Enabling charge-transfer/electrochemical surface reactions

The previous formulation will only consider a rection as electrochemical
if a beta value is supplied for that reaction *and* the reaction is an
'edge_reaction.'  This is problematic for two reasons: (1) many/most
charge-transfer reactions of interest occur at two-phase boundaries (see,
for example, Li-ion batteries and PEM fuel cells), not the three-phase-
boundary-like edges (which are most relevant for SOFCs).  (2) determining
whether a reaction is electrochemical or not should not rely at all upon
user input - the program itself should check to see whether charge is
transferred between phases, and the appropriate steps should be taken
during rate-of-progress calcuations.

This commit addresses the former issue.  Currently, if a charge-transfer
reaction is written as a surface_reaction, the code does not apply the
voltage correction to the forward rate.  By default, then, the entire
voltage correction is applied to the reverse reaction, which is the same
as setting beta = 0; not a good 'default' behavior (beta = 0.5 is a more
appropriate default).  With this change, surface reactions can now be
supplied with a beta value in cti or xml formats, and will be recognized
as a charge transfer reaction.

Longer term, it would be better to change the constructor routines such
that charge transfer is automatically detected and handled, rather than
relying upon user-specified flags.

interfaces/cython/cantera/ctml_writer.py

@@ -1296,7 +1296,7 @@ def build(self, p):
         elif self._type == 'chebyshev':
             self._kf = []
 
-        if self._type == 'edge':
+        if self._type == 'edge' or self._type == 'surface':
             if self._beta > 0:
                 electro = kfnode.addChild('electrochem')
                 electro['beta'] = repr(self._beta)
@@ -1605,7 +1605,8 @@ class surface_reaction(reaction):
     A heterogeneous chemical reaction with pressure-independent rate
     coefficient and mass-action kinetics.
     """
-    def __init__(self, equation='', kf=None, id='', order='', options=[]):
+    def __init__(self, equation='', kf=None, id='', order='', beta = 0.0,
+                 options=[]):
         """
         :param equation:
             A string specifying the chemical equation.
@@ -1625,9 +1626,16 @@ def __init__(self, equation='', kf=None, id='', order='', options=[]):
             reaction in the file.
         :param options:
             Processing options, as described in :ref:`sec-reaction-options`.
+        :param beta:
+            Charge transfer coefficient: A number between 0 and 1 which, for a
+            charge transfer reaction, determines how much of the electric
+            potential difference between two phases is applied to the
+            activiation energy of the fwd reaction.  The remainder is applied to
+            the reverse reaction.
         """
         reaction.__init__(self, equation, kf, id, order, options)
         self._type = 'surface'
+        self._beta = beta
 
 
 class edge_reaction(reaction):

src/kinetics/Reaction.cpp

@@ -605,9 +605,10 @@ shared_ptr<Reaction> newReaction(const XML_Node& rxn_node)
 {
     std::string type = ba::to_lower_copy(rxn_node["type"]);
 
-    // Modify the reaction type for edge reactions which contain electrochemical
-    // reaction data
-    if (rxn_node.child("rateCoeff").hasChild("electrochem") && type == "edge") {
+    // Modify the reaction type for interface reactions which contain
+    // electrochemical reaction data
+    if (rxn_node.child("rateCoeff").hasChild("electrochem")
+        && (type == "edge" || type == "surface")) {
         type = "electrochemical";
     }