WIP reaction model doc overhaul

doc/modelling/index.rst

@@ -8,5 +8,5 @@ This section gives complete information about the supported unit operations, bin
 .. toctree::
     unit_operations/index
     binding/index
-    reactions
+    reaction/index
     networks

doc/modelling/reaction/index.rst

@@ -0,0 +1,12 @@
+.. _reaction_models:
+
+Reaction models
+===============
+
+
+Reaction models describe the (net) fluxes :math:`f_{\mathrm{react}}` of a
+reaction mechanism.
+There are various reaction models implemented in CADET, please refer to the respective documentation below.
+
+- :ref:`mass_action_law_model`
+- :ref:`michaelis_menten_kinetics_model`

doc/modelling/reactions.rst → doc/modelling/reaction/mass_action_law.rst

@@ -1,13 +1,4 @@
-.. _reaction_models:
-
-Reaction models
-===============
-
-
-Reaction models describe the (net) fluxes :math:`f_{\mathrm{react}}` of a
-reaction mechanism. The most common mechanism is the mass action law.
-
-.. _MRMassActionLaw:
+.. _mass_action_law_model:
 
 Mass action law
 ---------------
@@ -59,7 +50,7 @@ where
 
 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`.
+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`.
 
 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}}`.
@@ -79,7 +70,7 @@ where
         - 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].
     \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:`MRMassActionLawExpMatDefault`, 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
@@ -141,7 +132,4 @@ Note that the parameter units have to be adapted to the unit of the external pro
 Each parameter of the externally dependent reaction model can depend on a different external source.
 The 0-based indices of the external source for each parameter is given in the dataset ``EXTFUN``.
 By assigning only one index to ``EXTFUN``, all parameters use the same source.
-The ordering of the parameters in ``EXTFUN`` is given by the ordering in the file format specification in Section :ref:`FFReaction`.
-
-The layout of the matrices in the file format is presented in Table :ref:`FFReactionMassActionLaw`.
-
+The ordering of the parameters in ``EXTFUN`` is given by the ordering in the file format specification in Section :ref:`FFReaction`.

doc/modelling/reaction/michaelis_menten_kinetics.rst

@@ -0,0 +1,5 @@
+.. _michaelis_menten_kinetics_model:
+
+Michaelis Menten kinetics
+-------------------------
+