diff --git a/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/groups.py b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/groups.py new file mode 100755 index 0000000000..392f689ed9 --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/groups.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Abstraction_vdW_Bidentate_Beta/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 is bonded to the surface (*5). The bond order between *1/*3 and the surface decreases. An example for this reaction is: COH* + CH2* = CO* + CH3*. The bond between *2 and *3 must be single. + + *4 + | + *1-*2=*3 *7 *1=*2=*3 *7-*4 + | : || ----> | +~*5~ +~*6~ + ~*8~~ ~*5~ + ~*8~~ + ~*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=["Donating", "Abstracting"], products=["Adsorbate2","Adsorbate3", "VacantSite"], ownReverse=False) + +reverse = "Surface_Abstraction_vdW_Bidentate_reverse_Beta" + +reactantNum=2 +productNum=3 + +recipe(actions=[ + ['FORM_BOND', '*4', 1, '*7'], + ['CHANGE_BOND', '*7', -1, '*8'], + ['CHANGE_BOND', '*1', -1, '*5'], + ['CHANGE_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*3', 1, '*6'], + ['BREAK_BOND', '*3', 1, '*6'], + ['BREAK_BOND', '*2', 1, '*4'], +]) + +entry( + index = 1, + label = "Donating", + group = +""" +1 *1 O u0 p2 {2,S} {5,S} +2 *2 R!H u0 {1,S} {3,D} {4,S} +3 *3 O u0 p2 {2,D} {6,vdW} +4 *4 R u0 {2,S} +5 *5 X u0 {1,S} +6 *6 X u0 {3,vdW} +""", + kinetics = None, +) + +entry( + index = 2, + label="Abstracting", + group = +""" +1 *8 Xo u0 {2,[D,T,Q]} +2 *7 R!H u0 px c0 {1,[D,T,Q]} +""", + kinetics = None, +) + +tree( +""" +L1: Abstracting +L1: Donating +""" +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/rules.py b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/rules.py new file mode 100644 index 0000000000..5ec08aa9be --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/rules.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Abstraction_vdW_Bidentate_Beta/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""" +These numbers for the general BEP are from the abstraction reaction of C-H to O. +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, DOI:10.1021/jp312593u +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) +""" +) diff --git a/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/template.cdx b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/template.cdx new file mode 100755 index 0000000000..5c379c196c Binary files /dev/null and b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/template.cdx differ diff --git a/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/template.eps b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/template.eps new file mode 100755 index 0000000000..fab2430dea --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/template.eps @@ -0,0 +1,669 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 18.2.0.48 +%%Title: template.eps +%%CreationDate: 26.08.2021 10:30 +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Times-Roman +%%BoundingBox: 104 338 425 386 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2019 PerkinElmer Informatics, Inc. 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sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +8187 +6959 M +8187 6979 l +8001 6979 l +8001 6959 l +cp +f +gr +gs +20 D sl/lW x +40 +/cW x +80 /bW x +54 /hS x +0 0 0 C +np +8372 7087 M +8392 7087 l +8395 7399 l +8375 7399 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/training/dictionary.txt b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/training/dictionary.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/training/reactions.py b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/training/reactions.py new file mode 100644 index 0000000000..4fa90f3a92 --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW_Bidentate_Beta/training/reactions.py @@ -0,0 +1,3 @@ +#!/usr/bin/env python +# encoding: utf-8 + diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/groups.py b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/groups.py new file mode 100644 index 0000000000..3553dc5cb4 --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/groups.py @@ -0,0 +1,53 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_vdW_Bidentate/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, double, and triple are possible. What matters is that the bond between *1 and *2 must be single. + # NOTE: we should probably include vdW, too! + + *1-*2=*3 *1 *2=*3 + | : ----> || | +~*4~ ~*5~~ ~*4~ + ~*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=["Combined"], products=["Adsorbate1", "Adsorbate2"], ownReverse=False) + +reverse = "Surface_Association_vdW_Bidentate" + +reactantNum=1 +productNum=2 + +recipe(actions=[ + ['CHANGE_BOND', '*1', 1, '*4'], + ['BREAK_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*3', 1, '*5'], + ['BREAK_BOND', '*3', 1, '*5'], + ['FORM_BOND', '*2', 1, '*5'], +]) + +entry( + index = 1, + label = "Combined", + group = +""" +1 *1 O u0 p2 {2,S} {4,S} +2 *2 R!H u0 {1,S} {3,D} +3 *3 O u0 p2 {2,D} {5,vdW} +4 *4 X u0 {1,S} +5 *5 X u0 {3,vdW} +""", + kinetics = None, +) + +tree( +""" +L1: Combined +""" +) diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/rules.py b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/rules.py new file mode 100644 index 0000000000..3d393f31f6 --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/rules.