkReaction = true; + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + else + { + _reaction.empty(); + } + + const bool transportSuccess = _convDispOp.configureModelDiscretization(paramProvider, helper, _disc.nComp, _disc.nCol, _disc.nRad, hasBulkReaction); // Setup the memory for tempState based on state vector _tempState = new double[numDofs()]; @@ -939,35 +997,25 @@ bool GeneralRateModel2D::configure(IParameterProvider& paramProvider) // Reconfigure reaction model bool dynReactionConfSuccess = true; - if (_dynReactionBulk && _dynReactionBulk->requiresConfiguration()) - { - paramProvider.pushScope("reaction_bulk"); - dynReactionConfSuccess = _dynReactionBulk->configure(paramProvider, _unitOpIdx, ParTypeIndep); - paramProvider.popScope(); - } + // Reconfigure reaction model + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; - if (_singleDynReaction) + for (unsigned int par = 0; par < _disc.nParType; par++) { - if (_dynReaction[0] && _dynReaction[0]->requiresConfiguration()) - { - paramProvider.pushScope("particle_type_000"); - paramProvider.pushScope("reaction"); - dynReactionConfSuccess = dynReactionConfSuccess && _dynReaction[0]->configure(paramProvider, _unitOpIdx, ParTypeIndep); - paramProvider.popScope(); - paramProvider.popScope(); - } - } - else - { - for (unsigned int type = 0; type < _disc.nParType; ++type) + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); + + if (paramProvider.exists(particleScope)) { - if (!_dynReaction[type] || !_dynReaction[type]->requiresConfiguration()) - continue; + paramProvider.pushScope(particleScope); + if (paramProvider.exists("NREAC_CROSS_PHASE")) + dynReactionConfSuccess = _reacParticle[par].configure("cross_phase", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reacParticle[par].configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_SOLID")) + dynReactionConfSuccess = _reacParticle[par].configure("solid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; - paramProvider.pushScope("particle_type_" + std::string(3 - std::to_string(type).length(), '0') + std::to_string(type)); - paramProvider.pushScope("adsorption"); - dynReactionConfSuccess = dynReactionConfSuccess && _dynReaction[type]->configure(paramProvider, _unitOpIdx, type); - paramProvider.popScope(); paramProvider.popScope(); } } @@ -986,12 +1034,12 @@ unsigned int GeneralRateModel2D::threadLocalMemorySize() const CADET_NOEXCEPT if (_binding[i] && _binding[i]->requiresWorkspace()) lms.fitBlock(_binding[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); - if (_dynReaction[i] && _dynReaction[i]->requiresWorkspace()) - lms.fitBlock(_dynReaction[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); + _reacParticle[i].setWorkspaceRequirements("cross_phase", 1, _disc.nComp, &_disc.strideBound[i], lms); + _reacParticle[i].setWorkspaceRequirements("liquid", 1, _disc.nComp, &_disc.strideBound[i], lms); + _reacParticle[i].setWorkspaceRequirements("solid", 1, _disc.nComp, &_disc.strideBound[i], lms); } + _reaction.setWorkspaceRequirements("liquid", _disc.nComp, 0, lms); - if (_dynReactionBulk && _dynReactionBulk->requiresWorkspace()) - lms.fitBlock(_dynReactionBulk->workspaceSize(_disc.nComp, 0, nullptr)); const unsigned int maxStrideBound = *std::max_element(_disc.strideBound, _disc.strideBound + _disc.nParType); lms.add(_disc.nComp + maxStrideBound); @@ -1359,7 +1407,7 @@ template ::enabled()); - if (!_dynReactionBulk || (_dynReactionBulk->numReactionsLiquid() == 0)) + if (! _reaction.getDynReactionVector("liquid")[0]) return 0; // Get offsets @@ -1376,12 +1424,18 @@ int GeneralRateModel2D::residualBulk(double t, unsigned int secIdx, StateType co const double z = (0.5 + static_cast(axialCell)) / static_cast(_disc.nCol); const ColumnPosition colPos{z, r, 0.0}; - _dynReactionBulk->residualLiquidAdd(t, secIdx, colPos, y, res, -1.0, tlmAlloc); + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) + { + if (!_reaction.getDynReactionVector("liquid")[i]) + continue; + + _reaction.getDynReactionVector("liquid")[i]->residualFluxAdd(t, secIdx, colPos, _disc.nComp, y, res, -1.0, tlmAlloc); if (wantJac) { // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - _dynReactionBulk->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(y), -1.0, _convDispOp.jacobian().row(colCell * idxr.strideColRadialCell()), tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _disc.nComp, reinterpret_cast(y), -1.0, _convDispOp.jacobian().row(colCell * idxr.strideColRadialCell()), tlmAlloc); + } } } @@ -1441,7 +1495,7 @@ int GeneralRateModel2D::residualParticle(double t, unsigned int parType, unsigne _parPorosity[parType], _poreAccessFactor.data() + _disc.nComp * parType, _binding[parType], - (_dynReaction[parType] && (_dynReaction[parType]->numReactionsCombined() > 0)) ? _dynReaction[parType] : nullptr + &_reacParticle[parType] }; // Loop over particle cells @@ -2368,7 +2422,7 @@ bool GeneralRateModel2D::setParameter(const ParameterId& pId, double value) if (_convDispOp.setParameter(pId, value)) return true; - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), true)) return true; } @@ -2388,7 +2442,7 @@ bool GeneralRateModel2D::setParameter(const ParameterId& pId, int value) if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), true)) return true; } @@ -2402,7 +2456,7 @@ bool GeneralRateModel2D::setParameter(const ParameterId& pId, bool value) if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), true)) return true; } @@ -2439,7 +2493,7 @@ void GeneralRateModel2D::setSensitiveParameterValue(const ParameterId& pId, doub if (_convDispOp.setSensitiveParameterValue(_sensParams, pId, value)) return; - if (model::setSensitiveParameterValue(pId, value, _sensParams, std::vector{ _dynReactionBulk }, true)) + if (model::setSensitiveParameterValue(pId, value, _sensParams, _reaction.getDynReactionVector("liquid"), true)) return; } @@ -2520,7 +2574,7 @@ bool GeneralRateModel2D::setSensitiveParameter(const ParameterId& pId, unsigned return true; } - if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, std::vector { _dynReactionBulk }, true)) + if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, _reaction.getDynReactionVector("liquid"), true)) { LOG(Debug) << "Found parameter " << pId << " in DynamicBulkReactionModel: Dir " << adDirection << " is set to " << adValue; return true; diff --git a/src/libcadet/model/GeneralRateModel2D.hpp b/src/libcadet/model/GeneralRateModel2D.hpp index 873333f3a..10e21b8b2 100644 --- a/src/libcadet/model/GeneralRateModel2D.hpp +++ b/src/libcadet/model/GeneralRateModel2D.hpp @@ -22,6 +22,7 @@ #include "cadet/StrongTypes.hpp" #include "cadet/SolutionExporter.hpp" #include "model/parts/TwoDimensionalConvectionDispersionOperator.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "AutoDiff.hpp" #include "linalg/SparseMatrix.hpp" #include "linalg/BandMatrix.hpp" @@ -277,7 +278,8 @@ class GeneralRateModel2D : public UnitOperationBase // IExternalFunction* _extFun; //!< External function (owned by library user) parts::TwoDimensionalConvectionDispersionOperator _convDispOp; //!< Convection dispersion operator for interstitial volume transport - IDynamicReactionModel* _dynReactionBulk; //!< Dynamic reactions in the bulk volume + ReactionSystem _reaction; //!< Reaction system for bulk + std::vector _reacParticle; //!< Reaction systems for particle bound states linalg::BandMatrix* _jacP; //!< Particle jacobian diagonal blocks (all of them) linalg::FactorizableBandMatrix* _jacPdisc; //!< Particle jacobian diagonal blocks (all of them) with time derivatives from BDF method diff --git a/src/libcadet/model/LumpedRateModelWithPores-InitialConditions.cpp b/src/libcadet/model/LumpedRateModelWithPores-InitialConditions.cpp index b0e1eacd1..8c74e0444 100644 --- a/src/libcadet/model/LumpedRateModelWithPores-InitialConditions.cpp +++ b/src/libcadet/model/LumpedRateModelWithPores-InitialConditions.cpp @@ -401,7 +401,7 @@ void LumpedRateModelWithPores::consistentInitialState(const Si _parPorosity[type], _poreAccessFactor.data() + _disc.nComp * type, _binding[type], - (_dynReaction[type] && (_dynReaction[type]->numReactionsCombined() > 0)) ? _dynReaction[type] : nullptr + &_reacParticle[type] }; const int localOffsetToParticle = idxr.offsetCp(ParticleTypeIndex{type}, ParticleIndex{static_cast(pblk)}); diff --git a/src/libcadet/model/LumpedRateModelWithPores.cpp b/src/libcadet/model/LumpedRateModelWithPores.cpp index f39024040..df8915eb4 100644 --- a/src/libcadet/model/LumpedRateModelWithPores.cpp +++ b/src/libcadet/model/LumpedRateModelWithPores.cpp @@ -63,7 +63,7 @@ int schurComplementMultiplierLRMPores(void* userData, double const* x, double* z template LumpedRateModelWithPores::LumpedRateModelWithPores(UnitOpIdx unitOpIdx) : UnitOperationBase(unitOpIdx), - _dynReactionBulk(nullptr), _filmDiffDep(nullptr), _jacP(0), _jacPdisc(0), _jacPF(0), _jacFP(0), _jacInlet(), _analyticJac(true), + _filmDiffDep(nullptr), _jacP(0), _jacPdisc(0), _jacPF(0), _jacFP(0), _jacInlet(), _analyticJac(true), _jacobianAdDirs(0), _factorizeJacobian(false), _tempState(nullptr), _initC(0), _initCp(0), _initCs(0), _initState(0), _initStateDot(0) { @@ -73,9 +73,8 @@ template LumpedRateModelWithPores::~LumpedRateModelWithPores() CADET_NOEXCEPT { delete[] _tempState; - - delete _dynReactionBulk; delete _filmDiffDep; + _reaction.clearDynamicReactionModels(); } template @@ -166,10 +165,9 @@ bool LumpedRateModelWithPores::configureModelDiscretization(IP clearBindingModels(); _binding = std::vector(_disc.nParType, nullptr); bool bindingConfSuccess = true; - clearDynamicReactionModels(); - _dynReaction = std::vector(_disc.nParType, nullptr); - bool reactionConfSuccess = true; + _reaction.clearDynamicReactionModels(); + bool reactionConfSuccess = true; for (int parType = 0; parType < _disc.nParType; parType++) { paramProvider.pushScope("particle_type_" + std::string(3 - std::to_string(parType).length(), '0') + std::to_string(parType)); @@ -202,13 +200,6 @@ bool LumpedRateModelWithPores::configureModelDiscretization(IP _singleBinding = !paramProvider.getInt("REACTION_PARTYPE_DEPENDENT"); else _singleBinding = _disc.nParType == 1; - - _dynReaction[parType] = helper.createDynamicReactionModel(dynReactModelName); - if (!_dynReaction[parType]) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactModelName); - - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction[parType]->usesParamProviderInDiscretizationConfig()); - reactionConfSuccess = reactionConfSuccess && _dynReaction[parType]->configureModelDiscretization(paramProvider, _disc.nComp, _disc.nBound + parType * _disc.nComp, _disc.boundOffset + parType * _disc.nComp) && reactionConfSuccess; } // Set particle geometry @@ -303,23 +294,91 @@ bool LumpedRateModelWithPores::configureModelDiscretization(IP // Set whether analytic Jacobian is used useAnalyticJacobian(analyticJac); - // ==== Construct and configure bulk dynamic reaction model - _dynReactionBulk = nullptr; - if (paramProvider.exists("REACTION_MODEL")) + // ==== Construct and configure dynamic reaction model + _reaction.clearDynamicReactionModels(); + + _reacParticle.clear(); + _reacParticle.resize(_disc.nParType); + + + + bool hasCrossPhaseReac = false; + bool hasSolidReac = false; + bool hasPoreReac = false; + bool hasLiquidReac = false; + + if (_disc.nParType > 0) { - const std::string dynReactName = paramProvider.getString("REACTION_MODEL"); - _dynReactionBulk = helper.createDynamicReactionModel(dynReactName); - if (!_dynReactionBulk) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactName); + + for (unsigned int par = 0; par < _disc.nParType; par++) + { - if (_dynReactionBulk->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope("reaction_bulk"); + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); + paramProvider.pushScope(particleScope); // particle_type_xxx - reactionConfSuccess = reactionConfSuccess && _dynReactionBulk->configureModelDiscretization(paramProvider, _disc.nComp, nullptr, nullptr); + ReactionSystem parReaction; + + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + int nReactions = paramProvider.getInt("NREAC_CROSS_PHASE"); + + reactionConfSuccess = _reacParticle[par].configureDiscretization("cross_phase", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + if (paramProvider.exists("NREAC_LIQUID")) + { + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + if (paramProvider.exists("NREAC_SOLID")) + { + int nReactions = paramProvider.getInt("NREAC_SOLID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("solid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + paramProvider.popScope(); // particle_type_xxx + + } - if (_dynReactionBulk->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); + } + if (paramProvider.exists("NREAC_LIQUID")) + { + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + else + { + _reaction.empty(); } // Setup the memory for tempState based on state vector @@ -500,6 +559,7 @@ bool LumpedRateModelWithPores::configure(IParameterProvider& p // Reconfigure binding model bool bindingConfSuccess = true; + bool dynReactionConfSuccess = true; if (!_binding.empty()) { if (_singleBinding) @@ -528,38 +588,25 @@ bool LumpedRateModelWithPores::configure(IParameterProvider& p } } } - // Reconfigure reaction model - bool dynReactionConfSuccess = true; - if (_dynReactionBulk && _dynReactionBulk->requiresConfiguration()) - { - paramProvider.pushScope("reaction_bulk"); - dynReactionConfSuccess = _dynReactionBulk->configure(paramProvider, _unitOpIdx, ParTypeIndep); - paramProvider.popScope(); - } + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; - if (_singleDynReaction) - { - if (_dynReaction[0] && _dynReaction[0]->requiresConfiguration()) - { - paramProvider.pushScope("particle_type_000"); - paramProvider.pushScope("reaction"); - dynReactionConfSuccess = dynReactionConfSuccess && _dynReaction[0]->configure(paramProvider, _unitOpIdx, ParTypeIndep); - paramProvider.popScope(); - paramProvider.popScope(); - } - } - else + for (unsigned int par = 0; par < _disc.nParType; par++) { - for (unsigned int type = 0; type < _disc.nParType; ++type) + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); + + if (paramProvider.exists(particleScope)) { - if (!_dynReaction[type] || !_dynReaction[type]->requiresConfiguration()) - continue; + paramProvider.pushScope(particleScope); + if (paramProvider.exists("NREAC_CROSS_PHASE")) + dynReactionConfSuccess = _reacParticle[par].configure("cross_phase", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reacParticle[par].configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_SOLID")) + dynReactionConfSuccess = _reacParticle[par].configure("solid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; - paramProvider.pushScope("particle_type_" + std::string(3 - std::to_string(type).length(), '0') + std::to_string(type)); - paramProvider.pushScope("adsorption"); - dynReactionConfSuccess = dynReactionConfSuccess && _dynReaction[type]->configure(paramProvider, _unitOpIdx, type); - paramProvider.popScope(); paramProvider.popScope(); } } @@ -572,18 +619,16 @@ unsigned int LumpedRateModelWithPores::threadLocalMemorySize() { LinearMemorySizer lms; - // Memory for residualImpl() - for (unsigned int i = 0; i < _disc.nParType; ++i) + // Handle all reactions + for (unsigned int parType = 0; parType < _disc.nParType; ++parType) { - if (_binding[i] && _binding[i]->requiresWorkspace()) - lms.fitBlock(_binding[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); + _reacParticle[parType].setWorkspaceRequirements("cross_phase", 1, _disc.nComp, &_disc.strideBound[parType], lms); + _reacParticle[parType].setWorkspaceRequirements("liquid", 1, _disc.nComp, &_disc.strideBound[parType], lms); + _reacParticle[parType].setWorkspaceRequirements("solid", 1, _disc.nComp, &_disc.strideBound[parType], lms); - if (_dynReaction[i] && _dynReaction[i]->requiresWorkspace()) - lms.fitBlock(_dynReaction[i]->workspaceSize(_disc.nComp, _disc.strideBound[i], _disc.nBound + i * _disc.nComp)); } + _reaction.setWorkspaceRequirements("liquid", _disc.nComp, 0, lms); - if (_dynReactionBulk && _dynReactionBulk->requiresWorkspace()) - lms.fitBlock(_dynReactionBulk->workspaceSize(_disc.nComp, 0, nullptr)); const unsigned int maxStrideBound = *std::max_element(_disc.strideBound, _disc.strideBound + _disc.nParType); lms.add(_disc.nComp + maxStrideBound); @@ -977,7 +1022,7 @@ int LumpedRateModelWithPores::residualBulk(double t, unsigned else _convDispOp.jacobian(*this, t, secIdx, yBase, nullptr, nullptr); - if (!_dynReactionBulk || (_dynReactionBulk->numReactionsLiquid() == 0)) + if (_reaction.getDynReactionVector("liquid").empty() || !_reaction.getDynReactionVector("liquid")[0]) return 0; // Get offsets @@ -988,14 +1033,22 @@ int LumpedRateModelWithPores::residualBulk(double t, unsigned for (unsigned int col = 0; col < _disc.nCol; ++col, y += idxr.strideColCell(), res += idxr.strideColCell()) { - const ColumnPosition colPos{(0.5 + static_cast(col)) / static_cast(_disc.nCol), 0.0, 0.0}; + const ColumnPosition colPos{ (0.5 + static_cast(col)) / static_cast(_disc.nCol), 0.0, 0.0 }; + + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) + { + + if (!_reaction.getDynReactionVector("liquid")[i]) + continue; + if (wantRes) - _dynReactionBulk->residualLiquidAdd(t, secIdx, colPos, y, res, -1.0, tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->residualFluxAdd(t, secIdx, colPos, _disc.nComp, y, res, -1.0, tlmAlloc); if (wantJac) { // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - _dynReactionBulk->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(y), -1.0, _convDispOp.jacobian().row(col * idxr.strideColCell()), tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _disc.nComp, reinterpret_cast(y), -1.0, _convDispOp.jacobian().row(col * idxr.strideColCell()), tlmAlloc); + } } } @@ -1029,7 +1082,7 @@ int LumpedRateModelWithPores::residualParticle(double t, unsig _parPorosity[parType], _poreAccessFactor.data() + _disc.nComp * parType, _binding[parType], - (_dynReaction[parType] && (_dynReaction[parType]->numReactionsCombined() > 0)) ? _dynReaction[parType] : nullptr + &_reacParticle[parType] }; // Handle time derivatives, binding, dynamic reactions @@ -1519,7 +1572,7 @@ bool LumpedRateModelWithPores::setParameter(const ParameterId& } } - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1531,7 +1584,11 @@ bool LumpedRateModelWithPores::setParameter(const ParameterId& { if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) + return true; + } + { + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1543,7 +1600,7 @@ bool LumpedRateModelWithPores::setParameter(const ParameterId& { if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, std::vector{ _dynReactionBulk }, true)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -1593,11 +1650,10 @@ void LumpedRateModelWithPores::setSensitiveParameterValue(cons if (param) { param->setValue(value); - return; } } - if (model::setSensitiveParameterValue(pId, value, _sensParams, std::vector{ _dynReactionBulk }, true)) + if (model::setSensitiveParameterValue(pId, value, _sensParams, _reaction.getDynReactionVector("liquid"), false)) return; } @@ -1680,7 +1736,7 @@ bool LumpedRateModelWithPores::setSensitiveParameter(const Par } } - if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, std::vector { _dynReactionBulk }, true)) + if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, _reaction.getDynReactionVector("liquid"), false)) { LOG(Debug) << "Found parameter " << pId << " in DynamicBulkReactionModel: Dir " << adDirection << " is set to " << adValue; return true; diff --git a/src/libcadet/model/LumpedRateModelWithPores.hpp b/src/libcadet/model/LumpedRateModelWithPores.hpp index 444886882..fe9026f75 100644 --- a/src/libcadet/model/LumpedRateModelWithPores.hpp +++ b/src/libcadet/model/LumpedRateModelWithPores.hpp @@ -29,6 +29,7 @@ #include "Memory.hpp" #include "model/ModelUtils.hpp" #include "ParameterMultiplexing.hpp" +#include "model/reaction/ReactionSystem.hpp" #include #include @@ -275,9 +276,11 @@ class LumpedRateModelWithPores : public UnitOperationBase // IExternalFunction* _extFun; //!< External function (owned by library user) ConvDispOperator _convDispOp; //!< Convection dispersion operator for interstitial volume transport - IDynamicReactionModel* _dynReactionBulk; //!< Dynamic reactions in the bulk volume IParameterParameterDependence* _filmDiffDep; //!< Film diffusion dependency on local velocity + ReactionSystem _reaction; //!< Reaction system for bulk + std::vector _reacParticle; //!< Reaction systems for particle bound states + std::vector _jacP; //!< Particle jacobian diagonal blocks (all of them for each particle type) std::vector _jacPdisc; //!< Particle jacobian diagonal blocks (all of them for each particle type) with time derivatives from BDF method diff --git a/src/libcadet/model/LumpedRateModelWithoutPores.cpp b/src/libcadet/model/LumpedRateModelWithoutPores.cpp index 4393a8720..9a31a644d 100644 --- a/src/libcadet/model/LumpedRateModelWithoutPores.cpp +++ b/src/libcadet/model/LumpedRateModelWithoutPores.cpp @@ -125,6 +125,7 @@ template LumpedRateModelWithoutPores::~LumpedRateModelWithoutPores() CADET_NOEXCEPT { delete[] _tempState; + _reaction.clearDynamicReactionModels(); } template @@ -260,23 +261,63 @@ bool LumpedRateModelWithoutPores::configureModelDiscretization // ==== Construct and configure dynamic reaction model bool reactionConfSuccess = true; - clearDynamicReactionModels(); - _dynReaction.push_back(nullptr); + _reaction.clearDynamicReactionModels(); - if (paramProvider.exists("REACTION_MODEL")) + bool hasCrossPhaseReac = false; + bool hasSolidReac = false; + bool hasLiquidReac = false; + + if (paramProvider.exists("NREAC_LIQUID")) { - _dynReaction[0] = helper.createDynamicReactionModel(paramProvider.getString("REACTION_MODEL")); - if (!_dynReaction[0]) - throw InvalidParameterException("Unknown dynamic reaction model " + paramProvider.getString("REACTION_MODEL")); + hasLiquidReac = true; + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } - if (_dynReaction[0]->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope("reaction"); + if (paramProvider.exists("particle_type_000")) + { + paramProvider.pushScope("particle_type_000"); - reactionConfSuccess = _dynReaction[0]->configureModelDiscretization(paramProvider, _disc.nComp, _disc.nBound, _disc.boundOffset); + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + hasCrossPhaseReac = true; + int nReactions = paramProvider.getInt("NREAC_CROSS_PHASE"); + reactionConfSuccess = _reaction.configureDiscretization("cross_phase", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + if (paramProvider.exists("NREAC_SOLID")) + { + hasSolidReac = true; + int nReactions = paramProvider.getInt("NREAC_SOLID"); + reactionConfSuccess = _reaction.configureDiscretization("solid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } - if (_dynReaction[0]->usesParamProviderInDiscretizationConfig()) paramProvider.popScope(); } + if (!hasLiquidReac && !hasCrossPhaseReac && !hasSolidReac) + { + _reaction.empty(); + } // Setup the memory for tempState based on state vector _tempState = new double[numDofs()]; @@ -311,7 +352,7 @@ bool LumpedRateModelWithoutPores::configure(IParameterProvider } // Reconfigure binding model - paramProvider.pushScope("particle_type_000"); + paramProvider.pushScope("particle_type_000"); // particle_type_000 bool bindingConfSuccess = true; if (_binding[0] && paramProvider.exists("adsorption") && _binding[0]->requiresConfiguration()) @@ -321,18 +362,19 @@ bool LumpedRateModelWithoutPores::configure(IParameterProvider paramProvider.popScope(); } - paramProvider.popScope(); - - // Reconfigure dynamic reaction model - bool reactionConfSuccess = true; - if (_dynReaction[0] && paramProvider.exists("reaction") && _dynReaction[0]->requiresConfiguration()) - { - paramProvider.pushScope("reaction"); - reactionConfSuccess = _dynReaction[0]->configure(paramProvider, _unitOpIdx, cadet::ParTypeIndep); - paramProvider.popScope(); - } - - return transportSuccess && bindingConfSuccess && reactionConfSuccess; + // Reconfigure reaction model + bool dynReactionConfSuccess = true; + if (paramProvider.exists("NREAC_CROSS_PHASE")) + dynReactionConfSuccess = _reaction.configure("cross_phase", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_SOLID")) + dynReactionConfSuccess = _reaction.configure("solid", 0, _unitOpIdx, paramProvider)&& dynReactionConfSuccess; + + paramProvider.popScope();// particle_type_000 + + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + + return transportSuccess && bindingConfSuccess && dynReactionConfSuccess; } template @@ -344,12 +386,10 @@ unsigned int LumpedRateModelWithoutPores::threadLocalMemorySiz if (_binding[0] && _binding[0]->requiresWorkspace()) lms.addBlock(_binding[0]->workspaceSize(_disc.nComp, _disc.strideBound, _disc.nBound)); - if (_dynReaction[0]) - { - lms.addBlock(_dynReaction[0]->workspaceSize(_disc.nComp, _disc.strideBound, _disc.nBound)); - lms.add(_disc.strideBound); - lms.add(_disc.strideBound * (_disc.strideBound + _disc.nComp)); - } + _reaction.setWorkspaceRequirements("cross_phase", _disc.nComp, _disc.strideBound, lms); + _reaction.setWorkspaceRequirements("solid", _disc.nComp, _disc.strideBound, lms); + _reaction.setWorkspaceRequirements("liquid", _disc.nComp, _disc.strideBound, lms); + lms.commit(); const std::size_t resKernelSize = lms.bufferSize(); @@ -680,7 +720,7 @@ int LumpedRateModelWithoutPores::residualImpl(double t, unsign _totalPorosity, nullptr, _binding[0], - (_dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)) ? _dynReaction[0] : nullptr + &_reaction }; // Midpoint of current column cell (z coordinate) - needed in externally dependent adsorption kinetic @@ -1193,7 +1233,7 @@ void LumpedRateModelWithoutPores::consistentInitialState(const _totalPorosity, nullptr, _binding[0], - (_dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)) ? _dynReaction[0] : nullptr + nullptr }; const int localOffsetToCell = idxr.offsetC() + col * idxr.strideColCell(); diff --git a/src/libcadet/model/LumpedRateModelWithoutPores.hpp b/src/libcadet/model/LumpedRateModelWithoutPores.hpp index 1d60db0f5..3eb9bde9a 100644 --- a/src/libcadet/model/LumpedRateModelWithoutPores.hpp +++ b/src/libcadet/model/LumpedRateModelWithoutPores.hpp @@ -28,6 +28,7 @@ #include "linalg/Gmres.hpp" #include "Memory.hpp" #include "model/ModelUtils.hpp" +#include "model/reaction/ReactionSystem.hpp" #include #include @@ -251,6 +252,8 @@ class LumpedRateModelWithoutPores : public UnitOperationBase std::vector _initState; //!< Initial conditions for state vector if given std::vector _initStateDot; //!< Initial conditions for time derivative + ReactionSystem _reaction; + BENCH_TIMER(_timerResidual) BENCH_TIMER(_timerResidualPar) BENCH_TIMER(_timerResidualSens) diff --git a/src/libcadet/model/LumpedRateModelWithoutPoresDG.cpp b/src/libcadet/model/LumpedRateModelWithoutPoresDG.cpp index 4741f8d3a..5e83edcfc 100644 --- a/src/libcadet/model/LumpedRateModelWithoutPoresDG.cpp +++ b/src/libcadet/model/LumpedRateModelWithoutPoresDG.cpp @@ -224,24 +224,67 @@ namespace cadet paramProvider.popScope(); // ==== Construct and configure dynamic reaction model - bool reactionConfSuccess = true; + _dynReaction.resize(1, nullptr); clearDynamicReactionModels(); - _dynReaction.push_back(nullptr); - if (paramProvider.exists("REACTION_MODEL")) + bool reactionConfSuccess = true; + _reaction.clearDynamicReactionModels(); + + bool hasCrossPhaseReac = false; + bool hasSolidReac = false; + bool hasLiquidReac = false; + + if (paramProvider.exists("NREAC_LIQUID")) { - _dynReaction[0] = helper.createDynamicReactionModel(paramProvider.getString("REACTION_MODEL")); - if (!