Halogen kinetics update

[davidfarinajr]

This PR adds some training reactions, regenerates trees, revises some A factors for rate rules, adds some forbidden groups, adds a new halocarbene_CO_dimerization family, and adds training + regenerate tree for 1,3_sigmatropic_rearrangement

[davidfarinajr]

I calculated some training reactions for 1,3_sigmatropic_rearrangement involving a halogen shift and a hydride (bonded to a halogen-bonded carbon) shift (1f15776) , and then regenerated the tree. I constructed the top of the tree by hand here 4bb10e6, the used auto tree gen script to generate extensions. We could make separate 1,3_hydride and 1,3_halogen shift families, put placing the nodes at the top of the tree essentially accomplishes this with the one family.

We are currently overestimating the rates of these types of reactions.

https://rmg.mit.edu/database/kinetics/families/1,3_sigmatropic_rearrangement/rate_rules/reactant1=1%20F%20u0%20p3%20c0%20%7B5,S%7D%0A2%20F%20u0%20p3%20c0%20%7B5,S%7D%0A3%20F%20u0%20p3%20c0%20%7B5,S%7D%0A4%20F%20u0%20p3%20c0%20%7B6,S%7D%0A5%20C%20u0%20p0%20c0%20%7B1,S%7D%20%7B2,S%7D%20%7B3,S%7D%20%7B6,S%7D%0A6%20C%20u0%20p0%20c0%20%7B4,S%7D%20%7B5,S%7D%20%7B7,D%7D%0A7%20C%20u0%20p0%20c0%20%7B6,D%7D%20%7B8,S%7D%20%7B9,S%7D%0A8%20H%20u0%20p0%20c0%20%7B7,S%7D%0A9%20H%20u0%20p0%20c0%20%7B7,S%7D%0A__product1=1%20F%20u0%20p3%20c0%20%7B5,S%7D%0A2%20F%20u0%20p3%20c0%20%7B6,S%7D%0A3%20F%20u0%20p3%20c0%20%7B7,S%7D%0A4%20F%20u0%20p3%20c0%20%7B7,S%7D%0A5%20C%20u0%20p0%20c0%20%7B1,S%7D%20%7B6,S%7D%20%7B8,S%7D%20%7B9,S%7D%0A6%20C%20u0%20p0%20c0%20%7B2,S%7D%20%7B5,S%7D%20%7B7,D%7D%0A7%20C%20u0%20p0%20c0%20%7B3,S%7D%20%7B4,S%7D%20%7B6,D%7D%0A8%20H%20u0%20p0%20c0%20%7B5,S%7D%0A9%20H%20u0%20p0%20c0%20%7B5,S%7D%0A__res=True

Here is the cross validation results for the tree:

tree_cross_val.pdf
tree_cross_validation.csv

[rwest]

@Nora-Khalil what's the status of all David's old PRs for halocarbons? Please can we figure out which to rebase / merge / abandon ?

[Nora-Khalil]

Status_of_Davids_halogen_PRs_.xlsx

[Nora-Khalil]

I will be attempting to rebase my PFAS database on to main in the next week or so. I built this database branching off of David's halogens database, so I think once I rebase the PFAS database, everything that should be integrated in main will be.