Fixed atomtype charge checking

Now includes checks for negative charges

temporary fix to an exponent overflow problem

Author: ssun30

rmgpy/molecule/group.py

@@ -1013,7 +1013,7 @@ def is_van_der_waals(self, wildcards=False):
         else:
             return abs(self.order[0]) <= 1e-9 and len(self.order) == 1
 
-            
+
     def is_reaction_bond(self, wildcards=False):
         """
         Return ``True`` if the bond represents a van der Waals bond or ``False`` if
@@ -1851,7 +1851,7 @@ def specify_bond_extensions(self, i, j, basename, r_bonds):
             else:
                 atom_type_j_str = atom_type_j[0].label
 
-            b = None 
+            b = None
             for v in bdict.keys():
                 if abs(v - bd) < 1e-4:
                     b = bdict[v]
@@ -2995,6 +2995,8 @@ def make_sample_molecule(self):
                                     'S0sc', 'S2sc', 'S2dc', 'S2tc', 'S4sc', 'S4dc', 'S4tdc', 'S6sc', 'S6dc', 'S6tdc']
                 if atom.charge > 0 and any([group_atom.atomtype[0] is ATOMTYPES[x] or ATOMTYPES[x].is_specific_case_of(group_atom.atomtype[0]) for x in positive_charged]):
                     pass
+                elif atom.charge < 0 and any([group_atom.atomtype[0] is ATOMTYPES[x] or ATOMTYPES[x].is_specific_case_of(group_atom.atomtype[0]) for x in negative_charged]):
+                    pass
                 elif atom.charge in group_atom.atomtype[0].charge:
                     # declared charge in original group is same as new charge
                     pass

rmgpy/rmg/reactors.py

@@ -601,18 +601,18 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         A = obj._A.value_si
         if obj._T0.value_si != 1.0:
             A /= ((obj._T0.value_si) ** obj._n.value_si)
-        if obj._V0.value_si != 0.0:
-            A *= np.exp(obj._alpha.value_si*obj._electrons.value_si*constants.F*obj.V0.value_si)
+        # if obj._V0.value_si != 0.0:
+        #     A *= np.exp(obj._alpha.value_si*obj._electrons.value_si*constants.F*obj.V0.value_si/constants.R/300)
         n = obj._n.value_si
         Ea = obj._Ea.value_si
-        q = obj._alpha.value_si*obj._electrons.value_si
+        q = obj._alpha.value_si*obj._electrons.value_si    
         return rms.Arrheniusq(A, n, Ea, q, rms.EmptyRateUncertainty())
     elif isinstance(obj, SurfaceChargeTransfer):
         A = obj._A.value_si
         if obj._T0.value_si != 1.0:
             A /= ((obj._T0.value_si) ** obj._n.value_si)
-        if obj._V0.value_si != 0.0:
-            A *= np.exp(obj._alpha.value_si*obj._electrons.value_si*constants.F*obj.V0.value_si)
+        # if obj._V0.value_si != 0.0:
+        #     A *= np.exp(obj._alpha.value_si*obj._electrons.value_si*constants.F*obj.V0.value_si/constants.R/300)
         n = obj._n.value_si
         Ea = obj._Ea.value_si
         q = obj._alpha.value_si*obj._electrons.value_si
@@ -784,7 +784,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         reactants = [rms_species_list[i] for i in reactantinds]
         products = [rms_species_list[i] for i in productinds]
         if isinstance(obj.kinetics, SurfaceChargeTransfer):
-            obj.set_reference_potential(obj.kinetics._T0.value_si)
+            obj.set_reference_potential(300)
         kinetics = to_rms(obj.kinetics, species_names=species_names, rms_species_list=rms_species_list, rmg_species=rmg_species)
         radchange = sum([spc.molecule[0].multiplicity-1 for spc in obj.products]) - sum([spc.molecule[0].multiplicity-1 for spc in obj.reactants])
         electronchange = -sum([spc.molecule[0].get_net_charge() for spc in obj.products]) + sum([spc.molecule[0].get_net_charge() for spc in obj.reactants])