_dynReaction[0]) - throw InvalidParameterException("Unknown dynamic reaction model " + paramProvider.getString("REACTION_MODEL")); + hasLiquidReac = true; + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } - if (_dynReaction[0]->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope("reaction"); + if (paramProvider.exists("particle_type_000")) + { + paramProvider.pushScope("particle_type_000"); - reactionConfSuccess = _dynReaction[0]->configureModelDiscretization(paramProvider, _disc.nComp, _disc.nBound, _disc.boundOffset); + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + hasCrossPhaseReac = true; + int nReactions = paramProvider.getInt("NREAC_CROSS_PHASE"); + reactionConfSuccess = _reaction.configureDiscretization("cross_phase", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + if (paramProvider.exists("NREAC_SOLID")) + { + hasSolidReac = true; + int nReactions = paramProvider.getInt("NREAC_SOLID"); + reactionConfSuccess = _reaction.configureDiscretization("solid", + 0, + nReactions, + _disc.nComp, + _disc.nBound, + _disc.boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } - if (_dynReaction[0]->usesParamProviderInDiscretizationConfig()) paramProvider.popScope(); } + if (!hasLiquidReac && !hasCrossPhaseReac && !hasSolidReac) + { + _reaction.empty(); + } // Setup the memory for tempState based on state vector if (firstConfigCall) @@ -286,25 +329,37 @@ namespace cadet paramProvider.popScope(); } - paramProvider.popScope(); - // Reconfigure dynamic reaction model - bool reactionConfSuccess = true; - if (_dynReaction[0] && paramProvider.exists("reaction") && _dynReaction[0]->requiresConfiguration()) + bool dynReactionConfSuccess = true; + bool hasReaction = false; + if (paramProvider.exists("NREAC_CROSS_PHASE")) { - paramProvider.pushScope("reaction"); - reactionConfSuccess = _dynReaction[0]->configure(paramProvider, _unitOpIdx, cadet::ParTypeIndep); - paramProvider.popScope(); + dynReactionConfSuccess = _reaction.configure("cross_phase", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + hasReaction = true; + } + if (paramProvider.exists("NREAC_SOLID")) + { + dynReactionConfSuccess = _reaction.configure("solid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + hasReaction = true; + } - setPattern(_jac, true, _dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)); - setPattern(_jacDisc, true, _dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)); + paramProvider.popScope();// particle_type_000 + + if (paramProvider.exists("NREAC_LIQUID")) + { + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + hasReaction = true; + } + + setPattern(_jac, true, hasReaction); + setPattern(_jacDisc, true, hasReaction); // the solver repetitively solves the linear system with a static pattern of the jacobian (set above). // The goal of analyzePattern() is to reorder the nonzero elements of the matrix, such that the factorization step creates less fill-in _linearSolver->analyzePattern(_jacDisc); - return bindingConfSuccess && reactionConfSuccess; + return bindingConfSuccess && dynReactionConfSuccess; } unsigned int LumpedRateModelWithoutPoresDG::threadLocalMemorySize() const CADET_NOEXCEPT @@ -315,12 +370,9 @@ namespace cadet if (_binding[0] && _binding[0]->requiresWorkspace()) lms.addBlock(_binding[0]->workspaceSize(_disc.nComp, _disc.strideBound, _disc.nBound)); - if (_dynReaction[0]) - { - lms.addBlock(_dynReaction[0]->workspaceSize(_disc.nComp, _disc.strideBound, _disc.nBound)); - lms.add(_disc.strideBound); - lms.add(_disc.strideBound * (_disc.strideBound + _disc.nComp)); - } + _reaction.setWorkspaceRequirements("cross_phase", _disc.nComp, _disc.strideBound, lms); + _reaction.setWorkspaceRequirements("solid", _disc.nComp, _disc.strideBound, lms); + _reaction.setWorkspaceRequirements("liquid", _disc.nComp, _disc.strideBound, lms); lms.commit(); const std::size_t resKernelSize = lms.bufferSize(); @@ -659,7 +711,7 @@ namespace cadet _totalPorosity, nullptr, _binding[0], - (_dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)) ? _dynReaction[0] : nullptr + &_reaction }; // Relative position of current node - needed in externally dependent adsorption kinetic @@ -1169,7 +1221,7 @@ namespace cadet _totalPorosity, nullptr, _binding[0], - (_dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)) ? _dynReaction[0] : nullptr + nullptr }; const int localOffsetToCell = idxr.offsetC() + point * idxr.strideColNode(); @@ -1296,7 +1348,7 @@ namespace cadet } CADET_PARFOR_END; // restore _jacDisc pattern - setPattern(_jacDisc, true, _dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)); + setPattern(_jacDisc, true, _reaction.hasReactions()); } @@ -1416,7 +1468,7 @@ namespace cadet } // reset jacobian pattern - setPattern(_jacDisc, true, _dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)); + setPattern(_jacDisc, true,_reaction.hasReactions()); } @@ -1647,7 +1699,7 @@ namespace cadet multiplyWithJacobian(simTime, simState, sensY, -1.0, 1.0, sensYdot); // Note that we have correctly negated the right hand side - setPattern(_jacDisc, true, _dynReaction[0] && (_dynReaction[0]->numReactionsCombined() > 0)); + setPattern(_jacDisc, true, _reaction.hasReactions()); //for (int entry = 0; entry < _jacDisc.nonZeros(); entry++) // _jacDisc.valuePtr()[entry] = 0.0; diff --git a/src/libcadet/model/LumpedRateModelWithoutPoresDG.hpp b/src/libcadet/model/LumpedRateModelWithoutPoresDG.hpp index d2ae655cc..da7c11d22 100644 --- a/src/libcadet/model/LumpedRateModelWithoutPoresDG.hpp +++ b/src/libcadet/model/LumpedRateModelWithoutPoresDG.hpp @@ -25,6 +25,7 @@ #include "cadet/SolutionExporter.hpp" #include "model/parts/ConvectionDispersionOperatorDG.hpp" #include "model/particle/ParticleModel.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "AutoDiff.hpp" #include "linalg/SparseMatrix.hpp" #include "linalg/BandMatrix.hpp" @@ -244,6 +245,8 @@ namespace cadet active _totalPorosity; //!< Total porosity \f$ \varepsilon_t \f$ + ReactionSystem _reaction; + bool _analyticJac; //!< Determines whether AD or analytic Jacobians are used unsigned int _jacobianAdDirs; //!< Number of AD seed vectors required for Jacobian computation bool _factorizeJacobian; //!< Determines whether the Jacobian needs to be factorized diff --git a/src/libcadet/model/MultiChannelTransportModel.cpp b/src/libcadet/model/MultiChannelTransportModel.cpp index 5ad64c1c9..c659f0b7d 100644 --- a/src/libcadet/model/MultiChannelTransportModel.cpp +++ b/src/libcadet/model/MultiChannelTransportModel.cpp @@ -317,7 +317,7 @@ namespace model { MultiChannelTransportModel::MultiChannelTransportModel(UnitOpIdx unitOpIdx) : UnitOperationBase(unitOpIdx), -_dynReactionBulk{ }, _jacInlet(), + _jacInlet(), _analyticJac(true), _jacobianAdDirs(0), _factorizeJacobian(false), _tempState(nullptr), _initC(0), _singleRadiusInitC(true), _initState(0), _initStateDot(0) { @@ -326,8 +326,7 @@ _dynReactionBulk{ }, _jacInlet(), MultiChannelTransportModel::~MultiChannelTransportModel() CADET_NOEXCEPT { delete[] _tempState; - for (auto* reac : _dynReactionBulk) - delete reac; + _reaction.clearDynamicReactionModels(); } unsigned int MultiChannelTransportModel::numDofs() const CADET_NOEXCEPT @@ -393,85 +392,16 @@ bool MultiChannelTransportModel::configureModelDiscretization(IParameterProvider // ==== Construct and configure dynamic reaction model bool reactionConfSuccess = true; - _oldReactionInterface = false; - - _dynReactionBulk.resize(1,nullptr); - if (paramProvider.exists("REACTION_MODEL")) + + _reaction.clearDynamicReactionModels(); + if (paramProvider.exists("NREAC_LIQUID")) { - _oldReactionInterface = true; - const std::string dynReactName = paramProvider.getString("REACTION_MODEL"); - _dynReactionBulk[0] = helper.createDynamicReactionModel(dynReactName); - if (!_dynReactionBulk[0]) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactName); - - if (_dynReactionBulk[0]->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope("reaction_bulk"); - - reactionConfSuccess = _dynReactionBulk[0]->configureModelDiscretization(paramProvider, _disc.nComp, nullptr, nullptr); - - if (_dynReactionBulk[0]->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", 0, nReactions, _disc.nComp, nullptr, nullptr, paramProvider, helper) && reactionConfSuccess; } - else if (paramProvider.exists("reaction_bulk")) + else { - paramProvider.pushScope("reaction_bulk"); - - if (paramProvider.exists("NREAC")) - { - int nReactions = paramProvider.getInt("NREAC"); - - if (nReactions <= 0) - { - paramProvider.popScope(); - throw InvalidParameterException("CSTR-Configuration: number of reaction must be positive, please check your configuration"); - } - _dynReactionBulk.resize(nReactions, nullptr); - - for (int i = 0; i < nReactions; ++i) { - - char reactionKey[32]; - snprintf(reactionKey, sizeof(reactionKey), "reaction_model_%03d", i); - - if (!paramProvider.exists(reactionKey)) { - paramProvider.popScope(); - throw InvalidParameterException("Missing reaction model definition for " + std::string(reactionKey)); - } - - paramProvider.pushScope(reactionKey); - - if (!paramProvider.exists("REACTION_TYPE")) { - paramProvider.popScope(); - throw InvalidParameterException("Missing 'type' parameter for " + std::string(reactionKey)); - } - - std::string reactionType = paramProvider.getString("REACTION_TYPE"); - paramProvider.popScope(); - _dynReactionBulk[i] = helper.createDynamicReactionModel(reactionType); - - if (!_dynReactionBulk[i]) { - paramProvider.popScope(); - throw InvalidParameterException("Unknown dynamic reaction model " + reactionType + - " for " + reactionKey); - } - - if (_dynReactionBulk[i]->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope(reactionKey); - - reactionConfSuccess = _dynReactionBulk[i]->configureModelDiscretization(paramProvider, _disc.nComp, nullptr, nullptr) && reactionConfSuccess; - - if (!reactionConfSuccess) { - if (_dynReactionBulk[i]->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); - paramProvider.popScope(); - throw InvalidParameterException("Failed to configure reaction model " + reactionType + - " for " + reactionKey); - } - - if (_dynReactionBulk[i]->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); - } - } - paramProvider.popScope(); + _reaction.empty(); } @@ -511,24 +441,9 @@ bool MultiChannelTransportModel::configure(IParameterProvider& paramProvider) // Reconfigure reaction model bool dynReactionConfSuccess = true; - for(auto i = 0; i < _dynReactionBulk.size(); i++) - { - if (_dynReactionBulk[i] && _dynReactionBulk[i]->requiresConfiguration()) - { - paramProvider.pushScope("reaction_bulk"); - if (!_oldReactionInterface) - { - char reactionKey[32]; - snprintf(reactionKey, sizeof(reactionKey), "reaction_model_%03d", i); - paramProvider.pushScope(reactionKey); - } - dynReactionConfSuccess = _dynReactionBulk[i]->configure(paramProvider, _unitOpIdx, ParTypeIndep) && dynReactionConfSuccess; - paramProvider.popScope(); - - if (!_oldReactionInterface) - paramProvider.popScope(); - } - } + + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; // Reconfigure exchange model bool exchangeConfSuccess = true; @@ -545,10 +460,10 @@ unsigned int MultiChannelTransportModel::threadLocalMemorySize() const CADET_NOE LinearMemorySizer lms; // Memory for residualImpl() - for (auto i = 0; i < _dynReactionBulk.size(); i++) + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) { - if (_dynReactionBulk[i] && _dynReactionBulk[i]->requiresWorkspace()) - lms.fitBlock(_dynReactionBulk[i]->workspaceSize(_disc.nComp, 0, nullptr)); + if (_reaction.getDynReactionVector("liquid")[i] && _reaction.getDynReactionVector("liquid")[i]->requiresWorkspace()) + lms.fitBlock(_reaction.getDynReactionVector("liquid")[i]->workspaceSize(_disc.nComp, 0, nullptr)); } return lms.bufferSize(); @@ -818,7 +733,7 @@ int MultiChannelTransportModel::residualImpl(double t, unsigned int secIdx, Stat } - if (!_dynReactionBulk[0]) + if (!_reaction.getDynReactionVector("liquid")[0]) return 0; // Get offsets @@ -835,16 +750,16 @@ int MultiChannelTransportModel::residualImpl(double t, unsigned int secIdx, Stat const ColumnPosition colPos{z, static_cast(channelCell), 0.0}; - for (auto i = 0; i < _dynReactionBulk.size(); i++) + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) { - if (_dynReactionBulk[i] && (_dynReactionBulk[i]->numReactionsLiquid() > 0)) + if (_reaction.getDynReactionVector("liquid")[i] && (_reaction.getDynReactionVector("liquid")[i]->numReactions() > 0)) { - _dynReactionBulk[i]->residualLiquidAdd(t, secIdx, colPos, yC, resC, -1.0, tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->residualFluxAdd(t, secIdx, colPos, _disc.nComp, yC, resC, -1.0, tlmAlloc); if (wantJac) { // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - _dynReactionBulk[i]->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(yC), -1.0, _convDispOp.jacobian().row(colCell * idxr.strideChannelCell()), tlmAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _disc.nComp, reinterpret_cast(yC), -1.0, _convDispOp.jacobian().row(colCell * idxr.strideChannelCell()), tlmAlloc); } } } diff --git a/src/libcadet/model/MultiChannelTransportModel.hpp b/src/libcadet/model/MultiChannelTransportModel.hpp index 887a1f55a..613c179d6 100644 --- a/src/libcadet/model/MultiChannelTransportModel.hpp +++ b/src/libcadet/model/MultiChannelTransportModel.hpp @@ -27,6 +27,7 @@ #include "Memory.hpp" #include "model/ModelUtils.hpp" #include "model/ParameterMultiplexing.hpp" +#include "reaction/ReactionSystem.hpp" #include #include @@ -203,8 +204,7 @@ class MultiChannelTransportModel : public UnitOperationBase // IExternalFunction* _extFun; //!< External function (owned by library user) parts::MultiChannelConvectionDispersionOperator _convDispOp; //!< Convection dispersion operator for interstitial volume transport - std::vector _dynReactionBulk; //!< Dynamic reactions in the bulk volume - bool _oldReactionInterface; + ReactionSystem _reaction; std::vector _exchange; //!< Exchange transition model linalg::DoubleSparseMatrix _jacInlet; //!< Jacobian inlet DOF block matrix connects inlet DOFs to first bulk cells diff --git a/src/libcadet/model/ParameterDependence.hpp b/src/libcadet/model/ParameterDependence.hpp index 4677f22de..d7511a732 100644 --- a/src/libcadet/model/ParameterDependence.hpp +++ b/src/libcadet/model/ParameterDependence.hpp @@ -191,8 +191,8 @@ class IParameterStateDependence * @param [in] row Row index * @param [in,out] jac Row iterator pointing to the row of component @p comp in the underlying matrix that stores the Jacobian */ - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::BandMatrix::RowIterator jac) const = 0; - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::DenseBandedRowIterator jac) const = 0; + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::BandMatrix::RowIterator jac) const = 0; + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::DenseBandedRowIterator jac) const = 0; /** * @brief Adds the analytical Jacobian of the parameter dependence for one liquid phase cell @@ -216,7 +216,7 @@ class IParameterStateDependence * @param [in] row Row index * @param [in,out] jac Jacobian */ - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const = 0; + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const = 0; /** * @brief Evaluates the parameter of component @p comp in the liquid phase of one combined phase cell diff --git a/src/libcadet/model/ReactionModel.hpp b/src/libcadet/model/ReactionModel.hpp index f468daf1e..c062635be 100644 --- a/src/libcadet/model/ReactionModel.hpp +++ b/src/libcadet/model/ReactionModel.hpp @@ -199,16 +199,16 @@ class IDynamicReactionModel * @param [in,out] workSpace Memory work space * @return @c 0 on success, @c -1 on non-recoverable error, and @c +1 on recoverable error */ - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, active const* y, active* res, const active& factor, LinearBufferAllocator workSpace) const = 0; - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, active const* y, active* res, double factor, LinearBufferAllocator workSpace) const = 0; - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, active* res, double factor, LinearBufferAllocator workSpace) const = 0; - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double* res, double factor, LinearBufferAllocator workSpace) const = 0; /** @@ -227,15 +227,17 @@ class IDynamicReactionModel * @param [in] t Current time point * @param [in] secIdx Index of the current section * @param [in] colPos Position in normalized coordinates (column inlet = 0, column outlet = 1; outer shell = 1, inner center = 0) + * @param [in] nStates number of states * @param [in] y Pointer to first component in the current cell * @param [in] factor Factor @f$ \gamma @f$ * @param [in,out] jac Row iterator pointing to the first component row of the underlying matrix in which the Jacobian is stored * @param [in,out] workSpace Memory work space */ - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandMatrix::RowIterator jac, LinearBufferAllocator workSpace) const = 0; - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::DenseBandedRowIterator jac, LinearBufferAllocator workSpace) const = 0; - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandedSparseRowIterator jac, LinearBufferAllocator workSpace) const = 0; - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandedEigenSparseRowIterator jac, LinearBufferAllocator workSpace) const = 0; + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::BandMatrix::RowIterator jac, LinearBufferAllocator workSpace) const = 0; + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::DenseBandedRowIterator jac, LinearBufferAllocator workSpace) const = 0; + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::BandedSparseRowIterator jac, LinearBufferAllocator workSpace) const = 0; + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::BandedEigenSparseRowIterator jac, LinearBufferAllocator workSpace) const = 0; + /** * @brief Evaluates the residual for one combined phase cell @@ -309,6 +311,7 @@ class IDynamicReactionModel */ virtual unsigned int numReactionsCombined() const CADET_NOEXCEPT = 0; + virtual unsigned int numReactions() const CADET_NOEXCEPT { return 0; }; protected: }; diff --git a/src/libcadet/model/StirredTankModel.cpp b/src/libcadet/model/StirredTankModel.cpp index b4ada0cab..30f6d7ed7 100644 --- a/src/libcadet/model/StirredTankModel.cpp +++ b/src/libcadet/model/StirredTankModel.cpp @@ -17,6 +17,7 @@ #include "cadet/SolutionRecorder.hpp" #include "model/BindingModel.hpp" #include "model/ReactionModel.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "SimulationTypes.hpp" #include "ParallelSupport.hpp" #include "linalg/Subset.hpp" @@ -62,7 +63,7 @@ namespace CSTRModel::CSTRModel(UnitOpIdx unitOpIdx) : UnitOperationBase(unitOpIdx), _nComp(0), _nParType(0), _nBound(nullptr), _boundOffset(nullptr), _strideBound(nullptr), _offsetParType(nullptr), - _totalBound(0), _analyticJac(true), _jac(), _jacFact(), _factorizeJac(false), _initConditions(0), _initConditionsDot(0), _dynReactionBulk{nullptr} + _totalBound(0), _analyticJac(true), _jac(), _jacFact(), _factorizeJac(false), _initConditions(0), _initConditionsDot(0) { // Mutliplexed binding and reaction models make no sense in CSTR _singleBinding = false; @@ -75,11 +76,8 @@ CSTRModel::~CSTRModel() CADET_NOEXCEPT delete[] _nBound; delete[] _strideBound; delete[] _offsetParType; + _reaction.clearDynamicReactionModels(); - for (auto i = 0; i < _dynReactionBulk.size(); i++) - { - delete _dynReactionBulk[i]; - } } unsigned int CSTRModel::numDofs() const CADET_NOEXCEPT @@ -223,107 +221,88 @@ bool CSTRModel::configureModelDiscretization(IParameterProvider& paramProvider, } // ==== Construct and configure dynamic reaction model - clearDynamicReactionModels(); bool reactionConfSuccess = true; - _old_interface = false; - _dynReactionBulk[0] = nullptr; - if (paramProvider.exists("REACTION_MODEL")) - { - _old_interface = true; - const std::string dynReactName = paramProvider.getString("REACTION_MODEL"); - _dynReactionBulk[0] = helper.createDynamicReactionModel(dynReactName); - if (!_dynReactionBulk[0]) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactName); + _reaction.clearDynamicReactionModels(); - if (_dynReactionBulk[0]->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope("reaction_bulk"); + _reacParticle.clear(); + _reacParticle.resize(_nParType); - reactionConfSuccess = _dynReactionBulk[0]->configureModelDiscretization(paramProvider, _nComp, nullptr, nullptr); - - if (_dynReactionBulk[0]->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); - } - else if (paramProvider.exists("reaction_bulk")) + if (_nParType > 0) { - paramProvider.pushScope("reaction_bulk"); - - if (paramProvider.exists("NREAC")) + for (unsigned int par = 0; par < _nParType; par++) { - int nReactions = paramProvider.getInt("NREAC"); - - if (nReactions <= 0) - { - paramProvider.popScope(); - throw InvalidParameterException("CSTR-Configuration: number of reaction must be positive, please check your configuration"); - } - _dynReactionBulk.resize(nReactions); - for (int i = 0; i < nReactions; ++i) { + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); - char reactionKey[32]; - snprintf(reactionKey, sizeof(reactionKey), "reaction_model_%03d", i); - - if (!paramProvider.exists(reactionKey)) { - paramProvider.popScope(); - throw InvalidParameterException("Missing reaction model definition for " + std::string(reactionKey)); - } - - paramProvider.pushScope(reactionKey); - - if (!paramProvider.exists("REACTION_TYPE")) { - paramProvider.popScope(); - throw InvalidParameterException("Missing 'type' parameter for " + std::string(reactionKey)); - } + if (paramProvider.exists(particleScope)) + { + paramProvider.pushScope(particleScope); // particle_type_xxx - std::string reactionType = paramProvider.getString("REACTION_TYPE"); - paramProvider.popScope(); - _dynReactionBulk[i] = helper.createDynamicReactionModel(reactionType); + //ReactionSystem parReaction; + + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + int nReactions = paramProvider.getInt("NREAC_CROSS_PHASE"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("cross_phase", + 0, + nReactions, + _nComp, + _nBound, + _boundOffset, + paramProvider, + helper) && reactionConfSuccess; - if (!_dynReactionBulk[i]) { - paramProvider.popScope(); - throw InvalidParameterException("Unknown dynamic reaction model " + reactionType + - " for " + reactionKey); } - - if (_dynReactionBulk[i]->usesParamProviderInDiscretizationConfig()) - paramProvider.pushScope(reactionKey); - - reactionConfSuccess = _dynReactionBulk[i]->configureModelDiscretization(paramProvider, _nComp, nullptr, nullptr); - - if (!reactionConfSuccess) { - if (_dynReactionBulk[i]->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); - paramProvider.popScope(); - throw InvalidParameterException("Failed to configure reaction model " + reactionType + - " for " + reactionKey); + if (paramProvider.exists("NREAC_LIQUID")) + { + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("liquid", + 0, + nReactions, + _nComp, + _nBound, + _boundOffset, + paramProvider, + helper) && reactionConfSuccess; } + if (paramProvider.exists("NREAC_SOLID")) + { + int nReactions = paramProvider.getInt("NREAC_SOLID"); + reactionConfSuccess = _reacParticle[par].configureDiscretization("solid", + 0, + nReactions, + _nComp, + _nBound, + _boundOffset, + paramProvider, + helper) && reactionConfSuccess; - if (_dynReactionBulk[i]->usesParamProviderInDiscretizationConfig()) - paramProvider.popScope(); - } } - paramProvider.popScope(); - } + paramProvider.popScope(); // particle_type_xxx + } + } - _dynReaction = std::vector(_nParType, nullptr); + } - if (paramProvider.exists("REACTION_MODEL_PARTICLES")) + if (paramProvider.exists("NREAC_LIQUID")) { - const std::vector dynReactModelNames = paramProvider.getStringArray("REACTION_MODEL_PARTICLES"); - if (dynReactModelNames.size() < _nParType) - throw InvalidParameterException("Field REACTION_MODEL_PARTICLES contains too few elements (" + std::to_string(_nParType) + " required)"); - - for (unsigned int i = 0; i < _nParType; ++i) - { - _dynReaction[i] = helper.createDynamicReactionModel(dynReactModelNames[i]); - if (!_dynReaction[i]) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactModelNames[i]); - - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction_particle", _nParType == 1, i, _nParType == 1, _dynReaction[i]->usesParamProviderInDiscretizationConfig()); - reactionConfSuccess = _dynReaction[i]->configureModelDiscretization(paramProvider, _nComp, _nBound + i * _nComp, _boundOffset + i * _nComp) && reactionConfSuccess; - } + int nReactions = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReactions, + _nComp, + _nBound, + _boundOffset, + paramProvider, + helper) && reactionConfSuccess; } + else + { + _reaction.empty(); + } + return bindingConfSuccess && reactionConfSuccess; } @@ -420,33 +399,29 @@ bool CSTRModel::configure(IParameterProvider& paramProvider) // Reconfigure reaction model bool dynReactionConfSuccess = true; - for (auto i = 0; i < _dynReactionBulk.size(); i++) - { - if (_dynReactionBulk[i] && _dynReactionBulk[i]->requiresConfiguration()) - { - paramProvider.pushScope("reaction_bulk"); - if (!_old_interface) + // Reconfigure reaction model + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + + for (unsigned int par = 0; par < _nParType; par++) { - char reactionKey[32]; - snprintf(reactionKey, sizeof(reactionKey), "reaction_model_%03d", i); - paramProvider.pushScope(reactionKey); - } - dynReactionConfSuccess = _dynReactionBulk[i]->configure(paramProvider, _unitOpIdx, ParTypeIndep); - paramProvider.popScope(); - - if(!_old_interface) + char particleScope[32]; + snprintf(particleScope, sizeof(particleScope), "particle_type_%03d", par); + + if (paramProvider.exists(particleScope)) + { + paramProvider.pushScope(particleScope); + if (paramProvider.exists("NREAC_CROSS_PHASE")) + dynReactionConfSuccess = _reacParticle[par].configure("cross_phase", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reacParticle[par].configure("liquid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_SOLID")) + dynReactionConfSuccess = _reacParticle[par].configure("solid", 0, _unitOpIdx, paramProvider) && dynReactionConfSuccess; + paramProvider.popScope(); } } - for (unsigned int type = 0; type < _nParType; ++type) - { - if (!_dynReaction[type] || !