Kinetic Search Error of [Pt]ON([Pt])[O] (Surface_Abstraction_vdW family)

[Tingchenlee]

Kinetic Search for this species

multiplicity 2
1 O u0 p2 c0 {3,S} {5,S}
2 O u1 p2 c0 {3,S}
3 N u0 p1 c0 {1,S} {2,S} {4,S}
4 X u0 p0 c0 {3,S}
5 X u0 p0 c0 {1,S} 

Error messages

rmgpy.exceptions.UndeterminableKineticsError: (TemplateReaction(reactants=[Molecule(smiles="[Pt]ON(N([Pt])[O])[O].[Pt]"), Molecule(smiles="O=[Pt]")], products=[Molecule(smiles="[Pt]ON([Pt])[O]"), Molecule(smiles="[Pt]ON([Pt])[O]")], pairs=[], family='Surface_Abstraction_vdW’), 'Kinetics could not be determined. 
Unable to find matching template for reaction <Molecule "[Pt]ON(N([Pt])[O])[O].[Pt]"> + <Molecule "O=[Pt]"> <=> <Molecule "[Pt]ON([Pt])[O]"> + <Molecule "[Pt]ON([Pt])[O]"> in reaction family <KineticsGroups "Surface_Abstraction_vdW/groups">.
Trying to match [<Entry index=1 label="AdsorbateVdW">, <Entry index=2 label="Adsorbate1">] but matched [<Entry index=5 label="*=O">]') 

If you add other reactants in the searching blocks, for example

multiplicity 2
1 O u0 p2 c0 {3,S} {5,S}
2 O u1 p2 c0 {3,S}
3 N u0 p1 c0 {1,S} {2,S} {4,S}
4 X u0 p0 c0 {3,S}
5 X u0 p0 c0 {1,S}

and

1 X u0

or

multiplicity 2
1 O u0 p2 c0 {3,S} {5,S}
2 O u1 p2 c0 {3,S}
3 N u0 p1 c0 {1,S} {2,S} {4,S}
4 X u0 p0 c0 {3,S}
5 X u0 p0 c0 {1,S}

and

1 O u0 p2 c0 {2,D}
2 C u0 p0 c0 {1,D} {3,D}
3 X u0 p0 c0 {2,D}

The results showed up

[Tingchenlee]

The same as [O]O[Pt] species, the error messages were:

rmgpy.exceptions.UndeterminableKineticsError: (TemplateReaction(reactants=[Molecule(smiles="[O]O[O].[Pt]"), Molecule(smiles="O=[Pt]")], products=[Molecule(smiles="[O]O[Pt]"), Molecule(smiles="[O]O[Pt]")], pairs=[], family='Surface_Abstraction_vdW'), 'Kinetics could not be determined. Unable to find matching template for reaction <Molecule "[O]O[O].[Pt]"> + <Molecule "O=[Pt]"> <=> <Molecule "[O]O[Pt]"> + <Molecule "[O]O[Pt]"> in reaction family <KineticsGroups "Surface_Abstraction_vdW/groups">.Trying to match [<Entry index=1 label="AdsorbateVdW">, <Entry index=2 label="Adsorbate1">] but matched [<Entry index=5 label="*=O">]')

The searching function of these two together was ok

multiplicity 2
1 O u0 p2 c0 {2,S} {3,S}
2 O u1 p2 c0 {1,S}
3 X u0 p0 c0 {1,S}

and

1 O u0 p2 c0 {2,D}
2 X u0 p0 c0 {1,D}

[xiaoruiDong]

@Tingchenlee Thanks for reporting this. When searching reactions for a single species (a single input structure), the RMG website will do the search twice: 1. generate reactions with the single reactant; 2. do another generation for bimolecular reactions for the same structure. The issue is in step 2. You can regenerate the bug in RMG-Py by running database.kinetics.generate_reactions_from_families(reactants,) where reactants is a list of two same molecules that have the geometry you posted (e.g., the first adjacency list on this page). So this problem is actually an RMG issue. From the website end, I don't know for catalytic systems do you want to do A + A searches (I found some examples from your post issues). my proposal will be we can forbid all automatic A+A reaction searches on the website for catalytic reactions while still allow A + A search when you manually input two geometries in the search.