From e856d91714946174d8becff73af966b89829af71 Mon Sep 17 00:00:00 2001 From: Matt Johnson Date: Sat, 9 Mar 2024 18:32:23 -0800 Subject: [PATCH] add lithium surface kinetics libraries based on Pynta calculations --- .../libraries/LithiumSurface/dictionary.txt | 143 ++++++++++++++ .../libraries/LithiumSurface/reactions.py | 98 ++++++++++ .../LithiumSurfaceAnalogy/dictionary.txt | 176 ++++++++++++++++++ .../LithiumSurfaceAnalogy/reactions.py | 30 +++ 4 files changed, 447 insertions(+) create mode 100644 input/kinetics/libraries/LithiumSurface/dictionary.txt create mode 100644 input/kinetics/libraries/LithiumSurface/reactions.py create mode 100644 input/kinetics/libraries/LithiumSurfaceAnalogy/dictionary.txt create mode 100644 input/kinetics/libraries/LithiumSurfaceAnalogy/reactions.py diff --git a/input/kinetics/libraries/LithiumSurface/dictionary.txt b/input/kinetics/libraries/LithiumSurface/dictionary.txt new file mode 100644 index 0000000000..a8a1807219 --- /dev/null +++ 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 new file mode 100644 index 0000000000..aa6e6372ea --- /dev/null +++ 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", +) \ No newline at end of file diff --git a/input/kinetics/libraries/LithiumSurfaceAnalogy/dictionary.txt b/input/kinetics/libraries/LithiumSurfaceAnalogy/dictionary.txt new file mode 100644 index 0000000000..d32bf18df8 --- /dev/null +++ b/input/kinetics/libraries/LithiumSurfaceAnalogy/dictionary.txt @@ -0,0 +1,176 @@ + +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} + +LiOCOOCH2CH2CH2CH2OCOOLi +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 C u0 p0 c0 {9,S} {13,S} {14,S} {15,S} +13 H u0 p0 c0 {12,S} +14 H u0 p0 c0 {12,S} +15 C u0 p0 c0 {12,S} {16,S} {17,S} {18,S} +16 H u0 p0 c0 {15,S} +17 H u0 p0 c0 {15,S} +18 O u0 p2 c0 {15,S} {19,S} +19 C u0 p0 c0 {18,S} {20,D} {21,S} +20 O u0 p2 c0 {19,D} +21 O u0 p2 c0 {19,S} {22,S} +22 Li u0 p0 c0 {21,S} + +LiOCOOOCOOLi +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 O u0 p2 c0 {5,S} {7,S} +7 C u0 p0 c0 {6,S} {8,D} {9,S} +8 O u0 p2 c0 {7,D} +9 O u0 p2 c0 {7,S} {10,S} +10 Li u0 p0 c0 {9,S} + diff --git a/input/kinetics/libraries/LithiumSurfaceAnalogy/reactions.py b/input/kinetics/libraries/LithiumSurfaceAnalogy/reactions.py new file mode 100644 index 0000000000..a19251b9db --- /dev/null +++ b/input/kinetics/libraries/LithiumSurfaceAnalogy/reactions.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "LithiumSurfaceAnalogy" +shortDesc = u"" +longDesc = u""" +Analogies to Reactions calculated with BEEF-vdW on Libcc110 with Pynta +""" + +#CFG: O2 is a special case: we need to treat it separately +# reverse of R10 +# entry( +# index = 1, +# label = "LiOCOOCH2CH2X + LiOCOOCH2CH2X <=> LiOCOOCH2CH2CH2CH2OCOOLi + 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"""analogy to LiOCOOCH2CH2X + LiOCOOX <=> LiOCOOCH2CH2OCOOLi + X + X""", +# longDesc = u"""""", +# metal = "Li", +# ) + +# entry( +# index = 2, +# label = "LiOCOOX + LiOCOOX <=> LiOCOOOCOOLi + 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"""analogy to LiOCOOCH2CH2X + LiOCOOX <=> LiOCOOCH2CH2OCOOLi + X + X""", +# longDesc = u"""""", +# metal = "Li", +# ) \ No newline at end of file