_dynReaction[type]->requiresConfiguration()) - continue; - - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction_particle", type, _nParType == 1, true); - dynReactionConfSuccess = _dynReaction[type]->configure(paramProvider, _unitOpIdx, type) && dynReactionConfSuccess; - } return bindingConfSuccess && dynReactionConfSuccess; } @@ -460,16 +435,17 @@ unsigned int CSTRModel::threadLocalMemorySize() const CADET_NOEXCEPT { if (_binding[i] && _binding[i]->requiresWorkspace()) lms.fitBlock(_binding[i]->workspaceSize(_nComp, _strideBound[i], _nBound + i * _nComp)); - if (_dynReaction[i] && _dynReaction[i]->requiresWorkspace()) - lms.fitBlock(_dynReaction[i]->workspaceSize(_nComp, _strideBound[i], _nBound + i * _nComp)); } - for (auto i = 0; i < _dynReactionBulk.size(); i++) + // Handle all reactions + for (unsigned int parType = 0; parType < _nParType; ++parType) { - if (_dynReactionBulk[i] && _dynReactionBulk[i]->requiresWorkspace()) - lms.fitBlock(_dynReactionBulk[i]->workspaceSize(_nComp, 0, nullptr)); - } + _reacParticle[parType].setWorkspaceRequirements("cross_phase", 1, _nComp, &_strideBound[parType], lms); + _reacParticle[parType].setWorkspaceRequirements("liquid", 1, _nComp, &_strideBound[parType], lms); + _reacParticle[parType].setWorkspaceRequirements("solid", 1, _nComp, &_strideBound[parType], lms); + } + _reaction.setWorkspaceRequirements("liquid", _nComp, 0, lms); const unsigned int maxStrideBound = _strideBound ? *std::max_element(_strideBound, _strideBound + _nParType) : 0; lms.add(_nComp + maxStrideBound); @@ -1397,15 +1373,15 @@ int CSTRModel::residualImpl(double t, unsigned int secIdx, StateType const* cons // Reactions in liquid phase const ColumnPosition colPos{0.0, 0.0, 0.0}; - for (auto i = 0; i < _dynReactionBulk.size(); i++) + for (auto i = 0; i < _reaction.getDynReactionVector("liquid").size(); i++) { - if (_dynReactionBulk[i] && (_dynReactionBulk[i]->numReactionsLiquid() > 0)) + if (_reaction.getDynReactionVector("liquid")[i]) { LinearBufferAllocator subAlloc = tlmAlloc.manageRemainingMemory(); BufferedArray flux = subAlloc.array(_nComp); std::fill_n(static_cast(flux), _nComp, 0.0); - _dynReactionBulk[i]->residualLiquidAdd(t, secIdx, colPos, c, static_cast(flux), -1.0, subAlloc); + _reaction.getDynReactionVector("liquid")[i]->residualFluxAdd(t, secIdx, colPos, _nComp, c, static_cast(flux), -1.0, subAlloc); for (unsigned int comp = 0; comp < _nComp; ++comp) resC[comp] += v * flux[comp]; @@ -1415,7 +1391,7 @@ int CSTRModel::residualImpl(double t, unsigned int secIdx, StateType const* cons for (unsigned int comp = 0; comp < _nComp; ++comp) _jac.native(comp, _nComp + _totalBound) += static_cast(flux[comp]); // dF/dvliquid = flux - _dynReactionBulk[i]->analyticJacobianLiquidAdd(t, secIdx, colPos, reinterpret_cast(c), -static_cast(v), _jac.row(0), subAlloc); + _reaction.getDynReactionVector("liquid")[i]->analyticJacobianAdd(t, secIdx, colPos, _nComp, reinterpret_cast(c), -static_cast(v), _jac.row(0), subAlloc); } } } @@ -1454,9 +1430,10 @@ int CSTRModel::residualImpl(double t, unsigned int secIdx, StateType const* cons _binding[type]->analyticJacobian(t, secIdx, colPos, reinterpret_cast(y) + 2 * _nComp + _offsetParType[type], _nComp + _offsetParType[type], _jac.row(_nComp + _offsetParType[type]), tlmAlloc); } - // Reaction - IDynamicReactionModel* const dynReaction = _dynReaction[type]; - if (dynReaction && (dynReaction->numReactionsCombined() > 0)) + // Cross Phase reaction + for (int reac = 0; reac < _reacParticle[type].getDynReactionVector("cross_phase").size(); reac++) + { + if (_reacParticle[type].getDynReactionVector("cross_phase")[reac]) { LinearBufferAllocator subAlloc = tlmAlloc.manageRemainingMemory(); @@ -1467,7 +1444,7 @@ int CSTRModel::residualImpl(double t, unsigned int secIdx, StateType const* cons std::fill_n(fluxLiquid, _nComp, 0.0); std::fill_n(fluxSolid, _strideBound[type], 0.0); - dynReaction->residualCombinedAdd(t, secIdx, colPos, c, c + _nComp + _offsetParType[type], fluxLiquid, fluxSolid, -1.0, subAlloc); + _reacParticle[type].getDynReactionVector("cross_phase")[reac]->residualCombinedAdd(t, secIdx, colPos, c, c + _nComp + _offsetParType[type], fluxLiquid, fluxSolid, -1.0, subAlloc); for (unsigned int comp = 0; comp < _nComp; ++comp) resC[comp] += v * fluxLiquid[comp]; @@ -1480,7 +1457,7 @@ int CSTRModel::residualImpl(double t, unsigned int secIdx, StateType const* cons for (unsigned int bnd = 0; bnd < _nBound[type * _nComp + comp]; ++bnd, ++idx) { // Add reaction term to mobile phase - resC[comp] += static_cast::type>(liquidFactor) * fluxSolid[idx]; + resC[comp] += static_cast::type>(liquidFactor)* fluxSolid[idx]; if (!qsReaction[idx]) { @@ -1498,7 +1475,7 @@ int CSTRModel::residualImpl(double t, unsigned int secIdx, StateType const* cons BufferedArray fluxJacobianMem = subAlloc.array((_strideBound[type] + _nComp) * (_strideBound[type] + _nComp)); linalg::DenseMatrixView jacFlux(static_cast(fluxJacobianMem), nullptr, _strideBound[type] + _nComp, _strideBound[type] + _nComp); jacFlux.setAll(0.0); - dynReaction->analyticJacobianCombinedAdd(t, secIdx, colPos, reinterpret_cast(c), reinterpret_cast(c + _nComp + _offsetParType[type]), + _reacParticle[type].getDynReactionVector("cross_phase")[reac]->analyticJacobianCombinedAdd(t, secIdx, colPos, reinterpret_cast(c), reinterpret_cast(c + _nComp + _offsetParType[type]), -1.0, jacFlux.row(0), jacFlux.row(_nComp), subAlloc); idx = 0; @@ -1529,6 +1506,72 @@ int CSTRModel::residualImpl(double t, unsigned int secIdx, StateType const* cons } } } + // solid reaction + for (int reac = 0; reac < _reacParticle[type].getDynReactionVector("solid").size(); reac++) + { + if (_reacParticle[type].getDynReactionVector("solid")[reac]) + { + LinearBufferAllocator subAlloc = tlmAlloc.manageRemainingMemory(); + + ResidualType* const resQ = resC + _nComp + _offsetParType[type]; + BufferedArray fluxBuffer = subAlloc.array(_nComp + _strideBound[type]); + ResidualType* const fluxLiquid = static_cast(fluxBuffer); + ResidualType* const fluxSolid = fluxLiquid + _nComp; + + std::fill_n(fluxSolid, _strideBound[type], 0.0); + _reacParticle[type].getDynReactionVector("solid")[reac]->residualFluxAdd(t, secIdx, colPos, _strideBound[type], c + _nComp + _offsetParType[type], fluxSolid, -1.0, subAlloc); + + typedef typename DoubleActivePromoter::type FactorType; + const FactorType liquidFactor = vsolid * static_cast(_parTypeVolFrac[type]); + unsigned int idx = 0; + for (unsigned int comp = 0; comp < _nComp; ++comp) + { + for (unsigned int bnd = 0; bnd < _nBound[type * _nComp + comp]; ++bnd, ++idx) + { + // Add reaction term to mobile phase + resC[comp] += static_cast::type>(liquidFactor)* fluxSolid[idx]; + + if (!qsReaction[idx]) + { + // Add reaction term to solid phase + resQ[idx] += fluxSolid[idx]; + } + } + } + + if (wantJac) + { + // Assemble Jacobian: Reaction + + // dRes / dC and dRes / dQ + BufferedArray fluxJacobianMem = subAlloc.array((_strideBound[type] + _nComp) * (_strideBound[type] + _nComp)); + linalg::DenseMatrixView jacFlux(static_cast(fluxJacobianMem), nullptr, _strideBound[type] + _nComp, _strideBound[type] + _nComp); + jacFlux.setAll(0.0); + _reacParticle[type].getDynReactionVector("solid")[reac]->analyticJacobianAdd(t, secIdx, colPos, _strideBound[type], reinterpret_cast(c + _nComp + _offsetParType[type]), + -1.0, jacFlux.row(_nComp), subAlloc); + + idx = 0; + const double liquidFactor = static_cast(vsolid) * static_cast(_parTypeVolFrac[type]); + for (unsigned int comp = 0; comp < _nComp; ++comp) + { + for (unsigned int bnd = 0; bnd < _nBound[type * _nComp + comp]; ++bnd, ++idx) + { + // Add Jacobian row to mobile phase + jacFlux.addSubmatrixTo(_jac, liquidFactor, _nComp + idx, 0, 1, _nComp, comp, 0); + jacFlux.addSubmatrixTo(_jac, liquidFactor, _nComp + idx, _nComp, 1, _strideBound[type], comp, _nComp + _offsetParType[type]); + + if (!qsReaction[idx]) + { + // Add Jacobian row to solid phase + jacFlux.addSubmatrixTo(_jac, 1.0, _nComp + idx, 0, 1, _nComp, _nComp + _offsetParType[type] + idx, 0); + jacFlux.addSubmatrixTo(_jac, 1.0, _nComp + idx, _nComp, 1, _strideBound[type], _nComp + _offsetParType[type] + idx, _nComp + _offsetParType[type]); + } + } + } + } + } + } + } // Volume: \dot{V} = F_{in} - F_{out} - F_{filter} res[2 * _nComp + _totalBound] = vDot - flowIn + flowOut + static_cast(_curFlowRateFilter); @@ -2006,7 +2049,7 @@ bool CSTRModel::setParameter(const ParameterId& pId, double value) { if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, _dynReactionBulk , false)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid") , false)) return true; } @@ -2017,7 +2060,7 @@ bool CSTRModel::setParameter(const ParameterId& pId, int value) { if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, _dynReactionBulk, false)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -2028,7 +2071,7 @@ bool CSTRModel::setParameter(const ParameterId& pId, bool value) { if (pId.unitOperation == _unitOpIdx) { - if (model::setParameter(pId, value, _dynReactionBulk, false)) + if (model::setParameter(pId, value, _reaction.getDynReactionVector("liquid"), false)) return true; } @@ -2039,7 +2082,7 @@ void CSTRModel::setSensitiveParameterValue(const ParameterId& pId, double value) { if (pId.unitOperation == _unitOpIdx) { - if (model::setSensitiveParameterValue(pId, value, _sensParams, _dynReactionBulk, false)) + if (model::setSensitiveParameterValue(pId, value, _sensParams, _reaction.getDynReactionVector("liquid"), false)) return; } @@ -2048,7 +2091,7 @@ void CSTRModel::setSensitiveParameterValue(const ParameterId& pId, double value) bool CSTRModel::setSensitiveParameter(const ParameterId& pId, unsigned int adDirection, double adValue) { - if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, _dynReactionBulk , false)) + if (model::setSensitiveParameter(pId, adDirection, adValue, _sensParams, _reaction.getDynReactionVector("liquid") , false)) { LOG(Debug) << "Found parameter " << pId << " in DynamicBulkReactionModel: Dir " << adDirection << " is set to " << adValue; return true; diff --git a/src/libcadet/model/StirredTankModel.hpp b/src/libcadet/model/StirredTankModel.hpp index c140d11c0..dff10f378 100644 --- a/src/libcadet/model/StirredTankModel.hpp +++ b/src/libcadet/model/StirredTankModel.hpp @@ -23,6 +23,7 @@ #include "AutoDiff.hpp" #include "linalg/DenseMatrix.hpp" #include "model/ModelUtils.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "Memory.hpp" #include @@ -175,8 +176,9 @@ class CSTRModel : public UnitOperationBase std::vector _initConditions; //!< Initial conditions, ordering: Liquid phase concentration, solid phase concentration, liquid volume std::vector _initConditionsDot; //!< Initial conditions for time derivative - std::vector _dynReactionBulk; //!< Dynamic reactions in the bulk volume - bool _old_interface; // + ReactionSystem _reaction; + std::vector _reacParticle; + class Exporter : public ISolutionExporter { diff --git a/src/libcadet/model/UnitOperationBase.cpp b/src/libcadet/model/UnitOperationBase.cpp index dde7cbb42..2037d024a 100644 --- a/src/libcadet/model/UnitOperationBase.cpp +++ b/src/libcadet/model/UnitOperationBase.cpp @@ -31,7 +31,7 @@ namespace model { UnitOperationBase::UnitOperationBase(UnitOpIdx unitOpIdx) : _unitOpIdx(unitOpIdx), _binding(0, nullptr), _singleBinding(false), - _dynReaction(0, nullptr), _singleDynReaction(false), _nonlinearSolver(nullptr) + _singleDynReaction(false), _nonlinearSolver(nullptr) { } diff --git a/src/libcadet/model/UnitOperationBase.hpp b/src/libcadet/model/UnitOperationBase.hpp index 4e99915a7..dccee22e8 100644 --- a/src/libcadet/model/UnitOperationBase.hpp +++ b/src/libcadet/model/UnitOperationBase.hpp @@ -82,7 +82,7 @@ class UnitOperationBase : public IUnitOperation std::vector _binding; //!< Binding model std::vector _exchange; //!< Exchange model bool _singleBinding; //!< Determines whether only a single binding model is present - std::vector _dynReaction; //!< Dynamic reaction model + std::vector _dynReaction; //!< Dynamic reaction model in partical bool _singleDynReaction; //!< Determines whether only a single dynamic reaction model is present typedef std::unordered_map paramMap_t; diff --git a/src/libcadet/model/paramdep/DummyParameterDependence.cpp b/src/libcadet/model/paramdep/DummyParameterDependence.cpp index 6f7365d43..288917382 100644 --- a/src/libcadet/model/paramdep/DummyParameterDependence.cpp +++ b/src/libcadet/model/paramdep/DummyParameterDependence.cpp @@ -42,7 +42,7 @@ class ConstantZeroParameterStateDependence : public ParameterStateDependenceBase virtual int jacobianElementsPerRowLiquid() const CADET_NOEXCEPT { return 0; } virtual int jacobianElementsPerRowCombined() const CADET_NOEXCEPT { return 0; } - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddLiquid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddSolid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int bnd, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } @@ -62,7 +62,7 @@ class ConstantZeroParameterStateDependence : public ParameterStateDependenceBase } template - void analyticJacobianLiquidAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } + void analyticJacobianAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } template typename DoubleActivePromoter::type combinedParameterLiquidImpl(const ColumnPosition& colPos, const ParamType& param, StateType const* yLiquid, StateType const* ySolid, int comp) const @@ -100,7 +100,7 @@ class ConstantOneParameterStateDependence : public ParameterStateDependenceBase virtual int jacobianElementsPerRowLiquid() const CADET_NOEXCEPT { return 0; } virtual int jacobianElementsPerRowCombined() const CADET_NOEXCEPT { return 0; } - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddLiquid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddSolid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int bnd, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } @@ -120,7 +120,7 @@ class ConstantOneParameterStateDependence : public ParameterStateDependenceBase } template - void analyticJacobianLiquidAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } + void analyticJacobianAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } template typename DoubleActivePromoter::type combinedParameterLiquidImpl(const ColumnPosition& colPos, const ParamType& param, StateType const* yLiquid, StateType const* ySolid, int comp) const diff --git a/src/libcadet/model/paramdep/IdentityParameterDependence.cpp b/src/libcadet/model/paramdep/IdentityParameterDependence.cpp index bfd7bd7e1..7fbc439d0 100644 --- a/src/libcadet/model/paramdep/IdentityParameterDependence.cpp +++ b/src/libcadet/model/paramdep/IdentityParameterDependence.cpp @@ -42,7 +42,7 @@ class IdentityParameterStateDependence : public ParameterStateDependenceBase virtual int jacobianElementsPerRowLiquid() const CADET_NOEXCEPT { return 0; } virtual int jacobianElementsPerRowCombined() const CADET_NOEXCEPT { return 0; } - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddLiquid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddSolid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int bnd, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } @@ -62,7 +62,7 @@ class IdentityParameterStateDependence : public ParameterStateDependenceBase } template - void analyticJacobianLiquidAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } + void analyticJacobianAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } template typename DoubleActivePromoter::type combinedParameterLiquidImpl(const ColumnPosition& colPos, const ParamType& param, StateType const* yLiquid, StateType const* ySolid, int comp) const diff --git a/src/libcadet/model/paramdep/LiquidSaltSolidParameterDependence.cpp b/src/libcadet/model/paramdep/LiquidSaltSolidParameterDependence.cpp index acb68c236..b2834271c 100644 --- a/src/libcadet/model/paramdep/LiquidSaltSolidParameterDependence.cpp +++ b/src/libcadet/model/paramdep/LiquidSaltSolidParameterDependence.cpp @@ -84,7 +84,7 @@ class ExpLiquidSaltSolidParameterStateDependence : public ParameterStateDependen virtual int jacobianElementsPerRowLiquid() const CADET_NOEXCEPT { return 0; } virtual int jacobianElementsPerRowCombined() const CADET_NOEXCEPT { return 1; } - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddLiquid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddSolid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int bnd, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const @@ -113,7 +113,7 @@ class ExpLiquidSaltSolidParameterStateDependence : public ParameterStateDependen } template - void analyticJacobianLiquidAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } + void analyticJacobianAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } template typename DoubleActivePromoter::type combinedParameterLiquidImpl(const ColumnPosition& colPos, const ParamType& param, StateType const* yLiquid, StateType const* ySolid, int comp) const @@ -154,7 +154,7 @@ class PowerLiquidSaltSolidParameterStateDependence : public ParameterStateDepend virtual int jacobianElementsPerRowLiquid() const CADET_NOEXCEPT { return 0; } virtual int jacobianElementsPerRowCombined() const CADET_NOEXCEPT { return 1; } - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddLiquid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddSolid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int bnd, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const @@ -183,7 +183,7 @@ class PowerLiquidSaltSolidParameterStateDependence : public ParameterStateDepend } template - void analyticJacobianLiquidAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } + void analyticJacobianAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } template typename DoubleActivePromoter::type combinedParameterLiquidImpl(const ColumnPosition& colPos, const ParamType& param, StateType const* yLiquid, StateType const* ySolid, int comp) const @@ -224,7 +224,7 @@ class ColloidalAffinityLiquidSaltSolidParameterStateDependence : public Paramete virtual int jacobianElementsPerRowLiquid() const CADET_NOEXCEPT { return 0; } virtual int jacobianElementsPerRowCombined() const CADET_NOEXCEPT { return 1; } - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddLiquid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int comp, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const { } virtual void analyticJacobianCombinedAddSolid(const ColumnPosition& colPos, double param, double const* yLiquid, double const* ySolid, int bnd, double factor, int offset, int row, linalg::DoubleSparseMatrix& jac) const @@ -269,7 +269,7 @@ class ColloidalAffinityLiquidSaltSolidParameterStateDependence : public Paramete } template - void analyticJacobianLiquidAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } + void analyticJacobianAddImpl(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, RowIterator jac) const { } template typename DoubleActivePromoter::type combinedParameterLiquidImpl(const ColumnPosition& colPos, const ParamType& param, StateType const* yLiquid, StateType const* ySolid, int comp) const diff --git a/src/libcadet/model/paramdep/ParameterDependenceBase.hpp b/src/libcadet/model/paramdep/ParameterDependenceBase.hpp index 735d11cff..1ad58025a 100644 --- a/src/libcadet/model/paramdep/ParameterDependenceBase.hpp +++ b/src/libcadet/model/paramdep/ParameterDependenceBase.hpp @@ -82,11 +82,11 @@ class ParameterStateDependenceBase : public IParameterStateDependence /** * @brief Inserts implementations of all parameter() and analyticJacobian() method variants * @details An IParameterStateDependence implementation has to provide liquidParameter(), combinedParameterLiquid(), - * combinedParameterSolid(), analyticJacobianLiquidAdd(), analyticJacobianCombinedAddLiquid(), and + * combinedParameterSolid(), analyticJacobianAdd(), analyticJacobianCombinedAddLiquid(), and * analyticJacobianCombinedAddSolid() methods for different variants of state and parameter type. * This macro saves some time by providing those implementations. It assumes that the implementation * provides templatized liquidParameterImpl(), combinedParameterLiquidImpl(), - * combinedParameterSolidImpl(), analyticJacobianLiquidAddImpl(), analyticJacobianCombinedAddLiquidImpl(), + * combinedParameterSolidImpl(), analyticJacobianAddImpl(), analyticJacobianCombinedAddLiquidImpl(), * and analyticJacobianCombinedAddSolidImpl() functions that realize all required variants. * * The implementation is inserted inline in the class declaration. @@ -112,14 +112,14 @@ class ParameterStateDependenceBase : public IParameterStateDependence return liquidParameterImpl(colPos, param, y, comp); \ } \ \ - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::BandMatrix::RowIterator jac) const \ + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::BandMatrix::RowIterator jac) const \ { \ - analyticJacobianLiquidAddImpl(colPos, param, y, comp, factor, offset, jac); \ + analyticJacobianAddImpl(colPos, param, y, comp, factor, offset, jac); \ } \ \ - virtual void analyticJacobianLiquidAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::DenseBandedRowIterator jac) const \ + virtual void analyticJacobianAdd(const ColumnPosition& colPos, double param, double const* y, int comp, double factor, int offset, linalg::DenseBandedRowIterator jac) const \ { \ - analyticJacobianLiquidAddImpl(colPos, param, y, comp, factor, offset, jac); \ + analyticJacobianAddImpl(colPos, param, y, comp, factor, offset, jac); \ } \ \ virtual active combinedParameterLiquid(const ColumnPosition& colPos, const active& param, active const* yLiquid, active const* ySolid, int comp) const \ diff --git a/src/libcadet/model/particle/GeneralRateParticle.cpp b/src/libcadet/model/particle/GeneralRateParticle.cpp index 3721cf903..1f556a7b5 100644 --- a/src/libcadet/model/particle/GeneralRateParticle.cpp +++ b/src/libcadet/model/particle/GeneralRateParticle.cpp @@ -118,27 +118,65 @@ namespace model // ==== Construct and configure dynamic reaction model - _dynReaction = nullptr; _reactionParDep = true; bool reactionConfSuccess = true; - if (paramProvider.exists("REACTION_MODEL")) - { - const std::vector dynReactModelNames = paramProvider.getStringArray("REACTION_MODEL"); + _reaction.clearDynamicReactionModels(); - if (dynReactModelNames.size() != 1) - throw InvalidParameterException("Field REACTION_MODEL_PARTICLES requires (only) 1 element"); + bool hasReaction = false; - _dynReaction = helper.createDynamicReactionModel(dynReactModelNames[0]); + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + hasReaction = true; + int nReac = paramProvider.getInt("NREAC_CROSS_PHASE"); + unsigned int noOfSet = 0; + + reactionConfSuccess = _reaction.configureDiscretization("cross_phase", + 0, + nReac, + _nComp, + _nBound.get(), + &noOfSet, + paramProvider, + helper) && reactionConfSuccess; - if (!_dynReaction) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactModelNames[0]); + } + if (paramProvider.exists("NREAC_LIQUID")) + { + hasReaction = true; + int nReac = paramProvider.getInt("NREAC_LIQUID"); + unsigned int noOfSet = 0; + + + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReac, + _nComp, + _nBound.get(), + &noOfSet, + paramProvider, + helper) && reactionConfSuccess; + } + if (paramProvider.exists("NREAC_SOLID")) + { + hasReaction = true; + int nReac = paramProvider.getInt("NREAC_SOLID"); + unsigned int noOfSet = 0; + + reactionConfSuccess = _reaction.configureDiscretization("solid", + 0, + nReac, + _nComp, + _nBound.get(), + &noOfSet, + paramProvider, + helper) && reactionConfSuccess; - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction->usesParamProviderInDiscretizationConfig()); - reactionConfSuccess = _dynReaction->configureModelDiscretization(paramProvider, _nComp, _nBound.get(), _parDiffOp->offsetBoundComp()) && reactionConfSuccess; - _reactionParDep = paramProvider.exists("REACTION_PARTYPE_DEPENDENT") ? paramProvider.getInt("REACTION_PARTYPE_DEPENDENT") : true; - } + } + + if (!hasReaction) + { + _reaction.empty(); } paramProvider.popScope(); // particle_type_{:03} @@ -162,11 +200,13 @@ namespace model // Reconfigure reaction model bool dynReactionConfSuccess = true; - if (_dynReaction && _dynReaction->requiresConfiguration()) - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction->requiresConfiguration()); - dynReactionConfSuccess = _dynReaction->configure(paramProvider, unitOpIdx, ParTypeIndep); - } + + if (paramProvider.exists("NREAC_CROSS_PHASE")) + dynReactionConfSuccess = _reaction.configure("cross_phase", 0, unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_SOLID")) + dynReactionConfSuccess = _reaction.configure("solid", 0, unitOpIdx, paramProvider) && dynReactionConfSuccess; // Reconfigure particle transport and discretization const bool parTransportConfigSuccess = _parDiffOp->configure(unitOpIdx, paramProvider, parameters, nParType, nBoundBeforeType, nTotalBound, _binding->reactionQuasiStationarity()); @@ -198,7 +238,7 @@ namespace model getPorosity(), getPoreAccessFactor(), _binding, - (_dynReaction && (_dynReaction->numReactionsCombined() > 0)) ? _dynReaction : nullptr + &_reaction }; } diff --git a/src/libcadet/model/particle/HomogeneousParticle.cpp b/src/libcadet/model/particle/HomogeneousParticle.cpp index f3dfda4cf..1afdb33b4 100644 --- a/src/libcadet/model/particle/HomogeneousParticle.cpp +++ b/src/libcadet/model/particle/HomogeneousParticle.cpp @@ -136,27 +136,62 @@ namespace model // ==== Construct and configure dynamic reaction model - _dynReaction = nullptr; _reactionParDep = true; bool reactionConfSuccess = true; - if (paramProvider.exists("REACTION_MODEL")) - { - const std::vector dynReactModelNames = paramProvider.getStringArray("REACTION_MODEL"); + _reaction.clearDynamicReactionModels(); - if (dynReactModelNames.size() != 1) - throw InvalidParameterException("Field REACTION_MODEL_PARTICLES requires (only) 1 element"); + bool hasCrossPhaseReac = false; + bool hasSolidReac = false; + bool hasLiquidReac = false; - _dynReaction = helper.createDynamicReactionModel(dynReactModelNames[0]); - if (!_dynReaction) - throw InvalidParameterException("Unknown dynamic reaction model " + dynReactModelNames[0]); - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction->usesParamProviderInDiscretizationConfig()); - reactionConfSuccess = _dynReaction->configureModelDiscretization(paramProvider, _nComp, _nBound.get(), _boundOffset) && reactionConfSuccess; - _reactionParDep = paramProvider.exists("REACTION_PARTYPE_DEPENDENT") ? paramProvider.getInt("REACTION_PARTYPE_DEPENDENT") : true; - } + if (paramProvider.exists("NREAC_CROSS_PHASE")) + { + hasCrossPhaseReac = true; + int nReac = paramProvider.getInt("NREAC_CROSS_PHASE"); + reactionConfSuccess = _reaction.configureDiscretization("cross_phase", + 0, + nReac, + _nComp, + _nBound.get(), + _boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + if (paramProvider.exists("NREAC_LIQUID")) + { + hasLiquidReac = true; + int nReac = paramProvider.getInt("NREAC_LIQUID"); + reactionConfSuccess = _reaction.configureDiscretization("liquid", + 0, + nReac, + _nComp, + _nBound.get(), + _boundOffset, + paramProvider, + helper) && reactionConfSuccess; + } + if (paramProvider.exists("NREAC_SOLID")) + { + hasLiquidReac = true; + int nReac = paramProvider.getInt("NREAC_SOLID"); + reactionConfSuccess = _reaction.configureDiscretization("solid", + 0, + nReac, + _nComp, + _nBound.get(), + _boundOffset, + paramProvider, + helper) && reactionConfSuccess; + + } + + if (!hasLiquidReac && !hasCrossPhaseReac && !hasSolidReac) + { + _reaction.empty(); } paramProvider.popScope(); // particle_type_{:03} @@ -265,11 +300,13 @@ namespace model // Reconfigure reaction model bool dynReactionConfSuccess = true; - if (_dynReaction && _dynReaction->requiresConfiguration()) - { - MultiplexedScopeSelector scopeGuard(paramProvider, "reaction", _dynReaction->requiresConfiguration()); - dynReactionConfSuccess = _dynReaction->configure(paramProvider, unitOpIdx, ParTypeIndep) && dynReactionConfSuccess; - } + + if (paramProvider.exists("NREAC_CROSS_PHASE")) + dynReactionConfSuccess = _reaction.configure("cross_phase", 0, unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_LIQUID")) + dynReactionConfSuccess = _reaction.configure("liquid", 0, unitOpIdx, paramProvider) && dynReactionConfSuccess; + if (paramProvider.exists("NREAC_SOLID")) + dynReactionConfSuccess = _reaction.configure("solid", 0, unitOpIdx, paramProvider) && dynReactionConfSuccess; paramProvider.popScope(); // particle_type_{:03} @@ -299,7 +336,7 @@ namespace model getPorosity(), getPoreAccessFactor(), _binding, - (_dynReaction && (_dynReaction->numReactionsCombined() > 0)) ? _dynReaction : nullptr + &_reaction }; } diff --git a/src/libcadet/model/particle/ParticleModel.hpp b/src/libcadet/model/particle/ParticleModel.hpp index f7cad869f..88da3e61f 100644 --- a/src/libcadet/model/particle/ParticleModel.hpp +++ b/src/libcadet/model/particle/ParticleModel.hpp @@ -19,6 +19,7 @@ #define LIBCADET_IPARTICLEMODEL_HPP_ #include "model/BindingModel.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "cadet/StrongTypes.hpp" #include "ParamIdUtil.hpp" #include "AutoDiff.hpp" @@ -126,13 +127,14 @@ namespace cadet { public: - IParticleModel() : _binding(nullptr), _dynReaction(nullptr) + IParticleModel() : _binding(nullptr) { } virtual ~IParticleModel() CADET_NOEXCEPT { delete _binding; - delete _dynReaction; + + _reaction.clearDynamicReactionModels(); } virtual bool configureModelDiscretization(IParameterProvider& paramProvider, const IConfigHelper& helper, const int nComp, const int parTypeIdx, const int nParType, const int strideBulkComp) = 0; @@ -174,7 +176,7 @@ namespace cadet inline IBindingModel* getBinding() const CADET_NOEXCEPT { return _binding; } inline bool bindingParDep() const CADET_NOEXCEPT { return _bindingParDep; } - inline IDynamicReactionModel* getReaction() const CADET_NOEXCEPT { return _dynReaction; } + inline const ReactionSystem* getReaction() const CADET_NOEXCEPT { return &_reaction; } inline bool reactionParDep() const CADET_NOEXCEPT { return _reactionParDep; } virtual inline const active& getPorosity() const CADET_NOEXCEPT = 0; @@ -238,7 +240,7 @@ namespace cadet IBindingModel* _binding; //!