diff --git a/families/images/Surface_Abstraction.png b/families/images/Surface_Abstraction.png index 5dc6094528..f5aa527aec 100644 Binary files a/families/images/Surface_Abstraction.png and b/families/images/Surface_Abstraction.png differ diff --git a/families/images/Surface_Abstraction_vdW.png b/families/images/Surface_Abstraction_vdW.png new file mode 100644 index 0000000000..94f0203927 Binary files /dev/null and b/families/images/Surface_Abstraction_vdW.png differ diff --git a/families/images/Surface_Addition_Single_vdW.png b/families/images/Surface_Addition_Single_vdW.png new file mode 100644 index 0000000000..51a5c6c371 Binary files /dev/null and b/families/images/Surface_Addition_Single_vdW.png differ diff --git a/families/images/Surface_Adsorption_Abstraction_vdW.png b/families/images/Surface_Adsorption_Abstraction_vdW.png new file mode 100644 index 0000000000..7c07e1c060 Binary files /dev/null and b/families/images/Surface_Adsorption_Abstraction_vdW.png differ diff --git a/families/images/Surface_Dissociation.png b/families/images/Surface_Dissociation.png index 0b29191d1f..caa61a4ba0 100644 Binary files a/families/images/Surface_Dissociation.png and b/families/images/Surface_Dissociation.png differ diff --git a/families/images/Surface_Dissociation_Double_vdW.png b/families/images/Surface_Dissociation_Double_vdW.png new file mode 100644 index 0000000000..beef9de4cb Binary files /dev/null and b/families/images/Surface_Dissociation_Double_vdW.png differ diff --git a/families/images/Surface_Dissociation_vdW.png b/families/images/Surface_Dissociation_vdW.png index 35a66fe987..73913ca6e1 100644 Binary files a/families/images/Surface_Dissociation_vdW.png and b/families/images/Surface_Dissociation_vdW.png differ diff --git a/families/images/Surface_Dual_Adsorption_vdW.png b/families/images/Surface_Dual_Adsorption_vdW.png new file mode 100644 index 0000000000..d7de4e9a06 Binary files /dev/null and b/families/images/Surface_Dual_Adsorption_vdW.png differ diff --git a/families/images/Surface_EleyRideal_Addition_Multiple_Bond.png b/families/images/Surface_EleyRideal_Addition_Multiple_Bond.png new file mode 100644 index 0000000000..2500fe4e54 Binary files /dev/null and b/families/images/Surface_EleyRideal_Addition_Multiple_Bond.png differ diff --git a/families/images/Surface_Migration.png b/families/images/Surface_Migration.png new file mode 100644 index 0000000000..59ed63c85a Binary files /dev/null and b/families/images/Surface_Migration.png differ diff --git a/families/images/Surface_Recombination_Single.png b/families/images/Surface_Recombination_Single.png new file mode 100644 index 0000000000..db52a381d1 Binary files /dev/null and b/families/images/Surface_Recombination_Single.png differ diff --git a/families/rmg_reaction_families.pdf b/families/rmg_reaction_families.pdf index 173e824ae9..e513fbf113 100644 Binary files a/families/rmg_reaction_families.pdf and b/families/rmg_reaction_families.pdf differ diff --git a/input/kinetics/families/Surface_Abstraction/groups.py b/input/kinetics/families/Surface_Abstraction/groups.py index e6be3bb6a3..8f8f5495cc 100644 --- a/input/kinetics/families/Surface_Abstraction/groups.py +++ b/input/kinetics/families/Surface_Abstraction/groups.py @@ -18,6 +18,9 @@ template(reactants=["Abstracting", "Donating"], products=["Abstracting", "Donating"], ownReverse=True) +reactantNum=2 +productNum=2 + recipe(actions=[ ['FORM_BOND', '*1', 1, '*4'], ['BREAK_BOND', '*3', 1, '*4'], diff --git a/input/kinetics/families/Surface_Abstraction/training/dictionary.txt b/input/kinetics/families/Surface_Abstraction/training/dictionary.txt index dba01f0809..3cd99757ec 100644 --- a/input/kinetics/families/Surface_Abstraction/training/dictionary.txt +++ b/input/kinetics/families/Surface_Abstraction/training/dictionary.txt @@ -16,12 +16,10 @@ CH3X_4 4 H u0 p0 {1,S} 5 *2 X u0 p0 {1,S} - OX_5 1 *5 X u0 p0 c0 {2,D} 2 *3 O u0 p2 c0 {1,D} - CHX_1 1 *1 C u0 p0 {2,S} {3,T} 2 H u0 p0 {1,S} @@ -33,7 +31,6 @@ CH2X_4 3 H u0 p0 {1,S} 4 *2 X u0 p0 {1,D} - CX_1 1 *1 C u0 p0 {2,Q} 2 *2 X u0 p0 {1,Q} @@ -43,3 +40,22 @@ CHX_4 2 *4 H u0 p0 {1,S} 3 *2 X u0 p0 {1,T} +O* +1 *2 X u0 p0 c0 {2,D} +2 *1 O u0 p2 c0 {1,D} + +HCO* +1 O u0 p2 c0 {2,D} +2 *3 C u0 p0 c0 {1,D} {3,S} {4,S} +3 *4 H u0 p0 c0 {2,S} +4 *5 X u0 p0 c0 {2,S} + +OH* +1 *1 O u0 p2 c0 {2,S} {3,S} +2 *4 H u0 p0 c0 {1,S} +3 *2 X u0 p0 c0 {1,S} + +CO* +1 O u0 p2 c0 {2,D} +2 *3 C u0 p0 c0 {1,D} {3,D} +3 *5 X u0 p0 c0 {2,D} \ No newline at end of file diff --git a/input/kinetics/families/Surface_Abstraction/training/reactions.py b/input/kinetics/families/Surface_Abstraction/training/reactions.py index 1341bb3fde..2f6d72c6a6 100644 --- a/input/kinetics/families/Surface_Abstraction/training/reactions.py +++ b/input/kinetics/families/Surface_Abstraction/training/reactions.py @@ -19,7 +19,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), - #rank = 3, + rank = 3, shortDesc = u"""Deutschmann Ni""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -39,7 +39,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), - #rank = 3, + rank = 3, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -80,7 +80,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), - #rank = 3, + rank = 3, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -89,3 +89,21 @@ """ ) +entry( + index = 39, + label = "O* + HCO* <=> OH* + CO*", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(1.0e13, 'm^2/(mol*s)'), + n = 0., + Ea=(0., 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 39 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) diff --git a/input/kinetics/families/Surface_Abstraction_vdW/groups.py b/input/kinetics/families/Surface_Abstraction_vdW/groups.py new file mode 100644 index 0000000000..9fa8ccd969 --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW/groups.py @@ -0,0 +1,125 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Abstraction_vdW/groups" +shortDesc = u"" +longDesc = u""" +A vdW species splitting, adsorbing to the surface, and transferring a functional group to a double, triple, or +quadruple bonded surface species. + + *2-*3 *4 *2 *4-*3 + : || ----> | | +~*1~ + ~*5~~ ~*1~ + ~*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=["AdsorbateVdW","Adsorbate1"], products=["Adsorbate2","Adsorbate3"], ownReverse=False) + +reverse = "Surface_Reverse_Abstraction_vdW" # maybe needs a better name? + +reactantNum=2 +productNum=2 + +recipe(actions=[ + ['BREAK_BOND', '*2', 1, '*3'], + ['FORM_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*4', -1, '*5'], + ['FORM_BOND', '*3', 1, '*4'], +]) + +entry( + index = 1, + label = "AdsorbateVdW", + group = +""" +1 *1 Xv ux px cx +2 *2 R ux px cx {3,S} +3 *3 R ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 2, + label = "Adsorbate1", + group = +""" +1 *5 X ux px cx {2,[D,T,Q]} +2 *4 R!H ux px cx {1,[D,T,Q]} +""", + kinetics = None, +) + +entry( + index = 3, + label = "O-R", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O ux p2 cx {3,S} +3 *3 R ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 4, + label = "C-R", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,S} +3 *3 R ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 5, + label = "O=*", + group = +""" +1 *5 X u0 p0 c0 {2,D} +2 *4 O u0 p2 c0 {1,D} +""", + kinetics = None, +) + +entry( + index = 6, + label = "C=*", + group = +""" +1 *5 X u0 p0 c0 {2,[D,T,Q]} +2 *4 C ux px cx {1,[D,T,Q]} +""", + kinetics = None, +) + +entry( + index = 7, + label = "H-H", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 H u0 p0 c0 {3,S} +3 *3 R ux px cx {2,S} +""", + kinetics = None, +) + +tree( +""" +L1: AdsorbateVdW + L2: H-H + L2: O-R + L2: C-R +L1: Adsorbate1 + L2: O=* + L2: C=* +""" +) diff --git a/input/kinetics/families/Surface_Abstraction_vdW/rules.py b/input/kinetics/families/Surface_Abstraction_vdW/rules.py new file mode 100644 index 0000000000..0be113bd19 --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW/rules.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Abstraction_vdW/rules" +shortDesc = u"" +longDesc = u""" +A vdW double bonded species dissociatively adsorbing to the surface with double +bonds. +""" + +entry( + index = 1, + label = "AdsorbateVdW;Adsorbate1", + kinetics = SurfaceArrheniusBEP( + A = (1.0e13, 'm^2/(mol*s)'), + n = 0, + alpha = 0.5, + E0 = (0, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""Made up""" +) + +# entry( +# index = 2, +# label = "O-H;O=*", +# kinetics = SurfaceArrheniusBEP( +# A = (1e13, 'm^2/(mol*s)'), +# n = 0, +# alpha = 0.65, +# E0 = (2.3060548, 'kcal/mol'), +# Tmin = (200, 'K'), +# Tmax = (3000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 17 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# +# E0 is Ea_fwd - deltaE and A is made up +# """ +# ) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Abstraction_vdW/template.cdx b/input/kinetics/families/Surface_Abstraction_vdW/template.cdx new file mode 100644 index 0000000000..2cc888a1b2 Binary files /dev/null and b/input/kinetics/families/Surface_Abstraction_vdW/template.cdx differ diff --git a/input/kinetics/families/Surface_Abstraction_vdW/template.eps b/input/kinetics/families/Surface_Abstraction_vdW/template.eps new file mode 100644 index 0000000000..dd8c3cbc52 --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW/template.eps @@ -0,0 +1,650 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:21 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 121 342 420 391 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2018 PerkinElmer Informatics, Inc. 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0 l cp +SM st}{Rr SM st}{rO Y M rO rO xl +0 Y X Y rO ac +X Y X 0 rO ac +X 0 0 0 rO ac +rO neg D xl X Y 0 Y rO ac +cp f +Rr st}{Ac st}{OrA gAc}{Ov st}{OrA 1 .4 sc gOv}{Asc LB whf}{Asc gLB} +{Asc gs gLB gr +-1 -1 sc LB whf}{Asc gs gLB gr +-0.4 -0.4 sc LB whf}{Asc LB gs whf gr +np -0.4 -0.4 sc gLB}{Asc DLB -1 -1 sc DLB gs whf gr +np 90 ro gs gDLB gr -1 -1 sc gDLB}{Asc gs -1 -1 sc ZLB whf gr +gs 3.6 12 sc gOv gr +ZLB whf}{Asc gs -1 -1 sc gZLB gr +gs 3.6 12 sc Cr whf gr +gZLB}{0 0 M X Y l SM st}{bW sl 0 0 M X Y l SM st} +{dL 0 0 M X Y l SM st}{OrA 1 16 dv D sc +0 -1 M +0 0 1 0 1 ac +8 0 8 1 1 ac +8 0 16 0 1 ac +16 0 16 -1 1 ac +SM st}{XY D 0 0 dt X Y dt}{XY 2 dv X Y dt}{XY D X Y dt 0 0 M SM cpt xl +2 dv D sc +1 0 M -1 0 l +0 1 M 0 -1 l +Ast}{XY D X Y dt 0 0 M SM cpt xl +2 dv D sc +1 0 M -1 0 l +Ast}{4.5 Aos +1 0 M -1 0 l +0 1 M 0 -1 l +2 0 M 0 0 2 0 360 arc +Ast}{4.5 Aos +1 0 M -1 0 l +2 0 M 0 0 2 0 360 arc +Ast}{2.25 Ath}{1.5 Ath}{1 Ath}{2.25 Aeq}{1.5 Aeq}{1 Aeq}{OrA 1 16 dv D sc +0 -1 M 0 0 l 16 0 l 16 -1 l SM st}{5 Aos +1 -1 M -1 -1 l +0 2 M 0 -2 l +Ast}{5 Aos +1 -1 M -1 -1 l +1 1 M -1 1 l +0 2 M 0 -2 l +Ast}{4.5 Aos +1 0 M -1 0 l +0 1 M 0 -1 l +Ast}{4.5 Aos +1 0 M -1 0 l +Ast}{gRc}{gRr}{Rc blf}{Rr blf}{Ac blf}{Ov blf}{Asc DLB -1 -1 sc DLB gs whf gr +np 90 ro DLB -1 -1 sc DLB blf}{Asc gs -1 -1 sc ZLB blf gr +gs 3.6 12 sc Cr whf gr +ZLB blf}{Asc gs -1 -1 sc ZLB whf gr +gs 3.6 12 sc Cr blf gr +ZLB whf}{Asc LB gs whf gr +np -0.4 -0.4 sc LB blf}{Asc LB gs f gr gs SM st gr +np -0.4 -0.4 sc LB whf}{Asc LB blf}{Asc LB gs f gr gs SM st gr +np -1 -1 sc LB whf}{Ac whf}{OrA gAc}{Ac blf}{Ov whf} +{OrA 1 .4 sc gOv}{Ov blf}{(Rac)Ach}{(Abs)Ach}{(Rel)Ach} +}e 39 s g xc gr}ie}b/DS{np M l st}b +/DD{gs dL DS gr}b/DB{gs 12 OB bW sl np 0 0 M 0 l st gr}b/ap{e 3 ix a +e 2 ix a}b/PT{D 2 4 gi al P OP D 1 sc +o length 6 gt{P 6 g}{e P 8 dv}ie +D lW 2 m lt{P lW 2 m}if +0 e +0 0 +3 -1 r s 3 1 r e s e +0 0 M 1 0 l +0 0 ap M 1 0 ap l +e n e n +0 0 ap M 1 0 ap l +P P}b/DT{gs np PT SM st gr}b +/NH{lW s D hS dv ru +cvi D 0 eq{P 1}if/nH x +D hS nH m s +D 0 lt{P .1 s nH dv}{nH 2 a dv D 0 xl 2 m s nH dv}ie}b +/Bd{D type/arraytype ne{bs e g}if{{P}{{{DS}{DD}{gs 12 OB np +bW 2 dv/bd x +lW 2 dv e D NH e{D bd M bd n l}for +st gr}{gs 12 OB np +lW 2 dv 0 xl NH 1 sc +bW 2 dv wF m nH 1 a dv/bd x +0 1 nH +{D 1 a bd m o o M n l}for SM st gr}{P}{DB}{gs 12 OB +np 0 lW 2 dv o o n M l bW 2 dv +wF m o o l n l +cp f gr}{P}{gs 12 OB/bL x +bW 2 dv D lW lt{P lW}if/bd x np 0 0 M +bL bd 4 m dv ru 2 o o lt{e}if P cvi/nSq x +bL nSq 2 m dv D sc +nSq{.135 .667 .865 .667 1 0 rcurveto +.135 -.667 .865 -.667 1 0 rcurveto}rp SM st gr}{gs 12 OB +np 0 lW 2 dv o o n M l bW 2 dv +wF m o o l n l +cp SM lW 0.8 m sl st gr}{P}{4 2 r gs OP/rad x 1 SA DA gr}{P} +}o 1 g 1 s g e 2 4 gi al P +5 -1 r xc}{al P 8 ix 1 eq{DD}{DS}ie 5 -1 r 2 eq{DB}{DS}ie P}{DT}}o 0 g g xc}b +/ed{gs cpt np cw 2 dv 0 360 arc f gr}b +/SPe{gs 0 e xl 1 1 S dv D n sc CMT currentmatrix P lW sl 4.0 setmiterlimit +np}b/ws{Wd 0 32 4 -1 roll widthshow}b/blank/Times-Roman findfont/CharStrings +g/space g d/mv 256 array d/NUL/SOH/STX/ETX/EOT/ENQ/ACK/BEL/BS/HT/LF/VT +/FF/CR/SO/SI +/DLE/DC1/DC2/DC3/DC4/NAK/SYN/ETB/CAN/EM/SUB/ESC/FS/GS/RS/US +mv 0 32 gi as P +mv 32/Times-Roman findfont/Encoding get +32 96 