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mjohnson541mjohnson541
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add Marcus kinetics type and allow dGrxn dependence of kinetics
1 parent 52a72f3 commit c8bb787

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+37
-17
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2 files changed

+37
-17
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‎src/Calculators/Rate.jl

Lines changed: 33 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@ export AbstractFalloffRate
1313
Ea::Q
1414
unc::P = EmptyRateUncertainty()
1515
end
16-
@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))
17-
@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))
16+
@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))
17+
@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))
1818
export Arrhenius
1919

2020
@with_kw struct StickingCoefficient{N<:Real,K<:Real,Q<:Real,P<:AbstractRateUncertainty} <: AbstractRate
@@ -23,8 +23,8 @@ export Arrhenius
2323
Ea::Q
2424
unc::P = EmptyRateUncertainty()
2525
end
26-
@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)
27-
@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)
26+
@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)
27+
@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)
2828
export StickingCoefficient
2929

3030
@with_kw struct Arrheniusq{N<:Real,K<:Real,Q<:Real,P<:AbstractRateUncertainty,B} <: AbstractRate
@@ -34,18 +34,38 @@ export StickingCoefficient
3434
q::B = 0.0
3535
unc::P = EmptyRateUncertainty()
3636
end
37-
@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))
38-
@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))
37+
@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))
38+
@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))
3939
export Arrheniusq
4040

41+
@with_kw struct Marcus{N<:Real,K<:Real,Q,P<:AbstractRateUncertainty,B} <: AbstractRate
42+
A::N
43+
n::K
44+
lmbd_i_coefs::Q
45+
lmbd_o::K
46+
wr::K
47+
wp::K
48+
beta::B
49+
unc::P = EmptyRateUncertainty()
50+
end
51+
@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}
52+
@fastmath lmbd = arr.lmbd_o + evalpoly(T,arr.lmbd_i_coefs)
53+
@fastmath arr.A*T^arr.n*exp(-lmbd/4.0*(1.0+dGrxn/lmbd)^2/(R*T)-arr.beta*d)
54+
end
55+
@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}
56+
@fastmath lmbd = arr.lmbd_o + evalpoly(T,arr.lmbd_i_coefs)
57+
@fastmath return arr.A*T^arr.n*exp(-lmbd/4.0*(1.0+dGrxn/lmbd)^2/(R*T)-arr.beta*d)
58+
end
59+
export Marcus
60+
4161
@with_kw struct PdepArrhenius{T<:Real,Q<:AbstractRateUncertainty,Z<:AbstractRate} <: AbstractRate
4262
Ps::Array{T,1}
4363
arrs::Array{Z,1}
4464
unc::Q = EmptyRateUncertainty()
4565
end
4666
PdepArrhenius(Ps::Array{Q,1},arrs::Array{Z,1}) where {Q<:Real,Z<:AbstractRate} = PdepArrhenius(sort(Ps),arrs)
4767

48-
@inline function (parr::PdepArrhenius)(;T::Q=nothing,P::V=nothing,C::S=0.0,phi=0.0) where {Q<:Real,V<:Real,S<:Real}
68+
@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}
4969
inds = getBoundingIndsSorted(P,parr.Ps)::Tuple{Int64,Int64}
5070

5171
if inds[2] == -1
@@ -65,7 +85,7 @@ export PdepArrhenius
6585
unc::Q = EmptyRateUncertainty()
6686
end
6787

68-
@inline function (marr::MultiArrhenius)(;T::Q,P::R=0.0,C::S=0.0,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
88+
@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}
6989
out = 0.0
7090
for arr in marr.arrs
7191
@fastmath out += arr(T)
@@ -79,7 +99,7 @@ export MultiArrhenius
7999
unc::Q = EmptyRateUncertainty()
80100
end
81101

82-
@inline function (parr::MultiPdepArrhenius)(;T::Q,P::R=0.0,C::S=0.0,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
102+
@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}
83103
out = 0.0
84104
for pdar in parr.parrs
85105
@fastmath out += pdar(T=T,P=P)
@@ -95,7 +115,7 @@ export MultiPdepArrhenius
95115
unc::Q = EmptyRateUncertainty()
96116
end
97117

98-
(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))
118+
(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))
99119
export ThirdBody
100120

101121
@with_kw struct Lindemann{N<:Integer,K<:AbstractFloat,Q<:AbstractRateUncertainty} <: AbstractFalloffRate
@@ -106,7 +126,7 @@ export ThirdBody
106126
unc::Q = EmptyRateUncertainty()
107127
end
108128

109-
@inline function (lnd::Lindemann)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
129+
@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}
110130
k0 = lnd.arrlow(T=T)
111131
kinf = lnd.arrhigh(T=T)
112132
@fastmath Pr = k0*C/kinf
@@ -126,7 +146,7 @@ export Lindemann
126146
unc::R = EmptyRateUncertainty()
127147
end
128148

129-
@inline function (tr::Troe)(;T::Q,P::R=0.0,C::S=nothing,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
149+
@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}
130150
k0 = tr.arrlow(T=T)
131151
kinf = tr.arrhigh(T=T)
132152
@fastmath Pr = k0*C/kinf
@@ -195,7 +215,7 @@ export getredtemp
195215
end
196216
export getredpress
197217

198-
@inline function (ch::Chebyshev)(;T::N,P::Q=0.0,C::B=0.0,phi=0.0) where {N<:Real,B<:Real,Q<:Real}
218+
@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}
199219
k = 0.0
200220
Tred = getredtemp(ch,T)
201221
Pred = getredpress(ch,P)

‎src/Calculators/Ratevec.jl

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ function Arrheniusvec(arrs::T) where {T<:AbstractArray}
2121
end
2222
return Arrheniusvec(A=A,n=n,Ea=Ea)
2323
end
24-
@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)))
24+
@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)))
2525
@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)))
2626
export Arrheniusvec
2727

@@ -86,7 +86,7 @@ export getredtemp
8686
end
8787
export getredpress
8888

89-
@inline function (ch::Chebyshevvec)(;T::N,P::Q=0.0,C::B=0.0,phi=0.0) where {N<:Real,B<:Real,Q<:Real}
89+
@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}
9090
k = zeros(N,size(ch.coefs)[1])
9191
Tred = getredtemp(ch,T)
9292
Pred = getredpress(ch,P)
@@ -170,7 +170,7 @@ function Troevec(troes::T) where {T<:AbstractArray}
170170
end
171171
export Troevec
172172

173-
@inline function (tr::Troevec)(;T::Q=nothing,P::R=0.0,C::S=nothing,phi=0.0) where {Q<:Real,R<:Real,S<:Real}
173+
@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}
174174
k0 = tr.arrlow(T=T)
175175
kinf = tr.arrhigh(T=T)
176176
@fastmath Pr = k0.*C./kinf
@@ -201,7 +201,7 @@ function PdepArrheniusvec(pdeparrs::T) where {T<:AbstractArray}
201201
end
202202
export PdepArrheniusvec
203203

204-
@inline function (parr::PdepArrheniusvec)(;T::Q=nothing,P::V=nothing,C::S=0.0,phi=0.0) where {Q<:Real,V<:Real,S<:Real}
204+
@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}
205205
inds = getBoundingIndsSorted(P,parr.Ps)::Tuple{Int64,Int64}
206206
if inds[2] == -1
207207
return @inbounds parr.arrvecs[inds[1]](T=T)

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