< Binding model std::shared_ptr _nBound; //!< Array with number of bound states for each component bool _bindingParDep; //!< Whether the binding model parameters depend on the particle type - IDynamicReactionModel* _dynReaction; //!< Dynamic reaction model + ReactionSystem _reaction; //!< Reaction system bool _reactionParDep; //!< Whether the binding model parameters depend on the particle type }; diff --git a/src/libcadet/model/parts/BindingCellKernel.hpp b/src/libcadet/model/parts/BindingCellKernel.hpp index cf89c703f..dcdf7ca53 100644 --- a/src/libcadet/model/parts/BindingCellKernel.hpp +++ b/src/libcadet/model/parts/BindingCellKernel.hpp @@ -21,6 +21,7 @@ #include "AutoDiff.hpp" #include "model/BindingModel.hpp" #include "model/ReactionModel.hpp" +#include "model/reaction/ReactionSystem.hpp" #include "SimulationTypes.hpp" #include "LoggingUtils.hpp" @@ -75,7 +76,7 @@ namespace cell const active& porosity; active const* poreAccessFactor; IBindingModel* binding; - IDynamicReactionModel* dynReaction; + const ReactionSystem* reaction; }; template @@ -152,54 +153,81 @@ namespace cell } } - // Reaction - if (params.dynReaction) + // Move pointers back to liquid phase + if (wantRes) + res -= params.nComp; + y -= params.nComp; + + // dim for reactions + const int numReacCrossPhase = + (params.reaction) + ? params.reaction->getDynReactionVector("cross_phase").size() + : 0; + + const int numReacLiquid = + (params.reaction) + ? params.reaction->getDynReactionVector("liquid").size() + : 0; + + const int numReacSolid = + (params.reaction) + ? params.reaction->getDynReactionVector("solid").size() + : 0; + + if (numReacCrossPhase > 0 || numReacLiquid > 0 || numReacSolid > 0) { + // Pre-calculate + std::vector invBetaP(params.nComp); + for (unsigned int comp = 0; comp < params.nComp; ++comp) + { + invBetaP[comp] = (1.0 - static_cast(params.porosity)) / + (params.poreAccessFactor ? static_cast(params.poreAccessFactor[comp]) * static_cast(params.porosity) : static_cast(params.porosity)); + } + // Cross phase reaction + for (unsigned int reac = 0; reac < numReacCrossPhase; ++reac) + { + if (!params.reaction->getDynReactionVector("cross_phase")[ reac]) + continue; + if (wantRes) { BufferedArray fluxSolid = buffer.template array(params.nTotalBound); std::fill_n(static_cast(fluxSolid), params.nTotalBound, 0.0); - params.dynReaction->residualCombinedAdd(t, secIdx, colPos, y - params.nComp, y, res - params.nComp, static_cast(fluxSolid), -1.0, buffer); + params.reaction->getDynReactionVector("cross_phase")[reac]->residualCombinedAdd(t, secIdx, colPos, y, y + params.nComp, res, static_cast(fluxSolid), -1.0, buffer); unsigned int idx = 0; for (unsigned int comp = 0; comp < params.nComp; ++comp) { - const ParamType invBetaP = (1.0 - static_cast(params.porosity)) / (params.poreAccessFactor ? static_cast(params.poreAccessFactor[comp]) * static_cast(params.porosity) : static_cast(params.porosity)); - for (unsigned int bnd = 0; bnd < params.nBound[comp]; ++bnd, ++idx) { // Add reaction term to mobile phase - res[-static_cast(params.nComp) + static_cast(comp)] += static_cast::type>(invBetaP)* fluxSolid[idx]; + res[static_cast(comp)] += static_cast::type>(invBetaP[comp])* fluxSolid[idx]; if (!params.qsReaction[idx]) { // Add reaction term to solid phase - res[idx] += fluxSolid[idx]; + res[idx + params.nComp] += fluxSolid[idx]; + } } } - } - } + if (wantJac) { - if (params.nTotalBound > 0) - { BufferedArray fluxSolidJacobian = buffer.template array(params.nTotalBound * (params.nTotalBound + params.nComp)); linalg::DenseMatrixView dmv(static_cast(fluxSolidJacobian), nullptr, params.nTotalBound, params.nTotalBound + params.nComp); dmv.setAll(0.0); // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - params.dynReaction->analyticJacobianCombinedAdd(t, secIdx, colPos, reinterpret_cast(y - params.nComp), reinterpret_cast(y), -1.0, jacBase, dmv.row(0, params.nComp), buffer); + params.reaction->getDynReactionVector("cross_phase")[ reac]->analyticJacobianCombinedAdd(t, secIdx, colPos, reinterpret_cast(y), reinterpret_cast(y + params.nComp), -1.0, jacBase, dmv.row(0, params.nComp), buffer); unsigned int idx = 0; for (unsigned int comp = 0; comp < params.nComp; ++comp) { - const double invBetaP = (1.0 - static_cast(params.porosity)) / (params.poreAccessFactor ? static_cast(params.poreAccessFactor[comp]) * static_cast(params.porosity) : static_cast(params.porosity)); - for (unsigned int bnd = 0; bnd < params.nBound[comp]; ++bnd, ++idx) { - // Add Jacobian row to mobile phase - (jacBase + comp).addArray(dmv.rowPtr(idx), -static_cast(comp), dmv.columns(), invBetaP); + // Add Jacobian row to mobile inline void addArray(double const* row, int startDiag, int length, double factor) + (jacBase + comp).addArray(dmv.rowPtr(idx), -static_cast(comp), dmv.columns(), invBetaP[comp]); if (!params.qsReaction[idx]) { @@ -209,14 +237,75 @@ namespace cell } } } - else + } + } + // Pore reactions + for (unsigned int reac = 0; reac < numReacLiquid; ++reac) + { + if (!params.reaction->getDynReactionVector("liquid")[reac]) + continue; + + if (wantRes) { - // We do not have bound states, but still need to obtain the Jacobian for the liquid phase. - // So we pass a row iterator for the solid phase that does not point anywhere and hope that the - // reaction model does not interact with it. + params.reaction->getDynReactionVector("liquid")[reac]->residualFluxAdd(t, secIdx, colPos, params.nComp, y, res, -1.0, buffer); + + if (wantJac) + { + params.reaction->getDynReactionVector("liquid")[reac]->analyticJacobianAdd(t, secIdx, colPos, params.nComp, reinterpret_cast(y), -1.0, jacBase, buffer); + } + } + } + // Solid reaction + for (unsigned int reac = 0; reac < numReacSolid; ++reac) + { + if (!params.reaction->getDynReactionVector("solid")[reac]) + continue; + + if (wantRes) + { + + BufferedArray fluxSolid = buffer.template array(params.nTotalBound); + std::fill_n(static_cast(fluxSolid), params.nTotalBound, 0.0); + params.reaction->getDynReactionVector("solid")[reac]->residualFluxAdd(t, secIdx, colPos, params.nTotalBound, y + params.nComp, static_cast(fluxSolid), -1.0, buffer);//todo params.strideBound[parType] + unsigned int idx = 0; + for (unsigned int comp = 0; comp < params.nComp; ++comp) + { + for (unsigned int bnd = 0; bnd < params.nBound[comp]; ++bnd, ++idx) + { + res[static_cast(comp)] += static_cast::type>(invBetaP[comp])* fluxSolid[idx]; + + if (!params.qsReaction[idx]) + { + // Add reaction term to solid phase + res[idx + params.nComp] += fluxSolid[idx]; + } + } + } + + if (wantJac) + { + BufferedArray fluxSolidJacobian = buffer.template array(params.nTotalBound * (params.nTotalBound + params.nComp)); + linalg::DenseMatrixView dmv(static_cast(fluxSolidJacobian), nullptr, params.nTotalBound, params.nTotalBound + params.nComp); + dmv.setAll(0.0); // static_cast should be sufficient here, but this statement is also analyzed when wantJac = false - params.dynReaction->analyticJacobianCombinedAdd(t, secIdx, colPos, reinterpret_cast(y - params.nComp), reinterpret_cast(y), -1.0, jacBase, linalg::DenseBandedRowIterator(), buffer); + params.reaction->getDynReactionVector("solid")[reac]->analyticJacobianAdd(t, secIdx, colPos, params.nTotalBound, reinterpret_cast(y + params.nComp), -1.0, dmv.row(0, params.nComp), buffer); + + unsigned int idx = 0; + for (unsigned int comp = 0; comp < params.nComp; ++comp) + { + for (unsigned int bnd = 0; bnd < params.nBound[comp]; ++bnd, ++idx) + { + (jacBase + comp).addArray(dmv.rowPtr(idx), -static_cast(comp), dmv.columns(), invBetaP[comp]); + + if (!params.qsReaction[idx]) + { + // Add Jacobian row to solid phase + (jacBase + params.nComp + idx).addArray(dmv.rowPtr(idx), -static_cast(params.nComp + idx), dmv.columns(), 1.0); + } + } + } + } } } } diff --git a/src/libcadet/model/reaction/CrystallizationReaction.cpp b/src/libcadet/model/reaction/CrystallizationReaction.cpp index 394b6334e..adb1a2669 100644 --- a/src/libcadet/model/reaction/CrystallizationReaction.cpp +++ b/src/libcadet/model/reaction/CrystallizationReaction.cpp @@ -1340,7 +1340,7 @@ class CrystallizationReaction : public IDynamicReactionModel } template - int residualLiquidImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, StateType const* y, ResidualType* res, const FactorType& factor, LinearBufferAllocator workSpace) const + int residualFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, StateType const* y, ResidualType* res, const FactorType& factor, LinearBufferAllocator workSpace) const { ResidualType B_0 = 0.0; ResidualType k_g_times_s_g = 0.0; @@ -1351,7 +1351,7 @@ class CrystallizationReaction : public IDynamicReactionModel StateType const* const yCrystal = y + 1; ResidualType* const resCrystal = res + 1; - const StateType sParam = (cadet_likely(y[0] / y[_nComp - 1] - 1.0 > 0)) ? y[0] / y[_nComp - 1] - 1.0 : 0.0; // s = (c_0 - c_eq) / c_eq = c_0 / c_eq - 1, rewrite it to zero if s drops below 0 + const StateType sParam = (cadet_likely(y[0] / y[_nComp - 1] - 1.0 > 0)) ? y[0] / y[_nComp - 1] - 1.0 : StateType(0.0); // s = (c_0 - c_eq) / c_eq = c_0 / c_eq - 1, rewrite it to zero if s drops below 0 const ParamType massDensityShapeFactor = static_cast(_nucleiMassDensity) * static_cast(_volShapeFactor); k_g_times_s_g = static_cast(_growthRateConstant) * pow(sParam, static_cast(_g)); @@ -1533,7 +1533,7 @@ class CrystallizationReaction : public IDynamicReactionModel int residualCombinedImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, StateType const* yLiquid, StateType const* ySolid, ResidualType* resLiquid, ResidualType* resSolid, double factor, LinearBufferAllocator workSpace) const { - return residualLiquidImpl(t, secIdx, colPos, yLiquid, resLiquid, factor, workSpace); + return residualFluxImpl(t, secIdx, colPos, 0, yLiquid, resLiquid, factor, workSpace); } template @@ -2396,7 +2396,7 @@ class CrystallizationReaction : public IDynamicReactionModel } template - void jacobianLiquidImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, RowIterator& jac, LinearBufferAllocator workSpace) const + void jacobianFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, RowIterator& jac, LinearBufferAllocator workSpace) const { if (_mode.hasPBM()) { @@ -2630,7 +2630,7 @@ class CrystallizationReaction : public IDynamicReactionModel template void jacobianCombinedImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* yLiquid, double const* ySolid, double factor, RowIteratorLiquid& jacLiquid, RowIteratorSolid& jacSolid, LinearBufferAllocator workSpace) const { - jacobianLiquidImpl(t, secIdx, colPos, yLiquid, factor, jacLiquid, workSpace); + jacobianFluxImpl(t, secIdx, colPos, 0, yLiquid, factor, jacLiquid, workSpace); } }; diff --git a/src/libcadet/model/reaction/DummyReaction.cpp b/src/libcadet/model/reaction/DummyReaction.cpp index 6eb36196a..03acd0393 100644 --- a/src/libcadet/model/reaction/DummyReaction.cpp +++ b/src/libcadet/model/reaction/DummyReaction.cpp @@ -62,22 +62,23 @@ class DummyDynamicReaction : public IDynamicReactionModel return 0; } - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, active const* y, active* res, const active& factor, LinearBufferAllocator workSpace) const { return 0; } - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, active const* y, active* res, double factor, LinearBufferAllocator workSpace) const { return 0; } - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, active* res, double factor, LinearBufferAllocator workSpace) const { return 0; } - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double* res, double factor, LinearBufferAllocator workSpace) const { return 0; } - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandMatrix::RowIterator jac, LinearBufferAllocator workSpace) const { } - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::DenseBandedRowIterator jac, LinearBufferAllocator workSpace) const { } - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandedSparseRowIterator jac, LinearBufferAllocator workSpace) const { } - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, linalg::BandedEigenSparseRowIterator jac, LinearBufferAllocator workSpace) const { } + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::BandMatrix::RowIterator jac, LinearBufferAllocator workSpace) const { } + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::DenseBandedRowIterator jac, LinearBufferAllocator workSpace) const { } + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::BandedSparseRowIterator jac, LinearBufferAllocator workSpace) const { } + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, linalg::BandedEigenSparseRowIterator jac, LinearBufferAllocator workSpace) const { } + virtual int residualCombinedAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* yLiquid, active const* ySolid, active* resLiquid, active* resSolid, double factor, LinearBufferAllocator workSpace) const { return 0; } diff --git a/src/libcadet/model/reaction/MassActionLawReaction.cpp b/src/libcadet/model/reaction/MassActionLawReaction.cpp index 2c11bff5d..4a78c1969 100644 --- a/src/libcadet/model/reaction/MassActionLawReaction.cpp +++ b/src/libcadet/model/reaction/MassActionLawReaction.cpp @@ -32,24 +32,16 @@ "externalName": "ExtMassActionLawParamHandler", "parameters": [ - { "type": "ScalarReactionDependentParameter", "varName": "kFwdBulk", "confName": "MAL_KFWD_BULK"}, - { "type": "ScalarReactionDependentParameter", "varName": "kBwdBulk", "confName": "MAL_KBWD_BULK"}, - { "type": "ScalarReactionDependentParameter", "varName": "kFwdLiquid", "confName": "MAL_KFWD_LIQUID"}, - { "type": "ScalarReactionDependentParameter", "varName": "kBwdLiquid", "confName": "MAL_KBWD_LIQUID"}, - { "type": "ScalarReactionDependentParameter", "varName": "kFwdSolid", "confName": "MAL_KFWD_SOLID"}, - { "type": "ScalarReactionDependentParameter", "varName": "kBwdSolid", "confName": "MAL_KBWD_SOLID"} + { "type": "ScalarReactionDependentParameter", "varName": "kFwd", "confName": "MAL_KFWD"}, + { "type": "ScalarReactionDependentParameter", "varName": "kBwd", "confName": "MAL_KBWD"} ] } */ /* Parameter description ------------------------ - kFwdBulk = Forward rate for reactions in bulk volume - kBwdBulk = Backward rate for reactions in bulk volume - kFwdLiquid = Forward rate for reactions in particle liquid phase - kBwdLiquid = Backward rate for reactions in particle liquid phase - kFwdSolid = Forward rate for reactions in particle solid phase - kBwdSolid = Backward rate for reactions in particle solid phase + kFwd = Forward rate for reactions + kBwd = Backward rate for reactions */ namespace cadet @@ -163,7 +155,7 @@ namespace * @param [in] exponents Matrix with exponents in the rate law * @param [in] y Array of concentrations */ - inline void fluxGradLiquid(double* fluxGrad, unsigned int r, unsigned int nComp, double rate, const cadet::linalg::ActiveDenseMatrix& exponents, double const* y) + inline void fluxGrad(double* fluxGrad, unsigned int r, unsigned int nComp, double rate, const cadet::linalg::ActiveDenseMatrix& exponents, double const* y) { for (unsigned int c = 0; c < nComp; ++c) { @@ -191,72 +183,10 @@ namespace } } } - - /** - * @brief Calculate gradient of reaction rate (flux) in liquid-solid phase cell - * @param [out] fluxGrad Array that holds the gradient of the reaction rate - * @param [in] r Index of the reaction - * @param [in] nComp Number of components - * @param [in] nTotalBoundStates Total number of bound states - * @param [in] rate Rate constant - * @param [in] expLiquid Matrix with exponents of the liquid phase concentrations in the rate law - * @param [in] expSolid Matrix with exponents of the solid phase concentrations in the rate law - * @param [in] yLiquid Array of liquid phase concentrations (points to first component of liquid phase concentrations) - * @param [in] ySolid Array of solid phase concentrations (points to first component of solid phase concentrations) - */ inline void fluxGradCombined(double* fluxGrad, unsigned int r, unsigned int nComp, unsigned int nTotalBoundStates, double rate, const cadet::linalg::ActiveDenseMatrix& expLiquid, const cadet::linalg::ActiveDenseMatrix& expSolid, double const* yLiquid, double const* ySolid) { - for (unsigned int c = 0; c < nComp; ++c) - { - if (cadet_unlikely(expLiquid.native(c, r) != 0.0)) - fluxGrad[c] = rate; - else - fluxGrad[c] = 0.0; - } - - for (unsigned int c = 0; c < nTotalBoundStates; ++c) - { - if (cadet_unlikely(expSolid.native(c, r) != 0.0)) - fluxGrad[nComp + c] = rate; - else - fluxGrad[nComp + c] = 0.0; - } - - // Calculate gradient - for (unsigned int c = 0; c < nComp; ++c) - { - if (cadet_unlikely(expLiquid.native(c, r) != 0.0)) - { - const double exponentValue = static_cast(expLiquid.native(c, r)); - const double v = pow(yLiquid[c], exponentValue); - for (unsigned int j = 0; j < c; ++j) - fluxGrad[j] *= v; - - fluxGrad[c] *= exponentValue * pow(yLiquid[c], exponentValue - 1.0); - - for (unsigned int j = c + 1; j < nComp + nTotalBoundStates; ++j) - fluxGrad[j] *= v; - - } - } - - for (unsigned int c = 0; c < nTotalBoundStates; ++c) - { - if (cadet_unlikely(expSolid.native(c, r) != 0.0)) - { - const double exponentValue = static_cast(expSolid.native(c, r)); - const double v = pow(ySolid[c], exponentValue); - for (unsigned int j = 0; j < nComp + c; ++j) - fluxGrad[j] *= v; - - fluxGrad[nComp + c] *= exponentValue * pow(ySolid[c], exponentValue - 1.0); - - for (unsigned int j = c + 1; j < nTotalBoundStates; ++j) - fluxGrad[nComp + j] *= v; - } - } } template @@ -287,17 +217,6 @@ namespace } } -/** - * @brief Defines the multi component Langmuir binding model - * @details Implements the Langmuir adsorption model: \f[ \begin{align} - * \frac{\mathrm{d}q_i}{\mathrm{d}t} &= k_{a,i} c_{p,i} q_{\text{max},i} \left( 1 - \sum_j \frac{q_j}{q_{\text{max},j}} \right) - k_{d,i} q_i - * \end{align} \f] - * Multiple bound states are not supported. - * Components without bound state (i.e., non-binding components) are supported. - * - * See @cite Langmuir1916. - * @tparam ParamHandler_t Type that can add support for external function dependence - */ template class MassActionLawReactionBase : public DynamicReactionModelBase { @@ -320,254 +239,119 @@ class MassActionLawReactionBase : public DynamicReactionModelBase virtual bool configureModelDiscretization(IParameterProvider& paramProvider, unsigned int nComp, unsigned int const* nBound, unsigned int const* boundOffset) { DynamicReactionModelBase::configureModelDiscretization(paramProvider, nComp, nBound, boundOffset); - - if (paramProvider.exists("MAL_STOICHIOMETRY_BULK")) + + if (paramProvider.exists("MAL_STOICHIOMETRY")) { - const std::size_t numElements = paramProvider.numElements("MAL_STOICHIOMETRY_BULK"); + const std::size_t numElements = paramProvider.numElements("MAL_STOICHIOMETRY"); if (numElements % nComp != 0) - throw InvalidParameterException("Size of field MAL_STOICHIOMETRY_BULK must be a positive multiple of NCOMP (" + std::to_string(nComp) + ")"); + throw InvalidParameterException("Size of field MAL_STOICHIOMETRY must be a positive multiple of NCOMP (" + std::to_string(nComp) + ")"); const unsigned int nReactions = numElements / nComp; - _stoichiometryBulk.resize(nComp, nReactions); - _expBulkFwd.resize(nComp, nReactions); - _expBulkBwd.resize(nComp, nReactions); + _stoichiometry.resize(nComp, nReactions); + _expFwd.resize(nComp, nReactions); + _expBwd.resize(nComp, nReactions); } if (!nBound || !boundOffset) return true; - if (paramProvider.exists("MAL_STOICHIOMETRY_LIQUID")) - { - const std::size_t numElements = paramProvider.numElements("MAL_STOICHIOMETRY_LIQUID"); - if (numElements % nComp != 0) - throw InvalidParameterException("Size of field MAL_STOICHIOMETRY_LIQUID must be a positive multiple of NCOMP (" + std::to_string(nComp) + ")"); - - const unsigned int nReactions = numElements / nComp; - - _stoichiometryLiquid.resize(nComp, nReactions); - _expLiquidFwd.resize(nComp, nReactions); - _expLiquidBwd.resize(nComp, nReactions); - - _expLiquidFwdSolid.resize(_nTotalBoundStates, nReactions); - _expLiquidBwdSolid.resize(_nTotalBoundStates, nReactions); - } - - if (paramProvider.exists("MAL_STOICHIOMETRY_SOLID") && (_nTotalBoundStates > 0)) - { - const std::size_t numElements = paramProvider.numElements("MAL_STOICHIOMETRY_SOLID"); - if (numElements % _nTotalBoundStates != 0) - throw InvalidParameterException("Size of field MAL_STOICHIOMETRY_SOLID must be a positive multiple of NTOTALBND (" + std::to_string(_nTotalBoundStates) + ")"); - - const unsigned int nReactions = numElements / _nTotalBoundStates; - - _stoichiometrySolid.resize(_nTotalBoundStates, nReactions); - _expSolidFwd.resize(_nTotalBoundStates, nReactions); - _expSolidBwd.resize(_nTotalBoundStates, nReactions); - - _expSolidFwdLiquid.resize(nComp, nReactions); - _expSolidBwdLiquid.resize(nComp, nReactions); - } - return true; } - virtual unsigned int numReactionsLiquid() const CADET_NOEXCEPT { return _stoichiometryBulk.columns(); } - virtual unsigned int numReactionsCombined() const CADET_NOEXCEPT { return _stoichiometryLiquid.columns() + _stoichiometrySolid.columns(); } + virtual unsigned int numReactions() const CADET_NOEXCEPT { return _stoichiometry.columns(); } + virtual unsigned int numReactionsLiquid() const CADET_NOEXCEPT { return 0; } + virtual unsigned int numReactionsCombined() const CADET_NOEXCEPT { return 0; } CADET_DYNAMICREACTIONMODEL_BOILERPLATE protected: ParamHandler_t _paramHandler; //!< Handles parameters and their dependence on external functions - linalg::ActiveDenseMatrix _stoichiometryBulk; - linalg::ActiveDenseMatrix _expBulkFwd; - linalg::ActiveDenseMatrix _expBulkBwd; - - linalg::ActiveDenseMatrix _stoichiometryLiquid; - linalg::ActiveDenseMatrix _expLiquidFwd; - linalg::ActiveDenseMatrix _expLiquidBwd; - linalg::ActiveDenseMatrix _expLiquidFwdSolid; - linalg::ActiveDenseMatrix _expLiquidBwdSolid; - - linalg::ActiveDenseMatrix _stoichiometrySolid; - linalg::ActiveDenseMatrix _expSolidFwd; - linalg::ActiveDenseMatrix _expSolidBwd; - linalg::ActiveDenseMatrix _expSolidFwdLiquid; - linalg::ActiveDenseMatrix _expSolidBwdLiquid; - - inline int maxNumReactions() const CADET_NOEXCEPT { return std::max(std::max(_stoichiometryBulk.columns(), _stoichiometryLiquid.columns()), _stoichiometrySolid.columns()); } + linalg::ActiveDenseMatrix _stoichiometry; + linalg::ActiveDenseMatrix _expFwd; + linalg::ActiveDenseMatrix _expBwd; + + + inline int maxNumReactions() const CADET_NOEXCEPT + { + return _stoichiometry.columns();; + } virtual bool configureImpl(IParameterProvider& paramProvider, UnitOpIdx unitOpIdx, ParticleTypeIdx parTypeIdx) { _paramHandler.configure(paramProvider, maxNumReactions(), _nComp, _nBoundStates); _paramHandler.registerParameters(_parameters, unitOpIdx, parTypeIdx, _nComp, _nBoundStates); - if ((_stoichiometryBulk.columns() > 0) && ((static_cast(_paramHandler.kFwdBulk().size()) < _stoichiometryBulk.columns()) || (static_cast(_paramHandler.kBwdBulk().size()) < _stoichiometryBulk.columns()))) - throw InvalidParameterException("MAL_KFWD_BULK and MAL_KBWD_BULK have to have the same size (number of reactions)"); - - if ((_stoichiometryLiquid.columns() > 0) && ((static_cast(_paramHandler.kFwdLiquid().size()) < _stoichiometryLiquid.columns()) || (static_cast(_paramHandler.kBwdLiquid().size()) < _stoichiometryLiquid.columns()))) - throw InvalidParameterException("MAL_KFWD_LIQUID and MAL_KBWD_LIQUID have to have the same size (number of reactions)"); - - if ((_stoichiometrySolid.columns() > 0) && ((static_cast(_paramHandler.kFwdSolid().size()) < _stoichiometrySolid.columns()) || (static_cast(_paramHandler.kBwdSolid().size()) < _stoichiometrySolid.columns()))) - throw InvalidParameterException("MAL_KFWD_SOLID and MAL_KBWD_SOLID have to have the same size (number of reactions)"); - - if (paramProvider.exists("MAL_STOICHIOMETRY_BULK")) - { - const std::vector s = paramProvider.getDoubleArray("MAL_STOICHIOMETRY_BULK"); - - if (static_cast(s.size()) != _stoichiometryBulk.elements()) - throw InvalidParameterException("MAL_STOICHIOMETRY_BULK has changed size (number of reactions changed)"); - - std::copy(s.begin(), s.end(), _stoichiometryBulk.data()); - } - registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_STOICHIOMETRY_BULK", _stoichiometryBulk); - - if (paramProvider.exists("MAL_EXPONENTS_BULK_FWD")) - { - const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_BULK_FWD"); - if (static_cast(s.size()) != _stoichiometryBulk.elements()) - throw InvalidParameterException("Expected MAL_EXPONENTS_BULK_FWD and MAL_STOICHIOMETRY_BULK to be of the same size (" + std::to_string(_stoichiometryBulk.elements()) + ")"); - - std::copy(s.begin(), s.end(), _expBulkFwd.data()); - } - else - { - // Obtain default values from stoichiometry - std::transform(_stoichiometryBulk.data(), _stoichiometryBulk.data() + _stoichiometryBulk.elements(), _expBulkFwd.data(), [](const active& v) { return std::max(0.0, -static_cast(v)); }); - } - registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_BULK_FWD", _expBulkFwd); - - if (paramProvider.exists("MAL_EXPONENTS_BULK_BWD")) - { - const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_BULK_BWD"); - if (static_cast(s.size()) != _stoichiometryBulk.elements()) - throw InvalidParameterException("Expected MAL_EXPONENTS_BULK_BWD and MAL_STOICHIOMETRY_BULK to be of the same size (" + std::to_string(_stoichiometryBulk.elements()) + ")"); - - std::copy(s.begin(), s.end(), _expBulkBwd.data()); - } - else + if ((_stoichiometry.columns() > 0) && ((static_cast(_paramHandler.kFwd().size()) < _stoichiometry.columns()) || (static_cast(_paramHandler.kBwd().size()) < _stoichiometry.columns()))) + throw InvalidParameterException("MAL_KFWD and MAL_KBWD have to have the same size (number of reactions)"); + + if (paramProvider.exists("MAL_STOICHIOMETRY")) { - // Obtain default values from stoichiometry - std::transform(_stoichiometryBulk.data(), _stoichiometryBulk.data() + _stoichiometryBulk.elements(), _expBulkBwd.data(), [](const active& v) { return std::max(0.0, static_cast(v)); }); - } - registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_BULK_BWD", _expBulkBwd); + const std::vector s = paramProvider.getDoubleArray("MAL_STOICHIOMETRY"); + if (static_cast(s.size()) != _stoichiometry.elements()) + throw InvalidParameterException("MAL_STOICHIOMETRY has changed size (number of reactions changed)"); - if (paramProvider.exists("MAL_STOICHIOMETRY_LIQUID")) - { - const std::vector s = paramProvider.getDoubleArray("MAL_STOICHIOMETRY_LIQUID"); - - if (static_cast(s.size()) != _stoichiometryLiquid.elements()) - throw InvalidParameterException("MAL_STOICHIOMETRY_LIQUID has changed size (number of reactions changed)"); - - std::copy(s.begin(), s.end(), _stoichiometryLiquid.data()); + std::copy(s.begin(), s.end(), _stoichiometry.data()); } - registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_STOICHIOMETRY_LIQUID", _stoichiometryLiquid); + registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_STOICHIOMETRY", _stoichiometry); - if (paramProvider.exists("MAL_EXPONENTS_LIQUID_FWD")) + if (paramProvider.exists("MAL_EXPONENTS_FWD")) { - const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_LIQUID_FWD"); - if (static_cast(s.size()) != _stoichiometryLiquid.elements()) - throw InvalidParameterException("Expected MAL_EXPONENTS_LIQUID_FWD and MAL_STOICHIOMETRY_LIQUID to be of the same size (" + std::to_string(_stoichiometryLiquid.elements()) + ")"); + const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_FWD"); + if (static_cast(s.size()) != _stoichiometry.elements()) + throw InvalidParameterException("Expected MAL_EXPONENTS_FWD and MAL_STOICHIOMETRY to be of the same size (" + std::to_string(_stoichiometry.elements()) + ")"); - std::copy(s.begin(), s.end(), _expLiquidFwd.data()); + std::copy(s.begin(), s.end(), _expFwd.data()); } else { // Obtain default values from stoichiometry - std::transform(_stoichiometryLiquid.data(), _stoichiometryLiquid.data() + _stoichiometryLiquid.elements(), _expLiquidFwd.data(), [](const active& v) { return std::max(0.0, -static_cast(v)); }); + std::transform(_stoichiometry.data(), _stoichiometry.data() + _stoichiometry.elements(), _expFwd.data(), [](const active& v) { return std::max(0.0, -static_cast(v)); }); } - registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_LIQUID_FWD", _expLiquidFwd); + registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_FWD", _expFwd); - if (paramProvider.exists("MAL_EXPONENTS_LIQUID_BWD")) + if (paramProvider.exists("MAL_EXPONENTS_BWD")) { - const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_LIQUID_BWD"); - if (static_cast(s.size()) != _stoichiometryLiquid.elements()) - throw InvalidParameterException("Expected MAL_EXPONENTS_LIQUID_BWD and MAL_STOICHIOMETRY_LIQUID to be of the same size (" + std::to_string(_stoichiometryLiquid.elements()) + ")"); + const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_BWD"); + if (static_cast(s.size()) != _stoichiometry.elements()) + throw InvalidParameterException("Expected MAL_EXPONENTS_BWD and MAL_STOICHIOMETRY to be of the same size (" + std::to_string(_stoichiometry.elements()) + ")"); - std::copy(s.begin(), s.end(), _expLiquidBwd.data()); + std::copy(s.begin(), s.end(), _expBwd.data()); } else { // Obtain default values from stoichiometry - std::transform(_stoichiometryLiquid.data(), _stoichiometryLiquid.data() + _stoichiometryLiquid.elements(), _expLiquidBwd.data(), [](const active& v) { return std::max(0.0, static_cast(v)); }); + std::transform(_stoichiometry.data(), _stoichiometry.data() + _stoichiometry.elements(), _expBwd.data(), [](const active& v) { return std::max(0.0, static_cast(v)); }); } - registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_LIQUID_BWD", _expLiquidBwd); - - if (!