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_vdW_Bidentate/rules" +shortDesc = u"" +longDesc = u""" +""" +entry( + index = 1, + label = "Combined", + kinetics = SurfaceArrheniusBEP( + A = (1e13, '1/s'), + n = 0, + alpha = 0.84, + E0 = (44.25, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +E0 and alpha are taken from: +"Universal Brønsted-Evans-Polanyi Relations for C–C, C–O, C–N, N–O, N–N, and O–O Dissociation Reactions" by Wang, ..., Norskov/ Catal. Lett (2011) 141:370-373, DOI: 10.1007/s10562-010-0477-y +(actual value for E0 was 1.92 eV.) +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) + """ +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/template.cdx b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/template.cdx new file mode 100644 index 0000000000..13de059092 Binary files /dev/null and b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/template.cdx differ diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/template.eps b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/template.eps new file mode 100644 index 0000000000..18017e122c --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/template.eps @@ -0,0 +1,545 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 6/4/2019 6:29 PM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Times-Roman +%%BoundingBox: 139 336 401 384 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2018 PerkinElmer Informatics, Inc. 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and 0 ne{ +64 and 0 ne{-0.5}{0.25}ie e 0.75 m}{P 0 e}ie +D 4 -1 r e scalefont setfont m cpt P e M}b +end +%%EndProcSet + +%%EndProlog +chemdict30 begin +/cW 40 def +/bW 80 def +/lW 20 def +/hS 54 def +/sh true def +720 SPe[ +/Helvetica +fD +/Times-Roman +fD]/ft x +2780 6720 M +8020 6720 l +8020 7680 l +2780 7680 l +cp +clip +np +65535 65535 65535 sBg +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +5577 7156 M +4871 7156 l +st +5015 7216 M +5721 7216 l +st +gs +20 sl +5751 7166 5751 7166 5751 +7166 5576 7166 5751 7166 5751 7166 5551 7104 5576 7133 5576 7166 5751 7166 +5551 7104 5551 7104 4 5751 7166 129 Sp +gr +gs +20 sl +4841 7206 4841 7206 4841 +7206 5041 7268 4841 7206 4841 7206 5016 7219 5041 7268 5041 7268 4841 7206 +5016 7206 5016 7206 4 4841 7206 129 Sp +gr +gr +0 4084 7600 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(X)show +gr +0 3062 7000 ts +65535 0 0 C +-227.856 0 M +64 10 0 tx +(1)show +0 10 0 tx +(R)show +gr +0 3435 7000 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +3400 6912 M +3400 6932 l +3097 6932 l +3097 6912 l +cp +f +gr +0 3501 7563 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +0 2840 7600 ts +0 32896 0 C +64 10 0 tx +(3)show +0 10 0 tx +(X)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +3000 7376 M +2980 7376 l +2980 7040 l +3000 7040 l +cp +f +gr +0 7058 7563 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +0 6518 7000 ts +65535 0 0 C +-227.856 0 M +64 10 0 tx +(1)show +0 10 0 tx +(R)show +gr +0 6297 7600 ts +0 32896 0 C +64 10 0 tx +(3)show +0 10 0 tx +(X)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +6492 7376 M +6472 7376 l +6472 7040 l +6492 7040 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +6420 7376 M +6400 7376 l +6400 7040 l +6420 7040 l +cp +f +gr +0 +7743 7600 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(X)show +gr +0 7738 7000 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +7903 7377 M +7883 7377 l +7884 7040 l +7904 7040 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/training/dictionary.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/training/reactions.py b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/training/reactions.py new file mode 100644 index 0000000000..3a048fe6dc --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate/training/reactions.py @@ -0,0 +1,9 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_vdW_Bidentate/training" +shortDesc = u"Reaction kinetics used to generate rate rules" +longDesc = u""" +Put kinetic parameters for specific reactions in this file to use as a +training set for generating rate rules to populate this kinetics family. +""" \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/groups.py b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/groups.py new file mode 100644 index 0000000000..952a545835 --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/groups.