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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
e410acb
Merge branch 'ReactionMechanismGenerator:main' into main
LekiaAnonim Sep 27, 2025
6f9ab99
Merge branch 'ReactionMechanismGenerator:main' into main
LekiaAnonim Nov 10, 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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@rwest rwest Jun 18, 2025

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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

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Copilot AI Nov 10, 2025

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[nitpick] Trailing whitespace detected. Consider removing the trailing spaces.

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def get_free_energy_of_non_charge_transfer_reaction(self, T):
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@rwest rwest Jun 18, 2025

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You'll notice the other method had cython.declare lines. This helps Cython create faster code.


Comment on lines +666 to 667
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Missing documentation for this new method. Consider adding a docstring that explains what this method calculates and when it should be used. Based on its usage in _get_free_energy_of_charge_transfer_reaction and get_reversible_potential, this method calculates the standard free energy of reaction (without the electrochemical potential term), which is used for both charge transfer and non-charge transfer reactions.

Suggested change
def get_free_energy_of_non_charge_transfer_reaction(self, T):
def get_free_energy_of_non_charge_transfer_reaction(self, T):
"""
Return the standard free energy of reaction (ΔG°) in J/mol at temperature `T` in K,
excluding any electrochemical potential (i.e., without the -nFE term).
This method sums the free energies of the products and subtracts those of the reactants,
and is used as the base calculation for both charge transfer and non-charge transfer reactions.
Parameters
----------
T : float
Temperature in Kelvin at which to evaluate the free energy of reaction.
Returns
-------
float
The standard free energy of reaction in J/mol.
"""

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Missing Cython type declarations. For consistency with other methods like get_enthalpy_of_reaction and get_entropy_of_reaction, this method should include Cython declarations. Consider adding:

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

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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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@rwest rwest Jun 18, 2025

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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)
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Unused Cython variable declarations. The variables reactant and product are declared but no longer used in this method since it now delegates to get_free_energy_of_non_charge_transfer_reaction. Consider removing them from the declaration:

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

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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
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The comment is misleading. The code calculates free energy from enthalpy and entropy (H - T*S) rather than directly using species free energies. Consider updating the comment to: "For non charge transfer reactions, calculate free energy from enthalpy and entropy"

Suggested change
# For non charge transfer reactions, we can use the free energy of the species
# For non charge transfer reactions, calculate free energy from enthalpy and entropy

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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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@rwest rwest Jun 18, 2025

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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

Expand Down
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