Reaction degeneracy for adsorption reactions has changed

[mazeau]

Because each atom matches the templates, we generated an adosorption reaction for each, and ended up with things like

! Template reaction: Surface_Adsorption_vdW
! Flux pairs: X(1), CH4OX(41); CH3OH(14), CH4OX(41); 
! Exact match found for rate rule (Adsorbate;VacantSite)
! Multiplied by reaction path degeneracy 6
X(1)+CH3OH(14)=CH4OX(41)                            6.000e-01 0.000     0.000  
STICK

but this appears to be fixed now after merging with the Master branch and we get

! Template reaction: Surface_Adsorption_vdW
! Flux pairs: X(1), CH3OH(46); CH3OH(14), CH3OH(46); 
! Exact match found for rate rule [Adsorbate;VacantSite]
! Euclidian distance = 0
! family: Surface_Adsorption_vdW
+X(1)+CH3OH(14)=CH3OH(46)                            1.000e-01 0.000     0.000  
STICK

which is 6 times slower.
This is probably an improvement, but we're reporting it here. It may be causing some changes

[mazeau]

Reaction path degeneracy has changed in other reaction families too.

This example has gone from 6 to 3...

-! Reaction index: Chemkin #15; RMG #33
+! Reaction index: Chemkin #27; RMG #46
 ! Template reaction: Surface_Adsorption_Dissociative
-! Flux pairs: CH3OH(14), CH3OX(39); CH3OH(14), HX(19); 
-! Exact match found for rate rule (Adsorbate;VacantSite1;VacantSite2)
-! Multiplied by reaction path degeneracy 6
-X(1)+X(1)+CH3OH(14)=HX(19)+CH3OX(39)                6.000e-02 0.000     10.000   
+! Flux pairs: CH3OH(14), CH3OX(45); CH3OH(14), HX(19); 
+! Exact match found for rate rule [Adsorbate;VacantSite1;VacantSite2]
+! Euclidian distance = 0
+! Multiplied by reaction path degeneracy 3.0
+! family: Surface_Adsorption_Dissociative
+X(1)+X(1)+CH3OH(14)=CH3OX(45)+HX(19)                3.000e-02 0.000     10.000   
     STICK

The species (45) is actually XCH2OH rather than CH3OX (the X is bonded to the C, not the O). So there are three possible C-H bonds that could have broken during the dissociative adsorption, hence the reaction path degeneracy of 3. ...?

Maybe it used to be 6 because there are two vacant X sites, and you could adsorb either way around....

but what should it be? (and why did it change)

[mazeau]

This one didn't change:

+! Reaction index: Chemkin #34; RMG #327
 ! Template reaction: Surface_Adsorption_Dissociative
-! Flux pairs: OCO(63), CH3OX(39); OCO(63), HOX(23); 
-! Exact match found for rate rule (Adsorbate;VacantSite1;VacantSite2)
-! Multiplied by reaction path degeneracy 4
-X(1)+X(1)+OCO(63)=HOX(23)+CH3OX(39)                 4.000e-02 0.000     10.000   
+! Flux pairs: OCO(139), CH3OX(45); OCO(139), HOX(23); 
+! Exact match found for rate rule [Adsorbate;VacantSite1;VacantSite2]
+! Euclidian distance = 0
+! Multiplied by reaction path degeneracy 4.0
+! family: Surface_Adsorption_Dissociative
+X(1)+X(1)+OCO(139)=CH3OX(45)+HOX(23)                4.000e-02 0.000     10.000   
     STICK

"OCO(139)" is HOCH2OH
"CH3OX(45)" is XCH2OH

two -OH bonds to break, two sites to stick to, four possible combinations, RPD=4.