New surface nitrogen families

input/kinetics/families/Surface_Abstraction_Charge_Separation/groups.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Charge_Separation/groups"
+shortDesc = u""
+longDesc = u"""
+Two adsorbates react. One has multiple bonds to the surface, the other has a
+bond to the surface and to some functional group with charge separation
+across the bond. The functional group is transferred to the multiple-bonded
+species.
+
+ *1   *4[-]-*3[+]          *1=*4  *3
+ |||          |      ---->  |      |
+~*2~~ +     ~*5~~         ~*2~ + ~*5~~
+
+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=["Abstracted", "Donated"], ownReverse=False)
+
+reactantNum=2
+productNum=2
+
+recipe(actions=[
+    ['FORM_BOND', '*1', 1, '*4'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['CHANGE_BOND', '*1', 1, '*4'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['LOSE_PAIR','*4','1'],
+    ['GAIN_PAIR', '*3', '1'],
+    ['LOSE_CHARGE','*3','1'],
+    ['GAIN_CHARGE', '*4', '1'],
+])
+
+entry(
+    index = 1,
+    label = "Abstracting",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,[T,Q]}
+2 *2 Xo  u0 p0 c0 {1,[T,Q]}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label="Donating",
+    group =
+"""
+1 *4 R!H u0 p[1,2,3] c-1 {2,S}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,[S,D]} {4,[S,D]}
+3 *5 Xo u0 p0 c0 {2,[S,D]}
+4 R u0 px c0 {2,[S,D]}
+""",
+    kinetics = None,
+)
+
+
+tree(
+"""
+L1: Abstracting
+L1: Donating
+"""
+)
+
+forbidden(
+    label = "Surf",
+    group =
+"""
+1 *4 R!H u0 p[1,2,3] c-1 {2,S} {5,[S,D,T]}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,[S,D]} {4,[S,D]}
+3 *5 Xo u0 p0 c0 {2,[S,D]}
+4 R u0 px c0 {2,[S,D]}
+5 Xo u0 c0 {1,[S,D,T]}
+""",
+)

input/kinetics/families/Surface_Abstraction_Charge_Separation/rules.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Charge_Separation/rules"
+shortDesc = u""
+longDesc = u"""
+"""
+entry(
+    index = 1,
+    label = "Abstracting;Donating",
+    kinetics = SurfaceArrheniusBEP(
+        A = (2.20e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.52,
+        E0 = (126, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data in literature taken from the following papers: 
+
+Ma and Schneider
+https://doi.org/10.1021/acscatal.8b04251
+
+Gomez-Díaz and Lopez
+https://pubs.acs.org/doi/10.1021/jp1093349
+
+Farberow et al.
+https://doi.org/10.1021/cs500668k
+
+Deng et al.
+https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra46544f
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+""",
+)

input/kinetics/families/Surface_Abstraction_Charge_Separation/training/dictionary.txt

@@ -0,0 +1 @@
+

input/kinetics/families/Surface_Abstraction_Charge_Separation/training/reactions.py

@@ -0,0 +1 @@
+

input/kinetics/families/Surface_Abstraction_Charge_Single/groups.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Charge_Single/groups"
+shortDesc = u""
+longDesc = u"""
+Two adsorbates react. One has multiple bonds to the surface, the other has a
+bond to the surface and some functional group with charge separation across it,
+and a functional group with no charge separation. The one with no separation is
+transferred to the multiple-bonded species.
+
+     *1  *4-*3[+]-*6[-]          *1-*4  *3=*6
+     ||      ||           ---->   |      |
+    ~*2~~ + ~*5~~               ~*2~ + ~*5~~
+
+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=["Abstracted", "Donated"], ownReverse=False)
+
+reactantNum=2
+productNum=2
+
+recipe(actions=[
+    ['FORM_BOND', '*1', 1, '*4'],
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['CHANGE_BOND', '*3', 1, '*6'],
+    ['CHANGE_BOND', '*3', -1, '*5'],
+    ['LOSE_PAIR','*6','1'],
+    ['GAIN_PAIR', '*3', '1'],
+    ['LOSE_CHARGE','*3','1'],
+    ['GAIN_CHARGE', '*6', '1'],
+])
+
+entry(
+    index = 1,
+    label = "Abstracting",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,[D,T,Q]}
+2 *2 Xo  u0 p0 c0 {1,[D,T,Q]}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label="Donating",
+    group =
+"""
+1 *4 R u0 px c0 {2,S}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,D} {4,S}
+3 *5 Xo u0 p0 c0 {2,D}
+4 *6 R!H u0 p[1,2,3] c-1 {2,S}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: Abstracting
+L1: Donating
+"""
+)
+
+forbidden(
+    label = "Surface_Atom",
+    group =
+"""
+1 *4 R u0 px c0 {2,S} {5,[S,D,T]}
+2 *3 Val5 u0 p0 c+1 {1,S} {3,D} {4,S}
+3 *5 Xo u0 p0 c0 {2,D}
+4 *6 R!H u0 p[1,2,3] c-1 {2,S}
+5 Xo u0 c0 {1,[S,D,T]}
+""",
+)

