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mjohnson541 wants to merge 16 commits into from
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Improve Rule Generation #2277

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e6110e9
add solute data to KineticsModel and Arrhenius
mjohnson541 Jan 11, 2022
a51925e
add ArrheniusChargeTransfer kinetics type
mjohnson541 Jan 11, 2022
aa39337
create ArrheniusChargeTransferBM type
mjohnson541 Jan 11, 2022
95db806
add ChargeTransfer types to kinetics/__init__.py
mjohnson541 Jan 11, 2022
25807c1
handle ChargeTransfer kinetics with in reaction.py
mjohnson541 Jan 11, 2022
908bad9
add handling ArrheniusChargeTransfer and fix handling SurfaceChargeTr…
mjohnson541 Jan 11, 2022
68d43d5
enable access to SoluteData object in kinetics database
mjohnson541 Jan 11, 2022
8d30987
when rule making is done on one processor don't use pool
mjohnson541 Jan 11, 2022
d81d824
add function for averaging kinetics
mjohnson541 Jan 11, 2022
1898402
update rule fitting
mjohnson541 Jan 11, 2022
5c727f1
enable use of non-surface charge transfer families
mjohnson541 Jan 11, 2022
321dbb8
add charge transfer types to database context
mjohnson541 Jan 11, 2022
1601dc8
standardize ascend option in cross validate
mjohnson541 Feb 28, 2022
58a9ef0
add comment to averaged kinetics
mjohnson541 Feb 28, 2022
ea72bf4
fix BM fitting
mjohnson541 Feb 28, 2022
4174c91
added Faraday's Constant `F`
davidfarinajr May 12, 2021
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27 changes: 10 additions & 17 deletions rmgpy/kinetics/arrhenius.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -611,27 +611,24 @@ cdef class ArrheniusBM(KineticsModel):
if len(rxns) == 1:
T = 1000.0
rxn = rxns[0]
dHrxn = rxn.get_enthalpy_of_reaction(T)
dHrxn = rxn.get_enthalpy_of_reaction(298.0)
A = rxn.kinetics.A.value_si
n = rxn.kinetics.n.value_si
Ea = rxn.kinetics.Ea.value_si

def kfcn(E0):
Vp = 2 * w0 * (2 * w0 + 2 * E0) / (2 * w0 - 2 * E0)
out = Ea - (w0 + dHrxn / 2.0) * (Vp - 2 * w0 + dHrxn) * (Vp - 2 * w0 + dHrxn) / (Vp * Vp - (2 * w0) * (2 * w0) + dHrxn * dHrxn)
return out

if abs(dHrxn) > 4 * w0 / 10.0:
E0 = w0 / 10.0
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@rwest rwest Jun 7, 2023

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can you explain why removing this? (in the commit message, ideally)

else:
E0 = fsolve(kfcn, w0 / 10.0)[0]
E0 = fsolve(kfcn, w0 / 10.0)[0]

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)
else:
# define optimization function
# define optimization function
def kfcn(xs, lnA, n, E0):
T = xs[:,0]
dHrxn = xs[:,1]
Expand All @@ -640,7 +637,7 @@ cdef class ArrheniusBM(KineticsModel):
Ea = np.where(dHrxn< -4.0*E0, 0.0, Ea)
Ea = np.where(dHrxn > 4.0*E0, dHrxn, Ea)
return lnA + np.log(T ** n * np.exp(-Ea / (8.314 * T)))

# get (T,dHrxn(T)) -> (Ln(k) mappings
xdata = []
ydata = []
Expand All @@ -649,7 +646,7 @@ cdef class ArrheniusBM(KineticsModel):
# approximately correct the overall uncertainties to std deviations
s = rank_accuracy_map[rxn.rank].value_si/2.0
for T in Ts:
xdata.append([T, rxn.get_enthalpy_of_reaction(T)])
xdata.append([T, rxn.get_enthalpy_of_reaction(298.0)])
ydata.append(np.log(rxn.get_rate_coefficient(T)))

sigmas.append(s / (8.314 * T))
Expand Down Expand Up @@ -1547,9 +1544,8 @@ cdef class ArrheniusChargeTransferBM(KineticsModel):
w0 = sum(w0s) / len(w0s)

if len(rxns) == 1:
T = 1000.0
rxn = rxns[0]
dHrxn = rxn.get_enthalpy_of_reaction(T)
dHrxn = rxn.get_enthalpy_of_reaction(298.0)
A = rxn.kinetics.A.value_si
n = rxn.kinetics.n.value_si
Ea = rxn.kinetics.Ea.value_si
Expand All @@ -1559,14 +1555,11 @@ cdef class ArrheniusChargeTransferBM(KineticsModel):
out = Ea - (w0 + dHrxn / 2.0) * (Vp - 2 * w0 + dHrxn) * (Vp - 2 * w0 + dHrxn) / (Vp * Vp - (2 * w0) * (2 * w0) + dHrxn * dHrxn)
return out

if abs(dHrxn) > 4 * w0 / 10.0:
E0 = w0 / 10.0
else:
E0 = fsolve(kfcn, w0 / 10.0)[0]
E0 = fsolve(kfcn, w0 / 10.0)[0]

self.Tmin = rxn.kinetics.Tmin
self.Tmax = rxn.kinetics.Tmax
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):
Expand All @@ -1586,7 +1579,7 @@ cdef class ArrheniusChargeTransferBM(KineticsModel):
# approximately correct the overall uncertainties to std deviations
s = rank_accuracy_map[rxn.rank].value_si/2.0
for T in Ts:
xdata.append([T, rxn.get_enthalpy_of_reaction(T)])
xdata.append([T, rxn.get_enthalpy_of_reaction(298.0)])
ydata.append(np.log(rxn.get_rate_coefficient(T)))

sigmas.append(s / (8.314 * T))
Expand Down