kinetics estimation

Non-Pressure Dependent Kinetics Estimation: What reactions are considered and what rate parameters are generated are governed by the libraries, seed mechanisms and families set in the input file. First when RMG starts, all reactions from any seed mechanisms and the associated rate information are included and used within the model. As RMG runs, whenever a new reaction is generated for a given family any available libraries are first searched for rate parameter data if rate data is found it is used, otherwise it estimates the rate using the families directly.

Family based rate estimation:

Family structure:
Families are composed of a tree or a series of trees whose nodes are groups. Each tree branches independent segments usually defining the reactants and reaction related sites although the independent segments can in practice be on any independent properties.
Example 1: X-H + Y. <=> Y-H + X. This one has one tree for X-H and one tree for Y. Example 2: H-R2R1. <=> .R2R1-H This one has three trees one for the backbone (~) between endgroups R1 and R2, one for R1 and one for R2. The backbone in general is usually defined as all atoms between the endgroups not directly participating in the reaction.

Groups:
Groups are more general versions of molecules. Unlike molecules groups permit extra types of nodes within the graph. For example a node in a group could be any of R,R!H,C,Cs,Cd,Cdd,Ct,CS,CO or Cb all of which could represent a carbon atom, additionally different bond structure possibilities are allowed.

for example:
atom-number label GroupAtom unpaired-electrons bonds 1 *1 R!H u1 {2,T} 2 *4 Ct u0 {1,T} {3,S} 3 *6 [Cd,Ct,Cb] u0 {2,S} {4,[D,T,B]} 4 *5 [Cd,Ct,Cb] u0 {3,[D,T,B]} {5,S} 5 *2 [Cd,Cdd,Ct,CO,N,CS] u0 {4,S} {6,[D,T]} 6 *3 [Cd,Ct,Od,Sd,Cdd,N] u0 {5,[D,T]}

This is a backbone group from Intra_R_Add_Endocyclic, the labels define the endgroups and the backbone structure. The GroupAtoms allow flexible definition of the atoms, Cd indicates a double bonded

• group/rate rules/libraries/ etc. (may already be in main documentation)
• degeneracy
• database usage
• small code to generate reactions