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Marcus Kinetics #247

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Marcus Kinetics #247

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64066e5
include electronchange in reaction reconstruction in phase
mjohnson541 Feb 4, 2024
3a6e483
add Marcus kinetics type and allow dGrxn dependence of kinetics
mjohnson541 Feb 4, 2024
c88e830
handle dGrxn and d dependence of reactions in interfaces and phase ca…
mjohnson541 Feb 4, 2024
f3b5f52
adapt Domains to dGrxn and d dependence of forward rate coefficient c…
mjohnson541 Feb 4, 2024
6755b49
add a Marcus reaction to the ORR.rms mechanism for testing
mjohnson541 Feb 4, 2024
80e9c39
fix variable naminng
mjohnson541 Mar 30, 2024
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46 changes: 33 additions & 13 deletions src/Calculators/Rate.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@ export AbstractFalloffRate
Ea::Q
unc::P = EmptyRateUncertainty()
end
@inline (arr::Arrhenius)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp(-arr.Ea/(R*T))
@inline (arr::Arrhenius)(T::Q;P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp(-arr.Ea/(R*T))
@inline (arr::Arrhenius)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp(-arr.Ea/(R*T))
@inline (arr::Arrhenius)(T::Q;P::N=0.0,C::S=0.0,phi=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp(-arr.Ea/(R*T))
export Arrhenius

@with_kw struct StickingCoefficient{N<:Real,K<:Real,Q<:Real,P<:AbstractRateUncertainty} <: AbstractRate
Expand All @@ -23,8 +23,8 @@ export Arrhenius
Ea::Q
unc::P = EmptyRateUncertainty()
end
@inline (arr::StickingCoefficient)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath min(arr.A*T^arr.n*exp(-arr.Ea/(R*T)),1.0)
@inline (arr::StickingCoefficient)(T::Q;P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath min(arr.A*T^arr.n*exp(-arr.Ea/(R*T)),1.0)
@inline (arr::StickingCoefficient)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath min(arr.A*T^arr.n*exp(-arr.Ea/(R*T)),1.0)
@inline (arr::StickingCoefficient)(T::Q;P::N=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath min(arr.A*T^arr.n*exp(-arr.Ea/(R*T)),1.0)
export StickingCoefficient

@with_kw struct Arrheniusq{N<:Real,K<:Real,Q<:Real,P<:AbstractRateUncertainty,B} <: AbstractRate
Expand All @@ -34,18 +34,38 @@ export StickingCoefficient
q::B = 0.0
unc::P = EmptyRateUncertainty()
end
@inline (arr::Arrheniusq)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp((-arr.Ea-arr.q*F*phi)/(R*T))
@inline (arr::Arrheniusq)(T::Q;P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp((-arr.Ea-arr.q*F*phi)/(R*T))
@inline (arr::Arrheniusq)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp((-arr.Ea-arr.q*F*phi)/(R*T))
@inline (arr::Arrheniusq)(T::Q;P::N=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath arr.A*T^arr.n*exp((-arr.Ea-arr.q*F*phi)/(R*T))
export Arrheniusq

@with_kw struct Marcus{N<:Real,K<:Real,Q,P<:AbstractRateUncertainty,B} <: AbstractRate
A::N
n::K
lmbd_i_coefs::Q
lmbd_o::K
wr::K
wp::K
beta::B
unc::P = EmptyRateUncertainty()
end
@inline function (arr::Marcus)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real}
@fastmath lmbd = arr.lmbd_o + evalpoly(T,arr.lmbd_i_coefs)
@fastmath arr.A*T^arr.n*exp(-lmbd/4.0*(1.0+dGrxn/lmbd)^2/(R*T)-arr.beta*d)
end
@inline function (arr::Marcus)(T::Q;P::N=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,N<:Real,S<:Real}
@fastmath lmbd = arr.lmbd_o + evalpoly(T,arr.lmbd_i_coefs)
@fastmath return arr.A*T^arr.n*exp(-lmbd/4.0*(1.0+dGrxn/lmbd)^2/(R*T)-arr.beta*d)
end
export Marcus

@with_kw struct PdepArrhenius{T<:Real,Q<:AbstractRateUncertainty,Z<:AbstractRate} <: AbstractRate
Ps::Array{T,1}
arrs::Array{Z,1}
unc::Q = EmptyRateUncertainty()
end
PdepArrhenius(Ps::Array{Q,1},arrs::Array{Z,1}) where {Q<:Real,Z<:AbstractRate} = PdepArrhenius(sort(Ps),arrs)

@inline function (parr::PdepArrhenius)(;T::Q=nothing,P::V=nothing,C::S=0.0,phi=0.0) where {Q<:Real,V<:Real,S<:Real}
@inline function (parr::PdepArrhenius)(;T::Q=nothing,P::V=nothing,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,V<:Real,S<:Real}
inds = getBoundingIndsSorted(P,parr.Ps)::Tuple{Int64,Int64}

if inds[2] == -1
Expand All @@ -65,7 +85,7 @@ export PdepArrhenius
unc::Q = EmptyRateUncertainty()
end

@inline function (marr::MultiArrhenius)(;T::Q,P::R=0.0,C::S=0.0,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
@inline function (marr::MultiArrhenius)(;T::Q,P::R=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,R<:Real,S<:Real}
out = 0.0
for arr in marr.arrs
@fastmath out += arr(T)
Expand All @@ -79,7 +99,7 @@ export MultiArrhenius
unc::Q = EmptyRateUncertainty()
end

