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fixups in SurfaceChargeTransfer class
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@davidfarinajr
davidfarinajr committed Jan 20, 2021
1 parent 1a8b368 commit e124de9
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Showing 2 changed files with 43 additions and 37 deletions.
2 changes: 1 addition & 1 deletion rmgpy/kinetics/surface.pxd
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ cdef class SurfaceChargeTransfer(KineticsModel):
cdef public ScalarQuantity _Ea
cdef public ScalarQuantity _T0
cdef public ScalarQuantity _V0
cdef public ScalarQuantity _a
cdef public ScalarQuantity _alpha
cdef public ScalarQuantity _ne

cpdef double get_activation_energy_from_potential(self, double V=?, bint non_negative=?)
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78 changes: 42 additions & 36 deletions rmgpy/kinetics/surface.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -533,22 +533,23 @@ cdef class SurfaceArrheniusBEP(ArrheniusEP):
cdef class SurfaceChargeTransfer(KineticsModel):

"""
A kinetics model based on (modified) Arrhenius for surface reactions.
A kinetics model for surface charge transfer reactions
It is very similar to the :class:`SurfaceArrhenius`, but the Ea is potential-dependent
It is very similar to the gas phase :class:`Arrhenius`
The attributes are:
=============== =============================================================
Attribute Description
=============== =============================================================
`a` The charge transfer coefficient
`A` The preexponential factor
`T0` The reference temperature
`V0` The reference potential
`n` The temperature exponent
`Ea` The activation energy
`ne` The stochiometry coeff for electrons (negative if reactant, positive if product)
`V0` The reversible potential
`alpha` The charge transfer coefficient
`Tmin` The minimum temperature at which the model is valid, or zero if unknown or undefined
`Tmax` The maximum temperature at which the model is valid, or zero if unknown or undefined
`Pmin` The minimum pressure at which the model is valid, or zero if unknown or undefined
Expand All @@ -558,23 +559,49 @@ cdef class SurfaceChargeTransfer(KineticsModel):
"""

def __init__(self, a=0.5, A=None, n=0.0, Ea=None, T0=(1.0, "K"), V0=(0.0, "V"), ne=-1, Tmin=None, Tmax=None, Pmin=None, Pmax=None,
uncertainty=None, comment=''):
def __init__(self, A=None, n=0.0, Ea=None, V0=None, alpha=0.5, ne=-1, T0=(1.0, "K"), Tmin=None, Tmax=None,
Pmin=None, Pmax=None, uncertainty=None, comment=''):

KineticsModel.__init__(self, Tmin=Tmin, Tmax=Tmax, Pmin=Pmin, Pmax=Pmax, uncertainty=uncertainty,
comment=comment)

self.alpha = alpha
self.A = A
self.n = n
self.Ea = Ea
self.T0 = T0
self.a = a
self.ne = ne
self.V0 = V0

def __repr__(self):
"""
Return a string representation that can be used to reconstruct the
Arrhenius object.
"""
string = 'SurfaceChargeTransfer(A={0!r}, n={1!r}, Ea={2!r}, V0={3!r}, alpha={4!r}, ne={5!r}, T0={6!r}'.format(
self.A, self.n, self.Ea, self.V0, self.alpha, self.ne, self.T0)
if self.Tmin is not None: string += ', Tmin={0!r}'.format(self.Tmin)
if self.Tmax is not None: string += ', Tmax={0!r}'.format(self.Tmax)
if self.Pmin is not None: string += ', Pmin={0!r}'.format(self.Pmin)
if self.Pmax is not None: string += ', Pmax={0!r}'.format(self.Pmax)
if self.uncertainty: string += ', uncertainty={0!r}'.format(self.uncertainty)
if self.comment != '': string += ', comment="""{0}"""'.format(self.comment)
string += ')'
return string

def __reduce__(self):
"""
A helper function used when pickling a SurfaceChargeTransfer object.
"""
return (SurfaceChargeTransfer, (self.A, self.n, self.Ea, self.V0, self.alpha, self.ne, self.T0, self.Tmin, self.Tmax, self.Pmin, self.Pmax,
self.uncertainty, self.comment))

property A:
"""The preexponential factor."""
def __get__(self):
return self._A
def __set__(self, value):
self._A = quantity.RateCoefficient(value)
self._A = quantity.SurfaceRateCoefficient(value)

property n:
"""The temperature exponent."""
Expand All @@ -598,7 +625,7 @@ cdef class SurfaceChargeTransfer(KineticsModel):
self._T0 = quantity.Temperature(value)

property V0:
"""The reference potential"""
"""The reversible potential."""
def __get__(self):
return self._V0
def __set__(self, value):
Expand All @@ -611,34 +638,12 @@ cdef class SurfaceChargeTransfer(KineticsModel):
def __set__(self, value):
self._ne = quantity.Dimensionless(value)

property a:
property alpha:
"""The charge transfer coefficient."""
def __get__(self):
return self._a
return self._alpha
def __set__(self, value):
self._a = quantity.Dimensionless(value)

def __repr__(self):
"""
Return a string representation that can be used to reconstruct the
Arrhenius object.
"""
string = 'SurfaceChargeTransfer(A={0!r}, n={1!r}, Ea={2!r}, T0={3!r}, a={4!r}, ne={5!r}, '.format(self.A, self.n, self.Ea, self.T0, self.a, self.ne)
if self.Tmin is not None: string += ', Tmin={0!r}'.format(self.Tmin)
if self.Tmax is not None: string += ', Tmax={0!r}'.format(self.Tmax)
if self.Pmin is not None: string += ', Pmin={0!r}'.format(self.Pmin)
if self.Pmax is not None: string += ', Pmax={0!r}'.format(self.Pmax)
if self.uncertainty: string += ', uncertainty={0!r}'.format(self.uncertainty)
if self.comment != '': string += ', comment="""{0}"""'.format(self.comment)
string += ')'
return string

def __reduce__(self):
"""
A helper function used when pickling an Arrhenius object.
"""
return (SurfaceChargeTransfer, (self.a, self.A, self.n, self.ne, self.Ea, self.T0, self.Tmin, self.Tmax, self.Pmin, self.Pmax,
self.uncertainty, self.comment))
self._alpha = quantity.Dimensionless(value)

cpdef double get_activation_energy_from_potential(self, double V=0.0, bint non_negative=True):
"""
Expand Down Expand Up @@ -699,7 +704,7 @@ cdef class SurfaceChargeTransfer(KineticsModel):
rate_sign_multiplier = 1

for i in range(len(Tlist)):
klist[i] /= np.exp((self.a * self.ne * constants.F * V) / (constants.R * Tlist[i])) # NOT SURE ABOUT SIGN HERE
klist[i] /= np.exp((self.alpha * self.ne * constants.F * V) / (constants.R * Tlist[i])) # NOT SURE ABOUT SIGN HERE

assert len(Tlist) == len(klist), "length of temperatures and rates must be the same"
if len(Tlist) < 3 + three_params:
Expand Down Expand Up @@ -756,7 +761,8 @@ cdef class SurfaceChargeTransfer(KineticsModel):
return False
if (not self.A.equals(other_kinetics.A) or not self.n.equals(other_kinetics.n)
or not self.Ea.equals(other_kinetics.Ea) or not self.T0.equals(other_kinetics.T0)
or not self.a.equals(other_kinetics.Ea) or not self.ne.equals(other_kinetics.ne)):
or not self.alpha.equals(other_kinetics.alpha) or not self.ne.equals(other_kinetics.ne)
or not self.V0.equals(other_kinetics.V0)):
return False

return True
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