gi putinterval +mv 39/quotesingle put +mv 96/grave put/unknown/unknown/quotesinglbase/florin/quotedblbase/ellipsis +/dagger/daggerdbl +/circumflex/perthousand/Scaron/guilsinglleft/OE/unknown/unknown/unknown +/unknown/quoteleft/quoteright/quotedblleft/quotedblright/bullet/endash +/emdash +/tilde/trademark/scaron/guilsinglright/oe/unknown/unknown/Ydieresis +/blank/exclamdown/cent/sterling/currency/yen/brokenbar/section +/dieresis/copyright/ordfeminine/guillemotleft/logicalnot/hyphen/registered +/macron +/degree/plusminus/twosuperior/threesuperior/acute/mu/paragraph +/periodcentered +/cedilla/onesuperior/ordmasculine/guillemotright/onequarter/onehalf +/threequarters/questiondown +/Agrave/Aacute/Acircumflex/Atilde/Adieresis/Aring/AE/Ccedilla +/Egrave/Eacute/Ecircumflex/Edieresis/Igrave/Iacute/Icircumflex/Idieresis +/Eth/Ntilde/Ograve/Oacute/Ocircumflex/Otilde/Odieresis/multiply +/Oslash/Ugrave/Uacute/Ucircumflex/Udieresis/Yacute/Thorn/germandbls +/agrave/aacute/acircumflex/atilde/adieresis/aring/ae/ccedilla +/egrave/eacute/ecircumflex/edieresis/igrave/iacute/icircumflex/idieresis +/eth/ntilde/ograve/oacute/ocircumflex/otilde/odieresis/divide +/oslash/ugrave/uacute/ucircumflex/udieresis/yacute/thorn/ydieresis +mv 128 128 gi as P/fSt 50 string d(ChemDraw)fSt copy P/fD{D/Symbol eq{ +findfont[1 0 0 -1 0 0]makefont}{D {findfont}stopped{/Helvetica findfont}if +D length dict/newdict x{ +1 index/FID ne{1 index/FontMatrix eq{[1 0 0 -1 0 0]matrix concatmatrix}if +newdict 3 1 r put}{P P}ie}forall +newdict/Encoding mv put +fSt 8 fSt length 8 sub gi cvs length 8 add +fSt 0 rot gi cvn newdict definefont}ie}b/ts{gs xl ro 0 0 M}b +/nl{0 e xl 0 0 M}b/tx{ft e g e sf m rot D 96 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 +733 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +2420 6840 M +8400 6840 l +8400 7820 l +2420 7820 l +cp +clip +np +65535 65535 65535 sBg +0 3731 7424 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +5698 7310 M +4992 7310 l +st +5136 7370 M +5842 7370 l +st +gs +20 sl +5872 7320 +5872 7320 5872 7320 5697 7320 5872 7320 5872 7320 5672 7258 5697 7287 5697 +7320 5872 7320 5672 7258 5672 7258 4 5872 7320 129 Sp +gr +gs +20 sl +4962 7360 +4962 7360 4962 7360 5162 7422 4962 7360 4962 7360 5137 7372 5162 7422 5162 +7422 4962 7360 5137 7360 5137 7360 4 4962 7360 129 Sp +gr +gr +0 4308 7736 ts +65535 32896 0 C +64 10 0 tx +(5)show +0 10 0 tx +(X)show +gr +0 4296 7136 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(R)show +gr +0 6307 7135 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +0 6319 7735 ts +65535 0 0 C +64 10 0 tx +(1)show +0 10 0 tx +(X)show +gr +0 2706 7109 ts +0 0 65535 C +-227.856 0 M +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +0 2728 7761 ts +65535 0 0 C +64 10 0 tx +(1)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 +4407 7175 M +4427 7175 l +4430 7514 l +4410 7515 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +4479 7175 M +4499 7174 l +4502 7514 l +4482 7514 l +cp +f +gr +0 +3086 7127 ts +0 32896 0 C +64 10 1 tx +(3)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +3053 7034 M +3053 7054 l +2741 7044 l +2742 7024 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7537 M +2867 7537 l +2867 7488 l +2887 7488 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7440 M +2867 7440 l +2867 7392 l +2887 7392 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 +0 0 C +np +2887 7343 M +2867 7343 l +2867 7295 l +2887 7295 l +cp +f +gr +gs +20 +D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7247 M +2867 7247 l +2867 +7198 l +2887 7198 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7150 M +2867 7150 l +2867 7102 l +2887 7102 l +cp +f +gr +gs +20 D sl/lW x +40 +/cW x +80 /bW x +54 /hS x +0 0 0 C +np +6454 7175 M +6474 7175 l +6478 7511 l +6458 +7511 l +cp +f +gr +0 6960 7424 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +0 8116 7136 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(R)show +gr +0 8128 7736 ts +65535 32896 0 C +64 10 0 tx +(5)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 +8263 7175 M +8283 7175 l +8287 7514 l +8267 7514 l +cp +f +gr +0 7750 7154 ts +0 32896 0 C +-227.856 0 M +64 10 1 tx +(3)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +7785 7082 M +7785 7062 l +8078 7053 l +8079 7073 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Abstraction_vdW/training/dictionary.txt b/input/kinetics/families/Surface_Abstraction_vdW/training/dictionary.txt new file mode 100644 index 0000000000..b6276f36cf --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW/training/dictionary.txt @@ -0,0 +1,62 @@ +OH_2* +1 *2 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 *1 X u0 p0 c0 {1,S} + +OH_4* +1 *4 O u0 p2 c0 {2,S} {3,S} +2 *3 H u0 p0 c0 {1,S} +3 *5 X u0 p0 c0 {1,S} + +H2O* +1 *2 O u0 p2 c0 {2,S} {3,S} +2 *3 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 *1 X u0 p0 c0 + +O* +1 *4 O u0 p2 c0 {2,D} +2 *5 X u0 p0 c0 {1,D} + +HCO* +1 O u0 p2 c0 {2,D} +2 *4 C u0 p0 c0 {1,D} {3,S} {4,S} +3 *3 H u0 p0 c0 {2,S} +4 *5 X u0 p0 c0 {2,S} + +CO* +1 O u0 p2 c0 {2,D} +2 *4 C u0 p0 c0 {1,D} {3,D} +3 *5 X u0 p0 c0 {2,D} + +HCOO* +1 *2 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 *1 X u0 p0 c0 {1,S} + +HCOOH* +1 *2 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 *3 H u0 p0 c0 {1,S} +6 *1 X u0 p0 c0 + +CH3O* +1 *2 O u0 p2 c0 {2,S} {6,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 *1 X u0 p0 c0 {1,S} + +CH3OH* +1 *2 O u0 p2 c0 {2,S} {6,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 *3 H u0 p0 c0 {1,S} +7 *1 X u0 p0 c0 \ No newline at end of file diff --git a/input/kinetics/families/Surface_Abstraction_vdW/training/reactions.py b/input/kinetics/families/Surface_Abstraction_vdW/training/reactions.py new file mode 100644 index 0000000000..cdcb75245a --- /dev/null +++ b/input/kinetics/families/Surface_Abstraction_vdW/training/reactions.py @@ -0,0 +1,85 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Abstraction_vdW/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. +""" + +# entry( +# index = 16, +# label = "OH_2* + OH_4* <=> H2O* + O*", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A = (1.675e12, 'm^2/(mol*s)'), +# n = 0., +# Ea = (14.0669343, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 16 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +# entry( +# index = 40, +# label = "OH_2* + HCO* <=> H2O* + CO*", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A = (9.597e12, 'm^2/(mol*s)'), +# n = 0., +# Ea = (6.9181644, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 40 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +# entry( +# index = 41, +# label = "HCOO* + HCO* <=> HCOOH* + CO*", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A = (2.2e14, 'm^2/(mol*s)'), +# n = 0., +# Ea = (13.8363288, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 41 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +# entry( +# index = 45, +# label = "CH3O* + HCO* <=> CH3OH* + CO*", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A = (1.934e12, 'm^2/(mol*s)'), +# n = 0., +# Ea = (8.76300824, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 45 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Addition_Single_vdW/groups.py b/input/kinetics/families/Surface_Addition_Single_vdW/groups.py new file mode 100644 index 0000000000..46ee0042c8 --- /dev/null +++ b/input/kinetics/families/Surface_Addition_Single_vdW/groups.py @@ -0,0 +1,193 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Addition_Single_vdW/groups" +shortDesc = u"" +longDesc = u""" +A single bonded surface species adding to a vdW double, triple, or quadruple bonded species and adsorbing to a surface. + +*2=*3 *4 *2-*3-*4 + : + | ----> | + +~*1~ ~*5~ ~*1~ ~*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=["AdsorbateVdW","Adsorbate1"], products=["VacantSite","Adsorbate2"], ownReverse=False) + +reverse = "Surface_Deletion_Single_vdW" + +reactantNum=2 +productNum=2 + +recipe(actions=[ + ['FORM_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*2', -1, '*3'], + ['FORM_BOND', '*3', 1, '*4'], + ['BREAK_BOND', '*4', 1, '*5'], +]) + +entry( + index = 1, + label = "AdsorbateVdW", + group = +""" +1 *1 Xv ux px cx +2 *2 R!H ux px cx {3,[D,T,Q]} +3 *3 R!H ux px cx {2,[D,T,Q]} +""", + kinetics = None, +) + +entry( + index = 2, + label = "Adsorbate1", + group = +""" +1 *5 X ux px cx {2,S} +2 *4 R ux px cx {1,S} +""", + kinetics = None, +) + +entry( + index = 3, + label = "O=R", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O ux p2 cx {3,D} +3 *3 R!H ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 4, + label = "C=R", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,[D,T,Q]} +3 *3 R!H ux px cx {2,[D,T,Q]} +""", + kinetics = None, +) + +entry( + index = 5, + label = "O=C=O", + group = +""" +1 O u0 p2 c0 {3,D} +2 *2 O u0 p2 c0 {3,D} +3 *3 C u0 p0 c0 {1,D} {2,D} +4 *1 Xv u0 p0 c0 +""", + kinetics = None, +) + +entry( + index = 6, + label = "H", + group = +""" +1 *5 X u0 p0 c0 {2,S} +2 *4 H u0 p0 c0 {1,S} +""", + kinetics = None, +) + +entry( + index = 7, + label = "O=C", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O ux p2 cx {3,D} +3 *3 C ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 8, + label = "O", + group = +""" +1 *5 X u0 p0 c0 {2,S} +2 *4 O u0 px c0 {1,S} +""", + kinetics = None, +) + +entry( + index = 9, + label = "OH", + group = +""" +1 *5 X u0 p0 c0 {2,S} +2 *4 O u0 p2 c0 {1,S} {3,S} +3 H u0 p0 c0 {2,S} +""", + kinetics = None, +) + +entry( + index = 10, + label = "C=O", + group = +""" +1 *1 Xv u0 p0 c0 +2 *3 O ux p2 cx {3,D} +3 *2 C ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 5, + label = "CO2", + group = +""" +1 O u0 p2 c0 {3,D} +2 *3 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,D} {2,D} +4 *1 Xv u0 p0 c0 +""", + kinetics = None, +) + +tree( +""" +L1: AdsorbateVdW + L2: C=R + L3: C=O + L4: CO2 + L2: O=R + L3: O=C + L4: O=C=O +L1: Adsorbate1 + L2: H + L2: O + L3: OH +""" +) + +# forbidden( +# label = "O=C", +# group = +# """ +# 1 *1 Xv ux px cx +# 2 *2 O ux px cx {3,D} +# 3 *3 C ux px cx {2,D} +# """, +# shortDesc = u"""""", +# longDesc =u""" +# Any O=C should not match *2 and *3 respectively because of duplicate reactions +# """, +# ) + diff --git a/input/kinetics/families/Surface_Addition_Single_vdW/rules.py b/input/kinetics/families/Surface_Addition_Single_vdW/rules.py new file mode 100644 index 0000000000..41fbc1b178 --- /dev/null +++ b/input/kinetics/families/Surface_Addition_Single_vdW/rules.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Addition_Single_vdW/rules" +shortDesc = u"" +longDesc = u""" +A single bonded surface species adding to a vdW double, triple, or quadruple bonded species and adsorbing to a surface. +""" + +# entry( +# index = 1, +# label = "AdsorbateVdW;Adsorbate1", +# kinetics = SurfaceArrheniusBEP( +# A = (1.0e13, 'm^2/(mol*s)'), +# n = 0, +# alpha = 0.5, +# E0 = (5, 'kcal/mol'), +# Tmin = (200, 'K'), +# Tmax = (3000, 'K'), +# ), +# rank = 5, +# shortDesc = u"""Default""", +# longDesc = u"""Made up""" +# ) + +entry( + index = 2, + label = "O=C=O;H", + kinetics = SurfaceArrheniusBEP( + A = (3.658e13, 'm^2/(mol*s)'), + n = 0, + alpha = 0.31, + E0 = (20.0626768, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 17 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d + +E0 is Ea +""" +) + +entry( + index = 3, + label = "O=C;H", + kinetics = SurfaceArrheniusBEP( + A = (1.815e13, 'm^2/(mol*s)'), + n = 0, + alpha = 0.37, + E0 = (5.53453152, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 24 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d + +E0 is Ea +""" +) + +entry( + index = 4, + label = "C=O;H", + kinetics = SurfaceArrheniusBEP( + A = (9.518e14, 'm^2/(mol*s)'), + n = 0, + alpha = 0.58, + E0 = (18.9096494, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 31 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d + +E0 is Ea +""" +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Addition_Single_vdW/template.cdx b/input/kinetics/families/Surface_Addition_Single_vdW/template.cdx new file mode 100644 index 0000000000..0c5d04882d Binary files /dev/null and b/input/kinetics/families/Surface_Addition_Single_vdW/template.cdx differ diff --git a/input/kinetics/families/Surface_Addition_Single_vdW/template.eps b/input/kinetics/families/Surface_Addition_Single_vdW/template.eps new file mode 100644 index 0000000000..d04cc48ac3 --- /dev/null +++ b/input/kinetics/families/Surface_Addition_Single_vdW/template.eps @@ -0,0 +1,648 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:23 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 121 347 447 398 +%%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 +745 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +2420 6940 M +8940 6940 l +8940 7960 l +2420 7960 l +cp +clip +np +65535 65535 65535 sBg +0 3719 7561 