GreenGroup/RMG-database — pull request #24 by bbuesser (2013-11-19 20:17:04+00:00)
Title: Adding Nitrogen to RMG-database

This extension brings the following features to RMG-database:

- all thermochemistry and kinetics databases have been extended to explicitly include all hydrogen atoms to be able to determine the lone electron pairs
- a new reaction family intra_NO2_ONO_conversion has been added to account for uni-molecular reactions from nitro- to nitrite species
- a new reaction family lone_electron_pair_bond has been added where a new bond is formed between two reactants solely by the two electrons of a lone electron pair of one of the reactants
- 115 rate rules and 76 functional groups for H_abstraction, 9 rate rules and 83 functional groups for R_Addition_MultipleBond and 58 rate rules and 88 functional groups for Disproportionation have been added following their derivation in the appendix of Robert Ashcraft’s PhD thesis based on data discussed by Dean and Bozzelli ('Gas-Phase Combustion Chemistry' (ISBN: 978-1-4612-7088-1), chapter 2, 'Combustion Chemistry of Nitrogen', Anthony M. Dean, Joseph W. Bozzelli)
- the thermochemistry group additivity values of Robert Ashcraft and nitrogen related values of Benson et al. have been added
- 5 thermochemistry libraries have been added for different atom combinations up to 6 carbon atoms (CH.py (117 species), CHN.py (135 species), CHO.py (386 species), CHON.py (97 species) and CN.py (1 species)) based on the data in Yaws' Critical Property Data for Chemical Engineers and Chemists (Table 30. Heat Capacity of Gas - Organic Compounds, Table 38. Enthalpy of Formation of Gas - Organic Compounds, Table 46. Entropy of Gas - Organic Compounds) found on www.Knovel.com
- a thermochemistry library based on data in the NIST database has been added (NISTThermoLibrary.py, currently 9 species)
- a thermochemistry library based on CCSD(T)F12A/cc-pVXZ-F12//B3LYP/6-311++g(d,p) calculations corrected by Bond Additivity Correction (BAC) has been added (thermo_DFT_CCSDTF12_BAC.py) containing soon more than 430 molecules and radicals, mostly related to nitrogen
- nitrogen has been enabled in the GRI-Mech3.0 mechanism and thermochemistry databases (GRI-Mech3.0-N)
- a kinetics library based on the reactions discussed in the book chapter of Dean and Bozzelli has been created ('Gas-Phase Combustion Chemistry' (ISBN: 978-1-4612-7088-1), chapter 2, 'Combustion Chemistry of Nitrogen', Anthony M. Dean, Joseph W. Bozzelli)
- three new seed mechanisms containing nitrogen (Nitrogen_Glarborg_Gimenez_et_al.py, Nitrogen_Glarborg_Lucassen_et_al.py, Nitrogen_Glarborg_Zhang_et_al.py) have been created based on recent publications by Glarborg et al.