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Marcus development #267

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72d7299
include electronchange in reaction reconstruction in phase
mjohnson541 Feb 4, 2024
839864d
add Marcus kinetics type and allow dGrxn dependence of kinetics
mjohnson541 Feb 4, 2024
34b324b
handle dGrxn and d dependence of reactions in interfaces and phase ca…
mjohnson541 Feb 4, 2024
ce77897
adapt Domains to dGrxn and d dependence of forward rate coefficient c…
mjohnson541 Feb 4, 2024
b7571b8
add a Marcus reaction to the ORR.rms mechanism for testing
mjohnson541 Feb 4, 2024
3a74a52
fix variable naminng
mjohnson541 Mar 30, 2024
955558b
Added reference potential to Arrheniusq
ssun30 May 28, 2024
2784fc2
Fixed interfaces not setting phi correctly
ssun30 Aug 6, 2024
94a39b7
Parser uses RMG if RDKit fails to get structure
ssun30 Aug 6, 2024
855af5a
Now runs CI upon pushing marcus_development
ssun30 Oct 1, 2024
1a59224
fix getKc call in ReactiveInternalInterface
mjohnson541 Sep 23, 2024
d7d99e0
add phi and d to newer domains
mjohnson541 Sep 23, 2024
5bf5919
phase electron change fixes
mjohnson541 Sep 25, 2024
774a8e0
missing domain tweaks for phi/d
mjohnson541 Sep 25, 2024
21cc358
fix FragmentBasedReactiveFilmGrowthInterfaceConstantT interface
mjohnson541 Sep 25, 2024
fcc4ddc
Added default values for wr/wp for Marcus Kinetics
ssun30 Oct 9, 2024
6379eb6
Fixed array input format in ORR.rms
ssun30 Oct 15, 2024
38cc7f4
Fixed processfluxes for interfaces
ssun30 Oct 22, 2024
6cbc147
Changed variable naming in TestReactors
ssun30 Nov 7, 2024
fbb66c4
Fixed typos
mjohnson541 Sep 25, 2024
526fa90
loosen solver tolerances for some tests
ssun30 Nov 8, 2024
3a5588b
TEMP: added checks to restrict barrier height
ssun30 Jan 5, 2025
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1 change: 1 addition & 0 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ on:
push:
branches:
- main
- marcus_development
jobs:
test:
runs-on: ubuntu-latest
Expand Down
59 changes: 44 additions & 15 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 @@ -23,29 +23,58 @@ 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
@with_kw struct Arrheniusq{N<:Real,K<:Real,Q<:Real,R<:Real,P<:AbstractRateUncertainty,B} <: AbstractRate
A::N
n::K
Ea::Q
q::B = 0.0
V0::R = 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} = begin
barrier = arr.Ea+arr.q*F*(phi-arr.V0)
corrected_barrier = max(0, dGrxn, barrier)
@fastmath arr.A*T^arr.n*exp(-corrected_barrier/(R*T))
end
@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} = begin
barrier = arr.Ea+arr.q*F*(phi-arr.V0)
corrected_barrier = max(0, dGrxn, barrier)
@fastmath arr.A*T^arr.n*exp(-corrected_barrier/(R*T))
end
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 = 0.0
wp::K = 0.0
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 +94,7 @@ 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 +108,7 @@ 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 +124,7 @@ 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 +135,7 @@ 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 +155,7 @@ 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 +224,7 @@ 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 Expand Up @@ -228,7 +257,7 @@ export getkineticstype

@inline extracttypename(typ::Symbol) = string(typ)
@inline extracttypename(typ) = string(typ.name)

@inline function _calcdkdCeff(tbarr::ThirdBody,T::Float64,Ceff::Float64)
return @fastmath tbarr.arr(T)
end
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
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