_nBoundStates || !_boundOffset) - return true; - - readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_LIQUID_FWD_MODSOLID", _expLiquidFwdSolid, _nComp, _boundOffset); - readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_LIQUID_BWD_MODSOLID", _expLiquidBwdSolid, _nComp, _boundOffset); - - - if (paramProvider.exists("MAL_STOICHIOMETRY_SOLID")) - { - const std::vector s = paramProvider.getDoubleArray("MAL_STOICHIOMETRY_SOLID"); - - if (static_cast(s.size()) != _stoichiometrySolid.elements()) - throw InvalidParameterException("MAL_STOICHIOMETRY_SOLID has changed size (number of reactions changed)"); - - std::copy(s.begin(), s.end(), _stoichiometrySolid.data()); - } - registerBoundStateRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_STOICHIOMETRY_SOLID", _stoichiometrySolid, _nComp, _boundOffset); - - if (paramProvider.exists("MAL_EXPONENTS_SOLID_FWD")) - { - const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_SOLID_FWD"); - if (static_cast(s.size()) != _stoichiometrySolid.elements()) - throw InvalidParameterException("Expected MAL_EXPONENTS_SOLID_FWD and MAL_STOICHIOMETRY_SOLID to be of the same size (" + std::to_string(_stoichiometrySolid.elements()) + ")"); - - std::copy(s.begin(), s.end(), _expSolidFwd.data()); - } - else - { - // Obtain default values from stoichiometry - std::transform(_stoichiometrySolid.data(), _stoichiometrySolid.data() + _stoichiometrySolid.elements(), _expSolidFwd.data(), [](const active& v) { return std::max(0.0, -static_cast(v)); }); - } - registerBoundStateRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_SOLID_FWD", _expSolidFwd, _nComp, _boundOffset); - - if (paramProvider.exists("MAL_EXPONENTS_SOLID_BWD")) - { - const std::vector s = paramProvider.getDoubleArray("MAL_EXPONENTS_SOLID_BWD"); - if (static_cast(s.size()) != _stoichiometrySolid.elements()) - throw InvalidParameterException("Expected MAL_EXPONENTS_SOLID_BWD and MAL_STOICHIOMETRY_SOLID to be of the same size (" + std::to_string(_stoichiometrySolid.elements()) + ")"); - - std::copy(s.begin(), s.end(), _expSolidBwd.data()); - } - else - { - // Obtain default values from stoichiometry - std::transform(_stoichiometrySolid.data(), _stoichiometrySolid.data() + _stoichiometrySolid.elements(), _expSolidBwd.data(), [](const active& v) { return std::max(0.0, static_cast(v)); }); - } - registerBoundStateRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_SOLID_BWD", _expSolidBwd, _nComp, _boundOffset); - - readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_SOLID_FWD_MODLIQUID", _expSolidFwdLiquid, _nComp, nullptr); - readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_SOLID_BWD_MODLIQUID", _expSolidBwdLiquid, _nComp, nullptr); + registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_EXPONENTS_BWD", _expBwd); + return true; } template - int residualLiquidImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, - StateType const* y, ResidualType* res, const FactorType& factor, LinearBufferAllocator workSpace) const + int residualFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, + const unsigned int nStates, StateType const* y, ResidualType* res, const FactorType& factor, LinearBufferAllocator workSpace) const { typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); // Calculate fluxes typedef typename DoubleActivePromoter::type flux_t; BufferedArray fluxes = workSpace.array(maxNumReactions()); - for (int r = 0; r < _stoichiometryBulk.columns(); ++r) + + for (int r = 0; r < _stoichiometry.columns(); ++r) { - flux_t fwd = rateConstantOrZero(static_cast::type>(p->kFwdBulk[r]), r, _expBulkFwd, _nComp); - for (int c = 0; c < _nComp; ++c) + flux_t fwd = rateConstantOrZero(static_cast::type>(p->kFwd[r]), r, _expFwd, nStates); + + for (int c = 0; c < nStates; ++c) { - if (_expBulkFwd.native(c, r) != 0.0) + if (_expFwd.native(c, r) != 0.0) { if (static_cast(y[c]) > 0.0) fwd *= pow(static_cast::type>(y[c]), - static_cast::type>(_expBulkFwd.native(c, r))); + static_cast::type>(_expFwd.native(c, r))); else { fwd *= 0.0; @@ -576,14 +360,15 @@ class MassActionLawReactionBase : public DynamicReactionModelBase } } - flux_t bwd = rateConstantOrZero(static_cast::type>(p->kBwdBulk[r]), r, _expBulkBwd, _nComp); - for (int c = 0; c < _nComp; ++c) - { - if (_expBulkBwd.native(c, r) != 0.0) + flux_t bwd = rateConstantOrZero(static_cast::type>(p->kBwd[r]), r, _expBwd, nStates); + for (int c = 0; c < nStates; ++c) + { + + if (_expBwd.native(c, r) != 0.0) { if (static_cast(y[c]) > 0.0) bwd *= pow(static_cast::type>(y[c]), - static_cast::type>(_expBulkBwd.native(c, r))); + static_cast::type>(_expBwd.native(c, r))); else { bwd *= 0.0; @@ -596,232 +381,56 @@ class MassActionLawReactionBase : public DynamicReactionModelBase } // Add reaction terms to residual - _stoichiometryBulk.multiplyVector(static_cast(fluxes), factor, res); + _stoichiometry.multiplyVector(static_cast(fluxes), factor, res); return 0; } - template - int residualCombinedImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, - StateType const* yLiquid, StateType const* ySolid, ResidualType* resLiquid, ResidualType* resSolid, double factor, LinearBufferAllocator workSpace) const - { - typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); - - // Calculate fluxes in liquid phase - typedef typename DoubleActivePromoter::type flux_t; - BufferedArray fluxes = workSpace.array(maxNumReactions()); - for (int r = 0; r < _stoichiometryLiquid.columns(); ++r) - { - flux_t fwd = rateConstantOrZero(static_cast::type>(p->kFwdLiquid[r]), r, _expLiquidFwd, _expLiquidFwdSolid, _nComp, _nTotalBoundStates); - for (int c = 0; c < _nComp; ++c) - { - if (_expLiquidFwd.native(c, r) != 0.0) - { - if (static_cast(yLiquid[c]) > 0.0) - fwd *= pow(static_cast::type>(yLiquid[c]), - static_cast::type>(_expLiquidFwd.native(c, r))); - else - { - fwd *= 0.0; - break; - } - } - } - for (int c = 0; c < _nTotalBoundStates; ++c) - { - if (_expLiquidFwdSolid.native(c, r) != 0.0) - { - if (static_cast(ySolid[c]) > 0.0) - fwd *= pow(static_cast::type>(ySolid[c]), - static_cast::type>(_expLiquidFwdSolid.native(c, r))); - else - { - fwd *= 0.0; - break; - } - } - } - - flux_t bwd = rateConstantOrZero(static_cast::type>(p->kBwdLiquid[r]), r, _expLiquidBwd, _expLiquidBwdSolid, _nComp, _nTotalBoundStates); - for (int c = 0; c < _nComp; ++c) - { - if (_expLiquidBwd.native(c, r) != 0.0) - { - if (static_cast(yLiquid[c]) > 0.0) - bwd *= pow(static_cast::type>(yLiquid[c]), - static_cast::type>(_expLiquidBwd.native(c, r))); - else - { - bwd *= 0.0; - break; - } - } - } - for (int c = 0; c < _nTotalBoundStates; ++c) - { - if (_expLiquidBwdSolid.native(c, r) != 0.0) - { - if (static_cast(ySolid[c]) > 0.0) - bwd *= pow(static_cast::type>(ySolid[c]), - static_cast::type>(_expLiquidBwdSolid.native(c, r))); - else - { - bwd *= 0.0; - break; - } - } - } - - fluxes[r] = fwd - bwd; - } - - // Add reaction terms to liquid phase residual - _stoichiometryLiquid.multiplyVector(static_cast(fluxes), factor, resLiquid); - - if (_nTotalBoundStates == 0) - return 0; - - // Calculate fluxes in solid phase - for (int r = 0; r < _stoichiometrySolid.columns(); ++r) - { - flux_t fwd = rateConstantOrZero(static_cast::type>(p->kFwdSolid[r]), r, _expSolidFwdLiquid, _expSolidFwd, _nComp, _nTotalBoundStates); - for (int c = 0; c < _nComp; ++c) - { - if (_expSolidFwdLiquid.native(c, r) != 0.0) - { - if (static_cast(yLiquid[c]) > 0.0) - fwd *= pow(static_cast::type>(yLiquid[c]), - static_cast::type>(_expSolidFwdLiquid.native(c, r))); - else - { - fwd *= 0.0; - break; - } - } - } - for (int c = 0; c < _nTotalBoundStates; ++c) - { - if (_expSolidFwd.native(c, r) != 0.0) - { - if (static_cast(ySolid[c]) > 0.0) - fwd *= pow(static_cast::type>(ySolid[c]), - static_cast::type>(_expSolidFwd.native(c, r))); - else - { - fwd *= 0.0; - break; - } - } - } - - flux_t bwd = rateConstantOrZero(static_cast::type>(p->kBwdSolid[r]), r, _expSolidBwdLiquid, _expSolidBwd, _nComp, _nTotalBoundStates); - for (int c = 0; c < _nComp; ++c) - { - if (_expSolidBwdLiquid.native(c, r) != 0.0) - { - if (static_cast(yLiquid[c]) > 0.0) - bwd *= pow(static_cast::type>(yLiquid[c]), - static_cast::type>(_expSolidBwdLiquid.native(c, r))); - else - { - bwd *= 0.0; - break; - } - } - } - for (int c = 0; c < _nTotalBoundStates; ++c) - { - if (_expSolidBwd.native(c, r) != 0.0) - { - if (static_cast(ySolid[c]) > 0.0) - bwd *= pow(static_cast::type>(ySolid[c]), - static_cast::type>(_expSolidBwd.native(c, r))); - else - { - bwd *= 0.0; - break; - } - } - } - - fluxes[r] = fwd - bwd; - } - - // Add reaction terms to solid phase residual - _stoichiometrySolid.multiplyVector(static_cast(fluxes), factor, resSolid); - - return 0; - } template - void jacobianLiquidImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, const RowIterator& jac, LinearBufferAllocator workSpace) const + void jacobianFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nState, double const* y, double factor, const RowIterator& jac, LinearBufferAllocator workSpace) const { typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); - BufferedArray fluxes = workSpace.array(2 * _nComp); + BufferedArray fluxes = workSpace.array(2 * nState); double* const fluxGradFwd = static_cast(fluxes); - double* const fluxGradBwd = fluxGradFwd + _nComp; - for (int r = 0; r < _stoichiometryBulk.columns(); ++r) + double* const fluxGradBwd = fluxGradFwd + nState; + + for (int r = 0; r < _stoichiometry.columns(); ++r) { // Calculate gradients of forward and backward fluxes - fluxGradLiquid(fluxGradFwd, r, _nComp, static_cast(p->kFwdBulk[r]), _expBulkFwd, y); - fluxGradLiquid(fluxGradBwd, r, _nComp, static_cast(p->kBwdBulk[r]), _expBulkBwd, y); + double kFwd = static_cast(p->kFwd[r]); + double kBwd = static_cast(p->kBwd[r]); + + + fluxGrad(fluxGradFwd, r, nState, kFwd, _expFwd, y); + fluxGrad(fluxGradBwd, r, nState, kBwd, _expBwd, y); // Add gradients to Jacobian RowIterator curJac = jac; - for (int row = 0; row < _nComp; ++row, ++curJac) + for (int row = 0; row < nState; ++row, ++curJac) { - const double colFactor = static_cast(_stoichiometryBulk.native(row, r)) * factor; - for (int col = 0; col < _nComp; ++col) + const double colFactor = static_cast(_stoichiometry.native(row, r)) * factor; + for (int col = 0; col < nState; ++col) curJac[col - static_cast(row)] += colFactor * (fluxGradFwd[col] - fluxGradBwd[col]); } } } + template + int residualCombinedImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, + StateType const* yLiquid, StateType const* ySolid, ResidualType* resLiquid, ResidualType* resSolid, double factor, LinearBufferAllocator workSpace) const + { + return 0; + } + template void jacobianCombinedImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* yLiquid, double const* ySolid, double factor, const RowIteratorLiquid& jacLiquid, const RowIteratorSolid& jacSolid, LinearBufferAllocator workSpace) const { - typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); - - BufferedArray fluxes = workSpace.array(2 * (_nComp + _nTotalBoundStates)); - double* const fluxGradFwd = static_cast(fluxes); - double* const fluxGradBwd = fluxGradFwd + _nComp + _nTotalBoundStates; - - for (int r = 0; r < _stoichiometryLiquid.columns(); ++r) - { - // Calculate gradients of forward and backward fluxes - fluxGradCombined(fluxGradFwd, r, _nComp, _nTotalBoundStates, static_cast(p->kFwdLiquid[r]), _expLiquidFwd, _expLiquidFwdSolid, yLiquid, ySolid); - fluxGradCombined(fluxGradBwd, r, _nComp, _nTotalBoundStates, static_cast(p->kBwdLiquid[r]), _expLiquidBwd, _expLiquidBwdSolid, yLiquid, ySolid); - // Add gradients to Jacobian - RowIteratorLiquid curJac = jacLiquid; - for (int row = 0; row < _nComp; ++row, ++curJac) - { - const double colFactor = static_cast(_stoichiometryLiquid.native(row, r)) * factor; - for (int col = 0; col < _nComp + _nTotalBoundStates; ++col) - curJac[col - static_cast(row)] += colFactor * (fluxGradFwd[col] - fluxGradBwd[col]); - } - } - - if (_nTotalBoundStates == 0) - return; + } - for (int r = 0; r < _stoichiometrySolid.columns(); ++r) - { - // Calculate gradients of forward and backward fluxes - fluxGradCombined(fluxGradFwd, r, _nComp, _nTotalBoundStates, static_cast(p->kFwdSolid[r]), _expSolidFwdLiquid, _expSolidFwd, yLiquid, ySolid); - fluxGradCombined(fluxGradBwd, r, _nComp, _nTotalBoundStates, static_cast(p->kBwdSolid[r]), _expSolidBwdLiquid, _expSolidBwd, yLiquid, ySolid); - // Add gradients to Jacobian - RowIteratorSolid curJac = jacSolid; - for (int row = 0; row < _nTotalBoundStates; ++row, ++curJac) - { - const double colFactor = static_cast(_stoichiometrySolid.native(row, r)) * factor; - for (int col = 0; col < _nComp + _nTotalBoundStates; ++col) - curJac[col - static_cast(_nComp) - static_cast(row)] += colFactor * (fluxGradFwd[col] - fluxGradBwd[col]); - } - } - } }; typedef MassActionLawReactionBase MassActionLawReaction; diff --git a/src/libcadet/model/reaction/MassActionLawReactionCrossPhase.cpp b/src/libcadet/model/reaction/MassActionLawReactionCrossPhase.cpp new file mode 100644 index 000000000..b61b81f91 --- /dev/null +++ b/src/libcadet/model/reaction/MassActionLawReactionCrossPhase.cpp @@ -0,0 +1,714 @@ +// ============================================================================= +// CADET +// +// Copyright © 2008-present: The CADET-Core Authors +// Please see the AUTHORS.md file. +// +// All rights reserved. This program and the accompanying materials +// are made available under the terms of the GNU Public License v3.0 (or, at +// your option, any later version) which accompanies this distribution, and +// is available at http://www.gnu.org/licenses/gpl.html +// ============================================================================= + +#include "model/reaction/ReactionModelBase.hpp" +#include "model/ExternalFunctionSupport.hpp" +#include "model/ModelUtils.hpp" +#include "cadet/Exceptions.hpp" +#include "model/Parameters.hpp" +#include "LocalVector.hpp" +#include "SimulationTypes.hpp" +#include "linalg/ActiveDenseMatrix.hpp" +#include "Memory.hpp" + +#include +#include +#include +#include +#include + +/* +{ + "name": "MassActionLawCrossPhaseParamHandler", + "externalName": "ExtMassActionLawCrossPhaseParamHandler", + "parameters": + [ + + { "type": "ScalarReactionDependentParameter", "varName": "kFwdLiquid", "confName": "MAL_KFWD_LIQUID"}, + { "type": "ScalarReactionDependentParameter", "varName": "kBwdLiquid", "confName": "MAL_KBWD_LIQUID"}, + { "type": "ScalarReactionDependentParameter", "varName": "kFwdSolid", "confName": "MAL_KFWD_SOLID"}, + { "type": "ScalarReactionDependentParameter", "varName": "kBwdSolid", "confName": "MAL_KBWD_SOLID"} + ] +} +*/ + +/* Parameter description + ------------------------ + kFwdLiquid = Forward rate for reactions in particle liquid phase + kBwdLiquid = Backward rate for reactions in particle liquid phase + kFwdSolid = Forward rate for reactions in particle solid phase + kBwdSolid = Backward rate for reactions in particle solid phase +*/ + +namespace cadet +{ + + namespace model + { + + inline const char* MassActionLawCrossPhaseParamHandler::identifier() CADET_NOEXCEPT { return "MASS_ACTION_LAW_CROSS_PHASE"; } + + inline bool MassActionLawCrossPhaseParamHandler::validateConfig(unsigned int nReactions, unsigned int nComp, unsigned int const* nBoundStates) + { + return true; + } + + inline const char* ExtMassActionLawCrossPhaseParamHandler::identifier() CADET_NOEXCEPT { return "EXT_MASS_ACTION_LAW_CROSS_PHASE"; } + + inline bool ExtMassActionLawCrossPhaseParamHandler::validateConfig(unsigned int nReactions, unsigned int nComp, unsigned int const* nBoundStates) + { + return true; + } + + + namespace + { + /** + * @brief Registers a matrix-valued parameter (row-major storage) with bound states as rows + * @details The matrix-valued parameter has as many rows as there are bound states in the system. + * @param [in,out] parameters Parameter map + * @param [in] unitOpIdx Unit operation id + * @param [in] parTypeIdx Particle type index + * @param [in] paramName Name of the parameter + * @param [in] mat Matrix to register + * @param [in] nComp Number of components + * @param [in] boundOffset Array with offsets to bound states of a specific component + */ + inline void registerBoundStateRowMatrix(std::unordered_map& parameters, UnitOpIdx unitOpIdx, ParticleTypeIdx parTypeIdx, const std::string& paramName, cadet::linalg::ActiveDenseMatrix& mat, + unsigned int nComp, unsigned int const* boundOffset) + { + const cadet::StringHash hashName = cadet::hashStringRuntime(paramName); + cadet::registerParam2DArray(parameters, mat.data(), mat.elements(), [=](bool multi, unsigned int row, unsigned int col) + { + const unsigned int comp = std::lower_bound(boundOffset, boundOffset + nComp, row) - boundOffset; + const unsigned int bnd = row - boundOffset[comp]; + return cadet::makeParamId(hashName, unitOpIdx, comp, parTypeIdx, bnd, col, cadet::SectionIndep); + }, + mat.columns() + ); + } + + /** + * @brief Registers a matrix-valued parameter (row-major storage) with components as rows + * @details The matrix-valued parameter has as many rows as there are components in the system. + * @param [in,out] parameters Parameter map + * @param [in] unitOpIdx Unit operation id + * @param [in] parTypeIdx Particle type index + * @param [in] paramName Name of the parameter + * @param [in] mat Matrix to register + */ + inline void registerCompRowMatrix(std::unordered_map& parameters, UnitOpIdx unitOpIdx, ParticleTypeIdx parTypeIdx, const std::string& paramName, cadet::linalg::ActiveDenseMatrix& mat) + { + const cadet::StringHash hashName = cadet::hashStringRuntime(paramName); + cadet::registerParam2DArray(parameters, mat.data(), mat.elements(), [=](bool multi, unsigned int row, unsigned int col) + { + return cadet::makeParamId(hashName, unitOpIdx, row, parTypeIdx, cadet::BoundStateIndep, col, cadet::SectionIndep); + }, + mat.columns() + ); + } + + /** + * @brief Reads reaction rate exponents and registers them + * @details Reads a matrix-valued parameter into the given pre-allocated matrix and registers the + * parameters in the map. If @p boundOffset is @c nullptr, the matrix has as many columns + * as there are components. Otherwise, the matrix has as many columns as there are bound states. + * @param [in] paramProvider Parameter provider + * @param [in,out] parameters Parameter map + * @param [in] unitOpIdx Unit operation id + * @param [in] parTypeIdx Particle type index + * @param [in] paramName Name of the parameter + * @param [out] mat Matrix that holds the values (pre-allocated) + * @param [in] nComp Number of components + * @param [in] boundOffset Array with offsets to bound states of a specific component, or @c nullptr + */ + inline void readAndRegisterExponents(cadet::IParameterProvider& paramProvider, std::unordered_map& parameters, UnitOpIdx unitOpIdx, ParticleTypeIdx parTypeIdx, + const std::string& paramName, cadet::linalg::ActiveDenseMatrix& mat, unsigned int nComp, unsigned int const* boundOffset) + { + if (paramProvider.exists(paramName)) + { + const std::vector s = paramProvider.getDoubleArray(paramName); + if (static_cast(s.size()) != mat.elements()) + throw InvalidParameterException("Expected " + paramName + " to be of size " + std::to_string(mat.elements()) + ""); + + std::copy(s.begin(), s.end(), mat.data()); + } + else + mat.setAll(0.0); + + if (boundOffset) + registerBoundStateRowMatrix(parameters, unitOpIdx, parTypeIdx, paramName, mat, nComp, boundOffset); + else + registerCompRowMatrix(parameters, unitOpIdx, parTypeIdx, paramName, mat); + } + + /** + * @brief Calculate gradient of reaction rate (flux) in liquid phase + * @param [out] fluxGrad Array that holds the gradient of the reaction rate + * @param [in] r Index of the reaction + * @param [in] nComp Number of components + * @param [in] rate Rate constant + * @param [in] exponents Matrix with exponents in the rate law + * @param [in] y Array of concentrations + */ + inline void fluxGradLiquid(double* fluxGrad, unsigned int r, unsigned int nComp, double rate, const cadet::linalg::ActiveDenseMatrix& exponents, double const* y) + { + for (unsigned int c = 0; c < nComp; ++c) + { + if (cadet_unlikely(exponents.native(c, r) != 0.0)) + fluxGrad[c] = rate; + else + fluxGrad[c] = 0.0; + } + + // Calculate gradient + for (unsigned int c = 0; c < nComp; ++c) + { + if (cadet_unlikely(exponents.native(c, r) != 0.0)) + { + const double exponentValue = static_cast(exponents.native(c, r)); + const double v = pow(y[c], exponentValue); + for (unsigned int j = 0; j < c; ++j) + fluxGrad[j] *= v; + + fluxGrad[c] *= exponentValue * pow(y[c], exponentValue - 1.0); + + for (unsigned int j = c + 1; j < nComp; ++j) + fluxGrad[j] *= v; + + } + } + } + + /** + * @brief Calculate gradient of reaction rate (flux) in liquid-solid phase cell + * @param [out] fluxGrad Array that holds the gradient of the reaction rate + * @param [in] r Index of the reaction + * @param [in] nComp Number of components + * @param [in] nTotalBoundStates Total number of bound states + * @param [in] rate Rate constant + * @param [in] expLiquid Matrix with exponents of the liquid phase concentrations in the rate law + * @param [in] expSolid Matrix with exponents of the solid phase concentrations in the rate law + * @param [in] yLiquid Array of liquid phase concentrations (points to first component of liquid phase concentrations) + * @param [in] ySolid Array of solid phase concentrations (points to first component of solid phase concentrations) + */ + inline void fluxGradCombined(double* fluxGrad, unsigned int r, unsigned int nComp, unsigned int nTotalBoundStates, double rate, + const cadet::linalg::ActiveDenseMatrix& expLiquid, const cadet::linalg::ActiveDenseMatrix& expSolid, double const* yLiquid, double const* ySolid) + { + for (unsigned int c = 0; c < nComp; ++c) + { + if (cadet_unlikely(expLiquid.native(c, r) != 0.0)) + fluxGrad[c] = rate; + else + fluxGrad[c] = 0.0; + } + + for (unsigned int c = 0; c < nTotalBoundStates; ++c) + { + if (cadet_unlikely(expSolid.native(c, r) != 0.0)) + fluxGrad[nComp + c] = rate; + else + fluxGrad[nComp + c] = 0.0; + } + + // Calculate gradient + for (unsigned int c = 0; c < nComp; ++c) + { + if (cadet_unlikely(expLiquid.native(c, r) != 0.0)) + { + const double exponentValue = static_cast(expLiquid.native(c, r)); + const double v = pow(yLiquid[c], exponentValue); + for (unsigned int j = 0; j < c; ++j) + fluxGrad[j] *= v; + + fluxGrad[c] *= exponentValue * pow(yLiquid[c], exponentValue - 1.0); + + for (unsigned int j = c + 1; j < nComp + nTotalBoundStates; ++j) + fluxGrad[j] *= v; + + } + } + + for (unsigned int c = 0; c < nTotalBoundStates; ++c) + { + if (cadet_unlikely(expSolid.native(c, r) != 0.0)) + { + const double exponentValue = static_cast(expSolid.native(c, r)); + const double v = pow(ySolid[c], exponentValue); + for (unsigned int j = 0; j < nComp + c; ++j) + fluxGrad[j] *= v; + + fluxGrad[nComp + c] *= exponentValue * pow(ySolid[c], exponentValue - 1.0); + + for (unsigned int j = c + 1; j < nTotalBoundStates; ++j) + fluxGrad[nComp + j] *= v; + + } + } + } + + template + inline num_t rateConstantOrZero(const num_t& rate, unsigned int idxReaction, const cadet::linalg::ActiveDenseMatrix& exponents, unsigned int nComp) + { + for (unsigned int c = 0; c < nComp; ++c) + { + if (cadet_unlikely(exponents.native(c, idxReaction) != 0.0)) + return rate; + } + return 0.0; + } + + template + inline num_t rateConstantOrZero(const num_t& rate, unsigned int idxReaction, const cadet::linalg::ActiveDenseMatrix& expLiquid, const cadet::linalg::ActiveDenseMatrix& expSolid, unsigned int nComp, unsigned int nTotalBoundStates) + { + for (unsigned int c = 0; c < nComp; ++c) + { + if (cadet_unlikely(expLiquid.native(c, idxReaction) != 0.0)) + return rate; + } + for (unsigned int c = 0; c < nTotalBoundStates; ++c) + { + if (cadet_unlikely(expSolid.native(c, idxReaction) != 0.0)) + return rate; + } + return 0.0; + } + } + + /** + * @brief Defines the multi component Langmuir binding model + * @details Implements the Langmuir adsorption model: \f[ \begin{align} + * \frac{\mathrm{d}q_i}{\mathrm{d}t} &= k_{a,i} c_{p,i} q_{\text{max},i} \left( 1 - \sum_j \frac{q_j}{q_{\text{max},j}} \right) - k_{d,i} q_i + * \end{align} \f] + * Multiple bound states are not supported. + * Components without bound state (i.e., non-binding components) are supported. + * + * See @cite Langmuir1916. + * @tparam ParamHandler_t Type that can add support for external function dependence + */ + template + class MassActionLawCrossPhaseReactionBase : public DynamicReactionModelBase + { + public: + + MassActionLawCrossPhaseReactionBase() { } + virtual ~MassActionLawCrossPhaseReactionBase() CADET_NOEXCEPT { } + + static const char* identifier() { return ParamHandler_t::identifier(); } + virtual const char* name() const CADET_NOEXCEPT { return ParamHandler_t::identifier(); } + + virtual void setExternalFunctions(IExternalFunction** extFuns, unsigned int size) { _paramHandler.setExternalFunctions(extFuns, size); } + virtual bool dependsOnTime() const CADET_NOEXCEPT { return ParamHandler_t::dependsOnTime(); } + virtual bool requiresWorkspace() const CADET_NOEXCEPT { return true; } + virtual unsigned int workspaceSize(unsigned int nComp, unsigned int totalNumBoundStates, unsigned int const* nBoundStates) const CADET_NOEXCEPT + { + return _paramHandler.cacheSize(maxNumReactions(), nComp, totalNumBoundStates) + std::max(maxNumReactions() * sizeof(active), 2 * (_nComp + totalNumBoundStates) * sizeof(double)); + } + + virtual bool configureModelDiscretization(IParameterProvider& paramProvider, unsigned int nComp, unsigned int const* nBound, unsigned int const* boundOffset) + { + DynamicReactionModelBase::configureModelDiscretization(paramProvider, nComp, nBound, boundOffset); + + + if (!nBound || !boundOffset) + return true; + + if (paramProvider.exists("MAL_STOICHIOMETRY_LIQUID")) + { + const std::size_t numElements = paramProvider.numElements("MAL_STOICHIOMETRY_LIQUID"); + if (numElements % nComp != 0) + throw InvalidParameterException("Size of field STOICHIOMETRY_LIQUID must be a positive multiple of NCOMP (" + std::to_string(nComp) + ")"); + + const unsigned int nReactions = numElements / nComp; + + _stoichiometryLiquid.resize(nComp, nReactions); + _expLiquidFwd.resize(nComp, nReactions); + _expLiquidBwd.resize(nComp, nReactions); + + _expLiquidFwdSolid.resize(_nTotalBoundStates, nReactions); + _expLiquidBwdSolid.resize(_nTotalBoundStates, nReactions); + } + + if (paramProvider.exists("MAL_STOICHIOMETRY_SOLID") && (_nTotalBoundStates > 0)) + { + const std::size_t numElements = paramProvider.numElements("MAL_STOICHIOMETRY_SOLID"); + if (numElements % _nTotalBoundStates != 0) + throw InvalidParameterException("Size of field STOICHIOMETRY_SOLID must be a positive multiple of NTOTALBND (" + std::to_string(_nTotalBoundStates) + ")"); + + const unsigned int nReactions = numElements / _nTotalBoundStates; + + _stoichiometrySolid.resize(_nTotalBoundStates, nReactions); + _expSolidFwd.resize(_nTotalBoundStates, nReactions); + _expSolidBwd.resize(_nTotalBoundStates, nReactions); + + _expSolidFwdLiquid.resize(nComp, nReactions); + _expSolidBwdLiquid.resize(nComp, nReactions); + } + + return true; + } + + virtual unsigned int numReactionsLiquid() const CADET_NOEXCEPT { return 0; } + virtual unsigned int numReactionsCombined() const CADET_NOEXCEPT { return _stoichiometryLiquid.columns() + _stoichiometrySolid.columns(); } + + CADET_DYNAMICREACTIONMODEL_BOILERPLATE + + protected: + ParamHandler_t _paramHandler; //!