wip changes for stickingcoeffcient issue

rmgpy/cantera.py

@@ -256,26 +256,40 @@ def reaction_to_dicts(obj, spcs):
     length 1, but a MultiArrhenius or MultiPDepArrhenius will be longer.
     """
 
-    try:
-        reaction_list = []
-        if isinstance(obj.kinetics, MultiArrhenius) or isinstance(obj.kinetics, MultiPDepArrhenius):
-            list_of_cantera_reactions = obj.to_cantera(use_chemkin_identifier=True)
-        else: 
-            list_of_cantera_reactions = [ obj.to_cantera(use_chemkin_identifier=True) ]
-
-        for reaction in list_of_cantera_reactions:
-            reaction_data = reaction.input_data     
-            efficiencies = getattr(obj.kinetics, 'efficiencies', {})
-            if efficiencies:      
-                reaction_data["efficiencies"] = {spcs[i].to_chemkin(): float(val) for i, val in enumerate(obj.kinetics.get_effective_collider_efficiencies(spcs)) if val != 1}
-
-            reaction_list.append(reaction_data)
-        return reaction_list
-    except: 
-        print('passing')
-        print(type(obj.kinetics))
-        print(str(obj))
-        return []
+    #try:
+    reaction_list = []
+    if isinstance(obj.kinetics, MultiArrhenius) or isinstance(obj.kinetics, MultiPDepArrhenius):
+        list_of_cantera_reactions = obj.to_cantera(use_chemkin_identifier=True)
+    else: 
+        list_of_cantera_reactions = [ obj.to_cantera(use_chemkin_identifier=True) ]
+
+    for reaction in list_of_cantera_reactions:
+        reaction_data = reaction.input_data   
+        efficiencies = getattr(obj.kinetics, 'efficiencies', {})
+        if efficiencies:      
+            reaction_data["efficiencies"] = {spcs[i].to_chemkin(): float(val) for i, val in enumerate(obj.kinetics.get_effective_collider_efficiencies(spcs)) if val != 1}
+        # if isinstance(obj.kinetics, StickingCoefficient):
+        #     reaction_data.pop('equation', None)
+        #     reaction_data['equation'] = str(obj)
+        reaction_list.append(reaction_data)
+
+    # for reaction in list_of_cantera_reactions:
+    #     reaction_data = reaction.input_data   
+    #     efficiencies = getattr(obj.kinetics, 'efficiencies', {})
+    #     if efficiencies:      
+    #         reaction_data["efficiencies"] = {spcs[i].to_chemkin(): float(val) for i, val in enumerate(obj.kinetics.get_effective_collider_efficiencies(spcs)) if val != 1}
+
+    #     reaction_list.append(reaction_data)
+
+    # if isinstance[obj.kinetics, StickingCoefficient]:  
+    #      print(str(obj))
+
+    return reaction_list
+    # except: 
+    #     print('passing')
+    #     print(type(obj.kinetics))
+    #     print(str(obj))
+    #     return []
 
 
 def obj_to_dict(obj, spcs, names=None, label="solvent"):

rmgpy/reaction.pxd

@@ -70,7 +70,7 @@ cdef class Reaction:
 
     cpdef bint is_surface_reaction(self)
 
-    cpdef bint has_template(self, list reactants, list products)
+    cpdef bint has_template(self, list ct_reactants, list ct_products)
 
     cpdef bint matches_species(self, list reactants, list products=?)
 

rmgpy/reaction.py

@@ -44,6 +44,7 @@
 import os.path
 from copy import deepcopy
 from functools import reduce
+from sre_parse import fix_flags
 from urllib.parse import quote
 
 import cython
@@ -245,6 +246,22 @@ def to_chemkin(self, species_list=None, kinetics=True):
         else:
             return rmgpy.chemkin.write_reaction_string(self)
 
+
+    def fix_reaction(self, ct_reactions, ct_products):
+        """
+        Fixes the formatting of StickingCoefficients reaction equations 
+        """    
+        rxn_stoic = [f'{v} {k}' for k,v in ct_reactions.items() if v !=1]
+        rxn_stoic.extend([k for k,v in ct_reactions.items() if v == 1])
+
+        prod_stoic = [f'{v} {k}' for k,v in ct_products.items() if v !=1]
+        prod_stoic.extend([k for k,v in ct_products.items() if v == 1])
+
+        equation = ' + '.join(rxn_stoic) + ' <=> '  + ' + '.join(prod_stoic)
+        return equation
+
+
+
     def to_cantera(self, species_list=None, use_chemkin_identifier=False):
         """
         Converts the RMG Reaction object to a Cantera Reaction object
@@ -281,9 +298,9 @@ def to_cantera(self, species_list=None, use_chemkin_identifier=False):
                 ct_products[product_name] += 1
             else:
                 ct_products[product_name] = 1
+
         if self.specific_collider:  # add a specific collider if exists
             ct_collider[self.specific_collider.to_chemkin() if use_chemkin_identifier else self.specific_collider.label] = 1
-
         if self.kinetics:
             if isinstance(self.kinetics, Arrhenius):
                 # Create an Elementary Reaction
@@ -340,7 +357,8 @@ def to_cantera(self, species_list=None, use_chemkin_identifier=False):
                 b = self.kinetics._n.value_si
                 Ea = self.kinetics._Ea.value_si * 1000  # convert from J/mol to J/kmol
                 rate = ct.StickingArrheniusRate(A, b, Ea)
-                ct_reaction = ct.Reaction(equation=str(self), rate=rate)
+                equation = self.fix_reaction(ct_reactants, ct_products)
+                ct_reaction = ct.Reaction(equation=equation, rate=rate)
 
 
             elif isinstance(self.kinetics, Lindemann):
@@ -378,6 +396,7 @@ def to_cantera(self, species_list=None, use_chemkin_identifier=False):
         else:
             raise Exception('Cantera reaction cannot be created because there was no kinetics.')
 
+
     def get_url(self):
         """
         Get a URL to search for this reaction in the rmg website.