Adding surface libraries

input/kinetics/libraries/Surface/Ammonia/Duan_Ni111/dictionary.txt

@@ -0,0 +1,32 @@
+X
+1 X u0 p0 c0
+
+H_X
+1 H u0 p0 c0 {2,S}
+2 X u0 p0 c0 {1,S}
+
+N_X
+1 N u0 p1 c0 {2,T}
+2 X u0 p0 c0 {1,T}
+
+N2
+1 N u0 p1 c0 {2,T}
+2 N u0 p1 c0 {1,T}
+
+NH_X
+1 N u0 p1 c0 {2,S} {3,D}
+2 H u0 p0 c0 {1,S}
+3 X u0 p0 c0 {1,D}
+
+NH2_X
+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}
+
+NH3_X
+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 H u0 p0 c0 {1,S}
+5 X u0 p0 c0

input/kinetics/libraries/Surface/Ammonia/Duan_Ni111/reactions.py

@@ -0,0 +1,163 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Duan_Ni111"
+shortDesc = u""
+longDesc = u"""
+This library is built to import training reactions, based on:
+"Ammonia decomposition on Fe(1 1 0), Co(1 1 1) and 
+Ni(1 1 1) surfaces: A density functional theory study"
+Duan et al. Journal of Molecular Catalysis A: Chemical 357 (2012) 81–86
+https://doi.org/10.1016/j.molcata.2012.01.023
+
+and
+
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+"""
+
+entry(
+    index = 1,
+    label = "NH3_X + X <=> NH2_X + H_X",
+    kinetics = SurfaceArrhenius(
+        A = (4.35E15, 'cm^2/(mol*s)'), 
+        n = 0.0,
+        Ea = (107103.9, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""Surface_Dissociation_vdW""",
+    longDesc = u"""
+"Ammonia decomposition on Fe(1 1 0), Co(1 1 1) and 
+Ni(1 1 1) surfaces: A density functional theory study"
+Duan et al. Journal of Molecular Catalysis A: Chemical 357 (2012) 81–86
+https://doi.org/10.1016/j.molcata.2012.01.023
+
+and
+
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni111 = 3.148E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(-Ea/RT) = 5.35(1/s)/exp(-107103.9(J/mol)/8.314(J/mol/K)/873K) =  1.37E7/s
+  = (1.37E7/s)/3.148E-9(mol/cm^2) = 4.35E15 cm^2/mol/s
+
+Ea = 1.11eV = 107103.9J/mol
+
+This is reaction 1 from Table 2
+""",
+    metal = "Ni",
+    facet = "111",
+)
+
+entry(
+    index = 2,
+    label = "NH2_X + X <=> NH_X + H_X",
+    kinetics = SurfaceArrhenius(
+        A = (8.34E19, 'cm^2/(mol*s)'), 
+        n = 0.0,
+        Ea = (56929.1, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""Surface_Dissociation""",
+    longDesc = u"""
+"Ammonia decomposition on Fe(1 1 0), Co(1 1 1) and 
+Ni(1 1 1) surfaces: A density functional theory study"
+Duan et al. Journal of Molecular Catalysis A: Chemical 357 (2012) 81–86
+https://doi.org/10.1016/j.molcata.2012.01.023
+
+and
+
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni111 = 3.148E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(Ea/RT) = 1.03E8(1/s)/exp(-56929.1(J/mol)/8.314(J/mol/K)/873K) = 2.63E11/s
+  = (2.63E11/s)/3.148E-9(mol/cm^2) = 8.34E19cm^2/mol/s
+
+Ea = 0.59eV = 56929.1J/mol
+
+This is reaction 2 from Table 2  
+""",
+    metal = "Ni",
+    facet = "111",
+)
+
+entry(
+    index = 3,
+    label = "NH_X + X <=> N_X + H_X",
+    kinetics = SurfaceArrhenius(
+        A = (2.46E19, 'cm^2/(mol*s)'), 
+        n = 0.0,
+        Ea = (107103.9, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""Surface_Dissociation""",
+    longDesc = u"""
+"Ammonia decomposition on Fe(1 1 0), Co(1 1 1) and 
+Ni(1 1 1) surfaces: A density functional theory study"
+Duan et al. Journal of Molecular Catalysis A: Chemical 357 (2012) 81–86
+https://doi.org/10.1016/j.molcata.2012.01.023
+
+and
+
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni111 = 3.148E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(-Ea/RT) = 3.02E4(1/s)/exp(-107103.9J/mol / 8.314(J/mol/K)/873K) =  7.74E10/s
+  = (7.74E10/s)/3.148E-9(mol/cm^2) = 2.46E19 cm^2/mol/s
+
+Ea = 1.11eV = 107103.9J/mol
+
+This is reaction 3 from Table 2  
+""",
+    metal = "Ni",
+    facet = "111",
+)
+
+entry(
+    index = 4,
+    label = "N_X + N_X <=> N2 + X + X",
+    kinetics = SurfaceArrhenius(
+        A = (3.62E20, 'cm^2/(mol*s)'),  
+        n = 0.0,
+        Ea = (179471.4, 'J/mol'),  
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""N2 Surface_Adsorption_Dissociative""",
+    longDesc = u"""
+"Ammonia decomposition on Fe(1 1 0), Co(1 1 1) and 
+Ni(1 1 1) surfaces: A density functional theory study"
+Duan et al. Journal of Molecular Catalysis A: Chemical 357 (2012) 81–86
+https://doi.org/10.1016/j.molcata.2012.01.023
+
+and
+
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni111 = 3.148E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(-Ea/RT) = 2.08E1(1/s)/exp(-179471.4(J/mol)/8.314(J/mol/K)/873K) = 1.14E12/s
+  = (1.14E12/s)/3.148E-9(mol/cm^2) = 3.62E20 cm^2/mol/s
+
+Ea = 1.86eV = 179471.4J/mol
+
+This is reaction 4 from Table 2   
+""",
+    metal = "Ni",
+    facet = "111",
+)