< Handles parameters and their dependence on external functions + + + linalg::ActiveDenseMatrix _stoichiometryLiquid; + linalg::ActiveDenseMatrix _expLiquidFwd; + linalg::ActiveDenseMatrix _expLiquidBwd; + linalg::ActiveDenseMatrix _expLiquidFwdSolid; + linalg::ActiveDenseMatrix _expLiquidBwdSolid; + + linalg::ActiveDenseMatrix _stoichiometrySolid; + linalg::ActiveDenseMatrix _expSolidFwd; + linalg::ActiveDenseMatrix _expSolidBwd; + linalg::ActiveDenseMatrix _expSolidFwdLiquid; + linalg::ActiveDenseMatrix _expSolidBwdLiquid; + + inline int maxNumReactions() const CADET_NOEXCEPT { return std::max(_stoichiometryLiquid.columns(), _stoichiometrySolid.columns()); } + + virtual bool configureImpl(IParameterProvider& paramProvider, UnitOpIdx unitOpIdx, ParticleTypeIdx parTypeIdx) + { + _paramHandler.configure(paramProvider, maxNumReactions(), _nComp, _nBoundStates); + _paramHandler.registerParameters(_parameters, unitOpIdx, parTypeIdx, _nComp, _nBoundStates); + + if ((_stoichiometryLiquid.columns() > 0) && ((static_cast(_paramHandler.kFwdLiquid().size()) < _stoichiometryLiquid.columns()) || (static_cast(_paramHandler.kBwdLiquid().size()) < _stoichiometryLiquid.columns()))) + throw InvalidParameterException("KFWD_LIQUID and KBWD_LIQUID have to have the same size (number of reactions)"); + + if ((_stoichiometrySolid.columns() > 0) && ((static_cast(_paramHandler.kFwdSolid().size()) < _stoichiometrySolid.columns()) || (static_cast(_paramHandler.kBwdSolid().size()) < _stoichiometrySolid.columns()))) + throw InvalidParameterException("KFWD_SOLID and KBWD_SOLID have to have the same size (number of reactions)"); + + + if (paramProvider.exists("MAL_STOICHIOMETRY_LIQUID")) + { + const std::vector s = paramProvider.getDoubleArray("MAL_STOICHIOMETRY_LIQUID"); + + if (static_cast(s.size()) != _stoichiometryLiquid.elements()) + throw InvalidParameterException("STOICHIOMETRY_LIQUID has changed size (number of reactions changed)"); + + std::copy(s.begin(), s.end(), _stoichiometryLiquid.data()); + } + registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MAL_STOICHIOMETRY_LIQUID", _stoichiometryLiquid); + + if (paramProvider.exists("EXPONENTS_LIQUID_FWD")) + { + const std::vector s = paramProvider.getDoubleArray("EXPONENTS_LIQUID_FWD"); + if (static_cast(s.size()) != _stoichiometryLiquid.elements()) + throw InvalidParameterException("Expected EXPONENTS_LIQUID_FWD and STOICHIOMETRY_LIQUID to be of the same size (" + std::to_string(_stoichiometryLiquid.elements()) + ")"); + + std::copy(s.begin(), s.end(), _expLiquidFwd.data()); + } + else + { + // Obtain default values from stoichiometry + std::transform(_stoichiometryLiquid.data(), _stoichiometryLiquid.data() + _stoichiometryLiquid.elements(), _expLiquidFwd.data(), [](const active& v) { return std::max(0.0, -static_cast(v)); }); + } + registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "EXPONENTS_LIQUID_FWD", _expLiquidFwd); + + if (paramProvider.exists("EXPONENTS_LIQUID_BWD")) + { + const std::vector s = paramProvider.getDoubleArray("EXPONENTS_LIQUID_BWD"); + if (static_cast(s.size()) != _stoichiometryLiquid.elements()) + throw InvalidParameterException("Expected EXPONENTS_LIQUID_BWD and STOICHIOMETRY_LIQUID to be of the same size (" + std::to_string(_stoichiometryLiquid.elements()) + ")"); + + std::copy(s.begin(), s.end(), _expLiquidBwd.data()); + } + else + { + // Obtain default values from stoichiometry + std::transform(_stoichiometryLiquid.data(), _stoichiometryLiquid.data() + _stoichiometryLiquid.elements(), _expLiquidBwd.data(), [](const active& v) { return std::max(0.0, static_cast(v)); }); + } + registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "EXPONENTS_LIQUID_BWD", _expLiquidBwd); + + if (!_nBoundStates || !_boundOffset) + return true; + + readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "EXPONENTS_LIQUID_FWD_MODSOLID", _expLiquidFwdSolid, _nComp, _boundOffset); + readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "EXPONENTS_LIQUID_BWD_MODSOLID", _expLiquidBwdSolid, _nComp, _boundOffset); + + + if (paramProvider.exists("MAL_STOICHIOMETRY_SOLID")) + { + const std::vector s = paramProvider.getDoubleArray("MAL_STOICHIOMETRY_SOLID"); + + if (static_cast(s.size()) != _stoichiometrySolid.elements()) + throw InvalidParameterException("STOICHIOMETRY_SOLID has changed size (number of reactions changed)"); + + std::copy(s.begin(), s.end(), _stoichiometrySolid.data()); + } + registerBoundStateRowMatrix(_parameters, unitOpIdx, parTypeIdx, "STOICHIOMETRY_SOLID", _stoichiometrySolid, _nComp, _boundOffset); + + if (paramProvider.exists("EXPONENTS_SOLID_FWD")) + { + const std::vector s = paramProvider.getDoubleArray("EXPONENTS_SOLID_FWD"); + if (static_cast(s.size()) != _stoichiometrySolid.elements()) + throw InvalidParameterException("Expected EXPONENTS_SOLID_FWD and STOICHIOMETRY_SOLID to be of the same size (" + std::to_string(_stoichiometrySolid.elements()) + ")"); + + std::copy(s.begin(), s.end(), _expSolidFwd.data()); + } + else + { + // Obtain default values from stoichiometry + std::transform(_stoichiometrySolid.data(), _stoichiometrySolid.data() + _stoichiometrySolid.elements(), _expSolidFwd.data(), [](const active& v) { return std::max(0.0, -static_cast(v)); }); + } + registerBoundStateRowMatrix(_parameters, unitOpIdx, parTypeIdx, "EXPONENTS_SOLID_FWD", _expSolidFwd, _nComp, _boundOffset); + + if (paramProvider.exists("EXPONENTS_SOLID_BWD")) + { + const std::vector s = paramProvider.getDoubleArray("EXPONENTS_SOLID_BWD"); + if (static_cast(s.size()) != _stoichiometrySolid.elements()) + throw InvalidParameterException("Expected EXPONENTS_SOLID_BWD and STOICHIOMETRY_SOLID to be of the same size (" + std::to_string(_stoichiometrySolid.elements()) + ")"); + + std::copy(s.begin(), s.end(), _expSolidBwd.data()); + } + else + { + // Obtain default values from stoichiometry + std::transform(_stoichiometrySolid.data(), _stoichiometrySolid.data() + _stoichiometrySolid.elements(), _expSolidBwd.data(), [](const active& v) { return std::max(0.0, static_cast(v)); }); + } + registerBoundStateRowMatrix(_parameters, unitOpIdx, parTypeIdx, "EXPONENTS_SOLID_BWD", _expSolidBwd, _nComp, _boundOffset); + + readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "EXPONENTS_SOLID_FWD_MODLIQUID", _expSolidFwdLiquid, _nComp, nullptr); + readAndRegisterExponents(paramProvider, _parameters, unitOpIdx, parTypeIdx, "EXPONENTS_SOLID_BWD_MODLIQUID", _expSolidBwdLiquid, _nComp, nullptr); + + return true; + } + + template + int residualFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, + const unsigned int nStates, StateType const* y, ResidualType* res, const FactorType& factor, LinearBufferAllocator workSpace) const + { + return 0; + } + + template + int residualCombinedImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, + StateType const* yLiquid, StateType const* ySolid, ResidualType* resLiquid, ResidualType* resSolid, double factor, LinearBufferAllocator workSpace) const + { + typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); + + // Calculate fluxes in liquid phase + typedef typename DoubleActivePromoter::type flux_t; + BufferedArray fluxes = workSpace.array(maxNumReactions()); + for (int r = 0; r < _stoichiometryLiquid.columns(); ++r) + { + flux_t fwd = rateConstantOrZero(static_cast::type>(p->kFwdLiquid[r]), r, _expLiquidFwd, _expLiquidFwdSolid, _nComp, _nTotalBoundStates); + for (int c = 0; c < _nComp; ++c) + { + if (_expLiquidFwd.native(c, r) != 0.0) + { + if (static_cast(yLiquid[c]) > 0.0) + fwd *= pow(static_cast::type>(yLiquid[c]), + static_cast::type>(_expLiquidFwd.native(c, r))); + else + { + fwd *= 0.0; + break; + } + } + } + for (int c = 0; c < _nTotalBoundStates; ++c) + { + if (_expLiquidFwdSolid.native(c, r) != 0.0) + { + if (static_cast(ySolid[c]) > 0.0) + fwd *= pow(static_cast::type>(ySolid[c]), + static_cast::type>(_expLiquidFwdSolid.native(c, r))); + else + { + fwd *= 0.0; + break; + } + } + } + + flux_t bwd = rateConstantOrZero(static_cast::type>(p->kBwdLiquid[r]), r, _expLiquidBwd, _expLiquidBwdSolid, _nComp, _nTotalBoundStates); + for (int c = 0; c < _nComp; ++c) + { + if (_expLiquidBwd.native(c, r) != 0.0) + { + if (static_cast(yLiquid[c]) > 0.0) + bwd *= pow(static_cast::type>(yLiquid[c]), + static_cast::type>(_expLiquidBwd.native(c, r))); + else + { + bwd *= 0.0; + break; + } + } + } + for (int c = 0; c < _nTotalBoundStates; ++c) + { + if (_expLiquidBwdSolid.native(c, r) != 0.0) + { + if (static_cast(ySolid[c]) > 0.0) + bwd *= pow(static_cast::type>(ySolid[c]), + static_cast::type>(_expLiquidBwdSolid.native(c, r))); + else + { + bwd *= 0.0; + break; + } + } + } + + fluxes[r] = fwd - bwd; + } + + // Add reaction terms to liquid phase residual + _stoichiometryLiquid.multiplyVector(static_cast(fluxes), factor, resLiquid); + + if (_nTotalBoundStates == 0) + return 0; + + // Calculate fluxes in solid phase + for (int r = 0; r < _stoichiometrySolid.columns(); ++r) + { + flux_t fwd = rateConstantOrZero(static_cast::type>(p->kFwdSolid[r]), r, _expSolidFwdLiquid, _expSolidFwd, _nComp, _nTotalBoundStates); + for (int c = 0; c < _nComp; ++c) + { + if (_expSolidFwdLiquid.native(c, r) != 0.0) + { + if (static_cast(yLiquid[c]) > 0.0) + fwd *= pow(static_cast::type>(yLiquid[c]), + static_cast::type>(_expSolidFwdLiquid.native(c, r))); + else + { + fwd *= 0.0; + break; + } + } + } + for (int c = 0; c < _nTotalBoundStates; ++c) + { + if (_expSolidFwd.native(c, r) != 0.0) + { + if (static_cast(ySolid[c]) > 0.0) + fwd *= pow(static_cast::type>(ySolid[c]), + static_cast::type>(_expSolidFwd.native(c, r))); + else + { + fwd *= 0.0; + break; + } + } + } + + flux_t bwd = rateConstantOrZero(static_cast::type>(p->kBwdSolid[r]), r, _expSolidBwdLiquid, _expSolidBwd, _nComp, _nTotalBoundStates); + for (int c = 0; c < _nComp; ++c) + { + if (_expSolidBwdLiquid.native(c, r) != 0.0) + { + if (static_cast(yLiquid[c]) > 0.0) + bwd *= pow(static_cast::type>(yLiquid[c]), + static_cast::type>(_expSolidBwdLiquid.native(c, r))); + else + { + bwd *= 0.0; + break; + } + } + } + for (int c = 0; c < _nTotalBoundStates; ++c) + { + if (_expSolidBwd.native(c, r) != 0.0) + { + if (static_cast(ySolid[c]) > 0.0) + bwd *= pow(static_cast::type>(ySolid[c]), + static_cast::type>(_expSolidBwd.native(c, r))); + else + { + bwd *= 0.0; + break; + } + } + } + + fluxes[r] = fwd - bwd; + } + + // Add reaction terms to solid phase residual + _stoichiometrySolid.multiplyVector(static_cast(fluxes), factor, resSolid); + + return 0; + } + + template + void jacobianFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, const RowIterator& jac, LinearBufferAllocator workSpace) const + { + } + + template + void jacobianCombinedImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* yLiquid, double const* ySolid, double factor, const RowIteratorLiquid& jacLiquid, const RowIteratorSolid& jacSolid, LinearBufferAllocator workSpace) const + { + typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); + + BufferedArray fluxes = workSpace.array(2 * (_nComp + _nTotalBoundStates)); + double* const fluxGradFwd = static_cast(fluxes); + double* const fluxGradBwd = fluxGradFwd + _nComp + _nTotalBoundStates; + + for (int r = 0; r < _stoichiometryLiquid.columns(); ++r) + { + // Calculate gradients of forward and backward fluxes + fluxGradCombined(fluxGradFwd, r, _nComp, _nTotalBoundStates, static_cast(p->kFwdLiquid[r]), _expLiquidFwd, _expLiquidFwdSolid, yLiquid, ySolid); + fluxGradCombined(fluxGradBwd, r, _nComp, _nTotalBoundStates, static_cast(p->kBwdLiquid[r]), _expLiquidBwd, _expLiquidBwdSolid, yLiquid, ySolid); + + // Add gradients to Jacobian + RowIteratorLiquid curJac = jacLiquid; + for (int row = 0; row < _nComp; ++row, ++curJac) + { + const double colFactor = static_cast(_stoichiometryLiquid.native(row, r)) * factor; + for (int col = 0; col < _nComp + _nTotalBoundStates; ++col) + curJac[col - static_cast(row)] += colFactor * (fluxGradFwd[col] - fluxGradBwd[col]); + } + } + + if (_nTotalBoundStates == 0) + return; + + for (int r = 0; r < _stoichiometrySolid.columns(); ++r) + { + // Calculate gradients of forward and backward fluxes + fluxGradCombined(fluxGradFwd, r, _nComp, _nTotalBoundStates, static_cast(p->kFwdSolid[r]), _expSolidFwdLiquid, _expSolidFwd, yLiquid, ySolid); + fluxGradCombined(fluxGradBwd, r, _nComp, _nTotalBoundStates, static_cast(p->kBwdSolid[r]), _expSolidBwdLiquid, _expSolidBwd, yLiquid, ySolid); + + // Add gradients to Jacobian + RowIteratorSolid curJac = jacSolid; + for (int row = 0; row < _nTotalBoundStates; ++row, ++curJac) + { + const double colFactor = static_cast(_stoichiometrySolid.native(row, r)) * factor; + for (int col = 0; col < _nComp + _nTotalBoundStates; ++col) + curJac[col - static_cast(_nComp) - static_cast(row)] += colFactor * (fluxGradFwd[col] - fluxGradBwd[col]); + } + } + } + }; + + typedef MassActionLawCrossPhaseReactionBase MassActionLawCrossPhaseReaction; + typedef MassActionLawCrossPhaseReactionBase ExternalMassActionLawCrossPhaseReaction; + + namespace reaction + { + void registerMassActionLawReactionCrossPhase(std::unordered_map>& reactions) + { + reactions[MassActionLawCrossPhaseReaction::identifier()] = []() { return new MassActionLawCrossPhaseReaction(); }; + reactions[ExternalMassActionLawCrossPhaseReaction::identifier()] = []() { return new ExternalMassActionLawCrossPhaseReaction(); }; + } + } // namespace reaction + + } // namespace model + +} // namespace cadet diff --git a/src/libcadet/model/reaction/MichaelisMentenReaction.cpp b/src/libcadet/model/reaction/MichaelisMentenReaction.cpp index f176187a5..f06ad46ff 100644 --- a/src/libcadet/model/reaction/MichaelisMentenReaction.cpp +++ b/src/libcadet/model/reaction/MichaelisMentenReaction.cpp @@ -128,8 +128,8 @@ class MichaelisMentenBase : public DynamicReactionModelBase virtual bool requiresWorkspace() const CADET_NOEXCEPT { return true; } virtual unsigned int workspaceSize(unsigned int nComp, unsigned int totalNumBoundStates, unsigned int const* nBoundStates) const CADET_NOEXCEPT { - return _paramHandler.cacheSize(_stoichiometryBulk.columns(), nComp, totalNumBoundStates) + - std::max(_stoichiometryBulk.columns() * sizeof(active), + return _paramHandler.cacheSize(_stoichiometry.columns(), nComp, totalNumBoundStates) + + std::max(_stoichiometry.columns() * sizeof(active), 2 * (_nComp + totalNumBoundStates) * sizeof(double)); } @@ -137,30 +137,30 @@ class MichaelisMentenBase : public DynamicReactionModelBase { DynamicReactionModelBase::configureModelDiscretization(paramProvider, nComp, nBound, boundOffset); - if (paramProvider.exists("MM_STOICHIOMETRY_BULK")) + if (paramProvider.exists("MM_STOICHIOMETRY")) { - const std::size_t numElements = paramProvider.numElements("MM_STOICHIOMETRY_BULK"); + const std::size_t numElements = paramProvider.numElements("MM_STOICHIOMETRY"); if (numElements % nComp != 0) - throw InvalidParameterException("Size of field MM_STOICHIOMETRY_BULK must be a positive multiple of NCOMP (" + std::to_string(nComp) + ")"); + throw InvalidParameterException("Size of field MM_STOICHIOMETRY must be a positive multiple of NCOMP (" + std::to_string(nComp) + ")"); const unsigned int nReactions = numElements / nComp; - _stoichiometryBulk.resize(nComp, nReactions); + _stoichiometry.resize(nComp, nReactions); _idxSubstrate.resize(nReactions); } - return true; - } - - virtual unsigned int numReactionsLiquid() const CADET_NOEXCEPT { return _stoichiometryBulk.columns(); } - virtual unsigned int numReactionsCombined() const CADET_NOEXCEPT { return 0; } + return true; + } + virtual unsigned int numReactions() const CADET_NOEXCEPT { return _stoichiometry.columns(); } + virtual unsigned int numReactionsLiquid() const CADET_NOEXCEPT { return 0; } + virtual unsigned int numReactionsCombined() const CADET_NOEXCEPT { return 0; } CADET_DYNAMICREACTIONMODEL_BOILERPLATE protected: ParamHandler_t _paramHandler; //!< Handles parameters and their dependence on external functions - linalg::ActiveDenseMatrix _stoichiometryBulk; + linalg::ActiveDenseMatrix _stoichiometry; std::vector> _idxSubstrate; //!< Indices of substrate components for each reaction [reaction][substrate indices] std::vector>> _idxCompInhibitors; //!< Indices of competitive inhibitors [reaction][substrate][inhibitor indices] std::vector>> _idxUncompInhibitors; //!< Indices of uncompetitive inhibitors [reaction][substrate][inhibitor indices] @@ -188,48 +188,48 @@ class MichaelisMentenBase : public DynamicReactionModelBase virtual bool configureImpl(IParameterProvider& paramProvider, UnitOpIdx unitOpIdx, ParticleTypeIdx parTypeIdx) { - _paramHandler.configure(paramProvider, _stoichiometryBulk.columns(), _nComp, _nBoundStates); + _paramHandler.configure(paramProvider, _stoichiometry.columns(), _nComp, _nBoundStates); _paramHandler.registerParameters(_parameters, unitOpIdx, parTypeIdx, _nComp, _nBoundStates); _oldInterface = false; // handle old interface // - kmm is the number of reactions // - kI refers to the non competative inhibition konstants - if ((_stoichiometryBulk.columns() > 0) && (_paramHandler.kMM().size() == _stoichiometryBulk.columns()) || (paramProvider.exists("MM_KI"))) + if ((_stoichiometry.columns() > 0) && (_paramHandler.kMM().size() == _stoichiometry.columns()) || (paramProvider.exists("MM_KI"))) { _oldInterface = true; LOG(Warning) << "MM_KI is only is only supported for backwards compatibility, but the implementation of Michaelis Menten kinetics has changed, please refer to the documentation for CADET version >= 5.2.0"; } // Parameter validations - if ((_stoichiometryBulk.columns() > 0) && ((_paramHandler.vMax().size() < _stoichiometryBulk.columns()))) + if ((_stoichiometry.columns() > 0) && ((_paramHandler.vMax().size() < _stoichiometry.columns()))) throw InvalidParameterException("MM_VMAX have to have the size (number of reactions)"); - if (_oldInterface && (_stoichiometryBulk.columns() > 0) && (_paramHandler.kMM().size() < _stoichiometryBulk.columns())) + if (_oldInterface && (_stoichiometry.columns() > 0) && (_paramHandler.kMM().size() < _stoichiometry.columns())) throw InvalidParameterException("MM_KMM have to have the size (number of reactions)"); - if (!_oldInterface && (_stoichiometryBulk.columns() > 0) && (_paramHandler.kMM().size() < _stoichiometryBulk.columns() * _nComp)) + if (!_oldInterface && (_stoichiometry.columns() > 0) && (_paramHandler.kMM().size() < _stoichiometry.columns() * _nComp)) throw InvalidParameterException("MM_KMM must have the size (number of reactions) x (number of components)"); // kInhibitComp and kInhibitUnComp are 3D parameters with size (number of reactions) x (number of substrates) x (number of components) - if (paramProvider.exists("MM_STOICHIOMETRY_BULK")) + if (paramProvider.exists("MM_STOICHIOMETRY")) { - const std::vector s = paramProvider.getDoubleArray("MM_STOICHIOMETRY_BULK"); - std::vector KIC(_stoichiometryBulk.columns() * _nComp * _nComp); - std::vector KIUC(_stoichiometryBulk.columns() * _nComp * _nComp); + const std::vector s = paramProvider.getDoubleArray("MM_STOICHIOMETRY"); + std::vector KIC(_stoichiometry.columns() * _nComp * _nComp); + std::vector KIUC(_stoichiometry.columns() * _nComp * _nComp); bool hasCompetiveInhibition = false; if (paramProvider.exists("MM_KI_C")) { KIC = paramProvider.getDoubleArray("MM_KI_C"); - if (KIC.size() != _stoichiometryBulk.columns() * _nComp * _nComp) + if (KIC.size() != _stoichiometry.columns() * _nComp * _nComp) throw InvalidParameterException("MM_KI_C must have the size (number of reactions) x (number of components) x (number of components)"); } if (paramProvider.exists("MM_KI_UC")) { KIUC = paramProvider.getDoubleArray("MM_KI_UC"); - if (KIUC.size() != _stoichiometryBulk.columns() * _nComp * _nComp) + if (KIUC.size() != _stoichiometry.columns() * _nComp * _nComp) throw InvalidParameterException("MM_KI_UC must have the size (number of reactions) x (number of components) x (number of components)"); } if (paramProvider.exists("MM_KI")) @@ -239,14 +239,14 @@ class MichaelisMentenBase : public DynamicReactionModelBase } - if (s.size() != _stoichiometryBulk.elements()) - throw InvalidParameterException("MM_STOICHIOMETRY_BULK size mismatch: Expected " + - std::to_string(_stoichiometryBulk.elements()) + " elements but got " + std::to_string(s.size())); + if (s.size() != _stoichiometry.elements()) + throw InvalidParameterException("MM_STOICHIOMETRY size mismatch: Expected " + + std::to_string(_stoichiometry.elements()) + " elements but got " + std::to_string(s.size())); - std::copy(s.begin(), s.end(), _stoichiometryBulk.data()); + std::copy(s.begin(), s.end(), _stoichiometry.data()); // Identify substrates (negative entries in stoichiometry matrix) - const unsigned int nReactions = static_cast(_stoichiometryBulk.columns()); + const unsigned int nReactions = static_cast(_stoichiometry.columns()); _idxSubstrate.clear(); _idxCompInhibitors.resize(nReactions); _idxUncompInhibitors.resize(nReactions); @@ -256,7 +256,7 @@ class MichaelisMentenBase : public DynamicReactionModelBase std::vector idxSubstrateReaction_r; for (unsigned int c = 0; c < _nComp; ++c) { - if (_stoichiometryBulk.native(c, r) < 0.0) + if (_stoichiometry.native(c, r) < 0.0) idxSubstrateReaction_r.push_back(static_cast(c)); } @@ -300,21 +300,21 @@ class MichaelisMentenBase : public DynamicReactionModelBase } } - registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MM_STOICHIOMETRY_BULK", _stoichiometryBulk); + registerCompRowMatrix(_parameters, unitOpIdx, parTypeIdx, "MM_STOICHIOMETRY", _stoichiometry); return true; } - template - int residualLiquidImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, - StateType const* y, ResidualType* res, const FactorType& factor, LinearBufferAllocator workSpace) const - { - typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); + template + int residualFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, + const unsigned int nStates, StateType const* y, ResidualType* res, const FactorType& factor, LinearBufferAllocator workSpace) const + { + typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); // Calculate fluxes typedef typename DoubleActivePromoter::type flux_t; - BufferedArray fluxes = workSpace.array(_stoichiometryBulk.columns()); + BufferedArray fluxes = workSpace.array(_stoichiometry.columns()); - for (unsigned int r = 0; r < static_cast(_stoichiometryBulk.columns()); ++r) + for (unsigned int r = 0; r < static_cast(_stoichiometry.columns()); ++r) { unsigned int nSub = _idxSubstrate[r].size(); flux_t vProd = 1.0; @@ -376,7 +376,7 @@ class MichaelisMentenBase : public DynamicReactionModelBase } // Add reaction terms to residual - _stoichiometryBulk.multiplyVector(static_cast(fluxes), factor, res); + _stoichiometry.multiplyVector(static_cast(fluxes), factor, res); return 0; } @@ -395,12 +395,12 @@ class MichaelisMentenBase : public DynamicReactionModelBase return 0; } - template - void jacobianLiquidImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, double factor, const RowIterator& jac, LinearBufferAllocator workSpace) const - { - typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); + template + void jacobianFluxImpl(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, double factor, const RowIterator& jac, LinearBufferAllocator workSpace) const + { + typename ParamHandler_t::ParamsHandle const p = _paramHandler.update(t, secIdx, colPos, _nComp, _nBoundStates, workSpace); - for (unsigned int r = 0; r < static_cast(_stoichiometryBulk.columns()); ++r) + for (unsigned int r = 0; r < static_cast(_stoichiometry.columns()); ++r) { unsigned int nSub = _idxSubstrate[r].size(); @@ -583,7 +583,7 @@ class MichaelisMentenBase : public DynamicReactionModelBase RowIterator curJac = jac; for (unsigned int row = 0; row < _nComp; ++row, ++curJac) { - const double colFactor = static_cast(_stoichiometryBulk.native(row, r)) * factor; + const double colFactor = static_cast(_stoichiometry.native(row, r)) * factor; curJac[static_cast(comp) - static_cast(row)] += colFactor * dvdy; } } diff --git a/src/libcadet/model/reaction/ReactionModelBase.hpp b/src/libcadet/model/reaction/ReactionModelBase.hpp index 417eba6a6..2f02ec37e 100644 --- a/src/libcadet/model/reaction/ReactionModelBase.hpp +++ b/src/libcadet/model/reaction/ReactionModelBase.hpp @@ -82,37 +82,37 @@ class DynamicReactionModelBase : public IDynamicReactionModel /** * @brief Inserts implementations of all residual() and analyticJacobian() method variants - * @details An IDynamicReactionModel implementation has to provide residualLiquidAdd(), residualCombinedAdd(), - * analyticJacobianLiquidAdd(), and analyticJacobianCombinedAdd() methods for different variants of state + * @details An IDynamicReactionModel implementation has to provide residualFluxAdd(), residualCombinedAdd(), + * analyticJacobianAdd(), and analyticJacobianCombinedAdd() methods for different variants of state * and parameter type. This macro saves some time by providing those implementations. It assumes that the - * implementation provides templatized residualLiquidImpl(), residualCombinedImpl(), jacobianLiquidImpl(), + * implementation provides templatized residualFluxImpl(), residualCombinedImpl(), jacobianFluxImpl(), * and jacobianCombinedImpl() function that realize all required variants. * * The implementation is inserted inline in the class declaration. */ #define CADET_DYNAMICREACTIONMODEL_BOILERPLATE \ - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* y, \ + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, active const* y, \ active* res, const active& factor, LinearBufferAllocator workSpace) const \ { \ - return residualLiquidImpl(t, secIdx, colPos, y, res, factor, workSpace); \ + return residualFluxImpl(t, secIdx, colPos, nStates,y, res, factor, workSpace); \ } \ \ - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* y, \ + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, active const* y, \ active* res, double factor, LinearBufferAllocator workSpace) const \ { \ - return