Dissociative adsorption generates wrong flux pairs? #2782
Description
Bug Description
I'm trying to make some flux diagrams for surface mechanisms, and I've noticed a few missing arrows for surface dissocative adsorption. For example, this reaction:
Is missing the arrow from NH3 to HX:
How To Reproduce
The flux diagram is experimental code, but you can see the annotated flux pairs RMG generates for the reaction:
! Reaction index: Chemkin #10; RMG #18
! Template reaction: Surface_Adsorption_Dissociative
! Flux pairs: NH3(8), H2NX(17); X(1), HX(3); X(1), HX(3);
! Estimated using template [Adsorbate;VacantSite1;VacantSite2] for rate rule [N;VacantSite1;VacantSite2]
! Euclidian distance = 1.0
! Multiplied by reaction path degeneracy 3.0
! family: Surface_Adsorption_Dissociative
X(1)+X(1)+NH3(8)<=>HX(3)+H2NX(17) 4.500e-02 0.000 1.195
STICK
Or generate them yourself with this code:
import rmgpy.species
import rmgpy.reaction
my_reaction = rmgpy.reaction.Reaction()
NH3 = rmgpy.species.Species(smiles='N')
X = rmgpy.species.Species().from_adjacency_list(
"""1 X u0 p0 c0"""
)
H2NX = rmgpy.species.Species().from_adjacency_list(
"""1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 X u0 p0 c0 {1,S}"""
)
HX = rmgpy.species.Species().from_adjacency_list(
"""1 H u0 p0 c0 {2,S}
2 X u0 p0 c0 {1,S}"""
)
my_reaction.reactants = [NH3, X, X]
my_reaction.products = [H2NX, HX]
display(my_reaction)
my_reaction.generate_pairs()
for pair in my_reaction.pairs:
print(f'{pair[0].smiles}\t->{pair[1].smiles}')
Expected Behavior
I would expect the NH3 and HX to also be a flux pair, but I also don't know very much about how these pairs get used in other parts of the RMG code and maybe there's a reason it's being done this way?
Installation Information
Describe your installation method and system information.
- OS: Ubuntu 20.04 LTS (in WSL)
- Installation method: source
- RMG version information:
- RMG-Py: 28c096d
- RMG-database: cbc8f9f5a11c179208ad078d4010afc8355698fa