input/kinetics/libraries/Surface/Ammonia/Duan_Ni211/dictionary.txt

@@ -0,0 +1,32 @@
+X
+1 X u0 p0 c0
+
+H_X
+1 H u0 p0 c0 {2,S}
+2 X u0 p0 c0 {1,S}
+
+N_X
+1 N u0 p1 c0 {2,T}
+2 X u0 p0 c0 {1,T}
+
+N2
+1 N u0 p1 c0 {2,T}
+2 N u0 p1 c0 {1,T}
+
+NH_X
+1 N u0 p1 c0 {2,S} {3,D}
+2 H u0 p0 c0 {1,S}
+3 X u0 p0 c0 {1,D}
+
+NH2_X
+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}
+
+NH3_X
+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 H u0 p0 c0 {1,S}
+5 X u0 p0 c0

input/kinetics/libraries/Surface/Ammonia/Duan_Ni211/reactions.py

@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Duan_Ni211"
+shortDesc = u""
+longDesc = u"""
+This library is built to import training reactions, based on:
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+"""
+
+entry(
+    index = 1,
+    label = "NH3_X + X <=> NH2_X + H_X",
+    kinetics = SurfaceArrhenius(
+        A = (5.52E19, 'cm^2/(mol*s)'), 
+        n = 0.0,
+        Ea = (63683.4, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""Surface_Dissociation_vdW""",
+    longDesc = u"""
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni211 = 3.339E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(-Ea/RT) = 2.85E7(1/s)/exp(-63683.4(J/mol)/8.314(J/mol/K)/873K) =  1.84E11/s
+  = (1.84E11/s)/3.339E-9(mol/cm^2) = 5.52E19 cm^2/mol/s
+
+Ea = 0.66eV = 63683.4J/mol
+
+This is reaction 1 from Table 2
+""",
+    metal = "Ni",
+    facet = "211",
+)
+
+entry(
+    index = 2,
+    label = "NH2_X + X <=> NH_X + H_X",
+    kinetics = SurfaceArrhenius(
+        A = (2.31E20, 'cm^2/(mol*s)'), 
+        n = 0.0,
+        Ea = (86841, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""Surface_Dissociation""",
+    longDesc = u"""
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni211 = 3.339E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(-Ea/RT) = 4.91E6(1/s)/exp(-86841(J/mol)/8.314(J/mol/K)/873K) = 7.71E11/s
+  = (7.71E11/s)/3.339E-9(mol/cm^2) = 2.31E20 cm^2/mol/s
+
+Ea = 0.9eV = 86841J/mol
+
+This is reaction 2 from Table 2  
+""",
+    metal = "Ni",
+    facet = "211",
+)
+
+entry(
+    index = 3,
+    label = "NH_X + X <=> N_X + H_X",
+    kinetics = SurfaceArrhenius(
+        A = (3.36E21, 'cm^2/(mol*s)'), 
+        n = 0.0,
+        Ea = (100349.6, 'J/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""Surface_Dissociation""",
+    longDesc = u"""
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni211 = 3.339E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(-Ea/RT) = 1.11E7(1/s)/exp(-100349.6(J/mol)/8.314(J/mol/K)/873K) = 1.12E13/s
+  = (1.12E13/s)/3.339E-9(mol/cm^2) = 3.36E21 cm^2/mol/s
+
+Ea = 1.04eV = 100349.6J/mol
+
+This is reaction 3 from Table 2  
+""",
+    metal = "Ni",
+    facet = "211",
+)
+
+entry(
+    index = 4,
+    label = "N_X + N_X <=> N2 + X + X",
+    kinetics = SurfaceArrhenius(
+        A = (4.90E20, 'cm^2/(mol*s)'),  
+        n = 0.0,
+        Ea = (285610.4, 'J/mol'),  
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    shortDesc = u"""N2 Surface_Adsorption_Dissociative""",
+    longDesc = u"""
+"Structure sensitivity of ammonia decomposition 
+over Ni catalysts: A computational and experimental study"
+Duan et al. Fuel Processing Technology 108 (2013) 112–117
+https://doi.org/10.1016/j.fuproc.2012.05.030
+
+This reaction used RMG's surface site density of Ni211 = 3.339E-9(mol/cm^2) to calculate the A factor.
+A = k/exp(-Ea/RT) = 1.33E-5(1/s)/exp(-285610.4(J/mol)/8.314(J/mol/K)/873K) =  1.64E12/s
+  = (1.64E12/s)/3.339E-9(mol/cm^2) = 4.90E20 cm^2/mol/s
+
+Ea = 2.96eV = 285610.4J/mol
+
+This is reaction 4 from Table 2   
+""",
+    metal = "Ni",
+    facet = "211",
+)