The seed mechanisms are stored in $RMG/databases/RMG_database/kinetics_libraries/
Currently, the reaction libraries that are included in RMG are:
the Leeds methane oxidation library the GRI-Mech 3.0 mechanism (w/o the nitrogen-containing species and the lumped C3H7 species) the Glarborg combustion mechanism for C1 - C3 species.
One or more species in these mechanisms would normally be forbidden by RMG, which may lead you to get an error message like “The molecular structure ... is forbidden by ...”. To avoid this, use a Primary Thermodynamic Library containing the species, as this will make it allowed. (e.g. the DFT_QCI_thermo library).
The species and reactions contained in the combustion_core\version5 directory correspond to the Leeds methane oxidation mechanism, version 1.5: http://garfield.chem.elte.hu/Combustion/mechanisms/metan15.dat
The species and reactions contained in the GRI-Mech3.0 directory are those reported in the GRI-Mech 3.0 mechanism, with the exception of the following species (and any reaction they participate in):
Any nitrogen-containing species C3H7
RMG cannot currently handle nitrogen atoms, and the C3H7 species in the GRI-Mech 3.0 mechanism is a lumped species, meant to represent n- and iso-propyl radical; RMG treats these two isomers as separate species.
RMG provides the option to use the rate coefficients in the master chemical mechanism developed by Peter Glarborg and coworkers at the Technical University of Denmark. The data are in the directory databases/kinetic_libraries/Glarborg. Within this directory are four subdirectories – C0, C1, C2, and C3 – where the index refers to the carbon number. The mechanisms are hierarchical in nature, so the contents of C0 are contained in C1, C1 in C2, and so forth. The C0 and C1 mechanisms include many small molecule reactions that would not necessarily fit the reaction families of RMG; consequently, they are useful Seed Mechanisms. The C2 and C3 mechanisms are optimized for high-temperature oxidation, and many of the species in the C2 and C3 mechanisms are relevant only for high-temperature chemistry. Therefore, if you are developing a mechanism for low- or moderate-temperature oxidation, it is suggested that you use C2 or C3 as a Primary Kinetic Library, rather than a Seed Mechanism.
One set of kinetics in the Glarborg kinetic_library has been changed: HO2 + OH = H2O + O2. The reason for the change is Glarborg uses the summation of three sets of modified Arrhenius parameters to reproduce their recommended rate coefficient. However, one of the temperature-independent pre-exponential (“A”) factors is negative, which neither RMG nor CHEMKIN can parse properly. Instead, the kinetics of Baulch et al. have been included.
“Evaluated kinetic data for combustion modelling. Supplement I” D.L. Baulch, C.J. Cobos, R.A. Cox, P. Frank, G. Hayman, Th. Just, J.A. Kerr, T. Murrells, M.J. Pilling, J. Troe, R.W. Walker, J. Warnatz J. Phys. Chem. Ref. Data 23 (1994) 847-1033
Details of the mechanism can be obtained in these three papers and references therein.
“Experimental measurements and kinetic modeling of CO/H-2/O-2/NO, conversion at high pressure.” Rasmussen CL, Hanson J, Marshall P, Glarborg P IJCK, 2008, 40, 8, 454-480 DOI: 10.1002/kin.20327
“Experimental Measurements and Kinetic Modeling of CH4/O-2 and CH4/C2H6/O-2 Conversion at High Pressure.” Rasmussen CL, Jakobsen JG, Glarborg P IJCK, 2008, 40, 12, 778-807 DOI: 10.1002/kin.20352
“Experimental and kinetic modeling study of C2H4 oxidation at high pressure.” Lopez JG, Rasmussen CL, Alzueta MU, Gao Y, Marshall P, Glarborg P Proc. Comb. Inst. 2009, 32, 367-375 DOI: 10.1016/j.proci.2008.06.188