residualLiquidImpl(t, secIdx, colPos, y, res, factor, workSpace); \ + return residualFluxImpl(t, secIdx, colPos,nStates, y, res, factor, workSpace); \ } \ \ - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, \ + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, \ active* res, double factor, LinearBufferAllocator workSpace) const \ { \ - return residualLiquidImpl(t, secIdx, colPos, y, res, factor, workSpace); \ + return residualFluxImpl(t, secIdx, colPos, nStates,y, res, factor, workSpace); \ } \ \ - virtual int residualLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, \ + virtual int residualFluxAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, \ double* res, double factor, LinearBufferAllocator workSpace) const \ { \ - return residualLiquidImpl(t, secIdx, colPos, y, res, factor, workSpace); \ + return residualFluxImpl(t, secIdx, colPos, nStates, y, res, factor, workSpace); \ } \ \ virtual int residualCombinedAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, active const* yLiquid, \ @@ -133,28 +133,28 @@ class DynamicReactionModelBase : public IDynamicReactionModel return residualCombinedImpl(t, secIdx, colPos, yLiquid, ySolid, resLiquid, resSolid, factor, workSpace); \ } \ \ - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, \ + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, \ double factor, linalg::BandMatrix::RowIterator jac, LinearBufferAllocator workSpace) const \ { \ - jacobianLiquidImpl(t, secIdx, colPos, y, factor, jac, workSpace); \ + jacobianFluxImpl(t, secIdx, colPos, nStates, y, factor, jac, workSpace); \ } \ \ - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, \ + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, \ double factor, linalg::DenseBandedRowIterator jac, LinearBufferAllocator workSpace) const \ { \ - jacobianLiquidImpl(t, secIdx, colPos, y, factor, jac, workSpace); \ + jacobianFluxImpl(t, secIdx, colPos, nStates, y, factor, jac, workSpace); \ } \ \ - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, \ + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos,const unsigned int nStates, double const* y, \ double factor, linalg::BandedSparseRowIterator jac, LinearBufferAllocator workSpace) const \ { \ - jacobianLiquidImpl(t, secIdx, colPos, y, factor, jac, workSpace); \ + jacobianFluxImpl(t, secIdx, colPos, nStates, y, factor, jac, workSpace); \ } \ \ - virtual void analyticJacobianLiquidAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* y, \ + virtual void analyticJacobianAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, const unsigned int nStates, double const* y, \ double factor, linalg::BandedEigenSparseRowIterator jac, LinearBufferAllocator workSpace) const \ { \ - jacobianLiquidImpl(t, secIdx, colPos, y, factor, jac, workSpace); \ + jacobianFluxImpl(t, secIdx, colPos, nStates, y, factor, jac, workSpace); \ } \ \ virtual void analyticJacobianCombinedAdd(double t, unsigned int secIdx, const ColumnPosition& colPos, double const* yLiquid, double const* ySolid, \ diff --git a/src/libcadet/model/reaction/ReactionSystem.hpp b/src/libcadet/model/reaction/ReactionSystem.hpp new file mode 100644 index 000000000..0f7b13e21 --- /dev/null +++ b/src/libcadet/model/reaction/ReactionSystem.hpp @@ -0,0 +1,349 @@ +// ============================================================================= +// CADET +// +// Copyright © 2008-present: The CADET-Core Authors +// Please see the AUTHORS.md file. +// +// All rights reserved. This program and the accompanying materials +// are made available under the terms of the GNU Public License v3.0 (or, at +// your option, any later version) which accompanies this distribution, and +// is available at http://www.gnu.org/licenses/gpl.html +// ============================================================================= + +#pragma once + +#include "model/reaction/ReactionModelBase.hpp" +#include "model/ReactionModel.hpp" +#include "cadet/Exceptions.hpp" +#include "ConfigurationHelper.hpp" + +#include "LoggingUtils.hpp" +#include "Logging.hpp" + +#include +#include +#include +#include +#include +#include +#include +namespace cadet +{ + +namespace model +{ + +/** + * @brief Manages reaction models across different phases in a unit operation + * + * The ReactionSystem organizes and manages dynamic reaction models for different + * phases (cross_phase, pore, solid, bulk, liquid) within a unit operation. + * It handles configuration, discretization, and memory management of reaction models. + */ +struct ReactionSystem + { + private: + /** + * @brief Data structure holding reaction information for a specific phase + */ + struct PhaseData + { + std::vector dynReactions; //!< Dynamic reactions in the phase + + /** + * @brief Default constructor initializing phase data with safe defaults + */ + PhaseData() + { + dynReactions = { nullptr }; + } + }; + + //!< Maps phase type strings to their corresponding phase data + std::map _phaseMap = { + {"cross_phase", PhaseData{}}, + {"solid", PhaseData{}}, + {"liquid", PhaseData{}}, // unit liquid phase + {"pore", PhaseData{}} // particle liquid phase + }; + + /** + * @brief Retrieves phase data for a given phase type + * @param phaseType The type of phase to retrieve data for + * @return Reference to the phase data + * @throws InvalidParameterException if phase type is unknown + */ + PhaseData& getPhaseData(const std::string& phaseType) + { + auto phase = _phaseMap.find(phaseType); + if (phase == _phaseMap.end()) + throw InvalidParameterException("Unknown phase type: " + phaseType); + + return phase->second; + } + + /** + * @brief Const version of getPhaseData + * @param phaseType The type of phase to retrieve data for + * @return Const reference to the phase data + * @throws InvalidParameterException if phase type is unknown + */ + const PhaseData& getPhaseData(const std::string& phaseType) const + { + auto phase = _phaseMap.find(phaseType); + if (phase == _phaseMap.end()) + throw InvalidParameterException("Unknown phase type: " + phaseType); + + return phase->second; + } + + public: + + bool hasReactions() + { + for(const auto& phasePair : _phaseMap) + { + const auto& dynReactions = phasePair.second.dynReactions; + if (!dynReactions.empty()) + { + for (const auto* reaction : dynReactions) + { + if (reaction != nullptr) + { + return true; + } + } + } + } + return false; + } + + + /** + * @brief Gets const reference to dynamic reaction vector for a phase + * @param phase_type The phase type to retrieve reactions for + * @return Const reference to the vector of dynamic reaction models + */ + const std::vector& getDynReactionVector(const std::string& phase_type) const + { + return getPhaseData(phase_type).dynReactions; + } + + /** + * @brief Gets mutable reference to dynamic reaction vector for a phase + * @param phase_type The phase type to retrieve reactions for + * @return Mutable reference to the vector of dynamic reaction models + */ + std::vector& getDynReactionVector(const std::string& phase_type) + { + return getPhaseData(phase_type).dynReactions; + } + + /** + * @brief Configures the dimensions of the dynamic reaction vector for a phase + * @param phaseType The phase type to configure + * @param numReac Number of reactions to allocate space for + */ + void configureDimensions(const std::string& phaseType, unsigned int numReac) + { + auto& reactionVector = getPhaseData(phaseType).dynReactions; + reactionVector.resize(numReac, nullptr); + } + + + /** + * @brief Configures discretization for reaction models in a specific phase + * @param phaseType The phase type to configure + * @param parType The particle type index + * @param nReactions Number of reactions to configure + * @param nComp Number of components + * @param nBound Array of bound states per component + * @param boundOffset Array of bound state offsets per component + * @param paramProvider Parameter provider for configuration + * @param helper Configuration helper for creating reaction models + * @return True if configuration succeeded, false otherwise + */ + bool configureDiscretization(std::string phaseType, unsigned int parType, unsigned int nReactions, unsigned int nComp, unsigned int* nBound, unsigned int* boundOffset, IParameterProvider& paramProvider, const IConfigHelper& helper) + { + auto& dynReaction = getDynReactionVector(phaseType); + configureDimensions(phaseType, nReactions); + + bool reactionConfSuccess = true; + // Determine the number of reactions to configure + const unsigned int nReac = nReactions; + + // Configure each reaction model + for (unsigned int i = 0; i < nReac; ++i) + { + // for finite volumen units where the particles are not handling their own reactions. + // neet to map between the unser interphase and the phase types + std::string interphase_type = phaseType; + if (interphase_type == "pore") + interphase_type = "liquid"; + + char reactionKey[32]; + snprintf(reactionKey, sizeof(reactionKey), "%s_reaction_%03d", interphase_type.c_str(), i); + + paramProvider.pushScope(reactionKey); + + // Check if reaction type is specified + if (!paramProvider.exists("TYPE")) + { + paramProvider.popScope(); + throw InvalidParameterException("Missing 'type' parameter for " + std::string(reactionKey)); + } + + // Create reaction model based on type + std::string reactionType = paramProvider.getString("TYPE"); + dynReaction[i] = helper.createDynamicReactionModel(reactionType); + + // Validate reaction model creation + if (!dynReaction[i]) + { + paramProvider.popScope(); + throw InvalidParameterException("Unknown dynamic reaction model " + reactionType + + " for " + reactionKey); + } + + // Configure the reaction model discretization + reactionConfSuccess = dynReaction[i]->configureModelDiscretization(paramProvider, nComp, nBound + parType * nComp, boundOffset + parType * nComp) && reactionConfSuccess; + + // Handle configuration failure + if (!reactionConfSuccess) + { + if (dynReaction[i]->usesParamProviderInDiscretizationConfig()) + paramProvider.popScope(); + paramProvider.popScope(); + throw InvalidParameterException("Failed to configure reaction model " + reactionType + + " for " + reactionKey); + } + + // Pop scope if reaction model used parameter provider + //if (dynReaction[i]->usesParamProviderInDiscretizationConfig()) + paramProvider.popScope(); + } + + return reactionConfSuccess; + } + + /** + * @brief Configures reaction models for a specific phase and particle type + * @param phaseType The phase type to configure + * @param parType The particle type index + * @param unitOpIdx Unit operation index + * @param paramProvider Parameter provider for configuration + * @return True if configuration succeeded, false otherwise + */ + bool configure(std::string phaseType, unsigned int parType, unsigned int unitOpIdx, IParameterProvider& paramProvider) + { + auto& dynReaction = getDynReactionVector(phaseType); + bool dynReactionConfSuccess = true; + + // Determine the number of reactions to configure + const unsigned int nReac = dynReaction.size(); + // Configure each reaction + for (unsigned int reac = 0; reac < nReac; ++reac) + { + // Skip null reactions or those that don't require configuration + if (!dynReaction[reac] || !dynReaction[ reac]->requiresConfiguration()) + continue; + + // Create reaction scope key + + std::string interphase_type = phaseType; + if (interphase_type == "pore") + interphase_type = "liquid"; + + char reactionKey[32]; + snprintf(reactionKey, sizeof(reactionKey), "%s_reaction_%03d", interphase_type.c_str(), reac); + paramProvider.pushScope(reactionKey); //scope reaction_xxx + + // Configure the reaction model + dynReactionConfSuccess = dynReaction[ reac]->configure(paramProvider, unitOpIdx, parType) && dynReactionConfSuccess; + + paramProvider.popScope();//scope reaction_xxx + } + + return dynReactionConfSuccess; + } + + /** + * @brief Sets workspace requirements for all reaction models across all phases + * @param lms Linear memory sizer to configure workspace requirements + * @param nComp Number of components in the system + */ + void setWorkspaceRequirements(std::string phaseType, unsigned int nParType, unsigned int nComp, unsigned int const* strideBound, LinearMemorySizer& lms) const + { + auto& dynReactionVector = getDynReactionVector(phaseType); + + for (auto par = 0; par < nParType; par++) + { + int numReacOfPartical = dynReactionVector.size(); + int offSet = 0; // getOffsetForPhase(phaseType, par); + + for (auto i = 0; i < numReacOfPartical; i++) + { + if (dynReactionVector[i] && dynReactionVector[i]->requiresWorkspace()) + { + lms.fitBlock(dynReactionVector[offSet+ i]->workspaceSize(nComp, strideBound[i], nullptr)); + } + } + } + } + + void setWorkspaceRequirements(std::string phaseType, unsigned int nComp, unsigned int const strideBound, LinearMemorySizer& lms) const + { + auto& dynReactionVector = getDynReactionVector(phaseType); + for (auto i = 0; i < dynReactionVector.size(); i++) + { + if (dynReactionVector[i] && dynReactionVector[i]->requiresWorkspace()) + { + lms.fitBlock(dynReactionVector[i]->workspaceSize(nComp, strideBound, nullptr)); + } + } + + } + + /** + * @brief Clears and deletes all dynamic reaction models in all phases + * Properly deallocates memory and resets vectors to safe state + */ + void clearDynamicReactionModels() + { + for (auto& phase: _phaseMap) + { + auto& dynReactionVector = getDynReactionVector(phase.first); + // Delete all reaction model pointers + for (auto* reac: dynReactionVector) + { + delete reac; + } + // Clear vector and reset to safe initial state + dynReactionVector.clear(); + dynReactionVector.resize(1, nullptr); + } + } + + /** + * @brief Empties all reaction vectors without deleting the models + * Used for cleanup without memory deallocation + */ + void empty() + { + for (auto& phase : _phaseMap) + { + auto& dynReacVec = getPhaseData(phase.first).dynReactions; + dynReacVec.clear(); + dynReacVec.resize(1, nullptr); + } + } + + /** + * @brief Default constructor - initializes phase map with default values + */ + ReactionSystem(){ } + + }; + +} // namespace model +} // namespace cadet \ No newline at end of file diff --git a/test/CellKernelTests.cpp b/test/CellKernelTests.cpp index 2ac93bb6d..f90b847fe 100644 --- a/test/CellKernelTests.cpp +++ b/test/CellKernelTests.cpp @@ -357,7 +357,7 @@ TEST_CASE("CellKernel time derivative Jacobian analytic vs FD with dummy reactio porosity, poreAccessFactor.data(), &cbm.model(), - &cdrm.model() + nullptr }; // Compare Jacobians @@ -445,7 +445,7 @@ TEST_CASE("CellKernel Jacobian analytic vs AD with dummy reaction", "[CellKernel porosity, poreAccessFactor.data(), &cbm.model(), - &cdrm.model() + nullptr }; // Calculate Jacobian via AD diff --git a/test/ColumnModel1D.cpp b/test/ColumnModel1D.cpp index 35e43eacd..3314e0981 100644 --- a/test/ColumnModel1D.cpp +++ b/test/ColumnModel1D.cpp @@ -408,22 +408,22 @@ TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD bulk", "[Column_1D] cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_GRM", "DG", true, false, false, 2e-12); } -TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_GRM", "DG", false, true, false, 1e-14); } -TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_GRM", "DG", false, true, true, 1e-14); } -TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_GRM", "DG", true, true, false, 1e-14); } -TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as GRM dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_GRM", "DG", true, true, true, 1e-14); } @@ -433,22 +433,22 @@ TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD bul cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_GRM", "DG", true, false, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_GRM", "DG", false, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_GRM", "DG", false, true, true, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_GRM", "DG", true, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("Column_1D as GRM dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_GRM", "DG", true, true, true, 1e-6, 1e-14, 9e-4); } @@ -470,25 +470,25 @@ TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs A cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, false, false); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, false, true, false); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, false, true, true); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, true, false); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, true, true); @@ -500,25 +500,25 @@ TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivati cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, false, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, true, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = create1DColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, true, 1e-6, 1e-14, 9e-4); @@ -580,22 +580,22 @@ TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD bulk", "[Column_1D { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_LRMP", "DG", true, false, false, std::numeric_limits::epsilon() * 100.0); } -TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_LRMP", "DG", false, true, false, std::numeric_limits::epsilon() * 100.0); } -TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_LRMP", "DG", false, true, true, std::numeric_limits::epsilon() * 100.0); } -TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_LRMP", "DG", true, true, false, std::numeric_limits::epsilon() * 100.0); } -TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("COLUMN_MODEL_1D_LRMP", "DG", true, true, true, std::numeric_limits::epsilon() * 100.0); } @@ -605,22 +605,22 @@ TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD bu cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_LRMP", "DG", true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_LRMP", "DG", false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_LRMP", "DG", false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_LRMP", "DG", true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_1D_LRMP", "DG", true, true, true, 1e-6, 1e-14, 8e-4); } @@ -642,25 +642,25 @@ TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, false, false, 1e-8); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, false, true, false, 1e-8); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, false, true, true, 1e-8); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, true, false, 1e-8); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions Jacobian vs AD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, true, true, 1e-8); @@ -672,25 +672,25 @@ TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivat cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_1D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_1D],[DG],[DG1D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createLRMPColumnWithTwoCompLinearBindingThreeParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, true, 1e-6, 1e-14, 8e-4); diff --git a/test/ColumnModel2D.cpp b/test/ColumnModel2D.cpp index 9c7a3c180..fbb45a879 100644 --- a/test/ColumnModel2D.cpp +++ b/test/ColumnModel2D.cpp @@ -238,22 +238,22 @@ TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD bu cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_LRMP", "DG", true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_LRMP", "DG", false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_LRMP", "DG", false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_LRMP", "DG", true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_LRMP", "DG", true, true, true, 1e-6, 1e-14, 8e-4); } @@ -275,25 +275,25 @@ TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivat cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeHomParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeHomParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeHomParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as LRMP multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeHomParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, true, 1e-6, 1e-14, 8e-4); @@ -536,22 +536,22 @@ TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD bul cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "DG", true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "DG", false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "DG", false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "DG", true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("Column_2D as GRM dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "DG", true, true, true, 1e-6, 1e-14, 8e-4); } @@ -573,25 +573,25 @@ TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivati cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeGRMParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeGRMParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeGRMParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("Column_2D as GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[Column_2D],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeGRMParticleTypes(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, true, 1e-6, 1e-14, 8e-4); diff --git a/test/Crystallization.cpp b/test/Crystallization.cpp index 944fa3f54..fb6c05df0 100644 --- a/test/Crystallization.cpp +++ b/test/Crystallization.cpp @@ -106,7 +106,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distrib pp_setup.pushScope("unit_001"); // set the discretization scheme - pp_setup.pushScope("reaction_bulk"); + pp_setup.pushScope("liquid_reaction_000"); pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 4); pp_setup.popScope(); @@ -124,7 +124,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distrib pp_setup.pushScope("unit_001"); // set the discretization scheme - pp_setup.pushScope("reaction_bulk"); + pp_setup.pushScope("liquid_reaction_000"); pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 3); pp_setup.popScope(); @@ -142,7 +142,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleat pp_setup.pushScope("unit_001"); // set the discretization scheme - pp_setup.pushScope("reaction_bulk"); + pp_setup.pushScope("liquid_reaction_000"); pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 1); pp_setup.popScope(); @@ -160,7 +160,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleat pp_setup.pushScope("unit_001"); // set the discretization scheme - pp_setup.pushScope("reaction_bulk"); + pp_setup.pushScope("liquid_reaction_000"); pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 1); pp_setup.popScope(); @@ -178,7 +178,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary and sec pp_setup.pushScope("unit_001"); // set the discretization scheme - pp_setup.pushScope("reaction_bulk"); + pp_setup.pushScope("liquid_reaction_000"); pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 3); pp_setup.popScope(); diff --git a/test/GeneralRateModel.cpp b/test/GeneralRateModel.cpp index 0cc65f874..1c31db6da 100644 --- a/test/GeneralRateModel.cpp +++ b/test/GeneralRateModel.cpp @@ -272,22 +272,22 @@ TEST_CASE("GRM dynamic reactions Jacobian vs AD bulk", "[GRM],[Jacobian],[AD],[R cadet::test::reaction::testUnitJacobianDynamicReactionsAD("GENERAL_RATE_MODEL", "FV", true, false, false); } -TEST_CASE("GRM dynamic reactions Jacobian vs AD particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM dynamic reactions Jacobian vs AD particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("GENERAL_RATE_MODEL", "FV", false, true, false); } -TEST_CASE("GRM dynamic reactions Jacobian vs AD modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM dynamic reactions Jacobian vs AD modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("GENERAL_RATE_MODEL", "FV", false, true, true); } -TEST_CASE("GRM dynamic reactions Jacobian vs AD bulk and particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM dynamic reactions Jacobian vs AD bulk and particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("GENERAL_RATE_MODEL", "FV", true, true, false); } -TEST_CASE("GRM dynamic reactions Jacobian vs AD bulk and modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM dynamic reactions Jacobian vs AD bulk and modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[CI]") { cadet::test::reaction::testUnitJacobianDynamicReactionsAD("GENERAL_RATE_MODEL", "FV", true, true, true); } @@ -297,22 +297,22 @@ TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD bulk", "[GRM],[F cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("GENERAL_RATE_MODEL", "FV", true, false, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("GENERAL_RATE_MODEL", "FV", false, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("GENERAL_RATE_MODEL", "FV", false, true, true, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("GENERAL_RATE_MODEL", "FV", true, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest],[FD]") +TEST_CASE("GRM dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[CI],[FD]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("GENERAL_RATE_MODEL", "FV", true, true, true, 1e-6, 1e-14, 9e-4); } @@ -328,31 +328,31 @@ inline cadet::JsonParameterProvider createColumnWithTwoCompLinearBindingThreePar return jpp; } -TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD bulk", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType],[CI]")// todofix +TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD bulk", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType]") // toFix toFix fails on aRelease mode but not on DEBUG { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, false, false); } -TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD particle", "[GRM],[Jacobian],[FV],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD particle", "[GRM],[Jacobian],[FV],[AD],[ReactionModel],[ParticleType]") // toFix toFix fails on aRelease mode but not on DEBUG { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, false, true, false); } -TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType]") // toFix toFix fails on aRelease mode but not on DEBUG { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, false, true, true); } -TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD bulk and particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD bulk and particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType]") // toFix toFix fails on aRelease mode but not on DEBUG { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); - cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, true, false); + cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, true, false); } -TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD bulk and modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM multi particle types dynamic reactions Jacobian vs AD bulk and modified particle", "[GRM],[FV],[Jacobian],[AD],[ReactionModel],[ParticleType]") // toFix fails on aRelease mode but not on DEBUG { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testUnitJacobianDynamicReactionsAD(jpp, true, true, true); @@ -364,25 +364,25 @@ TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian v cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, false, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest],[FD]") +TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI],[FD]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest],[FD]") +TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI],[FD]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, true, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest],[FD]") +TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI],[FD]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, false, 1e-6, 1e-14, 9e-4); } -TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest],[FD]") +TEST_CASE("GRM multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[CI],[FD]") { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, true, 1e-6, 1e-14, 9e-4); diff --git a/test/GeneralRateModel2D.cpp b/test/GeneralRateModel2D.cpp index 