Consistently use T=298. K for fitting and evaluating Blowers-Masel ra…

…tes. Closes #1748
ReactionMechanismGenerator · May 3, 2024 · 981f4be · 981f4be
1 parent 5d10f96
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/rmgpy/data/kinetics/family.py b/rmgpy/data/kinetics/family.py
@@ -3658,13 +3658,13 @@ def cross_validate(self, folds=5, template_rxn_map=None, test_rxn_inds=None, T=1
                         if kinetics.E0.value_si < 0.0 or len(L) == 1:
                             kinetics = average_kinetics([r.kinetics for r in L])
                         else:
-                            kinetics = kinetics.to_arrhenius(rxn.get_enthalpy_of_reaction(298.0))
+                            kinetics = kinetics.to_arrhenius(rxn.get_enthalpy_of_reaction(298.))
                     else:
                         kinetics = ArrheniusChargeTransferBM().fit_to_reactions(L, recipe=self.forward_recipe.actions)
                         if kinetics.E0.value_si < 0.0 or len(L) == 1:
                             kinetics = average_kinetics([r.kinetics for r in L])
                         else:
-                            kinetics = kinetics.to_arrhenius_charge_transfer(rxn.get_enthalpy_of_reaction(298.0))
+                            kinetics = kinetics.to_arrhenius_charge_transfer(rxn.get_enthalpy_of_reaction(298.))
 
                     k = kinetics.get_rate_coefficient(T)
                     errors[rxn] = np.log(k / krxn)
@@ -4596,15 +4596,15 @@ def _make_rule(rr):
             dlnks = np.array([
                 np.log(
                     arr().fit_to_reactions(rs[list(set(range(len(rs))) - {i})], recipe=recipe)
-                    .to_arrhenius(rxn.get_enthalpy_of_reaction(Tref))
+                    .to_arrhenius(rxn.get_enthalpy_of_reaction(298.))
                     .get_rate_coefficient(T=Tref) / rxn.get_rate_coefficient(T=Tref)
                 ) for i, rxn in enumerate(rs)
             ])  # 1) fit to set of reactions without the current reaction (k)  2) compute log(kfit/kactual) at Tref
         else: # SurfaceChargeTransfer or ArrheniusChargeTransfer
             dlnks = np.array([
                 np.log(
                     arr().fit_to_reactions(rs[list(set(range(len(rs))) - {i})], recipe=recipe)
-                    .to_arrhenius_charge_transfer(rxn.get_enthalpy_of_reaction(Tref))
+                    .to_arrhenius_charge_transfer(rxn.get_enthalpy_of_reaction(298.))
                     .get_rate_coefficient(T=Tref) / rxn.get_rate_coefficient(T=Tref)
                 ) for i, rxn in enumerate(rs)
             ])  # 1) fit to set of reactions without the current reaction (k)  2) compute log(kfit/kactual) at Tref

diff --git a/rmgpy/kinetics/arrhenius.pyx b/rmgpy/kinetics/arrhenius.pyx
@@ -559,7 +559,7 @@ cdef class ArrheniusBM(KineticsModel):
         """
         Return the rate coefficient in the appropriate combination of m^3,
         mol, and s at temperature `T` in K and enthalpy of reaction `dHrxn`
-        in J/mol.
+        in J/mol, evaluated at 298 K.
         """
         cdef double A, n, Ea
         Ea = self.get_activation_energy(dHrxn)
@@ -570,7 +570,7 @@ cdef class ArrheniusBM(KineticsModel):
     cpdef double get_activation_energy(self, double dHrxn) except -1:
         """
         Return the activation energy in J/mol corresponding to the given
-        enthalpy of reaction `dHrxn` in J/mol.
+        enthalpy of reaction `dHrxn` in J/mol, evaluated at 298 K.
         """
         cdef double w0, E0
         E0 = self._E0.value_si
@@ -586,7 +586,8 @@ cdef class ArrheniusBM(KineticsModel):
     cpdef Arrhenius to_arrhenius(self, double dHrxn):
         """
         Return an :class:`Arrhenius` instance of the kinetics model using the
-        given enthalpy of reaction `dHrxn` to determine the activation energy.
+        given enthalpy of reaction `dHrxn` (in J/mol, evaluated at 298 K)
+        to determine the activation energy.
         """
         return Arrhenius(
             A=self.A,
@@ -615,7 +616,6 @@ cdef class ArrheniusBM(KineticsModel):
             w0 = sum(w0s) / len(w0s)
 
         if len(rxns) == 1:
-            T = 1000.0
             rxn = rxns[0]
             dHrxn = rxn.get_enthalpy_of_reaction(298.0)
             A = rxn.kinetics.A.value_si
@@ -632,7 +632,7 @@ cdef class ArrheniusBM(KineticsModel):
             self.Tmin = rxn.kinetics.Tmin
             self.Tmax = rxn.kinetics.Tmax
             self.solute = None
-            self.comment = 'Fitted to {0} reaction at temperature: {1} K'.format(len(rxns), T)
+            self.comment = 'Fitted to 1 reaction.'
         else:
             # define optimization function
             def kfcn(xs, lnA, n, E0):