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +5671 7447 M +4965 7447 l +st +5109 7507 M +5815 7507 l +st +gs +20 sl +5845 7457 +5845 7457 5845 7457 5670 7457 5845 7457 5845 7457 5645 7395 5670 7424 5670 +7457 5845 7457 5645 7395 5645 7395 4 5845 7457 129 Sp +gr +gs +20 sl +4935 7497 +4935 7497 4935 7497 5135 7559 4935 7497 4935 7497 5110 7509 5135 7559 5135 +7559 4935 7497 5110 7497 5110 7497 4 4935 7497 129 Sp +gr +gr +0 4288 7873 ts +65535 32896 0 C +64 10 0 tx +(5)show +0 10 0 tx +(X)show +gr +0 4276 7272 ts +65535 0 65535 C +64 10 0 tx 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+7435 7185 M +7435 7205 l +7137 7206 l +7137 7186 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Addition_Single_vdW/training/dictionary.txt b/input/kinetics/families/Surface_Addition_Single_vdW/training/dictionary.txt new file mode 100644 index 0000000000..6803061dd7 --- /dev/null +++ b/input/kinetics/families/Surface_Addition_Single_vdW/training/dictionary.txt @@ -0,0 +1,93 @@ +H* +1 *5 X u0 p0 c0 {2,S} +2 *4 H u0 p0 c0 {1,S} + +CO2* +1 O u0 p2 c0 {3,D} +2 *2 O u0 p2 c0 {3,D} +3 *3 C u0 p0 c0 {1,D} {2,D} +4 *1 X u0 p0 c0 + +Cu5 +1 *5 X u0 p0 c0 + +HCOO* +1 *2 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 *3 C u0 p0 c0 {1,S} {2,D} {4,S} +4 *4 H u0 p0 c0 {3,S} +5 *1 X u0 p0 c0 {1,S} + +CH3O2* +1 *4 O u0 p2 c0 {3,S} {6,S} +2 *2 O u0 p2 c0 {3,S} {7,S} +3 *3 C u0 p0 c0 {1,S} {2,S} {4,S} {5,S} +4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {1,S} +7 *1 X u0 p0 c0 {2,S} + +CH2O* +1 *2 O u0 p2 c0 {2,D} +2 *3 C u0 p0 c0 {1,D} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 *1 X u0 p0 c0 + +OH* +1 *4 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 *5 X u0 p0 c0 {1,S} + +CH3O* +1 *2 O u0 p2 c0 {2,S} {6,S} +2 *3 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 *4 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 *1 X u0 p0 c0 {1,S} + +COOH* +1 *3 O u0 p2 c0 {3,S} {4,S} +2 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,S} {2,D} {5,S} +4 *4 H u0 p0 c0 {1,S} +5 *1 X u0 p0 c0 {3,S} + +CO2_2* +1 O u0 p2 c0 {3,D} +2 *3 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,D} {2,D} +4 *1 X u0 p0 c0 + +CH2O_2* +1 *3 O u0 p2 c0 {2,D} +2 *2 C u0 p0 c0 {1,D} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 *1 X u0 p0 c0 + +CH2OH* +1 *3 O u0 p2 c0 {2,S} {5,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 *4 H u0 p0 c0 {1,S} +6 *1 X u0 p0 c0 {2,S} + +HCOOH* +1 O u0 p2 c0 {3,S} {5,S} +2 *2 O u0 p2 c0 {3,D} +3 *3 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {1,S} +6 *1 X u0 p0 c0 + +CH3O2_2* +1 O u0 p2 c0 {3,S} {6,S} +2 *2 O u0 p2 c0 {3,S} {7,S} +3 *3 C u0 p0 c0 {1,S} {2,S} {4,S} {5,S} +4 *4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {1,S} +7 *1 X u0 p0 c0 {2,S} \ No newline at end of file diff --git a/input/kinetics/families/Surface_Addition_Single_vdW/training/reactions.py b/input/kinetics/families/Surface_Addition_Single_vdW/training/reactions.py new file mode 100644 index 0000000000..f2c4eed9b1 --- /dev/null +++ b/input/kinetics/families/Surface_Addition_Single_vdW/training/reactions.py @@ -0,0 +1,124 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Addition_Single_vdW/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. +""" + +# entry( +# index = 11, +# label = "COOH* + Cu5 <=> CO2_2* + H*", +# degeneracy = 2, +# kinetics = SurfaceArrhenius( +# A = (2.3626e13, 'm^2/(mol*s)'), +# n = 0., +# Ea = (28.3644741, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 11 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +entry( + index = 17, + label = "CO2* + H* <=> HCOO* + Cu5", + degeneracy = 2, + kinetics = SurfaceArrhenius( + A = (3.658e13, 'm^2/(mol*s)'), + n = 0., + Ea = (20.0626768, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 17 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +entry( + index = 20, + label = "HCOOH* + H* <=> CH3O2_2* + Cu5", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A = (6.244e14, 'm^2/(mol*s)'), + n = 0., + Ea = (23.9829699, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 20 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +# throws a quantity error if left in +# entry( +# index = 23, +# label = "CH3O2* + Cu5 <=> CH2O* + OH*", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A = (1.001e13, 'm^2/(mol*s)'), +# n = 0., +# Ea = (17.0648055, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 23 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +entry( + index = 24, + label = "CH2O* + H* <=> CH3O* + Cu5", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A = (1.815e13, 'm^2/(mol*s)'), + n = 0., + Ea = (5.53453152, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 24 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +# entry( +# index = 31, +# label = "CH2O_2* + H* <=> CH2OH* + Cu5", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A = (9.518e14, 'm^2/(mol*s)'), +# n = 0., +# Ea = (18.9096494, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 31 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/groups.py b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/groups.py new file mode 100644 index 0000000000..a8bd21d657 --- /dev/null +++ b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/groups.py @@ -0,0 +1,186 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Adsorption_Abstraction_vdW/groups" +shortDesc = u"" +longDesc = u""" +Adsorbtion of a vdw species to the surface with a surface species. + +*2=*3 *4-*5 *2-*3-*5 *4 + : + | ----> | + || +~*1~ ~*6~ ~*1~~ ~*6~ + +The rate, which should be in mol/m2/s, +will be given by k * (mol/m2) * (mol/m3) +so k should be in (m3/mol/s). We will use sticking coefficients. +""" + +template(reactants=["AdsorbateVdW", "Adsorbate1"], products=["Adsorbate2","Adsorbate3"], ownReverse=False) + +reverse = "Surface_Desorption_Abstraction_vdW" + +reactantNum=2 +productNum=2 + +recipe(actions=[ + ['CHANGE_BOND', '*2', -1, '*3'], + ['FORM_BOND', '*1', 1, '*2'], + ['BREAK_BOND', '*4', 1, '*5'], + ['FORM_BOND', '*3', 1, '*5'], + ['CHANGE_BOND', '*4', 1, '*6'], +]) + +entry( + index = 1, + label = "AdsorbateVdW", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 R!H ux px cx {3,[D,T]} +3 *3 R!H ux px cx {2,[D,T]} + +""", + kinetics = None, +) + +entry( + index = 2, + label="Adsorbate1", + group = +""" +1 *6 Xo ux px cx {2,S} +2 *4 R!H ux px cx {1,S} {3,S} +3 *5 R ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 3, + label = "O=", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O ux px cx {3,D} +3 *3 R!H ux px cx {2,D} + +""", + kinetics = None, +) + +entry( + index = 4, + label = "C", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,[D,T]} +3 *3 R!H ux px cx {2,[D,T]} + +""", + kinetics = None, +) + +entry( + index = 5, + label = "O=C", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O ux px cx {3,D} +3 *3 C ux px cx {2,D} + +""", + kinetics = None, +) + +entry( + index = 6, + label = "O=O", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O u0 p2 c0 {3,D} +3 *3 O u0 p2 c0 {2,D} + +""", + kinetics = None, +) + +entry( + index = 7, + label = "C=", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,D} +3 *3 R!H ux px cx {2,D} + +""", + kinetics = None, +) + +entry( + index = 8, + label = "C#", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,T} +3 *3 R!H ux px cx {2,T} + +""", + kinetics = None, +) + +entry( + index = 9, + label="C-R", + group = +""" +1 *6 Xo u0 p0 c0 {2,S} +2 *4 C ux px cx {1,S} {3,S} +3 *5 R ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 10, + label="O-R", + group = +""" +1 *6 Xo u0 p0 c0 {2,S} +2 *4 O u0 p2 c0 {1,S} {3,S} +3 *5 R ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 11, + label="C-H", + group = +""" +1 *6 Xo u0 p0 c0 {2,S} +2 *4 C u0 p0 c0 {1,S} {3,S} +3 *5 H u0 p0 c0 {2,S} +""", + kinetics = None, +) + +tree( +""" +L1: AdsorbateVdW + L2: O= + L3: O=C + L3: O=O + L2: C + L3: C= + L3: C# +L1: Adsorbate1 + L2: C-R + L3: C-H + L2: O-R +""" +) diff --git a/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/rules.py b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/rules.py new file mode 100644 index 0000000000..6077aa19cf --- /dev/null +++ b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/rules.py @@ -0,0 +1,49 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Adsorption_Abstraction_vdW/rules" +shortDesc = u"" +longDesc = u""" +Adsorbtion of a vdw species to the surface with a surface species.""" + +entry( + index = 43, + label = "AdsorbateVdW;Adsorbate1", + kinetics = SurfaceArrheniusBEP( + A = (5.43e11, 'm^2/(mol*s)'), + n = 0, + alpha = 0.42, + E0 = (9.68543017, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 2, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 43 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d + +E0 is Ea +""" +) + +# entry( +# index = 43, +# label = "O=C;C-H", +# kinetics = StickingArrheniusBEP( +# A = (5.43e11, 'm^2/(mol*s)'), +# n = 0, +# alpha = 0.42, +# E0 = (9.68543017, 'kcal/mol'), +# Tmin = (200, 'K'), +# Tmax = (3000, 'K'), +# ), +# rank = 2, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 43 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# +# E0 is Ea +# """ +# ) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/template.cdx b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/template.cdx new file mode 100644 index 0000000000..c88859f671 Binary files /dev/null and b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/template.cdx differ diff --git a/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/template.eps b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/template.eps new file mode 100644 index 0000000000..66dbef8367 --- /dev/null +++ b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/template.eps @@ -0,0 +1,706 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:26 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 121 341 439 390 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2018 PerkinElmer Informatics, Inc. 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+/Agrave/Aacute/Acircumflex/Atilde/Adieresis/Aring/AE/Ccedilla +/Egrave/Eacute/Ecircumflex/Edieresis/Igrave/Iacute/Icircumflex/Idieresis +/Eth/Ntilde/Ograve/Oacute/Ocircumflex/Otilde/Odieresis/multiply +/Oslash/Ugrave/Uacute/Ucircumflex/Udieresis/Yacute/Thorn/germandbls +/agrave/aacute/acircumflex/atilde/adieresis/aring/ae/ccedilla +/egrave/eacute/ecircumflex/edieresis/igrave/iacute/icircumflex/idieresis +/eth/ntilde/ograve/oacute/ocircumflex/otilde/odieresis/divide +/oslash/ugrave/uacute/ucircumflex/udieresis/yacute/thorn/ydieresis +mv 128 128 gi as P/fSt 50 string d(ChemDraw)fSt copy P/fD{D/Symbol eq{ +findfont[1 0 0 -1 0 0]makefont}{D {findfont}stopped{/Helvetica findfont}if +D length dict/newdict x{ +1 index/FID ne{1 index/FontMatrix eq{[1 0 0 -1 0 0]matrix concatmatrix}if +newdict 3 1 r put}{P P}ie}forall +newdict/Encoding mv put +fSt 8 fSt length 8 sub gi cvs length 8 add +fSt 0 rot gi cvn newdict definefont}ie}b/ts{gs xl ro 0 0 M}b +/nl{0 e xl 0 0 M}b/tx{ft e g e sf m rot D 96 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 +731 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +2420 6820 M +8780 6820 l +8780 7800 l +2420 7800 l +cp +clip +np +65535 65535 65535 sBg +0 3618 7417 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +5968 7303 M +5262 7303 l +st +5406 7363 M +6112 7363 l +st +gs +20 sl +6142 7313 +6142 7313 6142 7313 5967 7313 6142 7313 6142 7313 5942 7251 5967 7280 5967 +7313 6142 7313 5942 7251 5942 7251 4 6142 7313 129 Sp +gr +gs +20 sl +5232 7353 +5232 7353 5232 7353 5432 7415 5232 7353 5232 7353 5407 7366 5432 7415 5432 +7415 5232 7353 5407 7353 5407 7353 4 5232 7353 129 Sp +gr +gr +0 4087 7729 ts +0 +65535 65535 C +64 10 0 tx +(6)show +0 10 0 tx +(X)show +gr +0 4075 7128 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(R)show +gr +0 6470 7129 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +0 6482 7729 ts +65535 0 0 C +64 10 0 tx +(1)show +0 10 0 tx +(X)show +gr +0 2479 7103 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +0 2728 7755 ts +65535 0 0 C +64 10 0 tx +(1)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 +4222 7168 M +4242 7168 l +4246 7504 l +4226 7505 l +cp +f +gr +0 3081 7104 ts +0 32896 0 C +64 10 +1 tx +(3)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7530 M +2867 7530 l +2867 7482 l +2887 7482 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7433 M +2867 7433 l +2867 7385 l +2887 7385 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7337 M +2867 7337 l +2867 7288 l +2887 7288 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 +0 0 C +np +2887 7240 M +2867 7240 l +2867 7192 l +2887 7192 l +cp +f +gr +gs +20 +D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7143 M +2867 7143 l +2867 +7101 l +2887 7101 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +6616 7168 M +6636 7168 l +6640 7504 l +6620 7504 l +cp +f +gr +0 8051 7403 ts +0 +0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +0 8508 7128 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(R)show +gr +0 8520 7729 ts +0 65535 65535 C +64 10 0 tx +(6)show +0 10 0 tx +(X)show +gr +0 7071 7130 ts +0 32896 0 C +64 10 1 tx +(3)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +3048 6980 M +3048 7000 l +2742 6999 l +2743 6979 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +3048 7052 M +3048 7072 l +2742 7071 l +2742 7051 l +cp +f +gr +0 +4682 7146 ts +65535 32896 0 C +64 10 1 tx +(5)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +4649 7053 M +4648 7073 l +4338 7063 l +4338 7044 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +7038 7042 M +7038 7062 l +6733 7061 l +6733 7041 l +cp +f +gr +0 +7671 7131 ts +65535 32896 0 C +64 10 1 tx +(5)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +7638 7043 M +7638 7063 l +7334 7062 l +7334 7042 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +8715 7504 M +8695 7504 l +8691 7167 l +8711 7167 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +8643 7505 M +8623 7505 l +8619 7168 l +8639 7168 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/training/dictionary.txt b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/training/dictionary.