ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database
Singlet O=O vdW species in Surface_Adsorption_Abstraction_vdW
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Description
As we discussed in #458, the gas phase O2 will be represented as [O][O], which has the following adjaceny list notation:
1 O u1 p2 {2,S}
2 O u1 p2 {1,S}
Since we don’t use the singlet O=O for the gas phase oxygen, do we want the vdW O2 to have this form in Surface_Adsorption_Abstraction_vdW family?
entry(
index = 11,
label = "O=O",
group =
"""
multiplicity [1]
1 *1 Xv u0 p0 c0
2 *2 O u0 p2 c0 {3,D}
3 *3 O u0 p2 c0 {2,D}
""",
kinetics = None,
)
We didn’t add the forbidden entry O=O in Surface_Adsorption_Bidentate family as well, and the following reaction will be created:

For consistency, should we keep all of them or remove the O=O entry
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the Surface_Adsorption_Abstraction_vdW and Surface_Adsorption_Bidentate family definitions, then inspect the O=O entry at index 11 and the related forbidden-entry behavior. Compare these definitions with the [O][O] gas-phase representation and review the linked discussion and generated reaction example. Done means the project has a documented, consistent decision and the affected family entries reflect it.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- database
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100