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Make Arrheniusq Kinetics Compatible With PCET Reactions #265

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Make Arrheniusq Kinetics Compatible With PCET Reactions #265

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966bfac
Added reference potential to Arrheniusq
ssun30 May 28, 2024
53995f6
Fixed interfaces not setting phi correctly
ssun30 Aug 6, 2024
6b9e9ba
Parser uses RMG if RDKit fails to get structure
ssun30 Aug 6, 2024
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9 changes: 5 additions & 4 deletions src/Calculators/Rate.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -27,15 +27,16 @@ end
@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,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))
@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-arr.V0))/(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-arr.V0))/(R*T))
export Arrheniusq

@with_kw struct Marcus{N<:Real,K<:Real,Q,P<:AbstractRateUncertainty,B} <: AbstractRate
Expand Down Expand Up @@ -248,7 +249,7 @@ 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
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8 changes: 8 additions & 0 deletions src/Interface.jl
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Expand Up @@ -95,6 +95,14 @@ function ReactiveInternalInterfaceConstantTPhi(domain1,domain2,reactions,T,A,phi
M,Nrp1,Nrp2 = getstoichmatrix(domain1,domain2,reactions)
Gpart = ArrayPartition(domain1.Gs,domain2.Gs)
dGrxns = -M*Gpart
electronchanges = [hasproperty(reaction, :electronchange) ? reaction.electronchange : 0.0 for reaction in reactions]
referencepotentials = [hasproperty(reaction.kinetics, :V0) ? reaction.kinetics.V0 : 0.0 for reaction in reactions]
if isa(domain1.phase, IdealSurface)
phi = domain1.phi !== nothing ? domain1.phi : phi
elseif isa(domain2.phase, IdealSurface)
phi = domain2.phi !== nothing ? domain2.phi : phi
end
dGrxns .+= electronchanges.*(phi.-referencepotentials).*F
kfs = getkf.(reactions,nothing,T,0.0,0.0,Ref([]),A,phi,dGrxns,0.0)
Kc = getKcs(domain1.phase,domain2.phase,T,Nrp1,Nrp2,dGrxns)
krevs = kfs./Kc
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7 changes: 6 additions & 1 deletion src/Parse.jl
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Expand Up @@ -168,7 +168,12 @@ function getatomdictsmiles(smiles)
mol.assign_representative_molecule()
getatomdictfromrmg(mol.mol_repr)
else
getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(smiles)))
try
return getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(smiles)))
catch e
println("RDKit parsing failed, using RMG instead", e)
return getatomdictfromrmg(molecule.Molecule().from_smiles(smiles))
end
end
end

Expand Down