Adding new surface families

input/kinetics/families/Surface_Abstraction_Beta_vdW/groups.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Beta_vdW/groups"
+shortDesc = u""
+longDesc = u"""
+Surface abstraction of one atom to another adsorbate. The bond fission occurs not at the binding atom, but in the beta position of the adsorbate, that is the bond between Atom *2 and *3 is broken. Atom *1 binds to the surface (*5). A vdW species is formed. The bond order between *4 and the surface decreases. An example for this reaction is: COOH* + O* = OH* + CO2*. The bond between *2 and *3 must be single.
+
+
+ *1-*2--*3  *4            *1=*2   *3-*4
+  |         ||      ---->   :      |
+~*5~ +    ~*6~~           ~*5~ +  ~*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=["Abstracting", "Donating"], products=["Adsorbate2","Adsorbate3"], ownReverse=False)
+
+reverse = "Surface_Abstraction_reverse_Beta_vdW"
+
+reactantNum=2
+productNum=2
+
+recipe(actions=[
+    ['FORM_BOND', '*3', 1, '*4'],
+    ['BREAK_BOND', '*1', 1, '*5'],
+    ['FORM_BOND', '*1', 0, '*5'],
+    ['CHANGE_BOND', '*1', 1, '*2'],
+    ['BREAK_BOND', '*2', 1, '*3'],
+    ['CHANGE_BOND', '*4',-1,'*6']
+])
+
+entry(
+    index = 1,
+    label = "Donating",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 R   u0 px cx {1,S} {3,S}
+3 *3 R   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label="Abstracting",
+    group =
+"""
+1 *6 Xo  u0 {2,D}
+2 *4 R!H u0 px cx {1,D}	
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 3,
+    label = "R-C-H",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 C u0 px cx {1,S} {3,S}
+3 *3 H   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 4,
+    label = "R-O-H",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 O   u0 p2 cx {1,S} {3,S}
+3 *3 H   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 5,
+    label = "O",
+    group =
+"""
+1 *4 O   u0 p2 c0 {2,D}
+2 *6 Xo  u0 {1,D}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 6,
+    label = "R-CH3",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 C   u0 p0 c0 {1,S} {3,S} {5,S} {6,S}
+3 *3 H   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+5    H   u0 {2,S}
+6    H   u0 {2,S}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: Abstracting
+    L2: O
+L1: Donating
+    L2: R-C-H
+	L3: R-CH3
+    L2: R-O-H
+"""
+)
+
+forbidden(
+    label = "Donating_Bidentate",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 R   u0 px cx {1,S} {3,S}
+3 *3 R   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+5    Xo  u0 
+"""
+)
+
+forbidden(
+    label="Abstracting_Bidentate",
+    group =
+"""
+1 *6 Xo  u0 {2,D}
+2 *4 R!H u0 px cx {1,D}	
+3    Xo  u0 
+"""
+)
+

input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py

@@ -0,0 +1,104 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Beta_vdW/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"""
+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
+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)
+    """
+)
+
+entry(
+    index = 2,
+    label = "O;R-C-H",
+    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"""
+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
+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)
+"""
+)
+
+entry(
+    index = 3,
+    label = "O;R-O-H",
+    kinetics = SurfaceArrheniusBEP(
+        A = (4.18e17, 'm^2/(mol*s)'),
+        n = 0.,
+        alpha =0.65,
+        E0 = (15.4, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+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
+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)
+"""
+)
+
+entry(
+    index = 4,
+    label = "Abstracting;R-CH3",
+    kinetics = SurfaceArrheniusBEP(
+        A = (1.393e17, '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"""
+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
+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)
+Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
+"""
+)
+
+entry(
+    index = 5,
+    label = "O;R-CH3",
+    kinetics = SurfaceArrheniusBEP(
+        A = (1.393e17, '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"""
+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
+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)
+Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms)
+"""
+)