Closed bjkreitz closed 3 weeks ago
I think what it does, or used to do, is
I guess a couple of questions.
Oh, one thing that would probably be an improvement would be to replace "[Pt]" with "X" when it reverts to SMILES? Or someone could try to code up your algorithm you describe at https://github.com/ReactionMechanismGenerator/RMG-database/pull/640
X indicates a bond to the surface. It is always on the left hand site of an atom that is bonded to the surface e.g. XCCH2 it means that C is bonded to the surface. If the X is on the right hand side and at the end of a label, it means that this species is physisorbed e.g. H2OX.
Although if the "use names from thermo libraries" works as intended, at least all your species will already be named well.
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Bug Description
When generating mechanisms for surface reactions, there is a bug in the naming of the species in the output file. RMG used to replace the SMILES string of the species for example
C[Pt]
has the labelCH3X(8)
in the final mechanism. This still works for some species. However, for a bunch of species RMG uses now the SMILES string in the final mechanism e.g.[Pt]CC[Pt]
is[Pt]CC[Pt](26)
instead ofC2H4X2(26)
.How To Reproduce
Run the catalysis/ch4_o2 example
Installation Information
Describe your installation method and system information.