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_vdW_Bidentate_Beta/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, double, and triple are possible. What matters is that the bond between *1 and *2 must be single. + # NOTE: we should probably include vdW, too! + + *4 + | + *1-*2=*3 *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=["Combined"], products=["Adsorbate1", "Adsorbate2"], ownReverse=False) + +reverse = "Surface_Association_vdW_Bidentate_Beta" + +reactantNum=1 +productNum=2 + +recipe(actions=[ + ['CHANGE_BOND', '*1', -1, '*5'], + ['CHANGE_BOND', '*1', 1, '*2'], + ['BREAK_BOND', '*2', 1, '*4'], + ['CHANGE_BOND', '*3', 1, '*6'], + ['BREAK_BOND', '*3', 1, '*6'], + ['FORM_BOND', '*4', 1, '*6'], +]) + +entry( + index = 1, + label = "Combined", + group = +""" +1 *1 O u0 p2 {2,S} {5,S} +2 *2 R!H u0 {1,S} {3,D} {4,S} +3 *3 O u0 p2 {2,D} {6,vdW} +4 *4 R u0 {2,S} +5 *5 X u0 {1,S} +6 *6 X u0 {3,vdW} +""", + kinetics = None, +) + +tree( +""" +L1: Combined +""" +) diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/rules.py b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/rules.py new file mode 100644 index 0000000000..f3730d91ba --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/rules.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_vdW_Bidentate_Beta/rules" +shortDesc = u"" +longDesc = u""" +""" +entry( + index = 1, + label = "Combined", + kinetics = SurfaceArrheniusBEP( + A = (1e13, '1/s'), + n = 0, + alpha = 0.84, + E0 = (44.25, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +E0 and alpha are taken from: +"Universal Brønsted-Evans-Polanyi Relations for C–C, C–O, C–N, N–O, N–N, and O–O Dissociation Reactions" by Wang, ..., Norskov/ Catal. Lett (2011) 141:370-373, DOI: 10.1007/s10562-010-0477-y +(actual value for E0 was 1.92 eV.) +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) + """ +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/template.cdx b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/template.cdx new file mode 100644 index 0000000000..13de059092 Binary files /dev/null and b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/template.cdx differ diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/template.eps b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/template.eps new file mode 100644 index 0000000000..18017e122c --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/template.eps @@ -0,0 +1,545 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 6/4/2019 6:29 PM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Times-Roman +%%BoundingBox: 139 336 401 384 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2018 PerkinElmer Informatics, Inc. All rights reserved. +userdict/chemdict30 210 dict put +chemdict30 begin/version 24 def/sv 13 def +/b{bind def}bind def/L{load def}b/R{null def}b/d/def L/a/add L/al/aload L +/as/astore L/at/atan L/cp/closepath L/cv/curveto L/cw/currentlinewidth L +/cpt/currentpoint L/dv/div L/D/dup L/e/exch L/F/false L/f/fill L/fa/forall L +/g/get L/gi/getinterval L/gr/grestore L/gs/gsave L/ie/ifelse L/ix/index L +/l/lineto L/mt/matrix L/M/moveto L/m/mul L/n/neg L/np/newpath L/pb/pathbbox L +/P/pop L/r/roll L/rl/rlineto L/rm/rmoveto L/ro/rotate L/rp/repeat L +/ru/round L/sc/scale L/sl/setlinewidth L/sm/setmatrix L/st/stroke L +/sp/strokepath L/sq/sqrt L/s/sub L/T/true L/tr/transform L/xl/translate L +/xc/exec L/A R/N R/St R/X R/Y R/aL R/bL R/bS R/bd R/bs R/cX R/cY R/ch R/co R +/fB R/fI R/fS R/fZ R/fl R/ft R/iX R/iY R/idx R/lh R/llx R/lly R/lp R/nH R +/nSq R/newdict R/ps R/rad R/rev R/sL R/sba R/sbl R/sbs R/sn R/spa R/tB R +/typ R/urx R/ury R/w R/wF R/xX R/xY R/rBg R/gBg R/bBg R/gry R/rDst R/gDst R 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and 0 ne{ +64 and 0 ne{-0.5}{0.25}ie e 0.75 m}{P 0 e}ie +D 4 -1 r e scalefont setfont m cpt P e M}b +end +%%EndProcSet + +%%EndProlog +chemdict30 begin +/cW 40 def +/bW 80 def +/lW 20 def +/hS 54 def +/sh true def +720 SPe[ +/Helvetica +fD +/Times-Roman +fD]/ft x +2780 6720 M +8020 6720 l +8020 7680 l +2780 7680 l +cp +clip +np +65535 65535 65535 sBg +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +5577 7156 M +4871 7156 l +st +5015 7216 M +5721 7216 l +st +gs +20 sl +5751 7166 5751 7166 5751 +7166 5576 7166 5751 7166 5751 7166 5551 7104 5576 7133 5576 7166 5751 7166 +5551 7104 5551 7104 4 5751 7166 129 Sp +gr +gs +20 sl +4841 7206 4841 7206 4841 +7206 5041 7268 4841 7206 4841 7206 5016 7219 5041 7268 5041 7268 4841 7206 +5016 7206 5016 7206 4 4841 7206 129 Sp +gr +gr +0 4084 7600 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(X)show +gr +0 3062 7000 ts +65535 0 0 C +-227.856 0 M +64 10 0 tx +(1)show +0 10 0 tx +(R)show +gr +0 3435 7000 ts +0 0 65535 C +64 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10 0 tx +(2)show +0 10 0 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +7903 7377 M +7883 7377 l +7884 7040 l +7904 7040 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/training/dictionary.