ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

Adding halogen nodes, AtomType for monovalent (non-terminal) atoms

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@rwest is already working on this.

Since Mar 26, 2020.

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Description

This issue is related to halogens PR: https://github.com/ReactionMechanismGenerator/RMG-database/pull/392

When adding halogen atoms to the kinetics trees, I removed halogen atoms (F, Cl, and Br) from the R!H atomtype. Because I made general nodes with [H, Val7] atoms, I needed an atomtype that was not H and not Val7. My thinking was that, since we have more data for H than for Val7 atoms, creating nodes with [H, Val7] would provide better estimates of the kinetics of halogen reactions when data is laking for halogen species. General idea for tree looks like this (where R!H doesn't include Val7):

Screen Shot 2020-03-26 at 2 36 26 PM

So that if there is no data for Val7, the [H,Val7] node would be used.

Alternatively, I could do this:

Screen Shot 2020-03-26 at 2 43 28 PM

But then if there is no data for Val7, the R!H node would be used to estimate kinetics.

I don't think I should remove Val7 from R!H because it literally translates to R not H. I think it would be more appropriate to add a mono-valent atomtype (and a not mono-valent atomtype). The mono-valent atomtype could include H and Val7 (F1s,Cl1s,Br1s). Although this gets a little tricky because Cl and Br can have multiple bonds and exceed octet rule because it has access to d orbitals.

Any thoughts, comments, insight would be greatly appreciated!

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