Remove reaction path degeneracy adjustments in surface families

[bjkreitz]

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Description In our last RMG-Cat meeting, we extensively discussed the concept of reaction path degeneracy and whether we should consider this for surface reactions, too. In the general catalysis community, this effect is not considered in the pre-exponential coefficients. Since RMG applies a reaction path degeneracy by default, it was necessary to create extra nodes in the trees of the reaction families. These extra nodes contained rate rules with pre-exponential coefficients that were divided by the reaction path degeneracy that is later applied by RMG (typically 2 or 3). Based on our discussion, we reached the conclusion that the reaction path degeneracy is necessary to accurately estimate the kinetics of surface reactions. Thus, I removed all the extra nodes in the trees along with their rate rules. This makes the trees less bulky and gets rid of some confusion.

I removed nodes and rules from the following families:

• Surface_Abstraction
• Surface_Abstraction_Beta
• Surface_Abstraction_Beta_Double_vdW
• Surface_Abstraction_Beta_vdW
• Surface_Dissociation
• Surface_Dissociation_Beta
• Surface_Dissociation_Beta_vdW
• Surface_Dissociation_vdW

The only family that still contains pre-exponential coefficients adjusted by the degeneracy is Surface_Adsorption_Dissociative. Sticking coefficients are typically based on empirical estimates and are in the range between 0-1. We decided to turn off degeneracy for sticking coefficients, but I haven't looked into this yet. Once I turn it off in the RMG-Py, I'll go back and remove the extra nodes in this family, too.

Testing I generated a mechanism with and without the degeneracy-corrected nodes for the oxidation of C2H6 over Pt(111). I obtained identical mechanisms for both cases. This result was anticipated since reaction path degeneracy doesn't have a huge impact on the rates.

Review I suggest generating a mechanism with this branch and with the regular branch. The results should be almost the same. Otherwise, please double-check that I haven't accidentally deleted important nodes from the trees. The review should be fairly quick because I didn't make major changes.