add lithium surface kinetics libraries

based on Pynta calculations
ReactionMechanismGenerator · Mar 29, 2024 · f28e8b0 · f28e8b0
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diff --git a/input/kinetics/libraries/LithiumSurface/dictionary.txt b/input/kinetics/libraries/LithiumSurface/dictionary.txt
@@ -0,0 +1,143 @@
+
+X
+1 X u0 p0 c0
+
+NCCH3
+1 N u0 p1 c0 {2,T}
+2 C u0 p0 c0 {1,T} {3,S}
+3 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
+4 H u0 p0 c0 {3,S}
+5 H u0 p0 c0 {3,S}
+6 H u0 p0 c0 {3,S}
+
+CH3X
+1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,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 {1,S}
+
+NCX
+1 N u0 p1 c0 {2,T}
+2 C u0 p0 c0 {1,T} {3,S}
+3 X u0 p0 c0 {2,S}
+
+HX
+1 H u0 p0 c0 {2,S}
+2 X u0 p0 c0 {1,S}
+
+CH2CNX
+1 C u0 p0 c0 {2,S} {3,S} {4,D}
+2 H u0 p0 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+4 C u0 p0 c0 {1,D} {5,D}
+5 N u0 p1 c0 {4,D} {6,S}
+6 X u0 p0 c0 {5,S}
+
+LiOCOOCH2CH2X
+1 Li u0 p0 c0 {2,S}
+2 O u0 p2 c0 {1,S} {3,S}
+3 C u0 p0 c0 {2,S} {4,D} {5,S}
+4 O u0 p2 c0 {3,D}
+5 O u0 p2 c0 {3,S} {6,S}
+6 C u0 p0 c0 {5,S} {7,S} {8,S} {9,S}
+7 H u0 p0 c0 {6,S}
+8 H u0 p0 c0 {6,S}
+9 C u0 p0 c0 {6,S} {10,S} {11,S} {12,S}
+10 H u0 p0 c0 {9,S}
+11 H u0 p0 c0 {9,S}
+12 X u0 p0 c0 {9,S}
+
+LiOCH2CH2X
+1 Li u0 p0 c0 {2,S}
+2 O u0 p2 c0 {1,S} {3,S}
+3 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
+4 H u0 p0 c0 {3,S}
+5 H u0 p0 c0 {3,S} 
+6 C u0 p0 c0 {3,S} {7,S} {8,S} {9,S}
+7 H u0 p0 c0 {6,S}
+8 H u0 p0 c0 {6,S}
+9 X u0 p0 c0 {6,S}
+
+CO2
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,D}
+3 O u0 p2 c0 {2,D}
+
+C2H4
+1 C u0 p0 c0 {2,D} {3,S} {4,S}
+2 C u0 p0 c0 {1,D} {5,S} {6,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {1,S}
+5 H u0 p0 c0 {2,S}
+6 H u0 p0 c0 {2,S}
+
+LiOCOOX
+1 Li u0 p0 c0 {2,S}
+2 O u0 p2 c0 {1,S} {3,S}
+3 C u0 p0 c0 {2,S} {4,D} {5,S}
+4 O u0 p2 c0 {3,D}
+5 O u0 p2 c0 {3,S} {6,S}
+6 X u0 p0 c0 {5,S}
+
+LiOX 
+1 Li u0 p0 c0 {2,S}
+2 O u0 p2 c0 {1,S} {3,S}
+3 X u0 p0 c0 {2,S}
+
+LiOCOOCH2CH2OCOOLi
+1 Li u0 p0 c0 {2,S}
+2 O u0 p2 c0 {1,S} {3,S}
+3 C u0 p0 c0 {2,S} {4,D} {5,S}
+4 O u0 p2 c0 {3,D}
+5 O u0 p2 c0 {3,S} {6,S}
+6 C u0 p0 c0 {5,S} {7,S} {8,S} {9,S}
+7 H u0 p0 c0 {6,S}
+8 H u0 p0 c0 {6,S}
+9 C u0 p0 c0 {6,S} {10,S} {11,S} {12,S}
+10 H u0 p0 c0 {9,S}
+11 H u0 p0 c0 {9,S}
+12 O u0 p2 c0 {9,S} {13,S}
+13 C u0 p0 c0 {12,S} {14,D} {15,S}
+14 O u0 p2 c0 {13,D}
+15 O u0 p2 c0 {13,S} {16,S}
+16 Li u0 p0 c0 {15,S}
+
+XOCOOX
+1 X u0 p0 c0 {2,S}
+2 O u0 p2 c0 {1,S} {3,S}
+3 C u0 p0 c0 {2,S} {4,D} {5,S}
+4 O u0 p2 c0 {3,D}
+5 O u0 p2 c0 {3,S} {6,S}
+6 X u0 p0 c0 {5,S}
+
+OX
+1 O u0 p2 c0 {2,D}
+2 X u0 p0 c0 {1,D}
+
+LiNCCH3X
+1 Li u0 p0 c0 {2,S}
+2 N u0 p1 c0 {1,S} {3,D}
+3 C u0 p0 c0 {2,D} {4,S} {5,S}
+4 X u0 p0 c0 {3,S}
+5 C u0 p0 c0 {3,S} {6,S} {7,S} {8,S}
+6 H u0 p0 c0 {5,S}
+7 H u0 p0 c0 {5,S}
+8 H u0 p0 c0 {5,S}
+
+LiNX
+1 Li u0 p0 c0 {2,S}
+2 N u0 p1 c0 {1,S} {3,D}
+3 X u0 p0 c0 {2,D}
+
+CH3CX
+1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
+2 H u0 p0 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {1,S}
+5 C u0 p0 c0 {1,S} {6,T}
+6 X u0 p0 c0 {5,T}
+
+
+
+
diff --git a/input/kinetics/libraries/LithiumSurface/reactions.py b/input/kinetics/libraries/LithiumSurface/reactions.py
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "LithiumSurface"
+shortDesc = u""
+longDesc = u"""
+Reactions calculated with BEEF-vdW  on Libcc110 with Pynta
+"""
+
+
+# entry(
+#     index = 1,
+#     label = "NCCH3 + X + X <=> CH3X + NCX",
+#     kinetics = SurfaceArrhenius(A=(7.21071e-50,'m^5/(molecules^2*s)'), n=2.61372, Ea=(-81.9951,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), 