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/training/reactions.py b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/training/reactions.py new file mode 100644 index 0000000000..28c954e974 --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_vdW_Bidentate_Beta/training/reactions.py @@ -0,0 +1,9 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_vdW_Bidentate_Beta/training" +shortDesc = u"Reaction kinetics used to generate rate rules" +longDesc = u""" +Put kinetic parameters for specific reactions in this file to use as a +training set for generating rate rules to populate this kinetics family. +""" \ No newline at end of file diff --git a/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/groups.py b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/groups.py new file mode 100644 index 0000000000..5168540a9b --- /dev/null +++ b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/groups.py @@ -0,0 +1,60 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Monodentate_to_vdW_Bidentate" +shortDesc = u"" +longDesc = u""" +If a monodentate adsorbate has an internal double or triple bond, then it can fall over onto a vacant site, creating a bidentate. + + *1-*2=*3 *1=*2-*3 + | ----> : | +~*4~ + ~*5~~ ~*4~~~~*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=["Monodentate", "VacantSite"], products=["Bidentate"], ownReverse=False) + +reverse = "Surface_vdW_Bidentate_to_Monodentate" + +recipe(actions=[ + ['FORM_BOND', '*3', 1, '*5'], + ['CHANGE_BOND', '*2', -1, '*3'], + ['CHANGE_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*1', -1, '*4'], +]) + +entry( + index = 1, + label = "Monodentate", + group = +""" +1 *1 O u0 p2 {2,S} {4,S} +2 *2 C u0 p0 {1,S} {3,D} +3 *3 O u0 p2 {2,D} +4 *4 Xo u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 2, + label="VacantSite", + group = +""" +1 *5 Xv u0 +""", + kinetics = None, +) + + +tree( +""" +L1: Monodentate + +L1: VacantSite +""" +) + diff --git a/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/rules.py b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/rules.py new file mode 100644 index 0000000000..85bb72f2f5 --- /dev/null +++ b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/rules.py @@ -0,0 +1,35 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Monodentate_to_Bidentate/rules" +shortDesc = u"" +longDesc = u""" +""" +entry( + index = 1, + label = "Monodentate;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (7.15e20, 'cm^2/(mol*s)'), + n = 0.0, + alpha = 0, + E0 = (3, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +Pre-exponential value and E0 are from R6b in Table 2 of "Automatic mechanism generation involving +kinetics of surface reactions with bidentate adsorbates" +Authors: B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith +doi:10.1039/d3dd00184a + +The reaction R6b is + *CHCH2 + * -> *CH*CH2 + +Other monodentate to bidentate reactions in this publication were without reaction barriers. +""" +) + + + diff --git a/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.cdx b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.cdx new file mode 100644 index 0000000000..f9f5b9b74f Binary files /dev/null and b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.cdx differ diff --git a/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.eps b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.eps new file mode 100644 index 0000000000..496a95c73c --- /dev/null +++ b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.eps @@ -0,0 +1,763 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw +%%CreationDate: 11/13/24 +%%BoundingBox: 0 0 222 46 +%%DocumentProcessColors: Cyan Magenta Yellow Black 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a/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.pdf b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.pdf new file mode 100644 index 0000000000..481302dd0f Binary files /dev/null and b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/template.pdf differ diff --git a/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/training/dictionary.txt b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/training/dictionary.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/training/reactions.py b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/training/reactions.py new file mode 100644 index 0000000000..344a324807 --- /dev/null +++ b/input/kinetics/families/Surface_Monodentate_to_vdW_Bidentate/training/reactions.py @@ -0,0 +1,9 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Monodentate_to_vdW_Bidentate/training" +shortDesc = u"Reaction kinetics used to generate rate rules" +longDesc = u""" +Put kinetic parameters for specific reactions in this file to use as a +training set for generating rate rules to populate this kinetics family. +""" \ No newline at end of file diff --git a/input/kinetics/families/recommended.py b/input/kinetics/families/recommended.py index 6d4fd8b43e..88797f845e 100644 --- a/input/kinetics/families/recommended.py +++ b/input/kinetics/families/recommended.py @@ -129,6 +129,10 @@ 'Surface_Abstraction_Charge_Separation', 'Surface_Dissociation_Charge_Separation', 'Surface_Dissociation_Charge_Single', + 'Surface_Monodentate_to_vdW_Bidentate', + 'Surface_Dissociation_vdW_Bidentate', + 'Surface_Dissociation_vdW_Bidentate_Beta', + 'Surface_Abstraction_vdW_Bidentate_Beta', #'Surface_Carbonate_Deposition', #'Surface_Carbonate_F_CO_Decomposition', #'Surface_Carbonate_2F_Decomposition',