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/training/reactions.py b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/training/reactions.py new file mode 100644 index 0000000000..0d4459fee3 --- /dev/null +++ b/input/kinetics/families/Surface_Adsorption_Abstraction_vdW/training/reactions.py @@ -0,0 +1,9 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Adsorption_Abstraction_vdW/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. +""" diff --git a/input/kinetics/families/Surface_Dissociation/groups.py b/input/kinetics/families/Surface_Dissociation/groups.py index ec738f3f16..e359d0001c 100644 --- a/input/kinetics/families/Surface_Dissociation/groups.py +++ b/input/kinetics/families/Surface_Dissociation/groups.py @@ -21,6 +21,9 @@ reverse = "Surface_Association" +reactantNum=2 +productNum=2 + recipe(actions=[ ['FORM_BOND', '*2', 1, '*4'], ['CHANGE_BOND', '*1', 1, '*3'], @@ -49,11 +52,87 @@ kinetics = None, ) +entry( + index = 3, + label = "C", + group = +""" +1 *1 C u0 {2,S} {3,[S,D,T]} +2 *2 R u0 {1,S} +3 *3 Xo u0 {1,[S,D,T]} +""", + kinetics = None, +) + +entry( + index = 4, + label = "O", + group = +""" +1 *1 O u0 {2,S} {3,S} +2 *2 R u0 {1,S} +3 *3 Xo u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 5, + label = "C-H", + group = +""" +1 *1 C u0 {2,S} {3,[S,D,T]} +2 *2 H u0 {1,S} +3 *3 Xo u0 {1,[S,D,T]} +""", + kinetics = None, +) + +entry( + index = 6, + label = "C-O", + group = +""" +1 *1 C u0 {2,S} {3,[S,D,T]} +2 *2 O u0 {1,S} +3 *3 Xo u0 {1,[S,D,T]} +""", + kinetics = None, +) + +entry( + index = 7, + label = "O-H", + group = +""" +1 *1 O u0 {2,S} {3,S} +2 *2 H u0 {1,S} +3 *3 Xo u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 8, + label = "O-C", + group = +""" +1 *1 O u0 {2,S} {3,S} +2 *2 C u0 {1,S} +3 *3 Xo u0 {1,S} +""", + kinetics = None, +) tree( """ L1: Combined - + L2: C + L3: C-H + L3: C-O + L2: O + L3: O-H + L3: O-C L1: VacantSite """ ) diff --git a/input/kinetics/families/Surface_Dissociation/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation/training/dictionary.txt index 5f33ad0db5..602b363b33 100644 --- a/input/kinetics/families/Surface_Dissociation/training/dictionary.txt +++ b/input/kinetics/families/Surface_Dissociation/training/dictionary.txt @@ -18,7 +18,6 @@ HX_5 1 *2 H u0 p0 {2,S} 2 *4 X u0 p0 {1,S} - CHX_3 1 *1 C u0 p0 {2,S} {3,T} 2 H u0 p0 {1,S} @@ -30,13 +29,11 @@ CH2X_1 3 H u0 p0 {1,S} 4 *3 X u0 p0 {1,D} - HOX_1 1 *1 O u0 p2 {2,S} {3,S} 2 *2 H u0 p0 {1,S} 3 *3 X u0 p0 {1,S} - OX_3 1 *1 X u0 p0 c0 {2,D} 2 *3 O u0 p2 c0 {1,D} @@ -53,28 +50,67 @@ OCX_3 2 O u0 p2 {1,D} 3 *3 X u0 p0 {1,D} - HOX_5 1 *2 O u0 p2 {2,S} {3,S} 2 H u0 p0 {1,S} 3 *4 X u0 p0 {1,S} - CXHO_1 1 *1 C u0 p0 {2,D} {3,S} {4,S} 2 O u0 p2 {1,D} 3 *2 H u0 p0 {1,S} 4 *3 X u0 p0 {1,S} - - CHX_1 1 *1 C u0 p0 {2,S} {3,T} 2 *2 H u0 p0 {1,S} 3 *3 X u0 p0 {1,T} - CX_3 1 *1 C u0 p0 {2,Q} 2 *3 X u0 p0 {1,Q} +HCO* +1 O u0 p2 c0 {2,D} +2 *2 C u0 p0 c0 {1,D} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 *4 X u0 p0 c0 {2,S} + +HCOO* +1 *1 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 *3 X u0 p0 c0 {1,S} + +HCOH* +1 O u0 p2 c0 {2,S} {4,S} +2 *1 C u0 p0 c0 {1,S} {3,S} {5,D} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {1,S} +5 *3 X u0 p0 c0 {2,D} + +CH2OH* +1 O u0 p2 c0 {2,S} {5,S} +2 *1 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S} +3 *2 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {1,S} +6 *3 X u0 p0 c0 {2,S} + +CH3O2* +1 O u0 p2 c0 {3,S} {6,S} +2 *2 O u0 p2 c0 {3,S} {7,S} +3 *2 C u0 p0 c0 {1,S} {2,S} {4,S} {5,S} +4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {1,S} +7 *3 X u0 p0 c0 {2,S} + +CH2OH*_2 +1 O u0 p2 c0 {2,S} {5,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {1,S} +6 *3 X u0 p0 c0 {2,S} \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation/training/reactions.py b/input/kinetics/families/Surface_Dissociation/training/reactions.py index 21c25e2273..382903f560 100644 --- a/input/kinetics/families/Surface_Dissociation/training/reactions.py +++ b/input/kinetics/families/Surface_Dissociation/training/reactions.py @@ -8,6 +8,44 @@ training set for generating rate rules to populate this kinetics family. """ +entry( + index = 10, + label = "OCX_3 + HOX_5 <=> HOCXO_1 + Ni_4", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(4.667E11, 'm^2/(mol*s)'), + n = 0.0, + Ea=(12.9139069, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 10 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +entry( + index = 15, + label = "HOX_1 + Ni_4 <=> OX_3 + HX_5", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(2.193E13, 'm^2/(mol*s)'), + n = 0.0, + Ea=(38.7417207, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 15 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + entry( index = 16, label = "CH2X_3 + HX_5 <=> CH3X_1 + Ni_4", @@ -19,6 +57,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), + rank=1, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -39,6 +78,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), + rank=1, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -59,6 +99,7 @@ # Tmin = (298, 'K'), # Tmax = (2000, 'K'), # ), +# rank = 1, # shortDesc = u"""Default""", # longDesc = u""" #"Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -78,6 +119,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), + rank=1, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -86,7 +128,62 @@ """ ) +entry( + index = 26, + label = "OCX_3 + HX_5 <=> CXHO_1 + Ni_4", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(9.240E12, 'm^2/(mol*s)'), + n = 0.0, + Ea=(22.8299425, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank=1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 26 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +entry( + index = 28, + label = "HCOO* + Ni_4 <=> HCO* + OX_3", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(2.570E12, 'm^2/(mol*s)'), + n = 0.0, + Ea=(10.8384576, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank=1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 28 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) +entry( + index = 31, + label = "HCOH* + HX_5 <=> CH2OH* + Ni_4", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(3.698E12, 'm^2/(mol*s)'), + n = 0.0, + Ea=(54.4228933, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank=1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 32 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) entry( index = 32, @@ -99,6 +196,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), + rank=1, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -107,6 +205,24 @@ """ ) +# entry( +# index = 36, +# label = "CH3O2* + Ni_4 <=> CH2OH*_2 + OX_3", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A=(5.485E13, 'm^2/(mol*s)'), +# n = 0.0, +# Ea=(46.3517015, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 36 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) entry( index = 44, @@ -119,6 +235,7 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), + rank=1, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" @@ -139,10 +256,11 @@ Tmin = (298, 'K'), Tmax = (2000, 'K'), ), + rank=1, shortDesc = u"""Default""", longDesc = u""" "Surface Reaction Kinetics of Steam- and CO2-Reforming as well as Oxidation of Methane over Nickel-Based Catalysts" Delgado et al Catalysts, 2015, 5, 871-904. Reaction R8 """ -) +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation_Double_vdW/groups.py b/input/kinetics/families/Surface_Dissociation_Double_vdW/groups.py new file mode 100644 index 0000000000..b61a266743 --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_Double_vdW/groups.py @@ -0,0 +1,117 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_Double_vdW/groups" +shortDesc = u"" +longDesc = u""" +A vdW double bonded species dissociatively adsorbing to the surface with double +bonds. + +*2=*3 *2 *3 + : + ----> || + || +~*1~ ~*4~ ~*1~ ~*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=["AdsorbateVdW","VacantSite"], products=["Adsorbate1","Adsorbate2"], ownReverse=False) + +reverse = "Surface_Association_Double_vdW" + +reactantNum=2 +productNum=2 + +recipe(actions=[ + ['FORM_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*2', -1, '*3'], + ['BREAK_BOND', '*2', 1, '*3'], + ['FORM_BOND', '*3', 1, '*4'], + ['CHANGE_BOND', '*3', 1, '*4'], +]) + +entry( + index = 1, + label = "AdsorbateVdW", + group = +""" +1 *1 Xv ux px cx +2 *2 R!H ux px cx {3,D} +3 *3 R!H ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 2, + label = "VacantSite", + group = +""" +1 *4 Xv u0 p0 c0 +""", + kinetics = None, +) + +entry( + index = 3, + label = "C=C", + group = +""" +1 *1 Xv ux px cx +2 *2 C ux px cx {3,D} +3 *3 C ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 4, + label = "C=O", + group = +""" +1 *1 Xv ux px cx +2 *2 C ux px cx {3,D} +3 *3 O ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 5, + label = "O=C=O", + group = +""" +1 O u0 p2 c0 {3,D} +2 *3 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,D} {2,D} +4 *1 Xv u0 p0 c0 +""", + kinetics = None, +) + +tree( +""" +L1: AdsorbateVdW + L2: C=C + L2: C=O + L3: O=C=O +L1: VacantSite +""" +) + +forbidden( + label = "O=C", + group = +""" +1 *1 Xv ux px cx +2 *2 O ux px cx {3,D} +3 *3 C ux px cx {2,D} +""", + shortDesc = u"""""", + longDesc =u""" +Any O=C should not match *2 and *3 respectively because of duplicate reactions +""", +) diff --git a/input/kinetics/families/Surface_Dissociation_Double_vdW/rules.py b/input/kinetics/families/Surface_Dissociation_Double_vdW/rules.py new file mode 100644 index 0000000000..90cae9c36c --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_Double_vdW/rules.py @@ -0,0 +1,25 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_Double_vdW/rules" +shortDesc = u"" +longDesc = u""" +A vdW double bonded species dissociatively adsorbing to the surface with double +bonds. +""" + +entry( + index = 1, + label = "AdsorbateVdW;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (1.0e13, 'm^2/(mol*s)'), + n = 0, + alpha = 0.44, + E0 = (0, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""Made up""" +) diff --git a/input/kinetics/families/Surface_Dissociation_Double_vdW/template.cdx b/input/kinetics/families/Surface_Dissociation_Double_vdW/template.cdx new file mode 100644 index 0000000000..66d0fa1975 Binary files /dev/null and b/input/kinetics/families/Surface_Dissociation_Double_vdW/template.cdx differ diff --git a/input/kinetics/families/Surface_Dissociation_Double_vdW/template.eps b/input/kinetics/families/Surface_Dissociation_Double_vdW/template.eps new file mode 100644 index 0000000000..daec5264cb --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_Double_vdW/template.eps @@ -0,0 +1,634 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:29 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 121 341 439 390 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2018 PerkinElmer Informatics, Inc. 