@inline function (parr::MultiPdepArrhenius)(;T::Q,P::R=0.0,C::S=0.0,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
@inline function (parr::MultiPdepArrhenius)(;T::Q,P::R=0.0,C::S=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,R<:Real,S<:Real}
out = 0.0
for pdar in parr.parrs
@fastmath out += pdar(T=T,P=P)
Expand All @@ -95,7 +115,7 @@ export MultiPdepArrhenius
unc::Q = EmptyRateUncertainty()
end

(tbarr::ThirdBody)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0) where {Q<:Real,R<:Real,S<:Real} = C*(tbarr.arr(T))
(tbarr::ThirdBody)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,R<:Real,S<:Real} = C*(tbarr.arr(T))
export ThirdBody

@with_kw struct Lindemann{N<:Integer,K<:AbstractFloat,Q<:AbstractRateUncertainty} <: AbstractFalloffRate
Expand All @@ -106,7 +126,7 @@ export ThirdBody
unc::Q = EmptyRateUncertainty()
end

@inline function (lnd::Lindemann)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
@inline function (lnd::Lindemann)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,R<:Real,S<:Real}
k0 = lnd.arrlow(T=T)
kinf = lnd.arrhigh(T=T)
@fastmath Pr = k0*C/kinf
Expand All @@ -126,7 +146,7 @@ export Lindemann
unc::R = EmptyRateUncertainty()
end

@inline function (tr::Troe)(;T::Q,P::R=0.0,C::S=nothing,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
@inline function (tr::Troe)(;T::Q,P::R=0.0,C::S=nothing,phi=0.0,dGrxn=0.0,d=0.0) where {Q<:Real,R<:Real,S<:Real}
k0 = tr.arrlow(T=T)
kinf = tr.arrhigh(T=T)
@fastmath Pr = k0*C/kinf
Expand Down Expand Up @@ -195,7 +215,7 @@ export getredtemp
end
export getredpress

@inline function (ch::Chebyshev)(;T::N,P::Q=0.0,C::B=0.0,phi=0.0) where {N<:Real,B<:Real,Q<:Real}
@inline function (ch::Chebyshev)(;T::N,P::Q=0.0,C::B=0.0,phi=0.0,dGrxn=0.0,d=0.0) where {N<:Real,B<:Real,Q<:Real}
k = 0.0
Tred = getredtemp(ch,T)
Pred = getredpress(ch,P)
Expand Down
8 changes: 4 additions & 4 deletions src/Calculators/Ratevec.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ function Arrheniusvec(arrs::T) where {T<:AbstractArray}
end
return Arrheniusvec(A=A,n=n,Ea=Ea)
end
@inline (arr::Arrheniusvec)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath @inbounds arr.A.*exp.(arr.n.*log(T).-arr.Ea.*(1.0/(R*T)))
@inline (arr::Arrheniusvec)(;T::Q,P::N=0.0,C::S=0.0,phi=0.0,dGrxns=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath @inbounds arr.A.*exp.(arr.n.*log(T).-arr.Ea.*(1.0/(R*T)))
@inline (arr::Arrheniusvec)(T::Q;P::N=0.0,C::S=0.0,phi=0.0) where {Q<:Real,N<:Real,S<:Real} = @fastmath @inbounds arr.A.*exp.(arr.n.*log(T).-arr.Ea.*(1.0/(R*T)))
export Arrheniusvec

Expand Down Expand Up @@ -86,7 +86,7 @@ export getredtemp
end
export getredpress

@inline function (ch::Chebyshevvec)(;T::N,P::Q=0.0,C::B=0.0,phi=0.0) where {N<:Real,B<:Real,Q<:Real}
@inline function (ch::Chebyshevvec)(;T::N,P::Q=0.0,C::B=0.0,phi=0.0,dGrxns=0.0) where {N<:Real,B<:Real,Q<:Real}
k = zeros(N,size(ch.coefs)[1])
Tred = getredtemp(ch,T)
Pred = getredpress(ch,P)
Expand Down Expand Up @@ -170,7 +170,7 @@ function Troevec(troes::T) where {T<:AbstractArray}
end
export Troevec

@inline function (tr::Troevec)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
@inline function (tr::Troevec)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0,dGrxns=0.0) where {Q<:Real,R<:Real,S<:Real}
k0 = tr.arrlow(T=T)
kinf = tr.arrhigh(T=T)
@fastmath Pr = k0.*C./kinf
Expand Down Expand Up @@ -201,7 +201,7 @@ function PdepArrheniusvec(pdeparrs::T) where {T<:AbstractArray}
end
export PdepArrheniusvec

@inline function (parr::PdepArrheniusvec)(;T::Q=nothing,P::V=nothing,C::S=0.0,phi=0.0) where {Q<:Real,V<:Real,S<:Real}
@inline function (parr::PdepArrheniusvec)(;T::Q=nothing,P::V=nothing,C::S=0.0,phi=0.0,dGrxns=0.0) where {Q<:Real,V<:Real,S<:Real}
inds = getBoundingIndsSorted(P,parr.Ps)::Tuple{Int64,Int64}
if inds[2] == -1
return @inbounds parr.arrvecs[inds[1]](T=T)
Expand Down