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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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3 changes: 2 additions & 1 deletion rmgpy/kinetics/__init__.py
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Expand Up @@ -29,7 +29,8 @@

from rmgpy.kinetics.model import KineticsModel, PDepKineticsModel, TunnelingModel, \
get_rate_coefficient_units_from_reaction_order, get_reaction_order_from_rate_coefficient_units
from rmgpy.kinetics.arrhenius import Arrhenius, ArrheniusEP, PDepArrhenius, MultiArrhenius, MultiPDepArrhenius, ArrheniusBM
from rmgpy.kinetics.arrhenius import Arrhenius, ArrheniusEP, PDepArrhenius, MultiArrhenius, MultiPDepArrhenius, \
ArrheniusBM, ArrheniusChargeTransfer, ArrheniusChargeTransferBM
from rmgpy.kinetics.chebyshev import Chebyshev
from rmgpy.kinetics.falloff import ThirdBody, Lindemann, Troe
from rmgpy.kinetics.kineticsdata import KineticsData, PDepKineticsData
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51 changes: 51 additions & 0 deletions rmgpy/kinetics/arrhenius.pxd
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Expand Up @@ -128,4 +128,55 @@ cdef class MultiPDepArrhenius(PDepKineticsModel):

cpdef bint is_identical_to(self, KineticsModel other_kinetics) except -2


cpdef change_rate(self, double factor)

################################################################################
cdef class ArrheniusChargeTransfer(KineticsModel):

cdef public ScalarQuantity _A
cdef public ScalarQuantity _n
cdef public ScalarQuantity _Ea
cdef public ScalarQuantity _T0
cdef public ScalarQuantity _V0
cdef public ScalarQuantity _alpha
cdef public ScalarQuantity _electrons

cpdef double get_activation_energy_from_potential(self, double V=?, bint non_negative=?)

cpdef double get_rate_coefficient(self, double T, double V=?) except -1

cpdef change_rate(self, double factor)

cpdef change_t0(self, double T0)

cpdef change_v0(self, double V0)

cpdef fit_to_data(self, np.ndarray Tlist, np.ndarray klist, str kunits, double T0=?, np.ndarray weights=?, bint three_params=?)

cpdef bint is_identical_to(self, KineticsModel other_kinetics) except -2


################################################################################

cdef class ArrheniusChargeTransferBM(KineticsModel):

cdef public ScalarQuantity _A
cdef public ScalarQuantity _n
cdef public ScalarQuantity _E0
cdef public ScalarQuantity _w0
cdef public ScalarQuantity _V0
cdef public ScalarQuantity _alpha
cdef public ScalarQuantity _electrons

cpdef change_v0(self, double V0)

cpdef double get_activation_energy(self, double dGrxn) except -1

cpdef double get_rate_coefficient_from_potential(self, double T, double V, double dGrxn) except -1

cpdef ArrheniusChargeTransfer to_arrhenius_charge_transfer(self, double dGrxn)

cpdef bint is_identical_to(self, KineticsModel other_kinetics) except -2

cpdef change_rate(self, double factor)
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