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s D hS dv ru +cvi D 0 eq{P 1}if/nH x +D hS nH m s +D 0 lt{P .1 s nH dv}{nH 2 a dv D 0 xl 2 m s nH dv}ie}b +/Bd{D type/arraytype ne{bs e g}if{{P}{{{DS}{DD}{gs 12 OB np +bW 2 dv/bd x +lW 2 dv e D NH e{D bd M bd n l}for +st gr}{gs 12 OB np +lW 2 dv 0 xl NH 1 sc +bW 2 dv wF m nH 1 a dv/bd x +0 1 nH +{D 1 a bd m o o M n l}for SM st gr}{P}{DB}{gs 12 OB +np 0 lW 2 dv o o n M l bW 2 dv +wF m o o l n l +cp f gr}{P}{gs 12 OB/bL x +bW 2 dv D lW lt{P lW}if/bd x np 0 0 M +bL bd 4 m dv ru 2 o o lt{e}if P cvi/nSq x +bL nSq 2 m dv D sc +nSq{.135 .667 .865 .667 1 0 rcurveto +.135 -.667 .865 -.667 1 0 rcurveto}rp SM st gr}{gs 12 OB +np 0 lW 2 dv o o n M l bW 2 dv +wF m o o l n l +cp SM lW 0.8 m sl st gr}{P}{4 2 r gs OP/rad x 1 SA DA gr}{P} +}o 1 g 1 s g e 2 4 gi al P +5 -1 r xc}{al P 8 ix 1 eq{DD}{DS}ie 5 -1 r 2 eq{DB}{DS}ie P}{DT}}o 0 g g xc}b +/ed{gs cpt np cw 2 dv 0 360 arc f gr}b +/SPe{gs 0 e xl 1 1 S dv D n sc CMT currentmatrix P lW sl 4.0 setmiterlimit +np}b/ws{Wd 0 32 4 -1 roll widthshow}b/blank/Times-Roman findfont/CharStrings +g/space g d/mv 256 array d/NUL/SOH/STX/ETX/EOT/ENQ/ACK/BEL/BS/HT/LF/VT +/FF/CR/SO/SI +/DLE/DC1/DC2/DC3/DC4/NAK/SYN/ETB/CAN/EM/SUB/ESC/FS/GS/RS/US +mv 0 32 gi as P +mv 32/Times-Roman findfont/Encoding get +32 96 gi putinterval +mv 39/quotesingle put +mv 96/grave put/unknown/unknown/quotesinglbase/florin/quotedblbase/ellipsis +/dagger/daggerdbl +/circumflex/perthousand/Scaron/guilsinglleft/OE/unknown/unknown/unknown +/unknown/quoteleft/quoteright/quotedblleft/quotedblright/bullet/endash +/emdash +/tilde/trademark/scaron/guilsinglright/oe/unknown/unknown/Ydieresis +/blank/exclamdown/cent/sterling/currency/yen/brokenbar/section +/dieresis/copyright/ordfeminine/guillemotleft/logicalnot/hyphen/registered +/macron +/degree/plusminus/twosuperior/threesuperior/acute/mu/paragraph +/periodcentered +/cedilla/onesuperior/ordmasculine/guillemotright/onequarter/onehalf +/threequarters/questiondown +/Agrave/Aacute/Acircumflex/Atilde/Adieresis/Aring/AE/Ccedilla +/Egrave/Eacute/Ecircumflex/Edieresis/Igrave/Iacute/Icircumflex/Idieresis +/Eth/Ntilde/Ograve/Oacute/Ocircumflex/Otilde/Odieresis/multiply +/Oslash/Ugrave/Uacute/Ucircumflex/Udieresis/Yacute/Thorn/germandbls +/agrave/aacute/acircumflex/atilde/adieresis/aring/ae/ccedilla +/egrave/eacute/ecircumflex/edieresis/igrave/iacute/icircumflex/idieresis +/eth/ntilde/ograve/oacute/ocircumflex/otilde/odieresis/divide +/oslash/ugrave/uacute/ucircumflex/udieresis/yacute/thorn/ydieresis +mv 128 128 gi as P/fSt 50 string d(ChemDraw)fSt copy P/fD{D/Symbol eq{ +findfont[1 0 0 -1 0 0]makefont}{D {findfont}stopped{/Helvetica findfont}if +D length dict/newdict x{ +1 index/FID ne{1 index/FontMatrix eq{[1 0 0 -1 0 0]matrix concatmatrix}if +newdict 3 1 r put}{P P}ie}forall +newdict/Encoding mv put +fSt 8 fSt length 8 sub gi cvs length 8 add +fSt 0 rot gi cvn newdict definefont}ie}b/ts{gs xl ro 0 0 M}b +/nl{0 e xl 0 0 M}b/tx{ft e g e sf m rot D 96 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 +731 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +2420 6820 M +8780 6820 l +8780 7800 l +2420 7800 l +cp +clip +np +65535 65535 65535 sBg +0 3894 7417 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +6183 7303 M +5477 7303 l +st +5621 7363 M +6327 7363 l +st +gs +20 sl +6357 7313 +6357 7313 6357 7313 6182 7313 6357 7313 6357 7313 6157 7251 6182 7280 6182 +7313 6357 7313 6157 7251 6157 7251 4 6357 7313 129 Sp +gr +gs +20 sl +5447 7353 +5447 7353 5447 7353 5647 7415 5447 7353 5447 7353 5622 7366 5647 7415 5647 +7415 5447 7353 5622 7353 5622 7353 4 5447 7353 129 Sp +gr +gr +0 4626 7729 ts +65535 0 65535 C +64 10 0 tx +(4)show +0 10 0 tx +(X)show +gr +0 6960 7129 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +0 6972 7729 ts +65535 0 0 C +64 10 0 tx +(1)show +0 10 0 tx +(X)show +gr +0 2479 7103 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +0 2728 7755 ts +65535 0 0 C +64 10 0 tx +(1)show +0 10 0 tx +(X)show +gr +0 3081 7104 ts +0 32896 0 C +64 10 1 tx +(3)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7530 M +2867 7530 l +2867 7482 l +2887 7482 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7433 M +2867 7433 l +2867 7385 l +2887 7385 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7337 M +2867 7337 l +2867 7288 l +2887 7288 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 +0 0 C +np +2887 7240 M +2867 7240 l +2867 7192 l +2887 7192 l +cp +f +gr +gs +20 +D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2887 7143 M +2867 7143 l +2867 +7101 l +2887 7101 l +cp +f +gr +0 7780 7403 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +0 8508 7128 ts +0 32896 0 C +64 10 0 tx +(3)show +0 10 0 tx +(R)show +gr +0 8520 7729 ts +65535 0 65535 C +64 10 0 tx +(4)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 +3048 6980 M +3048 7000 l +2742 6999 l +2743 6979 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +3048 7052 M +3048 7072 l +2742 7071 l +2742 7051 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +8715 7505 M +8695 7505 l +8691 7167 l +8711 7167 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 +0 0 C +np +8643 7506 M +8623 7506 l +8619 7168 l +8639 7168 l +cp +f +gr +gs +20 +D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +7167 7504 M +7147 7504 l +7143 +7168 l +7163 7168 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +7095 7504 M +7075 7505 l +7071 7169 l +7091 7168 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Dissociation_Double_vdW/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation_Double_vdW/training/dictionary.txt new file mode 100644 index 0000000000..de3d7b8909 --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_Double_vdW/training/dictionary.txt @@ -0,0 +1,32 @@ +O* +1 *3 O u0 p2 c0 {2,D} +2 *4 X u0 p0 c0 {1,D} + +CO* +1 O u0 p2 c0 {2,D} +2 *2 C u0 p0 c0 {1,D} {3,D} +3 *1 X u0 p0 c0 {2,D} + +CO2* +1 O u0 p2 c0 {3,D} +2 *3 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,D} {2,D} +4 *1 X u0 p0 c0 + +Cu4 +1 *4 X u0 p0 c0 + +HCOOH* +1 O u0 p2 c0 {3,S} {5,S} +2 *3 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {1,S} +6 *1 X u0 p0 c0 + +HCOH* +1 O u0 p2 c0 {2,S} {4,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {5,D} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {1,S} +5 *1 X u0 p0 c0 {2,D} diff --git a/input/kinetics/families/Surface_Dissociation_Double_vdW/training/reactions.py b/input/kinetics/families/Surface_Dissociation_Double_vdW/training/reactions.py new file mode 100644 index 0000000000..e59d6ea30c --- /dev/null +++ b/input/kinetics/families/Surface_Dissociation_Double_vdW/training/reactions.py @@ -0,0 +1,47 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dissociation_Double_vdW/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. +""" + +entry( + index = 9, + label = "CO* + O* <=> CO2* + Cu4", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(1.195e12, 'm^2/(mol*s)'), + n = 0., + Ea=(14.9893562, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 9 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +entry( + index = 35, + label = "HCOOH* + Cu4 <=> HCOH* + O*", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(4.828e11, 'm^2/(mol*s)'), + n = 0., + Ea=(57.65137, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 35 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation_vdW/groups.py b/input/kinetics/families/Surface_Dissociation_vdW/groups.py index 46c52478d0..aec34f6580 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/groups.py +++ b/input/kinetics/families/Surface_Dissociation_vdW/groups.py @@ -20,6 +20,9 @@ reverse = "Surface_Association_vdW" +reactantNum=2 +productNum=2 + recipe(actions=[ ['FORM_BOND', '*1', 1, '*3'], ['FORM_BOND', '*2', 1, '*4'], @@ -29,11 +32,11 @@ entry( index = 1, label = "Combined", - group = + group = """ -1 *1 R u0 {2,S} -2 *2 R u0 {1,S} -3 *3 X u0 +1 *1 R!H ux px cx {2,S} +2 *2 R ux px cx {1,S} +3 *3 Xv u0 p0 c0 """, kinetics = None, ) @@ -41,19 +44,55 @@ entry( index = 2, label="VacantSite", - group = + group = +""" +1 *4 Xv u0 p0 c0 +""", + kinetics = None, +) + +entry( + index = 3, + label = "R-H", + group = +""" +1 *1 R!H ux px cx {2,S} +2 *2 H u0 p0 c0 {1,S} +3 *3 Xv u0 p0 c0 +""", + kinetics = None, +) + +entry( + index = 4, + label = "C-H", + group = """ -1 *4 Xv u0 +1 *1 C ux px cx {2,S} +2 *2 H u0 p0 c0 {1,S} +3 *3 Xv u0 p0 c0 """, kinetics = None, ) +entry( + index = 5, + label = "O-H", + group = +""" +1 *1 O ux px cx {2,S} +2 *2 H u0 p0 c0 {1,S} +3 *3 Xv u0 p0 c0 +""", + kinetics = None, +) tree( """ L1: Combined - + L2: R-H + L3: C-H + L3: O-H L1: VacantSite """ ) - diff --git a/input/kinetics/families/Surface_Dissociation_vdW/rules.py b/input/kinetics/families/Surface_Dissociation_vdW/rules.py index c45d4e9326..23fc62f2fb 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/rules.py +++ b/input/kinetics/families/Surface_Dissociation_vdW/rules.py @@ -1,37 +1,27 @@ #!/usr/bin/env python # encoding: utf-8 -name = "Surface_Dissociation/rules" +name = "Surface_Dissociation_vdW/rules" shortDesc = u"" longDesc = u""" """ + entry( index = 1, label = "Combined;VacantSite", kinetics = SurfaceArrheniusBEP( - A = (1.0e17, 'm^2/(mol*s)'), + A = (1.436e11, 'm^2/(mol*s)'), n = 0, - alpha = 0.84, - E0 = (44.25, 'kcal/mol'), + alpha = 0.6, + E0 = (10.8384576, 'kcal/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), rank = 0, shortDesc = u"""Default""", longDesc = u""" -"Arrhenius preexponential values for surface recombination...reactions -are, in the SI system,... 10^13 - 10^14 m2/mol/s ...for bimolecular reactions" -from page 54 of "Silicon epitaxy" -Author: Danilo Crippa; Daniel L Rode; Maurizio Masi -Publisher: San Diego : Academic Press, 2001. -Series: Semiconductors and semimetals, v. 72. - -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.) - """ +Reaction 30 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +E0 is Ea +""" ) - - - diff --git a/input/kinetics/families/Surface_Dissociation_vdW/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation_vdW/training/dictionary.txt index e69de29bb2..e978076db6 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/training/dictionary.txt +++ b/input/kinetics/families/Surface_Dissociation_vdW/training/dictionary.txt @@ -0,0 +1,91 @@ +HCO* +1 O u0 p2 c0 {2,D} +2 *1 C u0 p0 c0 {1,D} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 *3 X u0 p0 c0 {2,S} + +H* +1 *2 H u0 p0 c0 {2,S} +2 *4 X u0 p0 c0 {1,S} + +CH2O* +1 O u0 p2 c0 {2,D} +2 *1 C u0 p0 c0 {1,D} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 *2 H u0 p0 c0 {2,S} +5 *3 X u0 p0 c0 + +Cu4 +1 *4 X u0 p0 c0 + +H2O* +1 *1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 *2 H u0 p0 c0 {1,S} +4 *3 X u0 p0 c0 + +OH* +1 *1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 *3 X u0 p0 c0 {1,S} + +COOH* +1 O u0 p2 c0 {3,S} {4,S} +2 O u0 p2 c0 {3,D} +3 *1 C u0 p0 c0 {1,S} {2,D} {5,S} +4 H u0 p0 c0 {1,S} +5 *3 X u0 p0 c0 {3,S} + +HCOOH* +1 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 *1 C u0 p0 c0 {1,S} {2,D} {4,S} +4 *2 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {1,S} +6 *3 X u0 p0 c0 + + +HCOO* +1 *1 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 *3 X u0 p0 c0 {1,S} + +HCOOH_1* +1 *1 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 *2 H u0 p0 c0 {1,S} +6 *3 X u0 p0 c0 + +HCOOH_2* +1 *2 O u0 p2 c0 {3,S} {5,S} +2 O u0 p2 c0 {3,D} +3 *1 C u0 p0 c0 {1,S} {2,D} {4,S} +4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {1,S} +6 *3 X u0 p0 c0 + +OH_2* +1 *2 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 *4 X u0 p0 c0 {1,S} + +CH2OH* +1 O u0 p2 c0 {2,S} {5,S} +2 *1 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {1,S} +6 *3 X u0 p0 c0 {2,S} + +CH3OH* +1 O u0 p2 c0 {2,S} {6,S} +2 *1 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 *2 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {1,S} +7 *3 X u0 p0 c0 \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation_vdW/training/reactions.py b/input/kinetics/families/Surface_Dissociation_vdW/training/reactions.py index a7f6379ef7..f6ac3e0a9e 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/training/reactions.py +++ b/input/kinetics/families/Surface_Dissociation_vdW/training/reactions.py @@ -7,3 +7,117 @@ Put kinetic parameters for specific reactions in this file to use as a training set for generating rate rules to populate this kinetics family. """ + +# entry( +# index = 13, +# label = "COOH* + H* <=> HCOOH* + Cu4", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A=(6.793e13, 'm^2/(mol*s)'), +# n = 0., +# Ea=(16.8342, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 0, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 13 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +entry( + index = 14, + label = "H2O* + Cu4 <=> OH* + H*", + degeneracy = 2, + kinetics = SurfaceArrhenius( + A=(1.436e11, 'm^2/(mol*s)'), + n = 0., + Ea=(4.84271508, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 14 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +entry( + index = 19, + label = "HCOO* + H* <=> HCOOH_1* + Cu4", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(1.302e14, 'm^2/(mol*s)'), + n = 0., + Ea=(20.9850987, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 19 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) + +# entry( +# index = 30, +# label = "HCO* + H* <=> CH2O* + Cu4", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A=(5.685e12, 'm^2/(mol*s)'), +# n = 