def testGetEffectiveRate3to2(self):
"""
Tests that the effective rate is limited for a 3 -> 2 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.tri_bi_reaction, self.T)
self.assertTrue(effective_rate < self.intrinsic_rates[self.tri_bi_reaction])
self.assertTrue(effective_rate >= 0.2 * self.intrinsic_rates[self.tri_bi_reaction])
def testGetEffectiveRateUnimolecular(self):
"""
Tests that the effective rate is the same as the intrinsic rate for
unimiolecular reactions.
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.uni_reaction, self.T)
self.assertEqual(effective_rate, self.intrinsic_rates[self.uni_reaction])
def testGetEffectiveRate2to1(self):
"""
Tests that the effective rate is limited in the forward direction for
a 2 -> 1 reaction
"""
effective_rate = diffusionLimiter.getEffectiveRate(self.bi_uni_reaction, self.T)
self.assertTrue(effective_rate < self.intrinsic_rates[self.bi_uni_reaction])
self.assertTrue(effective_rate >= 0.2 * self.intrinsic_rates[self.bi_uni_reaction])
def getRateCoefficient(self, T, P=0):
"""
Return the overall rate coefficient for the forward reaction at
temperature `T` in K and pressure `P` in Pa, including any reaction
path degeneracies.
If diffusionLimiter is enabled, the reaction is in the liquid phase and we use
a diffusion limitation to correct the rate. If not, then use the intrinsic rate
coefficient.
"""
if diffusionLimiter.enabled:
try:
k = self.__k_effective_cache[T]
except KeyError:
k = diffusionLimiter.getEffectiveRate(self, T)
self.__k_effective_cache[T] = k
return k
else:
return self.kinetics.getRateCoefficient(T, P)
def getRateCoefficient(self, T, P=0):
"""
Return the overall rate coefficient for the forward reaction at
temperature `T` in K and pressure `P` in Pa, including any reaction
path degeneracies.
If diffusionLimiter is enabled, the reaction is in the liquid phase and we use
a diffusion limitation to correct the rate. If not, then use the intrinsic rate
coefficient.
"""
if diffusionLimiter.enabled:
try:
k = self.__k_effective_cache[T]
except KeyError:
k = diffusionLimiter.getEffectiveRate(self, T)
self.__k_effective_cache[T] = k
return k
else:
return self.kinetics.getRateCoefficient(T, P)
def fixDiffusionLimitedA(self, T):
"""
Decrease the pre-exponential factor (A) by the diffusion factor
to account for the diffusion limit at the specified temperature.
"""
if not diffusionLimiter.enabled:
return
# Obtain effective rate
try:
k = self.k_effective_cache[T]
except KeyError:
k = diffusionLimiter.getEffectiveRate(self, T)
self.k_effective_cache[T] = k
# calculate diffusion factor
diffusionFactor = k / self.kinetics.getRateCoefficient(T, P=0)
# update preexponential factor
self.kinetics.A = self.kinetics.A * diffusionFactor
# Add a comment to self.kinetics.comment
self.kinetics.comment.append(
("Pre-exponential factor A has been decreased by the "
"diffusion factor {0.2g} evaluated at {1} K.").format(
diffusionFactor, T))