39cddf15c..dea1bd633 100644 --- a/test/GeneralRateModel2D.cpp +++ b/test/GeneralRateModel2D.cpp @@ -205,22 +205,22 @@ TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD bulk", "[GRM2D cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "FV", true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "FV", false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "FV", false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "FV", true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[fixParReacTest]") +TEST_CASE("GRM2D dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[CI]") { cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD("COLUMN_MODEL_2D_GRM", "FV", true, true, true, 1e-6, 1e-14, 8e-4); } @@ -236,31 +236,31 @@ inline cadet::JsonParameterProvider createColumnWithTwoCompLinearBindingThreePar return jpp; } -TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD bulk", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fix2DGRMFDtest]") +TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD bulk", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType]") // todo: last enty of jacobian is off { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM2D(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, false, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType]") // todo: last enty of jacobian is off { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM2D(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType]") // / todo: last enty of jacobian is off { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM2D(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, false, true, true, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD bulk and particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType]") // / todo: last enty of jacobian is off { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM2D(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, false, 1e-6, 1e-14, 8e-4); } -TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType],[fixParReacTest]") +TEST_CASE("GRM2D multi particle types dynamic reactions time derivative Jacobian vs FD bulk and modified particle", "[GRM2D],[FV],[Jacobian],[Residual],[ReactionModel],[ParticleType]") // / todo: last enty of jacobian is off { cadet::JsonParameterProvider jpp = createColumnWithTwoCompLinearBindingThreeParticleTypesGRM2D(); cadet::test::reaction::testTimeDerivativeJacobianDynamicReactionsFD(jpp, true, true, true, 1e-6, 1e-14, 8e-4); diff --git a/test/JacobianHelper.hpp b/test/JacobianHelper.hpp index 74c3ee5da..69c69137f 100644 --- a/test/JacobianHelper.hpp +++ b/test/JacobianHelper.hpp @@ -271,6 +271,8 @@ inline void compareJacobianFD(const std::function& for (unsigned int col = 0; col < n; ++col) { std::copy(y, y + n, dir); + std::fill(colB, colB + m, 0.0); + std::fill(colA, colA + m, 0.0); if (y[col] != 0.0) dir[col] = y[col] * (1.0 + h); @@ -376,6 +378,9 @@ inline void checkJacobianPatternFD(const std::function stoichMat(nReactions * nComp, 0.0); std::vector expFwd(nReactions * nComp, 0.0); std::vector expBwd(nReactions * nComp, 0.0); @@ -198,44 +201,60 @@ namespace reaction util::populate(rateFwd.data(), [](unsigned int idx) { return std::sin(0.3 + idx * 0.2) * 0.5 + 1.5; }, rateFwd.size()); util::populate(rateBwd.data(), [](unsigned int idx) { return std::sin(0.4 + idx * 0.4) * 0.5 + 1.6; }, rateBwd.size()); - jpp.set("MAL_STOICHIOMETRY_BULK", stoichMat); - jpp.set("MAL_EXPONENTS_BULK_FWD", expFwd); - jpp.set("MAL_EXPONENTS_BULK_BWD", expBwd); - jpp.set("MAL_KFWD_BULK", rateFwd); - jpp.set("MAL_KBWD_BULK", rateBwd); + jpp.set("MAL_STOICHIOMETRY", stoichMat); + jpp.set("MAL_EXPONENTS_FWD", expFwd); + jpp.set("MAL_EXPONENTS_BWD", expBwd); + jpp.set("MAL_KFWD", rateFwd); + jpp.set("MAL_KBWD", rateBwd); } - if (!jpp.exists("NPARTYPE")) + if (!jpp.exists("NPARTYPE") && !isCSTR) return; - const int nParType = jpp.getInt("NPARTYPE"); + int nParType = 0; + if (!isCSTR) + nParType = jpp.getInt("NPARTYPE"); + else + nParType = jpp.getIntArray("NBOUND").size() / jpp.getInt("NCOMP"); - if ((!isLRM && particle) || (isLRM && bulk)) + if ((!isLRM && particle)) { - const int nReactions = 3; + const int nReactions = 1; for (int i = 0; i < nParType; ++i) { - if (!isCSTR) - jpp.pushScope("particle_type_" + std::string(3 - std::to_string(i).length(), '0') + std::to_string(i)); + std::vector nBound; + int nTotalBound; + if (isCSTR) + { + nBound = jpp.getIntArray("NBOUND"); - std::vector nBound = jpp.getIntArray("NBOUND"); - const int nTotalBound = std::accumulate(nBound.begin(), nBound.end(), 0); + int start = i * nComp; + int end = start + nComp; - std::string scope; - if (!isCSTR) - { - jpp.set("REACTION_MODEL", "MASS_ACTION_LAW"); - scope = "reaction"; + nTotalBound = std::accumulate( + nBound.begin() + start, + nBound.begin() + end, + 0 + ); + + jpp.addScope("particle_type_" + std::string(3 - std::to_string(i).length(), '0') + std::to_string(i)); + jpp.pushScope("particle_type_" + std::string(3 - std::to_string(i).length(), '0') + std::to_string(i)); // particle_type_xxx } else { - jpp.set("REACTION_MODEL_PARTICLE", "MASS_ACTION_LAW"); - scope = "reaction_particle"; + jpp.pushScope("particle_type_" + std::string(3 - std::to_string(i).length(), '0') + std::to_string(i)); // particle_type_xxx + nBound = jpp.getIntArray("NBOUND"); + nTotalBound = std::accumulate(nBound.begin(), nBound.end(), 0); } - jpp.addScope(scope); - auto gs2 = util::makeGroupScope(jpp, scope); + int nReac = 1; + jpp.set("NREAC_CROSS_PHASE", nReac); + + jpp.addScope("cross_phase_reaction_000"); //particle_type_xxx/cross_phase_reaction_000 + auto gs3 = util::makeGroupScope(jpp, "cross_phase_reaction_000"); + + jpp.set("TYPE", "MASS_ACTION_LAW_CROSS_PHASE"); std::vector stoichMatLiquid(nReactions * nComp, 0.0); std::vector expFwdLiquid(nReactions * nComp, 0.0); @@ -291,7 +310,6 @@ namespace reaction jpp.set("MAL_EXPONENTS_SOLID_BWD_MODLIQUID", expBwdSolidModLiquid); } - if (!isCSTR) jpp.popScope(); } } @@ -329,8 +347,8 @@ namespace reaction for (unsigned int i = 0; i < SMAData->numDataPoints(); ++i, outletMM += nCompMM, outletSMA += nCompSMA) { CAPTURE(i); - CHECK((outletMM[0]) == cadet::test::makeApprox(outletSMA[0], relTol, absTol)); - CHECK((outletMM[1]) == cadet::test::makeApprox(outletSMA[1], relTol, absTol)); + CHECK((outletMM[0]) == cadet::test::makeApprox(outletSMA[0], relTol, absTol)); // supstrate + CHECK((outletMM[1]) == cadet::test::makeApprox(outletSMA[1], relTol, absTol)); // product } } @@ -408,7 +426,7 @@ namespace reaction // Evaluate with AD ad::resetAd(adRes, numDofs); - crm.model().residualLiquidAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, adY, adRes, 1.0, crm.buffer()); + crm.model().residualFluxAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, crm.nComp(), adY, adRes, 1.0, crm.buffer()); // Extract Jacobian jacAD.setAll(0.0); @@ -416,7 +434,7 @@ namespace reaction // Calculate analytic Jacobian jacAna.setAll(0.0); - crm.model().analyticJacobianLiquidAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, yState.data(), 1.0, jacAna.row(0), crm.buffer()); + crm.model().analyticJacobianAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, crm.nComp(), yState.data(), 1.0, jacAna.row(0), crm.buffer()); delete[] adY; delete[] adRes; @@ -425,7 +443,7 @@ namespace reaction [&](double const* lDir, double* res) -> void { std::fill_n(res, nComp, 0.0); - crm.model().residualLiquidAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, lDir, res, 1.0, crm.buffer()); + crm.model().residualFluxAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, crm.nComp(), lDir, res, 1.0, crm.buffer()); }, [&](double const* lDir, double* res) -> void { @@ -437,7 +455,7 @@ namespace reaction [&](double const* lDir, double* res) -> void { std::fill_n(res, nComp, 0.0); - crm.model().residualLiquidAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, lDir, res, 1.0, crm.buffer()); + crm.model().residualFluxAdd(1.0, 0u, ColumnPosition{0.0, 0.0, 0.0}, crm.nComp(), lDir, res, 1.0, crm.buffer()); }, [&](double const* lDir, double* res) -> void { diff --git a/test/ReactionModels.cpp b/test/ReactionModels.cpp index 9c37134a8..f6ec39f79 100644 --- a/test/ReactionModels.cpp +++ b/test/ReactionModels.cpp @@ -19,17 +19,17 @@ TEST_CASE("MassActionLaw kinetic analytic Jacobian vs AD", "[MassActionLaw],[Rea { const unsigned int nBound[] = {1, 2, 1}; const double point[] = {1.0, 2.0, 1.4, 2.1, 0.2, 1.1, 1.8}; - cadet::test::reaction::testDynamicJacobianAD("MASS_ACTION_LAW", 3, nBound, + cadet::test::reaction::testDynamicJacobianAD("MASS_ACTION_LAW_CROSS_PHASE", 3, nBound, R"json({ - "MAL_KFWD_BULK": [1.0, 2.0, 0.4], - "MAL_KBWD_BULK": [0.0, 0.2, 1.5], - "MAL_STOICHIOMETRY_BULK": [ 1.0, -2.0, 3.0, + "MAL_KFWD_LIQUID": [1.0, 2.0, 0.4], + "MAL_KBWD_LIQUID": [0.0, 0.2, 1.5], + "MAL_STOICHIOMETRY_LIQUID": [ 1.0, -2.0, 3.0, -1.0, 0.0, -2.0, 0.0, 1.0, 1.0], - "MAL_EXPONENTS_BULK_FWD": [ 1.2, 0.0, 0.0, + "MAL_EXPONENTS_LIQUID_FWD": [ 1.2, 0.0, 0.0, 0.0, 1.3, 2.2, 0.0, 1.0, 1.1], - "MAL_EXPONENTS_BULK_BWD": [ 0.8, 2.1, 1.0, + "MAL_EXPONENTS_LIQUID_BWD": [ 0.8, 2.1, 1.0, 1.3, 1.0, 0.0, 0.0, 0.0, 1.4], @@ -155,7 +155,7 @@ TEST_CASE("MichaelisMenten kinetic analytic Jacobian vs AD without inhibition", "MM_KMM": [1.0, 2.0, 0.4], "MM_KI": [-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0], "MM_VMAX": [1.0, 0.2, 1.5], - "MM_STOICHIOMETRY_BULK": [ 1.0, -2.0, 3.0, + "MM_STOICHIOMETRY": [ 1.0, -2.0, 3.0, -1.0, 0.0, -2.0, 0.0, 1.0, 1.0] })json", @@ -172,7 +172,7 @@ TEST_CASE("MichaelisMenten kinetic analytic Jacobian vs AD with inhibition", "[M "MM_KMM": [1.0, 2.0, 0.4], "MM_KI": [-1.0, 1.0, -1.0, -1.0, -1.0, -1.0, 3.0, 2.0, -1.0], "MM_VMAX": [1.0, 0.2, 1.5], - "MM_STOICHIOMETRY_BULK": [ 1.0, -2.0, 3.0, + "MM_STOICHIOMETRY": [ 1.0, -2.0, 3.0, -1.0, 0.0, -2.0, 0.0, 1.0, 1.0] })json", diff --git a/test/data/configuration_CSTR_MichaelisMenten_twoSubs_benchmark1.json b/test/data/configuration_CSTR_MichaelisMenten_twoSubs_benchmark1.json index ab35365d7..ea808f48f 100644 --- a/test/data/configuration_CSTR_MichaelisMenten_twoSubs_benchmark1.json +++ b/test/data/configuration_CSTR_MichaelisMenten_twoSubs_benchmark1.json @@ -22,9 +22,10 @@ ], "INIT_LIQUID_VOLUME": 10, "NCOMP": 3, - "REACTION_MODEL": "MICHAELIS_MENTEN", + "NREAC_LIQUID": 1, "UNIT_TYPE": "CSTR", - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "MICHAELIS_MENTEN", "MM_KI_C": [ 0, 0, @@ -56,7 +57,7 @@ 0.8, 0.0 ], - "MM_STOICHIOMETRY_BULK": [ + "MM_STOICHIOMETRY": [ -1, 1, -1 diff --git a/test/data/configuration_CSTR_MichaelisMenten_twoSubs_twoInhib_benchmark1.json b/test/data/configuration_CSTR_MichaelisMenten_twoSubs_twoInhib_benchmark1.json index 4dd32baf2..b65995886 100644 --- a/test/data/configuration_CSTR_MichaelisMenten_twoSubs_twoInhib_benchmark1.json +++ b/test/data/configuration_CSTR_MichaelisMenten_twoSubs_twoInhib_benchmark1.json @@ -22,19 +22,20 @@ ], "INIT_LIQUID_VOLUME": 1000, "NCOMP": 3, - "REACTION_MODEL": "MICHAELIS_MENTEN", "UNIT_TYPE": "CSTR", - "reaction_bulk": { + "NREAC_LIQUID": 1, + "liquid_reaction_000": { + "TYPE": "MICHAELIS_MENTEN", "MM_KI_C": [ 0.0, 0.0, 0.0, - + 0.0, 0.0, 0.0, - + 0.0, 0.0, @@ -60,7 +61,7 @@ 0.8, 0.0 ], - "MM_STOICHIOMETRY_BULK": [ + "MM_STOICHIOMETRY": [ -1, -1, 1 diff --git a/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_benchmark1.json b/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_benchmark1.json index a724adc2e..5d67c075b 100644 --- a/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_benchmark1.json +++ b/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_benchmark1.json @@ -26,24 +26,25 @@ ], "INIT_LIQUID_VOLUME": 10, "NCOMP": 7, - "REACTION_MODEL": "MASS_ACTION_LAW", + "NREAC_LIQUID": 1, "UNIT_TYPE": "CSTR", - "reaction_bulk": { - "MAL_KBWD_BULK": [ + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ 700000000.0, 800000000.0, 800000000.0, 700000000.0, 0 ], - "MAL_KFWD_BULK": [ + "MAL_KFWD": [ 1000000000.0, 1000000000.0, 1000000000.0, 1000000000.0, 120000.0 ], - "MAL_STOICHIOMETRY_BULK": [ + "MAL_STOICHIOMETRY": [ -1, 0, 0, diff --git a/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_twoInhib_benchmark1.json b/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_twoInhib_benchmark1.json index c69d75bc9..c28f93b24 100644 --- a/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_twoInhib_benchmark1.json +++ b/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_twoInhib_benchmark1.json @@ -32,10 +32,11 @@ ], "INIT_LIQUID_VOLUME": 1, "NCOMP": 12, - "REACTION_MODEL": "MASS_ACTION_LAW", + "NREAC_LIQUID": 1, "UNIT_TYPE": "CSTR", - "reaction_bulk": { - "MAL_KBWD_BULK": [ + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ 7000.0, 8000.0, 0.0, @@ -44,7 +45,7 @@ 3000.0, 4000.0 ], - "MAL_KFWD_BULK": [ + "MAL_KFWD": [ 10000.0, 10000.0, 120.0, @@ -53,7 +54,7 @@ 10000.0, 10000.0 ], - "MAL_STOICHIOMETRY_BULK": [ + "MAL_STOICHIOMETRY": [ -1, 0, 0, @@ -150,7 +151,6 @@ 0, 1 ] - ] } } }, diff --git a/test/data/model_CSTR_MichaelisMenten_benchmark1.json b/test/data/model_CSTR_MichaelisMenten_benchmark1.json index ea479b98f..847feb942 100644 --- a/test/data/model_CSTR_MichaelisMenten_benchmark1.json +++ b/test/data/model_CSTR_MichaelisMenten_benchmark1.json @@ -1,1088 +1,1083 @@ { - "model": { - "NUNITS": 1, - "connections": { - "NSWITCHES": 1, - "switch_000": { - "CONNECTIONS": [], - "SECTION": 0 - } + "model": { + "NUNITS": 1, + "connections": { + "NSWITCHES": 1, + "switch_000": { + "CONNECTIONS": [], + "SECTION": 0 + } + }, + "solver": { + "GS_TYPE": 1, + "MAX_KRYLOV": 0, + "MAX_RESTARTS": 10, + "SCHUR_SAFETY": 1e-08 + }, + "unit_000": { + "INIT_C": [ + 500, + 0 + ], + "INIT_LIQUID_VOLUME": 1000, + "NCOMP": 2, + "UNIT_TYPE": "CSTR", + "NREAC_LIQUID": 1, + "liquid_reaction_000": { + "TYPE": "MICHAELIS_MENTEN", + "MM_KI": [ + 0, + 0, + 0, + 0 + ], + "MM_KMM": [ + 100 + ], + "MM_STOICHIOMETRY": [ + -1.0, + 1.0 + ], + "MM_VMAX": [ + 40, + 10 + ] + } + } }, - "solver": { - "GS_TYPE": 1, - "MAX_KRYLOV": 0, - "MAX_RESTARTS": 10, - "SCHUR_SAFETY": 1e-08 + "return": { + "SPLIT_COMPONENTS_DATA": false, + "SPLIT_PORTS_DATA": 0, + "unit_000": { + "WRITE_COORDINATES": 1, + "WRITE_SENS_OUTLET": 1, + "WRITE_SOLUTION_BULK": 1, + "WRITE_SOLUTION_FLUX": 1, + "WRITE_SOLUTION_INLET": 1, + "WRITE_SOLUTION_OUTLET": 1, + "WRITE_SOLUTION_PARTICLE": 1, + "WRITE_SOLUTION_SOLID": 1, + 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"reaction_model_000": { - "REACTION_TYPE": "MASS_ACTION_LAW", - "MAL_KBWD_BULK": [ - 60000.0, - 0.0, - 30000.0, - 20000.0, - 30000.0, - 20000.0 - ], - "MAL_KFWD_BULK": [ - 1000.0, - 40000, - 10000.0, - 10000.0, - 10000.0, - 10000.0 - ], - "MAL_STOICHIOMETRY_BULK": [ - -1, - 0, - 0, - 0, - 0, - 0, - 0, - 1, - 0, - 0, - 0, - 0, - 0, - 0, - -1, - 0, - -1, - 0, - 0, - 0, - 0, - -1, - 0, - -1, - -1, - 1, - -1, - -1, - 0, - 0, - 1, - -1, - 0, - 0, - -1, - -1, - 0, - 0, - 1, - 0, - 0, - 0, - 0, - 0, - 0, - 1, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 1, - 0, - 0, - 0, - 0, - 1, - 0 - ] - } - } + "NREAC_LIQUID": 1, + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ + 60000.0, + 0.0, + 30000.0, + 20000.0, + 30000.0, + 20000.0 + ], + "MAL_KFWD": [ + 1000.0, + 40000, + 10000.0, + 10000.0, + 10000.0, + 10000.0 + ], + "MAL_STOICHIOMETRY": [ + -1, + 0, + 0, + 0, + 0, + 0, + 0, + 1, + 0, + 0, + 0, + 0, + 0, + 0, + -1, + 0, + -1, + 0, + 0, + 0, + 0, + -1, + 0, + -1, + -1, + 1, + -1, + -1, + 0, + 0, + 1, + -1, + 0, + 0, + -1, + -1, + 0, + 0, + 1, + 0, + 0, + 0, + 0, + 0, + 0, + 1, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 1, + 0, + 0, + 0, + 0, + 1, + 0 + ] } + } }, "return": { "SPLIT_COMPONENTS_DATA": false, diff --git a/test/data/model_CSTR_reacMAL_2comp_sensbenchmark1.json b/test/data/model_CSTR_reacMAL_2comp_sensbenchmark1.json index 7707fbd95..9520f3d95 100644 --- a/test/data/model_CSTR_reacMAL_2comp_sensbenchmark1.json +++ b/test/data/model_CSTR_reacMAL_2comp_sensbenchmark1.json @@ -58,22 +58,20 @@ "NCOMP": 2, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 0, - "reaction_bulk": { - "NREAC": 1, - "reaction_model_000": { - "REACTION_TYPE": "MASS_ACTION_LAW", - "MAL_KBWD_BULK": [ + "NREAC_LIQUID": 1, + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ 3.0 ], - "MAL_KFWD_BULK": [ + "MAL_KFWD": [ 1.0 ], - "MAL_STOICHIOMETRY_BULK": [ + "MAL_STOICHIOMETRY": [ -1, 1 ] } - } }, "unit_002": { "NCOMP": 2, @@ -97,7 +95,7 @@ "param_000": { "SENS_BOUNDPHASE": -1, "SENS_COMP": -1, - "SENS_NAME": "MAL_KFWD_BULK", + "SENS_NAME": "MAL_KFWD", "SENS_PARTYPE": -1, "SENS_REACTION": 0, "SENS_SECTION": -1, @@ -106,7 +104,7 @@ "param_001": { "SENS_BOUNDPHASE": -1, "SENS_COMP": 0, - "SENS_NAME": "MAL_STOICHIOMETRY_BULK", + "SENS_NAME": "MAL_STOICHIOMETRY", "SENS_PARTYPE": -1, "SENS_REACTION": 0, "SENS_SECTION": -1, diff --git a/test/data/model_CSTR_reacMAL_3comp_nreac_2.json b/test/data/model_CSTR_reacMAL_3comp_nreac_2.json index 23696d2b8..93aa644bf 100644 --- a/test/data/model_CSTR_reacMAL_3comp_nreac_2.json +++ b/test/data/model_CSTR_reacMAL_3comp_nreac_2.json @@ -52,49 +52,47 @@ ] } }, - "unit_001": { - "CONST_SOLID_VOLUME": 1.0, - "INIT_C": [ - 1.0, - 0.0, - 1.0 - ], - "INIT_LIQUID_VOLUME": 1.0, - "NCOMP": 3, - "UNIT_TYPE": "CSTR", - "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { - "NREAC": 2, - "reaction_model_000": { - "REACTION_TYPE": "MASS_ACTION_LAW", - "MAL_KBWD_BULK": [ - 0.5 - ], - "MAL_KFWD_BULK": [ - 1.0 - ], - "MAL_STOICHIOMETRY_BULK": [ - -1, - 1, - 0 - ] - }, - "reaction_model_001": { - "REACTION_TYPE": "MASS_ACTION_LAW", - "MAL_KBWD_BULK": [ - 0.5 - ], - "MAL_KFWD_BULK": [ - 1.0 - ], - "MAL_STOICHIOMETRY_BULK": [ - 0, - 1, - -1 - ] - } - } + "unit_001": { + "CONST_SOLID_VOLUME": 1.0, + "INIT_C": [ + 1.0, + 0.0, + 1.0 + ], + "INIT_LIQUID_VOLUME": 1.0, + "NCOMP": 3, + "UNIT_TYPE": "CSTR", + "USE_ANALYTIC_JACOBIAN": 1, + "NREAC_LIQUID": 2, + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ + 0.5 + ], + "MAL_KFWD": [ + 1.0 + ], + "MAL_STOICHIOMETRY": [ + -1, + 1, + 0 + ] }, + "liquid_reaction_001": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ + 0.5 + ], + "MAL_KFWD": [ + 1.0 + ], + "MAL_STOICHIOMETRY": [ + 0, + 1, + -1 + ] + } + }, "unit_002": { "NCOMP": 3, "UNIT_TYPE": "OUTLET" diff --git a/test/data/model_MCT1ch_noEx_noReac_benchmark1.json b/test/data/model_MCT1ch_noEx_noReac_benchmark1.json index fff06a9ba..a819473f3 100644 --- a/test/data/model_MCT1ch_noEx_noReac_benchmark1.json +++ b/test/data/model_MCT1ch_noEx_noReac_benchmark1.json @@ -652,23 +652,24 @@ "INIT_C": [ 0 ], - "MAL_EXPONENTS_BULK_FWD": [ + "MAL_EXPONENTS_FWD": [ 0, 1, 1, 0 ], "NCOMP": 1, - "REACTION_MODEL": "MASS_ACTION_LAW", + "NREAC_LIQUID": 1, "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT", - "reaction_bulk": { - "MAL_KBWD_BULK": [ + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ 0 ], - "MAL_KFWD_BULK": [ + "MAL_KFWD": [ 0 ], - "MAL_STOICHIOMETRY_BULK": [ + "MAL_STOICHIOMETRY": [ -1 ] } diff --git a/test/data/model_MCT1ch_noEx_reac_benchmark1.json b/test/data/model_MCT1ch_noEx_reac_benchmark1.json index 6ee0750aa..f1c440a12 100644 --- a/test/data/model_MCT1ch_noEx_reac_benchmark1.json +++ b/test/data/model_MCT1ch_noEx_reac_benchmark1.json @@ -652,23 +652,24 @@ "INIT_C": [ 0 ], - "MAL_EXPONENTS_BULK_FWD": [ + "MAL_EXPONENTS_FWD": [ 0, 1, 1, 0 ], "NCOMP": 1, - "REACTION_MODEL": "MASS_ACTION_LAW", "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT", - "reaction_bulk": { - "MAL_KBWD_BULK": [ + "NREAC_LIQUID": 1, + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ 0 ], - "MAL_KFWD_BULK": [ + "MAL_KFWD": [ 0.000567 ], - "MAL_STOICHIOMETRY_BULK": [ + "MAL_STOICHIOMETRY": [ -1 ] } diff --git a/test/data/model_MCT2ch_oneWayEx_reac_benchmark1.json b/test/data/model_MCT2ch_oneWayEx_reac_benchmark1.json index 9bd2ae1d3..8311a62e2 100644 --- a/test/data/model_MCT2ch_oneWayEx_reac_benchmark1.json +++ b/test/data/model_MCT2ch_oneWayEx_reac_benchmark1.json @@ -663,23 +663,24 @@ "INIT_C": [ 0 ], - "MAL_EXPONENTS_BULK_FWD": [ + "MAL_EXPONENTS_FWD": [ 0, 1, 1, 0 ], "NCOMP": 1, - "REACTION_MODEL": "MASS_ACTION_LAW", + "NREAC_LIQUID": 1, "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT", - "reaction_bulk": { - "MAL_KBWD_BULK": [ + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ 0 ], - "MAL_KFWD_BULK": [ + "MAL_KFWD": [ 0.000567 ], - "MAL_STOICHIOMETRY_BULK": [ + "MAL_STOICHIOMETRY": [ -1 ] } diff --git a/test/data/model_MCT3ch_twoWayExc_reac_benchmark1.json b/test/data/model_MCT3ch_twoWayExc_reac_benchmark1.json index ff1d96760..b89d63739 100644 --- a/test/data/model_MCT3ch_twoWayExc_reac_benchmark1.json +++ b/test/data/model_MCT3ch_twoWayExc_reac_benchmark1.json @@ -664,23 +664,24 @@ "INIT_C": [ 0 ], - "MAL_EXPONENTS_BULK_FWD": [ + "MAL_EXPONENTS_FWD": [ 0, 1, 1, 0 ], "NCOMP": 1, - "REACTION_MODEL": "MASS_ACTION_LAW", "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT", - "reaction_bulk": { - "MAL_KBWD_BULK": [ + "NREAC_LIQUID": 1, + "liquid_reaction_000": { + "TYPE": "MASS_ACTION_LAW", + "MAL_KBWD": [ 0 ], - "MAL_KFWD_BULK": [ + "MAL_KFWD": [ 0.000567 ], - "MAL_STOICHIOMETRY_BULK": [ + "MAL_STOICHIOMETRY": [ -1 ] } diff --git a/test/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json b/test/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json index e50f50fa4..80176d85f 100644 --- a/test/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json +++ b/test/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json @@ -307,10 +307,11 @@ ], "INIT_VOLUME": 0.0005, "NCOMP": 52, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_AGGREGATION_INDEX": 0, "CRY_AGGREGATION_RATE_CONSTANT": 5e-13, diff --git a/test/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json b/test/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json index ec217bfbd..635e088f7 100644 --- a/test/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json +++ b/test/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json @@ -557,11 +557,12 @@ "INIT_LIQUID_VOLUME": 0.0005, "NCOMP": 102, "CONST_SOLID_VOLUME": 0.0, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "CRYSTALLIZATION_MODE": 0, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_B": 2.0, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_PBM_growth_benchmark1.json b/test/data/model_cry_CSTR_PBM_growth_benchmark1.json index c5f3c3ba2..78159fe7e 100644 --- a/test/data/model_cry_CSTR_PBM_growth_benchmark1.json +++ b/test/data/model_cry_CSTR_PBM_growth_benchmark1.json @@ -557,11 +557,12 @@ "INIT_LIQUID_VOLUME": 0.0005, "NCOMP": 102, "CONST_SOLID_VOLUME": 0.0, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "CRYSTALLIZATION_MODE": 0, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_B": 2.0, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json b/test/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json index bcbc2bb18..2d912db4c 100644 --- a/test/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json +++ b/test/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json @@ -557,11 +557,12 @@ "INIT_LIQUID_VOLUME": 0.0005, "NCOMP": 102, "CONST_SOLID_VOLUME": 0.0, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "CRYSTALLIZATION_MODE": 0, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_B": 2.0, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json b/test/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json index 6a3565759..435cb687e 100644 --- a/test/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json +++ b/test/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json @@ -557,11 +557,12 @@ "INIT_LIQUID_VOLUME": 0.0005, "NCOMP": 102, "CONST_SOLID_VOLUME": 0.0, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "CRYSTALLIZATION_MODE": 0, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_B": 2.0, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json b/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json index 782403b02..9febffeab 100644 --- a/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json +++ b/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json @@ -557,11 +557,12 @@ "INIT_LIQUID_VOLUME": 0.0005, "NCOMP": 102, "CONST_SOLID_VOLUME": 0.0, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "CRYSTALLIZATION_MODE": 0, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_B": 2.0, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationGrowth_benchmark1.json b/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationGrowth_benchmark1.json index e54161a43..81a43e9f3 100644 --- a/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationGrowth_benchmark1.json +++ b/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationGrowth_benchmark1.json @@ -362,7 +362,7 @@ 0.0 ], "NCOMP": 52, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "CRYSTALLIZATION_MODE": 0, "TOTAL_POROSITY": 0.21, "UNIT_TYPE": "LUMPED_RATE_MODEL_WITHOUT_PORES", @@ -434,7 +434,8 @@ "WENO_ORDER": 2 } }, - "reaction": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_B": 2.0, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_aggFrag_benchmark1.json b/test/data/model_cry_CSTR_aggFrag_benchmark1.json index 40a0c6f5e..1b108cc5e 100644 --- a/test/data/model_cry_CSTR_aggFrag_benchmark1.json +++ b/test/data/model_cry_CSTR_aggFrag_benchmark1.json @@ -527,10 +527,11 @@ ], "INIT_VOLUME": 0.0005, "NCOMP": 96, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_AGGREGATION_INDEX": 0, "CRY_AGGREGATION_RATE_CONSTANT": 0.2, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_aggregation_benchmark1.json b/test/data/model_cry_CSTR_aggregation_benchmark1.json index c5d2abfa1..f8ed45df4 100644 --- a/test/data/model_cry_CSTR_aggregation_benchmark1.json +++ b/test/data/model_cry_CSTR_aggregation_benchmark1.json @@ -527,10 +527,11 @@ ], "INIT_VOLUME": 0.0005, "NCOMP": 96, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_AGGREGATION_INDEX": 3, "CRY_AGGREGATION_RATE_CONSTANT": 1.0, "CRY_BINS": [ diff --git a/test/data/model_cry_CSTR_fragmentation_benchmark1.json b/test/data/model_cry_CSTR_fragmentation_benchmark1.json index 54b04173a..00c3879bd 100644 --- a/test/data/model_cry_CSTR_fragmentation_benchmark1.json +++ b/test/data/model_cry_CSTR_fragmentation_benchmark1.json @@ -527,10 +527,11 @@ ], "INIT_VOLUME": 0.0005, "NCOMP": 96, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "UNIT_TYPE": "CSTR", "USE_ANALYTIC_JACOBIAN": 1, - "reaction_bulk": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_BINS": [ 0.01, 0.011006941712522098, diff --git a/test/data/model_cry_DPFR_PBM_aggregation_benchmark1.json b/test/data/model_cry_DPFR_PBM_aggregation_benchmark1.json index 86982c5bf..c57f6259e 100644 --- a/test/data/model_cry_DPFR_PBM_aggregation_benchmark1.json +++ b/test/data/model_cry_DPFR_PBM_aggregation_benchmark1.json @@ -218,7 +218,7 @@ ], "NCOMP": 34, "NPARTYPE": 1, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "TOTAL_POROSITY": 1.0, "UNIT_TYPE": "LUMPED_RATE_MODEL_WITHOUT_PORES", "particle_type_000": { @@ -313,7 +313,8 @@ "WENO_ORDER": 1 } }, - "reaction": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_AGGREGATION_INDEX": 0, "CRY_AGGREGATION_RATE_CONSTANT": 5e-13, diff --git a/test/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json b/test/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json index 5f69fe2d2..a1e79ef93 100644 --- a/test/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json +++ b/test/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json @@ -309,7 +309,7 @@ 0.4 ], "NCOMP": 52, - "REACTION_MODEL": "CRYSTALLIZATION", + "NREAC_LIQUID": 1, "CRYSTALLIZATION_MODE": 0, "TOTAL_POROSITY": 0.21, "particle_type_000": { @@ -386,7 +386,8 @@ "WENO_ORDER": 2 } }, - "reaction": { + "liquid_reaction_000": { + "TYPE": "CRYSTALLIZATION", "CRY_A": 1.0, "CRY_B": 2.0, "CRY_BINS": [ diff --git a/test/data/ref_CSTR_reacMAL_2comp_sensbenchmark1.h5 b/test/data/ref_CSTR_reacMAL_2comp_sensbenchmark1.h5 index 7fa5282e3..fcfe93403 100644 Binary files a/test/data/ref_CSTR_reacMAL_2comp_sensbenchmark1.h5 and b/test/data/ref_CSTR_reacMAL_2comp_sensbenchmark1.h5 differ