0., +# Ea=(10.8384576, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 0, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 30 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +# entry( +# index = 33, +# label = "CH2OH* + H* <=> CH3OH* + Cu4", +# degeneracy = 1, +# kinetics = SurfaceArrhenius( +# A=(5.242e12, 'm^2/(mol*s)'), +# n = 0., +# Ea=(37.5886933, 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 0, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 33 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) + +entry( + index = 34, + label = "HCOOH_2* + Cu4 <=> HCO* + OH_2*", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(5.242e12, 'm^2/(mol*s)'), + n = 0., + Ea=(37.5886933, 'kcal/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 34 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +""" +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dual_Adsorption_vdW/groups.py b/input/kinetics/families/Surface_Dual_Adsorption_vdW/groups.py new file mode 100644 index 0000000000..9de89db724 --- /dev/null +++ b/input/kinetics/families/Surface_Dual_Adsorption_vdW/groups.py @@ -0,0 +1,271 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dual_Adsorption_vdW/groups" +shortDesc = u"" +longDesc = u""" +Two vdW species reacting together and abstracting a functional group and then forming a single bond to the surface. + +*2=*3 *4-*6 *2-*3-*4 *6 + : : ----> | | +~*1~ + ~*5~~ ~*1~ + ~*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=["Adsorbate1","Adsorbate2"], products=["Adsorbate3","Adsorbate4"], ownReverse=False) + +reverse = "Surface_Dual_Desorption_vdW" + +reactantNum=2 +productNum=2 + +recipe(actions=[ + ['CHANGE_BOND','*2', -1, '*3'], + ['FORM_BOND', '*1', 1, '*2'], + ['BREAK_BOND', '*4', 1, '*6'], + ['FORM_BOND', '*3', 1, '*4'], + ['FORM_BOND', '*5', 1, '*6'], +]) + +entry( + index = 1, + label = "Adsorbate1", + group = +""" +1 *1 Xv ux px cx +2 *2 R!H ux px cx {3,[D,T,Q]} +3 *3 R!H ux px cx {2,[D,T,Q]} +""", + kinetics = None, +) + +entry( + index = 2, + label = "Adsorbate2", + group = +""" +1 *5 Xv ux px cx +2 *4 R ux px cx {3,S} +3 *6 R ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 3, + label = "CR", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,[D,T,Q]} +3 *3 R!H ux px cx {2,[D,T,Q]} +""", + kinetics = None, +) + +entry( + index = 4, + label = "O=R", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O ux px cx {3,D} +3 *3 R!H ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 5, + label = "C=O", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C u0 p0 c0 {3,D} +3 *3 O u0 p2 c0 {2,D} +""", + kinetics = None, +) + +entry( + index = 6, + label = "O=C", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O u0 p2 c0 {3,D} +3 *3 C ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 7, + label = "C=", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,D} +3 *3 R!H ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 8, + label = "C#", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,T} +3 *3 R!H ux px cx {2,T} +""", + kinetics = None, +) + +entry( + index = 9, + label = "C$", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 C ux px cx {3,Q} +3 *3 R!H ux px cx {2,Q} +""", + kinetics = None, +) + +entry( + index = 10, + label = "O=O", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 O u0 p2 c0 {3,D} +3 *3 O u0 p2 c0 {2,D} +""", + kinetics = None, +) + +entry( + index = 11, + label = "RR", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 R!H ux px cx {3,S} +3 *6 R!H ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 12, + label = "C-H", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 C ux px cx {3,S} +3 *6 H u0 p0 c0 {2,S} +""", + kinetics = None, +) + +entry( + index = 13, + label = "O-H", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 O u0 p2 c0 {3,S} +3 *6 H u0 p0 c0 {2,S} +""", + kinetics = None, +) + +entry( + index = 14, + label = "HH", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 H u0 p0 c0 {3,S} +3 *6 H u0 p0 c0 {2,S} +""", + kinetics = None, +) + +entry( + index = 15, + label = "RH", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 R!H ux px cx {3,S} +3 *6 H u0 p0 c0 {2,S} +""", + kinetics = None, +) + +entry( + index = 16, + label = "HR", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 H u0 p0 c0 {3,S} +3 *6 R!H ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 17, + label = "H-C", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 H u0 p0 c0 {3,S} +3 *6 C ux px cx {2,S} +""", + kinetics = None, +) + +entry( + index = 18, + label = "H-O", + group = +""" +1 *5 Xv u0 p0 c0 +2 *4 H u0 p0 c0 {3,S} +3 *6 O u0 p2 c0 {2,S} +""", + kinetics = None, +) + +tree( +""" +L1: Adsorbate1 + L2: CR + L3: C= + L4: C=O + L3: C# + L3: C$ + L2: O=R + L3: O=C + L3: O=O +L1: Adsorbate2 + L2: RR + L2: HH + L2: RH + L3: C-H + L3: O-H + L2: HR + L3: H-C + L3: H-O +""" +) diff --git a/input/kinetics/families/Surface_Dual_Adsorption_vdW/rules.py b/input/kinetics/families/Surface_Dual_Adsorption_vdW/rules.py new file mode 100644 index 0000000000..d443503da2 --- /dev/null +++ b/input/kinetics/families/Surface_Dual_Adsorption_vdW/rules.py @@ -0,0 +1,25 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dual_Adsorption_vdW/rules" +shortDesc = u"" +longDesc = u""" +A vdW double bonded species dissociatively adsorbing to the surface with double +bonds. +""" + +entry( + index = 1, + label = "Adsorbate1;Adsorbate2", + kinetics = SurfaceArrheniusBEP( + A = (1.0e13, 'm^2/(mol*s)'), + n = 0, + alpha = 0.0, + E0 = (0, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""Made up""" +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dual_Adsorption_vdW/template.cdx b/input/kinetics/families/Surface_Dual_Adsorption_vdW/template.cdx new file mode 100644 index 0000000000..e02b9d36c2 Binary files /dev/null and b/input/kinetics/families/Surface_Dual_Adsorption_vdW/template.cdx differ diff --git a/input/kinetics/families/Surface_Dual_Adsorption_vdW/template.eps b/input/kinetics/families/Surface_Dual_Adsorption_vdW/template.eps new file mode 100644 index 0000000000..cf40d48266 --- /dev/null +++ b/input/kinetics/families/Surface_Dual_Adsorption_vdW/template.eps @@ -0,0 +1,765 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:33 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 81 334 458 385 +%%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 +719 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +1620 6680 M +9160 6680 l +9160 7700 l +1620 7700 l +cp +clip +np +65535 65535 65535 sBg +0 2975 7293 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +5666 7178 M +4960 7178 l +st +5104 7238 M +5810 7238 l +st +gs +20 sl +5840 7188 +5840 7188 5840 7188 5665 7188 5840 7188 5840 7188 5640 7126 5665 7155 5665 +7188 5840 7188 5640 7126 5640 7126 4 5840 7188 129 Sp +gr +gs +20 sl +4930 7228 +4930 7228 4930 7228 5130 7290 4930 7228 4930 7228 5105 7241 5130 7290 5130 +7290 4930 7228 5105 7228 5105 7228 4 4930 7228 129 Sp +gr +gr +0 3872 7642 ts +65535 32896 0 C +64 10 0 tx +(5)show +0 10 0 tx +(X)show +gr +0 6340 7004 ts +0 0 65535 C +64 10 0 tx 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x +54 /hS x +0 0 0 C +np +7514 6945 M +7513 6965 l +7209 6957 l +7210 6937 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Dual_Adsorption_vdW/training/dictionary.txt b/input/kinetics/families/Surface_Dual_Adsorption_vdW/training/dictionary.txt new file mode 100644 index 0000000000..a2aacddca5 --- /dev/null +++ b/input/kinetics/families/Surface_Dual_Adsorption_vdW/training/dictionary.txt @@ -0,0 +1,23 @@ +OH* +1 *6 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 *5 X u0 p0 c0 {1,S} + +COOH* +1 *3 O u0 p2 c0 {3,S} {4,S} +2 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,S} {2,D} {5,S} +4 *4 H u0 p0 c0 {1,S} +5 *1 X u0 p0 c0 {3,S} + +CO2* +1 O u0 p2 c0 {3,D} +2 *3 O u0 p2 c0 {3,D} +3 *2 C u0 p0 c0 {1,D} {2,D} +4 *1 X u0 p0 c0 + +H2O* +1 *6 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 *4 H u0 p0 c0 {1,S} +4 *5 X u0 p0 c0 \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dual_Adsorption_vdW/training/reactions.py b/input/kinetics/families/Surface_Dual_Adsorption_vdW/training/reactions.py new file mode 100644 index 0000000000..28d9cf539a --- /dev/null +++ b/input/kinetics/families/Surface_Dual_Adsorption_vdW/training/reactions.py @@ -0,0 +1,28 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Dual_Adsorption_vdW/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. +""" + +# entry( +# index = 12, +# label = "COOH* + OH* <=> CO2* + H2O*", +# # degeneracy = 4, +# kinetics = SurfaceArrhenius( +# A = (1.0e13, 'm^2/(mol*s)'), +# n = 0., +# Ea = (0., 'kcal/mol'), +# Tmin = (298, 'K'), +# Tmax = (2000, 'K'), +# ), +# rank = 1, +# shortDesc = u"""Default""", +# longDesc = u""" +# Reaction 12 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +# and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d +# """ +# ) \ No newline at end of file diff --git a/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/groups.py b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/groups.py new file mode 100644 index 0000000000..fdd716ba12 --- /dev/null +++ b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/groups.py @@ -0,0 +1,301 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_EleyRideal_Addition_Multiple_Bond/groups" +shortDesc = u"" +longDesc = u""" +Eeley Rideal reaction with a gas phase double, triple, or quadruple bonded species with a species (most likely hydrogen) directly bonded to the surface. + + *2 *4=*3 *3-*4-*2 + | ----> | +~*1~ + ~*1~ + +The rate, which should be in mol/m2/s, +will be given by k * (mol/m2) * (mol/m3) +so k should be in (m3/mol/s). + +This is from Theoretical Investigation of the Mechanisms for Olefinic Hydrogenation on +Pt(110) and Pt(111) Surfaces +Vincent Maurice & Christian Minot, J. Phys. Chem. 1990, 94, 8579-8588 + +and inspired by Ethylene Dimerization and Oligomerization to 1-Butene and Higher Olefins with Chromium-Promoted Cobalt on Carbon Catalyst by Xu et al. Doi:10.1021/acscatal.7b03205 + +""" + +template(reactants=["Adsorbate1", "Gas"], products=["Adsorbate2"], ownReverse=False) + +reverse = "Surface_EleyRideal_Deletion_Multiple_Bond" + +reactantNum=2 +productNum=1 + +recipe(actions=[ + ['BREAK_BOND', '*1', 1, '*2'], + ['CHANGE_BOND', '*3', -1, '*4'], + ['FORM_BOND', '*1', 1, '*3'], + ['FORM_BOND', '*2', 1, '*4'], +]) + +entry( + index = 1, + label = "Adsorbate1", + group = +""" +1 *1 X ux px cx {2,S} +2 *2 R ux px cx {1,S} +""", + kinetics = None, +) + +entry( + index = 2, + label="Gas", + group = +""" +1 *3 R!H ux px cx {2,[D,T,Q]} +2 *4 R!H ux px cx {1,[D,T,Q]} +""", + kinetics = None, +) + +entry( + index = 3, + label="*H", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 H u0 p0 c0 {1,S} +""", + kinetics = None, +) + +entry( + index = 4, + label="*C", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} +""", + kinetics = None, +) + +entry( + index = 5, + label="R=R", + group = +""" +1 *3 R!H ux px cx {2,D} +2 *4 R!H ux px cx {1,D} +""", + kinetics = None, +) + +entry( + index = 6, + label="R#R", + group = +""" +1 *3 R!H ux px cx {2,T} +2 *4 R!H ux px cx {1,T} +""", + kinetics = None, +) + +entry( + index = 7, + label="C=C", + group = +""" +1 *3 C u0 p0 c0 {2,D} {3,S} {4,S} +2 *4 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} +""", + kinetics = None, +) + +entry( + index = 8, + label="C#C", + group = +""" +1 *3 C u0 p0 c0 {2,T} {3,S} +2 *4 C u0 p0 c0 {1,T} {4,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {2,S} +""", + kinetics = None, +) + +entry( + index = 9, + label="*C2", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 C u0 p0 c0 {2,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} +""", + kinetics = None, +) + +entry( + index = 10, + label="*C12+", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 C u0 p0 c0 {2,S} {6,S} {16,S} {17,S} +6 C u0 p0 c0 {5,S} {7,S} {18,S} {19,S} +7 C u0 p0 c0 {6,S} {8,S} {20,S} {21,S} +8 C u0 p0 c0 {7,S} {9,S} {22,S} {23,S} +9 C u0 p0 c0 {8,S} {10,S} {24,S} {25,S} +10 C u0 p0 c0 {9,S} {11,S} {26,S} {27,S} +11 C u0 p0 c0 {10,S} {12,S} {28,S} {29,S} +12 C u0 p0 c0 {11,S} {13,S} {30,S} {31,S} +13 C u0 p0 c0 {12,S} {14,S} {32,S} {33,S} +14 C u0 p0 c0 {13,S} {15,S} {34,S} {35,S} +15 C u0 p0 c0 {14,S} {36,S} {37,S} {38,S} +16 H u0 p0 c0 {5,S} +17 H u0 p0 c0 {5,S} +18 H u0 p0 c0 {6,S} +19 H u0 p0 c0 {6,S} +20 H u0 p0 c0 {7,S} +21 H u0 p0 c0 {7,S} +22 H u0 p0 c0 {8,S} +23 H u0 p0 c0 {8,S} +24 H u0 p0 c0 {9,S} +25 H u0 p0 c0 {9,S} +26 H u0 p0 c0 {10,S} +27 H u0 p0 c0 {10,S} +28 H u0 p0 c0 {11,S} +29 H u0 p0 c0 {11,S} +30 H u0 p0 c0 {12,S} +31 H u0 p0 c0 {12,S} +32 H u0 p0 c0 {13,S} +33 H u0 p0 c0 {13,S} +34 H u0 p0 c0 {14,S} +35 H u0 p0 c0 {14,S} +36 H u0 p0 c0 {15,S} +37 H u0 p0 c0 {15,S} +38 R u0 p0 c0 {15,S} +""", + kinetics = None, +) + +entry( + index = 11, + label="*C4", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 