Refit Intra R Add Endo/Exocyclic Rate Rules

[kspieks]

This PR adds 1 training reaction to each of the Intra_R_Add_Endocyclic and Intra_R_Add_Exocyclic reaction families and also refits the rate rules. All calculations were done at CCSD(T)-F12a/cc-pVDZ-F12//ωB97X-D3/def2-TZVP and include conformer searches and 1D rotor scans. The notebooks for refitting the rate rules as well as a slide deck that summarizes the improved rate estimate for these reactions is included in the zip file below.

The training reaction added to Intra_R_Add_Exocyclic brings substantial improvements. Previously, the rate rules gave an estimate for k(T=673K) that was over 1000x smaller than the actual rate calculated from TST.

The training reaction added to Intra_R_Add_Endocyclic brings minor improvements. Previously, this training reaction, which just came from group additivity, gave an estimate for k(T=673K) that was ~5x smaller than the actual rate calculated from TST. Note that since the product for this training reaction is chiral, the A-factor had to be multiplied by 2 since the reactant can attack itself from either the top or the bottom (both options are possible and equally likely).

Hopefully these new training reactions and rate rules improve people's mechanisms :)
20220321.zip

[lily90502]

This looks good to me

[kspieks]

For completeness, I actually refit these reaction families when rebasing and pushing using a better list of thermo libraries. The list I used is

thermo_libraries = [
                'heavy_oil_ccsdtf12_1dHR', 'Spiekermann_refining_elementary_reactions', 
                'Klippenstein_Glarborg2016', 'BurkeH2O2', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo',
                'primaryThermoLibrary', 'primaryNS', 'NitrogenCurran', 'NOx2018', 'FFCM1(-)',
                'SulfurLibrary', 'SulfurGlarborgH2S', 'SABIC_aromatics',
            ],

This is the same lists that are given by default in our ATG notebook as well as our ATG script but I also appended my thermo libraries to the front which have very good calculations. I made a mistake the first time I pushed this branch in that I only used 'heavy_oil_ccsdtf12_1dHR', 'primaryThermoLibrary' the first time around.

[amarkpayne]

Thanks for the PR @kspieks ! I'll merge this in as soon as the tests pass

[xiaoruiDong]

Merged as both checks passed