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Remove external references to Conformer._E0 #214

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Merged
merged 1 commit into from
May 20, 2014
Merged

Remove external references to Conformer._E0 #214

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4 changes: 2 additions & 2 deletions rmgpy/reaction.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -765,10 +765,10 @@ def calculateTSTRateCoefficient(self, T):
for spec in self.reactants:
logging.debug(' Calculating Partition function for ' + spec.label)
Qreac *= spec.getPartitionFunction(T) / (constants.R * T / 101325.)
E0 -= spec.conformer._E0.value_si
E0 -= spec.conformer.E0.value_si
logging.debug(' Calculating Partition function for ' + self.transitionState.label)
Qts = self.transitionState.getPartitionFunction(T) / (constants.R * T / 101325.)
E0 += self.transitionState.conformer._E0.value_si
E0 += self.transitionState.conformer.E0.value_si
k = (constants.kB * T / constants.h * Qts / Qreac) * math.exp(-E0 / constants.R / T)

# Apply tunneling correction
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4 changes: 2 additions & 2 deletions rmgpy/species.py
100644 → 100755
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Expand Up @@ -285,7 +285,7 @@ def getEnthalpy(self, T):
if self.hasThermo():
H = self.thermo.getEnthalpy(T)
elif self.hasStatMech():
H = self.conformer.getEnthalpy(T) + self.conformer._E0.value_si
H = self.conformer.getEnthalpy(T) + self.conformer.E0.value_si
else:
raise Exception('Unable to calculate enthalpy for species {0!r}: no thermo or statmech data available.'.format(self.label))
return H
Expand Down Expand Up @@ -315,7 +315,7 @@ def getFreeEnergy(self, T):
if self.hasThermo():
G = self.thermo.getFreeEnergy(T)
elif self.hasStatMech():
G = self.conformer.getFreeEnergy(T) + self.conformer._E0.value_si
G = self.conformer.getFreeEnergy(T) + self.conformer.E0.value_si
else:
raise Exception('Unable to calculate free energy for species {0!r}: no thermo or statmech data available.'.format(self.label))
return G
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