C u0 p0 c0 {2,S} {6,S} {8,S} {9,S} +6 C u0 p0 c0 {5,S} {7,S} {10,S} {11,S} +7 C u0 p0 c0 {6,S} {12,S} {13,S} {14,S} +8 H u0 p0 c0 {5,S} +9 H u0 p0 c0 {5,S} +10 H u0 p0 c0 {6,S} +11 H u0 p0 c0 {6,S} +12 H u0 p0 c0 {7,S} +13 H u0 p0 c0 {7,S} +14 H u0 p0 c0 {7,S} +""", + kinetics = None, +) + +entry( + index = 12, + label="*C6", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 C u0 p0 c0 {2,S} {6,S} {8,S} {9,S} +6 C u0 p0 c0 {5,S} {7,S} {10,S} {11,S} +7 C u0 p0 c0 {6,S} {12,S} {13,S} {14,S} +8 H u0 p0 c0 {5,S} +9 H u0 p0 c0 {5,S} +10 H u0 p0 c0 {6,S} +11 H u0 p0 c0 {6,S} +12 H u0 p0 c0 {7,S} +13 H u0 p0 c0 {7,S} +14 C u0 p0 c0 {7,S} {15,S} {16,S} {17,S} +15 C u0 p0 c0 {14,S} {18,S} {19,S} {20,S} +16 H u0 p0 c0 {14,S} +17 H u0 p0 c0 {14,S} +18 H u0 p0 c0 {15,S} +19 H u0 p0 c0 {15,S} +20 H u0 p0 c0 {15,S} +""", + kinetics = None, +) + +entry( + index = 12, + label="*C8", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 C u0 p0 c0 {2,S} {6,S} {8,S} {9,S} +6 C u0 p0 c0 {5,S} {7,S} {10,S} {11,S} +7 C u0 p0 c0 {6,S} {12,S} {13,S} {14,S} +8 H u0 p0 c0 {5,S} +9 H u0 p0 c0 {5,S} +10 H u0 p0 c0 {6,S} +11 H u0 p0 c0 {6,S} +12 H u0 p0 c0 {7,S} +13 H u0 p0 c0 {7,S} +14 C u0 p0 c0 {7,S} {15,S} {16,S} {17,S} +15 C u0 p0 c0 {14,S} {18,S} {19,S} {20,S} +16 H u0 p0 c0 {14,S} +17 H u0 p0 c0 {14,S} +18 H u0 p0 c0 {15,S} +19 H u0 p0 c0 {15,S} +20 C u0 p0 c0 {15,S} {21,S} {22,S} {23,S} +21 C u0 p0 c0 {20,S} {24,S} {25,S} {26,S} +22 H u0 p0 c0 {20,S} +23 H u0 p0 c0 {20,S} +24 H u0 p0 c0 {21,S} +25 H u0 p0 c0 {21,S} +26 H u0 p0 c0 {21,S} +""", + kinetics = None, +) + +tree( +""" +L1: Adsorbate1 + L2: *H + L2: *C + L3: *C2 + L3: *C4 + L3: *C6 + L3: *C8 + L3: *C12+ +L1: Gas + L2: R=R + L3: C=C + L2: R#R + L3: C#C +""" +) + diff --git a/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/rules.py b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/rules.py new file mode 100644 index 0000000000..53cc8167ac --- /dev/null +++ b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/rules.py @@ -0,0 +1,135 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_EleyRideal_Addition_Multiple_Bond/rules" +shortDesc = u"" +longDesc = u""" +Eley Rideal mechanism for a gas phase double or triple bonded species. +""" +entry( + index = 1, + label = "Adsorbate1;Gas", + kinetics = StickingCoefficientBEP( + A = 5e-6, + n = 0, + alpha = 0, + E0 = (68.66, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""E0 is Ea from Xu et al. Doi:10.1021/acscatal.7b03205""" +) + +entry( + index = 2, + label = "*C;R=R", + kinetics = StickingCoefficientBEP( + A = 5e-2, + n = 0, + alpha = 0, + E0 = (68.66, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""E0 is Ea from Xu et al. Doi:10.1021/acscatal.7b03205""" +) + +entry( + index = 3, + label = "*C12+;Gas", + kinetics = StickingCoefficientBEP( + A = 5e-3, + n = 0, + alpha = 0, + E0 = (85., 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""Made up""" +) + +entry( + index = 4, + label = "*C6;R=R", + kinetics = StickingCoefficientBEP( + A = 5e-2, + n = 0, + alpha = 0, + E0 = (77.62, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""E0 is Ea from Xu et al. Doi:10.1021/acscatal.7b03205""" +) + +entry( + index = 5, + label = "*C8;R=R", + kinetics = StickingCoefficientBEP( + A = 5e-2, + n = 0, + alpha = 0, + E0 = (77.62, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""Same as *C6. E0 is Ea from Xu et al. Doi:10.1021/acscatal.7b03205""" +) + +entry( + index = 6, + label = "*H;R=R", + kinetics = StickingCoefficientBEP( + A = 5e-2, + n = 0, + alpha = 0, + E0 = (68.66, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""Same as *C""" +) + +entry( + index = 7, + label = "*C2;R=R", + kinetics = StickingCoefficientBEP( + A = 5e-2, + n = 0, + alpha = 0, + E0 = (68.66, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""E0 is Ea from Xu et al. Doi:10.1021/acscatal.7b03205""" +) + +entry( + index = 8, + label = "*C4;R=R", + kinetics = StickingCoefficientBEP( + A = 5e-2, + n = 0, + alpha = 0, + E0 = (68.34, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""E0 is Ea from Xu et al. Doi:10.1021/acscatal.7b03205""" +) diff --git a/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/template.cdx b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/template.cdx new file mode 100644 index 0000000000..70bfa459db Binary files /dev/null and b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/template.cdx differ diff --git a/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/template.eps b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/template.eps new file mode 100644 index 0000000000..537444a7c3 --- /dev/null +++ b/input/kinetics/families/Surface_EleyRideal_Addition_Multiple_Bond/template.eps @@ -0,0 +1,541 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:35 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 125 336 414 383 +%%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 +719 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +2500 6720 M +8280 6720 l +8280 7660 l +2500 7660 l +cp +clip +np +65535 65535 65535 sBg +0 3310 7293 ts +0 0 0 C +0 12 0 tx +0 0 0 C +(+)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +20 D sl/lW x +6086 7179 M +5380 7179 l +st +5524 7239 M +6230 7239 l +st +gs +20 sl +6260 7189 +6260 7189 6260 7189 6085 7189 6260 7189 6260 7189 6060 7127 6085 7156 6085 +7189 6260 7189 6060 7127 6060 7127 4 6260 7189 129 Sp +gr +gs +20 sl +5350 7229 +5350 7229 5350 7229 5550 7291 5350 7229 5350 7229 5525 7241 5550 7291 5550 +7291 5350 7229 5525 7229 5525 7229 4 5350 7229 129 Sp +gr +gr +0 6801 7004 ts +0 +32896 0 C +64 10 0 tx +(3)show +0 10 0 tx +(R)show +gr +0 6813 7604 ts +65535 0 0 C +64 10 0 tx +(1)show 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x +80 /bW x +54 /hS x +0 0 0 C +np +7968 6918 M +7968 6938 l +7666 6938 l +7666 6918 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Migration/groups.py b/input/kinetics/families/Surface_Migration/groups.py new file mode 100644 index 0000000000..647f8d6577 --- /dev/null +++ b/input/kinetics/families/Surface_Migration/groups.py @@ -0,0 +1,156 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Migration/groups" +shortDesc = u"" +longDesc = u""" +Surface species migrating where it binds to the surface. + + *4 *4 + | | + *2--*3 *2--*3 + | ----> | +~*1~ ~*1~ + +The rate, which should be in mol/m2/s, +will be given by k * (mol/m2) +so k should be in (1/s). + +""" + +template(reactants=["Adsorbate1"], products=["Adsorbate2"], ownReverse=False) + +reverse = "Surface_Migration_Reverse" + +reactantNum=1 +productNum=1 + +recipe(actions=[ + ['BREAK_BOND', '*1', 1, '*2'], + ['BREAK_BOND', '*3', 1, '*4'], + ['FORM_BOND', '*1', 1, '*3'], + ['FORM_BOND', '*2', 1, '*4'], +]) + +entry( + index = 1, + label = "Adsorbate1", + group = +""" +1 *1 X ux px cx {2,S} +2 *2 R!H ux px cx {1,S} {3,[S,D]} +3 *3 R!H ux px cx {2,[S,D]} {4,S} +4 *4 R ux px cx {3,S} +""", + kinetics = None, +) + +entry( + index = 2, + label="*C", + group = +""" +1 *1 X ux px cx {2,S} +2 *2 C ux px cx {1,S} {3,[S,D]} +3 *3 C ux px cx {2,[S,D]} {4,S} +4 *4 R ux px cx {3,S} +""", + kinetics = None, +) + +entry( + index = 3, + label="*nbutane", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S} +3 *3 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S} +4 *4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 C u0 p0 c0 {3,S} {9,S} {10,S} {11,S} +9 H u0 p0 c0 {8,S} +10 H u0 p0 c0 {8,S} +11 C u0 p0 c0 {8,S} {12,S} {13,S} {14,S} +12 H u0 p0 c0 {11,S} +13 H u0 p0 c0 {11,S} +14 H u0 p0 c0 {11,S} +""", + kinetics = None, +) + +entry( + index = 4, + label="*nhexane", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S} +3 *3 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S} +4 *4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 C u0 p0 c0 {3,S} {9,S} {10,S} {11,S} +9 H u0 p0 c0 {8,S} +10 H u0 p0 c0 {8,S} +11 C u0 p0 c0 {8,S} {12,S} {13,S} {14,S} +12 H u0 p0 c0 {11,S} +13 H u0 p0 c0 {11,S} +14 C u0 p0 c0 {11,S} {15,S} {16,S} {17,S} +15 H u0 p0 c0 {14,S} +16 H u0 p0 c0 {14,S} +17 C u0 p0 c0 {14,S} {18,S} {19,S} {20,S} +18 H u0 p0 c0 {17,S} +19 H u0 p0 c0 {17,S} +20 H u0 p0 c0 {17,S} +""", + kinetics = None, +) + +entry( + index = 5, + label="*noctane", + group = +""" +1 *1 X u0 p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S} +3 *3 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S} +4 *4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 C u0 p0 c0 {3,S} {9,S} {10,S} {11,S} +9 H u0 p0 c0 {8,S} +10 H u0 p0 c0 {8,S} +11 C u0 p0 c0 {8,S} {12,S} {13,S} {14,S} +12 H u0 p0 c0 {11,S} +13 H u0 p0 c0 {11,S} +14 C u0 p0 c0 {11,S} {15,S} {16,S} {17,S} +15 H u0 p0 c0 {14,S} +16 H u0 p0 c0 {14,S} +17 C u0 p0 c0 {14,S} {18,S} {19,S} {20,S} +18 H u0 p0 c0 {17,S} +19 H u0 p0 c0 {17,S} +20 C u0 p0 c0 {17,S} {21,S} {22,S} {23,S} +21 H u0 p0 c0 {20,S} +22 H u0 p0 c0 {20,S} +23 C u0 p0 c0 {20,S} {24,S} {25,S} {26,S} +24 H u0 p0 c0 {23,S} +25 H u0 p0 c0 {23,S} +26 H u0 p0 c0 {23,S} +""", + kinetics = None, +) + +tree( +""" +L1: Adsorbate1 + L2: *C + L3: *nbutane + L3: *nhexane + L3: *noctane +""" +) diff --git a/input/kinetics/families/Surface_Migration/rules.py b/input/kinetics/families/Surface_Migration/rules.py new file mode 100644 index 0000000000..ace1018acb --- /dev/null +++ b/input/kinetics/families/Surface_Migration/rules.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Migration/rules" +shortDesc = u"" +longDesc = u""" +Surface species migrating where it binds to the surface +""" +entry( + index = 1, + label = "Adsorbate1", + kinetics = SurfaceArrheniusBEP( + A = (1.0e13, '1/s'), + n = 0, + alpha = 0, + E0 = (100, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""From Xu et al. Doi:10.1021/acscatal.7b03205 sort of, made up the rest -E""" +) + +entry( + index = 2, + label = "*nbutane", + kinetics = SurfaceArrheniusBEP( + A = (7.336e12, '1/s'), + n = 0, + alpha = 0, + E0 = (59.33, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""n-butane migration from C1 to C2""", + longDesc = u"""From Xu et al. Doi:10.1021/acscatal.7b03205 + +Given Ea = 59.33 kJ/mol, and fwd rate of 1.22e4/s: +A = 1.22e4/s / exp(-59.33 kJ/mol / R / 353 K) = 7.336e12/s +""" +) + +entry( + index = 3, + label = "*nhexane", + kinetics = SurfaceArrheniusBEP( + A = (7.346e12, '1/s'), + n = 0, + alpha = 0, + E0 = (58.93, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""n-hexane migration from C1 to C2""", + longDesc = u"""From Xu et al. Doi:10.1021/acscatal.7b03205 + +Given Ea = 58.93 kJ/mol, and fwd rate of 1.40e4/s: +A = 1.40e4/s / exp(-58.93 kJ/mol / R / 353 K) = 7.346e12/s +""" +) + +entry( + index = 4, + label = "*noctane", + kinetics = SurfaceArrheniusBEP( + A = (7.327e12, '1/s'), + n = 0, + alpha = 0, + E0 = (63.31, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""n-octane migration from C1 to C2""", + longDesc = u"""From Xu et al. Doi:10.1021/acscatal.7b03205 + +Given Ea = 63.31 kJ/mol, and fwd rate of 3.14e3/s: +A = 3.14e3/s / exp(-63.31 kJ/mol / R / 353 K) = 7.327e12/s +""" +) + + +entry( + index = 5, + label = "*C", + kinetics = SurfaceArrheniusBEP( + A = (7.336e12, '1/s'), + n = 0, + alpha = 0, + E0 = (59.33, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u"""See *C4""" +) diff --git a/input/kinetics/families/Surface_Migration/template.cdx b/input/kinetics/families/Surface_Migration/template.cdx new file mode 100644 index 0000000000..27c399d454 Binary files /dev/null and b/input/kinetics/families/Surface_Migration/template.cdx differ diff --git a/input/kinetics/families/Surface_Migration/template.eps b/input/kinetics/families/Surface_Migration/template.eps new file mode 100644 index 0000000000..0355f68335 --- /dev/null +++ b/input/kinetics/families/Surface_Migration/template.eps @@ -0,0 +1,551 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:36 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 188 321 351 398 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2018 PerkinElmer Informatics, Inc. 