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Refactored reaction.py to add get_free_energy_of_non_charge_transfer_reaction for code reuse and circular dependency prevention #2810

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Refactored reaction.py to add get_free_energy_of_non_charge_transfer_reaction for code reuse and circular dependency prevention #2810

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a4b7a4e
Corrected the typo that repeated self.electrons twice in ReactionErro…
LekiaAnonim Jun 17, 2025
62dbf3a
Add get_free_energy_of_non_charge_transfer_reaction method to reactio…
LekiaAnonim Jun 17, 2025
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37 changes: 15 additions & 22 deletions rmgpy/reaction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -624,7 +624,7 @@ def _apply_CHE_model(self, T):

if self.electrons != self.protons:
raise ReactionError("Number of electrons must equal number of protons! "
f"{self} has {self.electrons} protons and {self.electrons} electrons")
f"{self} has {self.protons} protons and {self.electrons} electrons")
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this typo fix looks good



H2_thermo = ThermoData(Tdata=([300,400,500,600,800,1000,1500],'K'),
Expand Down Expand Up @@ -662,25 +662,29 @@ def get_entropy_of_reaction(self, T):
for product in self.products:
dSrxn += product.get_entropy(T)
return dSrxn

def get_free_energy_of_non_charge_transfer_reaction(self, T):
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You'll notice the other method had cython.declare lines. This helps Cython create faster code.


def _get_free_energy_of_charge_transfer_reaction(self, T, potential=0.):

cython.declare(dGrxn=cython.double, reactant=Species, product=Species)

dGrxn = 0
dGrxn = 0.0
for reactant in self.reactants:
try:
dGrxn -= reactant.get_free_energy(T)
except Exception:
logging.error("Problem with reactant {!r} in reaction {!s}".format(reactant, self))
raise

for product in self.products:
try:
dGrxn += product.get_free_energy(T)
except Exception:
logging.error("Problem with product {!r} in reaction {!s}".format(reactant, self))
logging.error("Problem with product {!r} in reaction {!s}".format(product, self))
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this typo fix looks good (but you could turn it into an f-string while you're at it)

raise
return dGrxn

def _get_free_energy_of_charge_transfer_reaction(self, T, potential=0.):

cython.declare(dGrxn=cython.double, reactant=Species, product=Species)

dGrxn = self.get_free_energy_of_non_charge_transfer_reaction(T)

if potential != 0.:
dGrxn -= self.electrons * constants.F * potential
Expand All @@ -697,19 +701,8 @@ def get_free_energy_of_reaction(self, T, potential=0.):
if self.is_charge_transfer_reaction():
return self._get_free_energy_of_charge_transfer_reaction(T, potential=potential)

dGrxn = 0.0
for reactant in self.reactants:
try:
dGrxn -= reactant.get_free_energy(T)
except Exception:
logging.error("Problem with reactant {!r} in reaction {!s}".format(reactant, self))
raise
for product in self.products:
try:
dGrxn += product.get_free_energy(T)
except Exception:
logging.error("Problem with product {!r} in reaction {!s}".format(reactant, self))
raise
# For non charge transfer reactions, we can use the free energy of the species
dGrxn = self.get_enthalpy_of_reaction(T) - T * self.get_entropy_of_reaction(T)

return dGrxn

Expand All @@ -721,7 +714,7 @@ def get_reversible_potential(self, T):
if not self.is_charge_transfer_reaction():
raise KineticsError("Cannot get reversible potential for non charge transfer reactions")

deltaG = self._get_free_energy_of_charge_transfer_reaction(T) #J/mol
deltaG = self.get_free_energy_of_non_charge_transfer_reaction(T) #J/mol
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I don't like renaming _get_free_energy_of_charge_transfer_reaction into self.get_free_energy_of_non_charge_transfer_reaction and calling it a refactoring. They sound like opposites! Was the previous wrong? what is it actually doing?

V0 = deltaG / self.electrons / constants.F # V = deltaG / n / F
return V0

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