Merge pull request #144 from ReactionMechanismGenerator/edge_analysis

Edge analysis

Author: mjohnson541

Manifest.toml

@@ -14,6 +14,7 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"

Project.toml

@@ -91,6 +91,7 @@ export MultiPdepArrhenius
 @with_kw struct ThirdBody{N<:Integer,K<:AbstractFloat,Q<:AbstractRateUncertainty} <: AbstractFalloffRate
     arr::Arrhenius
     efficiencies::Dict{N,K} = Dict()
+    nameefficiencies::Dict{String,K} = Dict{String,Float64}()
     unc::Q = EmptyRateUncertainty()
 end
 
@@ -101,6 +102,7 @@ export ThirdBody
     arrhigh::Arrhenius
     arrlow::Arrhenius
     efficiencies::Dict{N,K} = Dict()
+    nameefficiencies::Dict{String,K} = Dict{String,Float64}()
     unc::Q = EmptyRateUncertainty()
 end
 
@@ -120,6 +122,7 @@ export Lindemann
     T1::F
     T2::L
     efficiencies::Dict{N,K} = Dict()
+    nameefficiencies::Dict{String,K} = Dict{String,Float64}()
     unc::R = EmptyRateUncertainty()
 end
 

src/Calculators/Rate.jl

@@ -2177,12 +2177,7 @@ end
 export jacobianp!
 
 function getreactionindices(ig::Q) where {Q<:AbstractPhase}
-    arr = zeros(Int64,(6,length(ig.reactions)))
-    for (i,rxn) in enumerate(ig.reactions)
-        arr[1:length(rxn.reactantinds),i] = rxn.reactantinds
-        arr[4:length(rxn.productinds)+3,i] = rxn.productinds
-    end
-    return arr
+    return deepcopy(ig.rxnarray)
 end
 export getreactionindices
 
@@ -2243,9 +2238,9 @@ export getreactionindices
         @inbounds sensrxns[i] = ElementaryReaction(
             index=i,
             reactants=SVector(reactants...),
-            reactantinds=SVector(reactantinds...),
+            reactantinds=MVector(reactantinds...),
             products=SVector(products...),
-            productinds=SVector(productinds...),
+            productinds=MVector(productinds...),
             kinetics=rxn.kinetics,
             radicalchange=rxn.radicalchange,
             pairs=rxn.pairs