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s D hS dv ru +cvi D 0 eq{P 1}if/nH x +D hS nH m s +D 0 lt{P .1 s nH dv}{nH 2 a dv D 0 xl 2 m s nH dv}ie}b +/Bd{D type/arraytype ne{bs e g}if{{P}{{{DS}{DD}{gs 12 OB np +bW 2 dv/bd x +lW 2 dv e D NH e{D bd M bd n l}for +st gr}{gs 12 OB np +lW 2 dv 0 xl NH 1 sc +bW 2 dv wF m nH 1 a dv/bd x +0 1 nH +{D 1 a bd m o o M n l}for SM st gr}{P}{DB}{gs 12 OB +np 0 lW 2 dv o o n M l bW 2 dv +wF m o o l n l +cp f gr}{P}{gs 12 OB/bL x +bW 2 dv D lW lt{P lW}if/bd x np 0 0 M +bL bd 4 m dv ru 2 o o lt{e}if P cvi/nSq x +bL nSq 2 m dv D sc +nSq{.135 .667 .865 .667 1 0 rcurveto +.135 -.667 .865 -.667 1 0 rcurveto}rp SM st gr}{gs 12 OB +np 0 lW 2 dv o o n M l bW 2 dv +wF m o o l n l +cp SM lW 0.8 m sl st gr}{P}{4 2 r gs OP/rad x 1 SA DA gr}{P} +}o 1 g 1 s g e 2 4 gi al P +5 -1 r xc}{al P 8 ix 1 eq{DD}{DS}ie 5 -1 r 2 eq{DB}{DS}ie P}{DT}}o 0 g g xc}b +/ed{gs cpt np cw 2 dv 0 360 arc f gr}b +/SPe{gs 0 e xl 1 1 S dv D n sc CMT currentmatrix P lW sl 4.0 setmiterlimit +np}b/ws{Wd 0 32 4 -1 roll widthshow}b/blank/Times-Roman findfont/CharStrings +g/space g d/mv 256 array d/NUL/SOH/STX/ETX/EOT/ENQ/ACK/BEL/BS/HT/LF/VT +/FF/CR/SO/SI +/DLE/DC1/DC2/DC3/DC4/NAK/SYN/ETB/CAN/EM/SUB/ESC/FS/GS/RS/US +mv 0 32 gi as P +mv 32/Times-Roman findfont/Encoding get +32 96 gi putinterval +mv 39/quotesingle put +mv 96/grave put/unknown/unknown/quotesinglbase/florin/quotedblbase/ellipsis +/dagger/daggerdbl +/circumflex/perthousand/Scaron/guilsinglleft/OE/unknown/unknown/unknown +/unknown/quoteleft/quoteright/quotedblleft/quotedblright/bullet/endash +/emdash +/tilde/trademark/scaron/guilsinglright/oe/unknown/unknown/Ydieresis +/blank/exclamdown/cent/sterling/currency/yen/brokenbar/section +/dieresis/copyright/ordfeminine/guillemotleft/logicalnot/hyphen/registered +/macron +/degree/plusminus/twosuperior/threesuperior/acute/mu/paragraph +/periodcentered +/cedilla/onesuperior/ordmasculine/guillemotright/onequarter/onehalf +/threequarters/questiondown +/Agrave/Aacute/Acircumflex/Atilde/Adieresis/Aring/AE/Ccedilla +/Egrave/Eacute/Ecircumflex/Edieresis/Igrave/Iacute/Icircumflex/Idieresis +/Eth/Ntilde/Ograve/Oacute/Ocircumflex/Otilde/Odieresis/multiply +/Oslash/Ugrave/Uacute/Ucircumflex/Udieresis/Yacute/Thorn/germandbls +/agrave/aacute/acircumflex/atilde/adieresis/aring/ae/ccedilla +/egrave/eacute/ecircumflex/edieresis/igrave/iacute/icircumflex/idieresis +/eth/ntilde/ograve/oacute/ocircumflex/otilde/odieresis/divide +/oslash/ugrave/uacute/ucircumflex/udieresis/yacute/thorn/ydieresis +mv 128 128 gi as P/fSt 50 string d(ChemDraw)fSt copy P/fD{D/Symbol eq{ +findfont[1 0 0 -1 0 0]makefont}{D {findfont}stopped{/Helvetica findfont}if +D length dict/newdict x{ +1 index/FID ne{1 index/FontMatrix eq{[1 0 0 -1 0 0]matrix concatmatrix}if +newdict 3 1 r put}{P P}ie}forall +newdict/Encoding mv put +fSt 8 fSt length 8 sub gi cvs length 8 add +fSt 0 rot gi cvn newdict definefont}ie}b/ts{gs xl ro 0 0 M}b +/nl{0 e xl 0 0 M}b/tx{ft e g e sf m rot D 96 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 +719 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +3760 6420 M +7020 6420 l +7020 7960 l +3760 7960 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 +5671 7178 M +4965 7178 l +st +5109 7238 M +5815 7238 l +st +gs +20 sl +5845 7188 5845 7188 5845 +7188 5670 7188 5845 7188 5845 7188 5645 7126 5670 7156 5670 7188 5845 7188 +5645 7126 5645 7126 4 5845 7188 129 Sp +gr +gs +20 sl +4935 7228 4935 7228 4935 +7228 5135 7290 4935 7228 4935 7228 5110 7241 5135 7290 5135 7290 4935 7228 +5110 7228 5110 7228 4 4935 7228 129 Sp +gr +gr +0 6746 7304 ts +0 32896 0 C +64 +10 0 tx +(3)show +0 10 0 tx +(R)show +gr +0 6758 7904 ts +65535 0 0 C +64 10 0 tx +(1)show +0 10 0 tx +(X)show +gr +0 3805 7304 ts +0 0 65535 C +64 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6744 l +4572 7081 l +4552 7081 l +cp +f +gr +gs +20 +D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +6293 6745 M +6313 6745 l +6313 +7081 l +6293 7081 l +cp +f +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/Surface_Recombination_Single/groups.py b/input/kinetics/families/Surface_Recombination_Single/groups.py new file mode 100644 index 0000000000..38d52f8a28 --- /dev/null +++ b/input/kinetics/families/Surface_Recombination_Single/groups.py @@ -0,0 +1,162 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Recombination_Single/groups" +shortDesc = u"" +longDesc = u""" +Surface addition where two single bonds combine to make a double bonded species. + + *2=*3 *4 *2-*3-*4 + | + | ----> || + +~*1~ ~*5~ ~*1~ ~*5~ + +The rate, which should be in mol/m2/s, +will be given by k * (mol/m2) * (mol/m2) * (mol/m3) +so k should be in (m5/mol2/s). We will use sticking coefficients. +""" + +template(reactants=["Adsorbate1", "Adsorbate2"], products=["Adsorbate3","VacantSite"], ownReverse=False) + +reverse = "Surface_Bond_Fission_Single" + +reactantNum=2 +productNum=2 + +recipe(actions=[ + ['CHANGE_BOND', '*2', -1, '*3'], + ['CHANGE_BOND', '*1', 1, '*2'], + ['BREAK_BOND', '*4', 1, '*5'], + ['FORM_BOND', '*3', 1, '*4'], +]) + +entry( + index = 1, + label = "Adsorbate1", + group = +""" +1 *1 Xo ux p0 c0 {2,S} +2 *2 R!H ux px cx {1,S} {3,[D,T]} +3 *3 R!H ux px cx {2,[D,T]} +""", + kinetics = None, +) + +entry( + index = 2, + label="Adsorbate2", + group = +""" +1 *5 Xo ux px cx {2,S} +2 *4 R ux px cx {1,S} +""", + kinetics = None, +) + +entry( + index = 3, + label = "C", + group = +""" +1 *1 Xo ux p0 c0 {2,S} +2 *2 C ux px cx {1,S} {3,[D,T]} +3 *3 R!H ux px cx {2,[D,T]} +""", + kinetics = None, +) + +entry( + index = 4, + label = "C=", + group = +""" +1 *1 Xo ux p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,D} +3 *3 R!H ux px cx {2,D} +""", + kinetics = None, +) + + +entry( + index = 5, + label = "C=O", + group = +""" +1 *1 Xo ux p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,D} +3 *3 O ux px cx {2,D} +""", + kinetics = None, +) + +entry( + index = 6, + label = "C=C", + group = +""" +1 *1 Xo ux p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,D} +3 *3 C u0 p0 c0 {2,D} +""", + kinetics = None, +) + +entry( + index = 7, + label = "C#", + group = +""" +1 *1 Xo ux p0 c0 {2,S} +2 *2 C u0 p0 c0 {1,S} {3,T} +3 *3 C ux px cx {2,T} +""", + kinetics = None, +) + +entry( + index = 8, + label="H-*", + group = +""" +1 *5 Xo u0 p0 c0 {2,S} +2 *4 H u0 p0 c0 {1,S} +""", + kinetics = None, +) + +entry( + index = 9, + label="O-*", + group = +""" +1 *5 Xo u0 p0 c0 {2,S} +2 *4 O u0 p2 c0 {1,S} +""", + kinetics = None, +) + +entry( + index = 10, + label="C-*", + group = +""" +1 *5 Xo u0 p0 c0 {2,S} +2 *4 C u0 p0 c0 {1,S} +""", + kinetics = None, +) + +tree( +""" +L1: Adsorbate1 + L2: C + L3: C= + L4: C=O + L4: C=C + L3: C# +L1: Adsorbate2 + L2: H-* + L2: O-* + L2: C-* +""" +) diff --git a/input/kinetics/families/Surface_Recombination_Single/rules.py b/input/kinetics/families/Surface_Recombination_Single/rules.py new file mode 100644 index 0000000000..ae8982337b --- /dev/null +++ b/input/kinetics/families/Surface_Recombination_Single/rules.py @@ -0,0 +1,28 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Surface_Addition_Dangling/rules" +shortDesc = u"" +longDesc = u""" +Eley Rideal mechanism for a gas phase double or triple bonded species. +""" +entry( + index = 29, + label = "C=O;H-*", + kinetics = SurfaceArrheniusBEP( + A = (8.97112, 'm^2/(mol*s)'), + n = 0., + alpha = 0.54, + E0 = (20.9850987, 'kcal/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 1, + shortDesc = u"""Default""", + longDesc = u""" +Reaction 29 from table 2 in "Mechanism of Methanol Synthesis on Cu through CO2 +and CO Hydrogenation", Grabow and Mavrikakis. doi:10.1021/cs200055d + +E0 is Ea +""" +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Recombination_Single/template.cdx b/input/kinetics/families/Surface_Recombination_Single/template.cdx new file mode 100644 index 0000000000..fec8e122e7 Binary files /dev/null and b/input/kinetics/families/Surface_Recombination_Single/template.cdx differ diff --git a/input/kinetics/families/Surface_Recombination_Single/template.eps b/input/kinetics/families/Surface_Recombination_Single/template.eps new file mode 100644 index 0000000000..4251b8615c --- /dev/null +++ b/input/kinetics/families/Surface_Recombination_Single/template.eps @@ -0,0 +1,603 @@ +%!PS-Adobe-2.0 EPSF-1.2 +%%Creator: ChemDraw 17.1.0.105 +%%Title: template.eps +%%CreationDate: 12/6/2019 11:37 AM +%%DocumentSuppliedProcSets: chemdict30 24 13 +%%DocumentFonts: Helvetica Helvetica Times-Roman +%%BoundingBox: 80 336 459 383 +%%DocumentProcessColors: Cyan Magenta Yellow Black +%%EndComments +%%BeginProcSet: chemdict30 24 13 +% ChemDraw Laser Prep +% © 1985-2018 PerkinElmer Informatics, Inc. 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+/Agrave/Aacute/Acircumflex/Atilde/Adieresis/Aring/AE/Ccedilla +/Egrave/Eacute/Ecircumflex/Edieresis/Igrave/Iacute/Icircumflex/Idieresis +/Eth/Ntilde/Ograve/Oacute/Ocircumflex/Otilde/Odieresis/multiply +/Oslash/Ugrave/Uacute/Ucircumflex/Udieresis/Yacute/Thorn/germandbls +/agrave/aacute/acircumflex/atilde/adieresis/aring/ae/ccedilla +/egrave/eacute/ecircumflex/edieresis/igrave/iacute/icircumflex/idieresis +/eth/ntilde/ograve/oacute/ocircumflex/otilde/odieresis/divide +/oslash/ugrave/uacute/ucircumflex/udieresis/yacute/thorn/ydieresis +mv 128 128 gi as P/fSt 50 string d(ChemDraw)fSt copy P/fD{D/Symbol eq{ +findfont[1 0 0 -1 0 0]makefont}{D {findfont}stopped{/Helvetica findfont}if +D length dict/newdict x{ +1 index/FID ne{1 index/FontMatrix eq{[1 0 0 -1 0 0]matrix concatmatrix}if +newdict 3 1 r put}{P P}ie}forall +newdict/Encoding mv put +fSt 8 fSt length 8 sub gi cvs length 8 add +fSt 0 rot gi cvn newdict definefont}ie}b/ts{gs xl ro 0 0 M}b +/nl{0 e xl 0 0 M}b/tx{ft e g e sf m rot D 96 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 +719 SPe[ +/Helvetica +fD +/Helvetica +fD +/Times-Roman +fD]/ft x +1600 6720 M +9180 6720 l +9180 7660 l +1600 7660 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 +5379 7178 M +4673 7178 l +st +4817 7238 M +5523 7238 l +st +gs +20 sl +5553 7188 5553 7188 5553 +7188 5378 7188 5553 7188 5553 7188 5353 7126 5378 7155 5378 7188 5553 7188 +5353 7126 5353 7126 4 5553 7188 129 Sp +gr +gs +20 sl +4643 7228 4643 7228 4643 +7228 4843 7290 4643 7228 4643 7228 4818 7241 4843 7290 4843 7290 4643 7228 +4818 7228 4818 7228 4 4643 7228 129 Sp +gr +gr +0 6755 7004 ts +0 32896 0 C +64 +10 0 tx +(3)show +0 10 0 tx +(R)show +gr +0 6167 7604 ts +65535 0 0 C +64 10 0 tx +(1)show +0 10 0 tx +(X)show +gr +0 1657 7004 ts +0 0 65535 C +64 10 0 tx +(2)show +0 10 0 tx +(R)show +gr +0 1669 7604 ts +65535 0 0 C +64 10 0 tx +(1)show +0 10 0 tx +(X)show +gr +0 2259 7005 ts +0 32896 0 C +64 10 1 tx +(3)show +0 10 1 tx +(R)show +gr +0 6157 7005 ts +0 0 65535 C +64 10 1 tx +(2)show +0 10 1 tx +(R)show +gr +0 7357 7005 ts +65535 0 65535 C +64 10 1 tx +(4)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +1804 7043 M +1824 7043 l +1828 7379 l +1808 7379 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 6937 M +6420 6917 l +6722 6916 l +6722 6936 l +cp +f +gr +0 +3078 7269 ts +0 0 0 C +0 12 2 tx +(+)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2226 6881 M +2226 6901 l +1920 6900 l +1920 6880 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +2226 6953 M +2226 6973 l +1920 6972 l +1920 6952 l +cp +f +gr +0 +3821 7605 ts +65535 32896 0 C +64 10 0 tx +(5)show +0 10 0 tx +(X)show +gr +0 3811 7005 ts +65535 0 65535 C +64 10 1 tx +(4)show +0 10 1 tx +(R)show +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +3957 7045 M +3977 7045 l +3980 7383 l +3960 7383 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +6267 7045 M +6287 7045 l +6290 7379 l +6270 7380 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 0 0 C +np +6339 7044 M +6359 7044 l +6362 7379 l +6342 7379 l +cp +f +gr +gs +20 D sl/lW x +40 /cW x +80 /bW x +54 /hS x +0 +0 0 C +np +7319 6917 M +7319 6937 l +7018 6936 l +7018 6916 l +cp +f +gr +0 8176 7269 +ts +0 0 0 C +0 12 2 tx +(+)show +gr +0 8906 7605 ts +65535 32896 0 C +64 10 0 tx +(5)show +0 10 0 tx +(X)show +gr +gr +end +%%Trailer +showpage diff --git a/input/kinetics/families/recommended.py b/input/kinetics/families/recommended.py index 2da5bb3acc..3af70acea3 100644 --- a/input/kinetics/families/recommended.py +++ b/input/kinetics/families/recommended.py @@ -81,12 +81,20 @@ 'Surface_Adsorption_Dissociative', 'Surface_Dissociation', 'Surface_Abstraction', + 'Surface_EleyRideal_Addition_Multiple_Bond', + 'Surface_Migration', + 'Surface_Dissociation_Double_vdW', + 'Surface_Addition_Single_vdW', + 'Surface_Dissociation_vdW', + 'Surface_Abstraction_vdW', + 'Surface_Dual_Adsorption_vdW', + 'Surface_Recombination_Single', + 'Surface_Adsorption_Abstraction_vdW', } # Surface chemistry families that are under development and not yet working well. surface_development = { 'Surface_Adsorption_Double', - 'Surface_Dissociation_vdW', 'Surface_Adsorption_Bidentate', 'Surface_Bidentate_Dissociation' # 'Surface_Recombination' #DEPRECATED. USE Surface_Dissociation INSTEAD diff --git a/scripts/process_family_images.py b/scripts/process_family_images.py index ba23d21d6d..c6a9c51720 100644 --- a/scripts/process_family_images.py +++ b/scripts/process_family_images.py @@ -64,7 +64,9 @@ def generate_family_pdf(): database_directory = os.path.abspath(os.path.join(os.path.dirname(__file__), '..')) fam_dir = os.path.join(database_directory, 'input', 'kinetics', 'families') dir_list = os.listdir(fam_dir) + dir_list.remove('__pycache__') fam_list = sorted([item for item in dir_list if os.path.isdir(os.path.join(fam_dir, item))]) # Only keep folders + print(fam_list) temp_dir = os.path.join(database_directory, 'temp') img_dir = os.path.join(temp_dir, 'images')