Merge pull request #2497 from ChrisBNEU to add documentation

Closes #2085 by adding the missing documentation for surface kinetics classes in the api reference

Author: rwest

documentation/source/reference/kinetics/index.rst

@@ -57,6 +57,19 @@ Class                   Description
 ======================= ========================================================
 
 
+
+Heterogenous catalysis kinetics models
+======================================
+
+.. currentmodule:: rmgpy.kinetics
+
+============================ ========================================================
+Class                        Description
+============================ ========================================================
+:class:`StickingCoefficient` A kinetics model to give Sticking Coefficients for surface adsorption, following Arrhenius form.
+:class:`SurfaceArrhenius`    A kinetics model based on (modified) Arrhenius for surface reactions.
+============================ ========================================================
+
 .. toctree::
     :hidden:
 
@@ -72,3 +85,5 @@ Class                   Description
     troe
     wigner
     eckart
+    surfacearrhenius
+    stickingcoefficient

documentation/source/reference/kinetics/stickingcoefficient.rst

@@ -0,0 +1,22 @@
+**********************************
+rmgpy.kinetics.StickingCoefficient
+**********************************
+
+.. autoclass:: rmgpy.kinetics.StickingCoefficient
+
+    The Sticking coefficient class uses an Arrhenius-like expression to determine
+    the sticking coefficient :math:`\gamma` of a species on a surface.
+
+    .. math:: \gamma = A (T/T_0)^{n} \exp\left(-\frac{E_\mathrm{a}}{RT}\right)
+
+    Above, :math:`A` is the preexponential factor, :math:`T_0` is the reference
+    temperature, :math:`n` is the temperature exponent, and :math:`E_\mathrm{a}`
+    is the activation energy.
+
+    The sticking coefficient is then used to calculate the rate coefficient :math:`k`
+    using the following expression:
+
+    .. math:: k = \frac{\gamma}{\Gamma} \sqrt{\frac{RT}{2 \pi W}}
+
+    where :math:`\Gamma` is the surface site density and :math:`W` is the molecular 
+    weight of the gas phase species. 

documentation/source/reference/kinetics/surfacearrhenius.rst

@@ -0,0 +1,17 @@
+*******************************
+rmgpy.kinetics.SurfaceArrhenius
+*******************************
+
+.. autoclass:: rmgpy.kinetics.SurfaceArrhenius
+
+    The SurfaceArrhenius class uses a rate expression that is identical to the 
+    Arrhenius class:
+
+    .. math:: k(T) = A \left( \frac{T}{T_0} \right)^n \exp \left( -\frac{E_\mathrm{a}}{RT} \right)
+
+    Above, :math:`A` is the preexponential factor, :math:`T_0` is the reference
+    temperature, :math:`n` is the temperature exponent, and :math:`E_\mathrm{a}`
+    is the activation energy.
+
+    The only difference is the units for :math:`A` are in terms of surface concentration 
+    (:math:`\mathrm{mol/m^2}`) instead of volume concentration (:math:`\mathrm{mol/m^3}`).