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Make Arrheniusq Kinetics Compatible With PCET Reactions #265

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9 changes: 5 additions & 4 deletions src/Calculators/Rate.jl
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
Expand Down
8 changes: 8 additions & 0 deletions src/Interface.jl
Original file line number Diff line number Diff line change
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
Expand Down
7 changes: 6 additions & 1 deletion src/Parse.jl
Original file line number Diff line number Diff line change
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
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