input/kinetics/families/Surface_Abstraction_Charge_Single/rules.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Abstraction_Charge_Single/rules"
+shortDesc = u""
+longDesc = u"""
+"""
+entry(
+    index = 1,
+    label = "Abstracting;Donating",
+    kinetics = SurfaceArrheniusBEP(
+        A = (2.20e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.52,
+        E0 = (126, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data in literature taken from the following papers: 
+
+Ma and Schneider
+https://doi.org/10.1021/acscatal.8b04251
+
+Gomez-Díaz and Lopez
+https://pubs.acs.org/doi/10.1021/jp1093349
+
+Farberow et al.
+https://doi.org/10.1021/cs500668k
+
+Deng et al.
+https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra46544f
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+""",
+)

input/kinetics/families/Surface_Abstraction_Charge_Single/training/dictionary.txt

@@ -0,0 +1 @@
+

input/kinetics/families/Surface_Abstraction_Charge_Single/training/reactions.py

@@ -0,0 +1 @@
+

input/kinetics/families/Surface_Adsorption_Single/groups.py

@@ -248,15 +248,15 @@
 """,
 )
 
-forbidden(
-    label = "chargedSpecies",
-    group =
-"""
-1 *1 R u1 c[+1,-1]
-""",
-    shortDesc = u"""""",
-    longDesc =
-u"""
-The adsorbing atom should not have a charge
-""",
-)
+# forbidden(
+#     label = "chargedSpecies",
+#     group =
+# """
+# 1 *1 R u1 c[+1,-1]
+# """,
+#     shortDesc = u"""""",
+#     longDesc =
+# u"""
+# The adsorbing atom should not have a charge
+# """,
+# )

input/kinetics/families/Surface_Dissociation_Charge_Separation/groups.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Dissociation_Charge_Separation/groups"
+shortDesc = u""
+longDesc = u"""
+Surface bond fission of one species into two distinct adsorbates.
+Atom *1 is bonded to the surface (*3). The image below shows a single bond,
+but single and double are possible. What matters is that the bond
+between *1 and *2 must be single and have charge separation across it.
+
+   *1[+]--*2[-]          *1      *2
+    |            ---->    |      ||
+  ~*3~ + ~*4~~           ~*3~ + ~*4~~
+
+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=["Combined", "VacantSite"], products=["Adsorbate1", "Adsorbate2"], ownReverse=False)
+
+reverse = "Surface_Association_Charge_Separation"
+
+reactantNum=2
+productNum=2
+
+recipe(actions=[
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['FORM_BOND', '*2', 1, '*4'],
+    ['CHANGE_BOND', '*2', 1, '*4'],
+    ['LOSE_PAIR','*2','1'],
+    ['GAIN_PAIR', '*1', '1'],
+    ['LOSE_CHARGE','*1','1'],
+    ['GAIN_CHARGE', '*2', '1'],
+])
+
+entry(
+    index = 1,
+    label = "Combined",
+    group =
+"""
+1 *1 Val5 u0 p0 c+1 {2,S} {3,[S,D]}
+2 *2 R!H u0 p[1,2,3] c-1 {1,S}
+3 *3 Xo u0 p0 c0 {1,[S,D]}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label="VacantSite",
+    group =
+"""
+1 *4 Xv u0 p0 c0
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: Combined
+L1: VacantSite
+"""
+)
+
+forbidden(
+    label = "Surf",
+    group =
+"""
+1 *1 Val5 u0 p0 c+1 {2,S} {3,[S,D]}
+2 *2 R!H u0 p[1,2,3] c-1 {1,S} {4,[S,D,T]}
+3 *3 Xo u0 p0 c0 {1,[S,D]}
+4 Xo u0 c0 {2,[S,D,T]}
+""",
+)

input/kinetics/families/Surface_Dissociation_Charge_Separation/rules.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Dissociation_Charge_Separation/rules"
+shortDesc = u""
+longDesc = u"""
+"""
+entry(
+    index = 1,
+    label = "Combined;VacantSite",
+    kinetics = SurfaceArrheniusBEP(
+        A = (9.88e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.52,
+        E0 = (126, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data in literature taken from the following papers: 
+
+Ma and Schneider
+https://doi.org/10.1021/acscatal.8b04251
+
+Gomez-Díaz and Lopez
+https://pubs.acs.org/doi/10.1021/jp1093349
+
+Farberow et al.
+https://doi.org/10.1021/cs500668k
+
+Deng et al.
+https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra46544f
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+"""
+)

input/kinetics/families/Surface_Dissociation_Charge_Separation/training/reactions.py

@@ -0,0 +1,3 @@
+#!/usr/bin/env python
+# encoding: utf-8
+