Formate families

.github/workflows/CI.yml

@@ -37,7 +37,7 @@ concurrency:
 env:
   # if running on RMG-Database but requiring changes on an un-merged branch of RMG-Py, replace
   # main with the name of the branch
-  RMG_PYBRANCH: main
+  RMG_PY_BRANCH: main
   # RMS branch to use for ReactionMechanismSimulator installation
   RMS_BRANCH: for_rmg
   # RMS mode used for install_rms.sh

input/kinetics/families/Surface_Abstraction_vdWBidentate_Beta/groups.py

@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_vdWBidentate_Beta/groups"
+shortDesc = u""
+longDesc = u"""
+Surface abstraction of the beta R!H-R atom of a vdW bidentate by a neighboring surface adsorbate. 
+Example:  [X]~OC(H)O[X] + O=[X]-> OCO.[X] + O[X] + [X]
+The bond fission occurs at the beta position: the R!H-H bond (*2-*4) breaks, and *4 (R) 
+is transferred to the abstracting adsorbate *7, which weakens its own surface bond (*7-*8) upon 
+gaining R. Simultaneously, the *1-*2 bond (O-R) strengthens and *3 (O) detaches from surface 
+site *6, releasing CO2. A vacant site (*6) is produced as a product.
+
+    *4
+     |
+ *1-*2=*3          *7            *1=*2=*3    *7-*4
+  |     :          ||      ---->              |
+~*5~ +~*6~  +     ~*8~~           ~*5~  +   ~*8~~  + ~*6~
+
+The rate, which should be in mol/m2/s,
+will be given by k * (mol/m2) * (mol/m2)
+so k should be in (m2/mol/s). 
+"""
+
+template(reactants=["Donating", "Abstracting"], products=["Adsorbate2","Adsorbate3", "VacantSite"], ownReverse=False)
+
+reverse = "Surface_Abstraction_vdWBidentate_reverse_Beta"
+
+reactantNum=2
+productNum=3
+
+recipe(actions=[
+    ['FORM_BOND', '*4', 1, '*7'],
+    ['CHANGE_BOND', '*7', -1, '*8'],
+    ['CHANGE_BOND', '*1', -1, '*5'],
+    ['CHANGE_BOND', '*1', 1, '*2'],
+    ['CHANGE_BOND', '*3', 1, '*6'],
+    ['BREAK_BOND', '*3', 1, '*6'],
+    ['BREAK_BOND', '*2', 1, '*4'],
+])
+
+entry(
+    index = 1,
+    label = "Donating",
+    group =
+"""
+1 *1 O   u0 p2 {2,S} {5,S}
+2 *2 R!H u0 {1,S} {3,D} {4,S}
+3 *3 O   u0 p2 {2,D} {6,vdW}
+4 *4 R u0 {2,S}
+5 *5 X  u0 {1,S}
+6 *6 X  u0 {3,vdW}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label="Abstracting",
+    group =
+"""
+1 *8 Xo  u0 {2,[D,T,Q]}
+2 *7 R!H u0 px c0 {1,[D,T,Q]}	
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: Abstracting
+L1: Donating
+"""
+)

input/kinetics/families/Surface_Abstraction_vdWBidentate_Beta/rules.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_vdWBidentate_Beta/rules"
+shortDesc = u""
+longDesc = u"""
+"""
+
+entry(
+    index = 1,
+    label = "Abstracting;Donating",
+    kinetics = SurfaceArrheniusBEP(
+        A = (4.18e17, 'm^2/(mol*s)'),
+        n = 0.,
+        alpha = 0.94,
+        E0 = (129.3, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u""" 
+These numbers for the general BEP are from the abstraction reaction of C-H to O.
+BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
+From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
+"""
+)