Incorrect behavior of kinetic entries

[xiaoruiDong]

Bug Description

Kinetics search on the RMG website can't calculate the reactions rates for some mechanisms, which look like this one:

While their reverse reactions rates can be found:

How to Reproduce

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}

react with

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}

Expected Behavior

RMG can calculate the rates of these reactions

Installation Information

• RMG-website

Additional Context

other examples:

• N2H4_X ⇔ N2H4 + X , in Surface_Adsorption_vdW
• H2_X ⇔ H2 + X , in Surface_Adsorption_vdW
• H_X + NH2_X ⇔ NH3 + X + X , in Surface_Adsorption_Dissociative
• N2H_X ⇔ H_X + N2 , in Surface_EleyRideal_Addition_Multiple_Bond
• X_O2_X ⇔ O2 + X + X , in Surface_Adsorption_Bidentate
• N_X + N_X ⇔ N2 + X + X , in Nitrogen

Originally posted by @Tingchenlee in ReactionMechanismGenerator/RMG-Py#2079

[xiaoruiDong]

@Tingchenlee Hi Ting-Chen, thank you for reporting this issue. The example you showed (and also other examples you mentioned) is a reaction whose kinetics is defined from the reverse direction. That is the reason why you can get the reverse rate coefficient with no problem. In RMG-website's implementation, generate_reverse_rate_coefficient (a method of Reaction) is called to get the forward rate of those reactions. However, many kinetics model defined in the surface.pyx (e.g., StickingCoefficientBEP) don't support this method. Therefore, in order to get those forward rates and visualize them on RMG-website, you need to modify the generate_reverse_rate_coefficient function first. Please let me know after you or someone in your group makes such modifications, and I can help you with further testing. Thanks!