+#                                 Tmax=(2500,'K'), 
+#                                 comment="""Fitted to 50 data points; dA = *|/ 1.09361, dn = +|- 0.0113301, dEa = +|- 0.0787021 kJ/mol"""),
+#     shortDesc = u"""""",
+#     longDesc = u"""""",
+# 	metal = "Li",
+#     facet = "110",
+# )
+
+# entry(
+#     index = 2,
+#     label = "NCCH3 + X + X <=> HX + CH2CNX",
+#     kinetics = SurfaceArrhenius(A=(2.07084e-51,'m^5/(molecules^2*s)'), n=3.09905, Ea=(-37.6145,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), 
+#                                 comment="""Fitted to 50 data points; dA = *|/ 1.1121, dn = +|- 0.0134532, dEa = +|- 0.0934501 kJ/mol"""),
+#     shortDesc = u"""note this was not a target reaction NCCH3 + Li + Li => HX + NCCH2X was targetted and resulting in three TSs for this reaction""",
+#     longDesc = u"""""",
+# 	metal = "Li",
+#     facet = "110",
+# )
+
+entry(
+    index = 3,
+    label = "LiOCOOCH2CH2X <=> CO2 + LiOCH2CH2X",
+    kinetics = SurfaceArrhenius(A=(2.66452e+11,'s^-1'), n=1.27462, Ea=(70.1461,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), 
+                                comment="""Fitted to 50 data points; dA = *|/ 1.11209, dn = +|- 0.0134516, dEa = +|- 0.0934388 kJ/mol"""),
+    shortDesc = u"""""",
+    longDesc = u"""""",
+	metal = "Li",
+    facet = "110",
+)
+
+entry(
+    index = 4,
+    label = "LiOCOOCH2CH2X + X <=> C2H4 + LiOCOOX + X",
+    kinetics = SurfaceArrhenius(A=(3.5183e-07,'m^2/(molecule*s)'), n=0.128046, Ea=(-11.0304,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), 
+                                comment="""Fitted to 50 data points; dA = *|/ 1.05314, dn = +|- 0.00655564, dEa = +|- 0.0455374 kJ/mol"""),
+    shortDesc = u"""""",
+    longDesc = u"""""",
+	metal = "Li",
+    facet = "110",
+)
+
+entry(
+    index = 5,
+    label = "LiOCOOX + X <=> CO2 + LiOX + X",
+    kinetics = SurfaceArrhenius(A=(3.5183e-07,'m^2/(molecule*s)'), n=0.128046, Ea=(-11.0304,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), 
+                                comment="""Fitted to 50 data points; dA = *|/ 1.05314, dn = +|- 0.00655564, dEa = +|- 0.0455374 kJ/mol"""),
+    shortDesc = u"""""",
+    longDesc = u"""""",
+	metal = "Li",
+    facet = "110",
+)
+
+# entry(
+#     index = 6,
+#     label = "LiOCOOCH2CH2X + LiOCOOX <=> LiOCOOCH2CH2OCOOLi + X + X",
+#     kinetics = SurfaceArrhenius(A=(7.76425e-10,'m^2/(molecule*s)'), n=1.17184, Ea=(224.131,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), 
+#                                 comment="""Fitted to 50 data points; dA = *|/ 1.05424, dn = +|- 0.00668821, dEa = +|- 0.0464584 kJ/mol"""),
+#     shortDesc = u"""""",
+#     longDesc = u"""""",
+# 	metal = "Li",
+#     facet = "110",
+# )
+
+entry(
+    index = 7,
+    label = "XOCOOX <=> CO2 + OX + X",
+    kinetics = SurfaceArrhenius(A=(1.10312e+12,'s^-1'), n=0.682037, Ea=(95.3188,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), 
+                                comment="""Fitted to 50 data points; dA = *|/ 1.2104, dn = +|- 0.0241775, dEa = +|- 0.167944 kJ/mol"""),
+    shortDesc = u"""""",
+    longDesc = u"""""",
+	metal = "Li",
+    facet = "110",
+)
+
+entry(
+    index = 8,
+    label = "LiNCCH3X + X <=> LiNX + CH3CX",
+    kinetics = SurfaceArrhenius(A=(7.71978e-11,'m^2/(molecule*s)'), n=1.32625, Ea=(170.986,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), 
+                                comment="""Fitted to 50 data points; dA = *|/ 1.03899, dn = +|- 0.00484281, dEa = +|- 0.0336396 kJ/mol"""),
+    shortDesc = u"""""",
+    longDesc = u"""""",
+	metal = "Li",
+    facet = "110",
+)