Automatic Mechanism Analysis

Running Automatic Mechanism Analysis

Automatic mechanism analysis can be run for a single species at a single time point using the function analyzespc(sim,spcname,t;N=10,tol=1e-3,branchthreshold=0.9, pathbranchthreshold=0.2,branchtol=1e-2,steptol=1e-2, transitorysensitivitymethod=transitorysensitivitiesfulltrapezoidal, eliminate=true ). This returns an array of ReactionAnalysis objects corresponding to each reaction found in the analysis (based on N and tol choices).

ReactionAnalysis Object

The ReactionAnalysis object has seven attributes, branchings the array of potentially important Branching objects, paths the array of potentially important ReactionPath objects, radprodlossfract the fraction of production (+) or loss (-) of radicals that this reaction accounts for, spcind the index of the target species, spcname the name of the target species, rxnind the index of the reaction and sens the transitory sensitivity value. Can be dumpped to a string report by getrxnanalysisstring(sim,ra;branchingcutoff=1e-2,radbranchfract=0.01) or simply printed with printrxnanalysis(sim,ra;branchingcutoff=1e-2,radbranchfract=0.01) where the branchingcutoff is the fraction of the branching at which reactions will no longer show up as part of a branching and radbranchfract is the fraction of radical production/loss above which the value is displayed as important.

Branching Object

The Branching object has three attributes, spcind the index of the target species, rxninds the array of the indices of the reactions in order of branching fraction, branchingratios the fraction of the branching accounted for by each reaction. Can be used to generate a flux diagram with getfluxdiagram(bsol,t,b::Branching; branchtol=1.0e-2, kwargs...) where branchtol is the fraction of the branching at which the product of a reaction will not be included in the flux diagram. Note this flux diagram includes all reaction between species part of the important branching reactions and not just the branching reactions themselves.

ReactionPath Object

The ReactionPath object has six important attributes, forward indices whether the path was generated following the flux forward from the target species or backwards from the target species, spcsinds is the array of the species indices followed in order along the flux path, rxninds is the array of reactions that connect these spcsinds, spcind is the index of the target species, branchfracts is the branching fraction of the reaction in rxninds for the species in spcsinds, branchfract is the fraction of the flux following from the start of the path to the end. Can be used to generate a flux diagram with getfluxdiagram(bsol,t,rp::ReactionPath; radius=0, kwargs...). Note this flux diagram includes all reactions between species that are parts of the ReactionPath and not just the reaction path itself.