From bccb8e65b8c2a5a97f579ccb4d5630981e1014d6 Mon Sep 17 00:00:00 2001 From: Yunsie Chung Date: Mon, 19 Jul 2021 12:08:30 -0400 Subject: [PATCH] 1,3_Insertion_CO2 tree fitting --- .../families/1,3_Insertion_CO2/groups.py | 833 ++---------------- .../families/1,3_Insertion_CO2/rules.py | 118 ++- .../1,3_Insertion_CO2/training/reactions.py | 79 +- 3 files changed, 185 insertions(+), 845 deletions(-) diff --git a/input/kinetics/families/1,3_Insertion_CO2/groups.py b/input/kinetics/families/1,3_Insertion_CO2/groups.py index bc1653b831..3298fa7438 100644 --- a/input/kinetics/families/1,3_Insertion_CO2/groups.py +++ b/input/kinetics/families/1,3_Insertion_CO2/groups.py @@ -2,16 +2,21 @@ # encoding: utf-8 name = "1,3_Insertion_CO2/groups" -shortDesc = u"" -longDesc = u""" +shortDesc = "" +longDesc = """ """ -template(reactants=["CO2_CS2", "RR'"], products=["R_(CS2)_R'"], ownReverse=False) +template(reactants=["Root"], products=["R_(CS2)_R'"], ownReverse=False) reverse = "1,2_Elimination_CO2" reversible = True +reactantNum = 2 +productNum = 1 + +autoGenerated = True + recipe(actions=[ ['BREAK_BOND', '*3', 1, '*4'], ['CHANGE_BOND', '*1', -1, '*2'], @@ -21,827 +26,107 @@ entry( index = 0, - label = "CO2_CS2", - group = "OR{CO2, CS2}", - kinetics = None, -) - -entry( - index = 1, - label = "RR'", - group = "OR{R_H, R_R'}", - kinetics = None, -) - -entry( - index = 2, - label = "CO2", - group = "OR{CO2_Od, CO2_Cdd}", - kinetics = None, -) - -entry( - index = 3, - label = "CO2_Od", - group = -""" -1 *2 Cdd u0 {2,D} {3,D} -2 *1 O2d u0 {1,D} -3 O2d u0 {1,D} -""", - kinetics = None, -) - -entry( - index = 4, - label = "CO2_Cdd", - group = -""" -1 *1 Cdd u0 {2,D} {3,D} -2 *2 O2d u0 {1,D} -3 O2d u0 {1,D} -""", - kinetics = None, -) - -entry( - index = 5, - label = "CS2", - group = "OR{CS2_Sd, CS2_Cdd}", - kinetics = None, -) - -entry( - index = 6, - label = "CS2_Sd", - group = -""" -1 *2 Cdd u0 {2,D} {3,D} -2 *1 S2d u0 {1,D} -3 S2d u0 {1,D} -""", - kinetics = None, -) - -entry( - index = 7, - label = "CS2_Cdd", - group = -""" -1 *1 Cdd u0 {2,D} {3,D} -2 *2 S2d u0 {1,D} -3 S2d u0 {1,D} -""", - kinetics = None, -) - -entry( - index = 8, - label = "R_H", - group = -""" -1 *3 [H,Cs,Cd,Cb,Sis,Sid,N] u0 c0 {2,S} -2 *4 H u0 p0 c0 {1,S} -""", - kinetics = None, -) - -entry( - index = 9, - label = "H2", - group = -""" -1 *3 H u0 p0 c0 {2,S} -2 *4 H u0 p0 c0 {1,S} -""", - kinetics = None, -) - -entry( - index = 10, - label = "Cb_H", - group = -""" -1 *3 Cb u0 c0 {2,B} {3,S} -2 [Cb,Cbf] u0 {1,B} -3 *4 H u0 p0 c0 {1,S} -""", - kinetics = None, -) - -entry( - index = 11, - label = "Cd_H", - group = -""" -1 *3 Cd u0 c0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} -3 *4 H u0 p0 c0 {1,S} -4 R u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 12, - label = "Cd_pri", - group = -""" -1 *3 Cd u0 c0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} -3 *4 H u0 p0 c0 {1,S} -4 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 13, - label = "Cd_sec", - group = -""" -1 *3 Cd u0 c0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} -3 *4 H u0 p0 c0 {1,S} -4 R!H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 14, - label = "Cd/H/NonDeC", - group = -""" -1 *3 Cd u0 c0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} -3 *4 H u0 p0 c0 {1,S} -4 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 15, - label = "Cd/H/NonDeO", - group = -""" -1 *3 Cd u0 c0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} -3 *4 H u0 p0 c0 {1,S} -4 O2s u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 16, - label = "Cd/H/OneDe", - group = -""" -1 *3 Cd u0 c0 {2,D} {3,S} {4,S} -2 Cd u0 {1,D} -3 *4 H u0 p0 c0 {1,S} -4 [Cd,Ct,Cb,CO,CS] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 17, - label = "Cs_H", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 R u0 {1,S} -4 R u0 {1,S} -5 R u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 18, - label = "C_methane", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 19, - label = "C_pri", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 R!H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 20, - label = "C_pri/NonDeC", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 21, - label = "C_pri/NonDeO", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 O2s u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 22, - label = "C_pri/NonDeS", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 S2s u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 23, - label = "C_pri/De", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 [Cd,Ct,Cb,CO,CS] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 24, - label = "C_sec", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 R!H u0 {1,S} -5 R!H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 25, - label = "C/H2/NonDeC", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 Cs u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 26, - label = "C/H2/NonDeO", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 O u0 {1,S} -5 [Cs,O,S] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 27, - label = "C/H2/CsO", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 O u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 28, - label = "C/H2/O2", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 O u0 {1,S} -5 O u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 29, - label = "C/H2/NonDeS", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 S u0 {1,S} -5 [Cs,O,S] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 30, - label = "C/H2/CsS", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 S u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 31, - label = "C/H2/S2", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 S u0 {1,S} -5 S u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 32, - label = "C/H2/OneDe", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 [Cd,Ct,CO,CS,Cb] u0 {1,S} -5 [Cs,O] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 33, - label = "C/H2/OneDeC", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 [Cd,Ct,CO,CS,Cb] u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 34, - label = "C/H2/OneDeO", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 [Cd,Ct,CO,CS,Cb] u0 {1,S} -5 O u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 35, - label = "C/H2/TwoDe", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 H u0 {1,S} -4 [Cd,Ct,CO,CS,Cb] u0 {1,S} -5 [Cd,Ct,CO,CS,Cb] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 36, - label = "C_ter", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 R!H u0 {1,S} -4 R!H u0 {1,S} -5 R!H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 37, - label = "C/H/NonDeC", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cs,O,S] u0 {1,S} -4 [Cs,O,S] u0 {1,S} -5 [Cs,O,S] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 38, - label = "C/H/Cs3", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 Cs u0 {1,S} -4 Cs u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 39, - label = "C/H/NDMustO", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 O u0 {1,S} -4 [Cs,O,S] u0 {1,S} -5 [Cs,O,S] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 40, - label = "C/H/OneDe", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 [Cs,O,S] u0 {1,S} -5 [Cs,O,S] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 41, - label = "C/H/Cs2", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 Cs u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 42, - label = "C/H/ODMustO", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 O u0 {1,S} -5 [Cs,O,S] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 43, - label = "C/H/TwoDe", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 [Cd,Ct,Cb,CO,CS] u0 {1,S} -5 [Cs,O,S] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 44, - label = "C/H/Cs", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 [Cd,Ct,Cb,CO,CS] u0 {1,S} -5 Cs u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 45, - label = "C/H/TDMustO", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 [Cd,Ct,Cb,CO,CS] u0 {1,S} -5 O u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 46, - label = "C/H/ThreeDe", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 H u0 p0 c0 {1,S} -3 [Cd,Ct,Cb,CO,CS] u0 {1,S} -4 [Cd,Ct,Cb,CO,CS] u0 {1,S} -5 [Cd,Ct,Cb,CO,CS] u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 47, - label = "R_R'", - group = -""" -1 *3 [Cs,Sis,N,S] u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 [Cs,Cd,Cb,Sis,Sid,N,S] u0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 48, - label = "Cs_Cs", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cs u0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -""", - kinetics = None, -) - -entry( - index = 49, - label = "C_methyl_C_methyl", - group = -""" -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cs u0 c0 {1,S} {6,S} {7,S} {8,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -6 H u0 {2,S} -7 H u0 {2,S} -8 H u0 {2,S} -""", - kinetics = None, -) - -entry( - index = 50, - label = "C_methyl_C_pri", + label = "Root", group = """ -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cs u0 c0 {1,S} {6,S} {7,S} {8,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -6 H u0 {2,S} -7 H u0 {2,S} -8 C u0 {2,S} +1 *3 [H,Cs,Cd,Cb,Sis,Sid,N,S] u0 c0 {2,S} +2 *4 [H,Cs,Cd,Cb,Sis,Sid,N,S] u0 c0 {1,S} +3 *2 [Cdd,O2d,S2d] u0 {4,D} +4 *1 [Cdd,O2d,S2d] u0 {3,D} """, kinetics = None, ) entry( - index = 51, - label = "C_methyl_C_sec", + index = 1, + label = "Root_2CbCdCsHNSSidSis->H", group = """ -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cs u0 c0 {1,S} {6,S} {7,S} {8,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -6 H u0 {2,S} -7 C u0 {2,S} -8 C u0 {2,S} +1 *3 [H,Cs,Cd,Cb,Sis,Sid,N,S] u0 c0 {2,S} +2 *4 H u0 c0 {1,S} +3 *2 O2d u0 {4,D} +4 *1 Cdd u0 {3,D} """, kinetics = None, ) entry( - index = 52, - label = "C_methyl_C_ter", + index = 2, + label = "Root_2CbCdCsHNSSidSis->H_1CbCdCsHNSSidSis->H", group = """ -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cs u0 c0 {1,S} {6,S} {7,S} {8,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -6 C u0 {2,S} -7 C u0 {2,S} -8 C u0 {2,S} +1 *3 H u0 c0 r0 {2,S} +2 *4 H u0 c0 r0 {1,S} +3 *2 O2d u0 r0 {4,D} +4 *1 Cdd u0 r0 {3,D} """, kinetics = None, ) entry( - index = 53, - label = "Cs_Cd", + index = 3, + label = "Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H", group = """ -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cd u0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} +1 *3 Cs u0 c0 {2,S} +2 *4 H u0 c0 {1,S} +3 *2 O2d u0 {4,D} +4 *1 Cdd u0 {3,D} """, kinetics = None, ) entry( - index = 54, - label = "C_methyl_Cd_pri", + index = 4, + label = "Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R", group = """ -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cd u0 c0 {1,S} {6,S} {7,D} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -6 H u0 {2,S} -7 C u0 {2,D} +1 *3 Cs u0 c0 {2,S} {5,[S,D,T,B,Q]} +2 *4 H u0 c0 {1,S} +3 *2 O2d u0 {4,D} +4 *1 Cdd u0 {3,D} +5 R!H ux {1,[S,D,T,B,Q]} """, kinetics = None, ) entry( - index = 55, - label = "C_methyl_Cd_sec", + index = 5, + label = "Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R_Ext-1Cs-R", group = """ -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cd u0 c0 {1,S} {6,S} {7,D} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} -6 C u0 {2,S} -7 C u0 {2,D} +1 *3 Cs u0 c0 r0 {2,S} {5,[S,D,T,B,Q]} {6,[S,D,T,B,Q]} +2 *4 H u0 c0 r0 {1,S} +3 *2 O2d u0 r0 {4,D} +4 *1 Cdd u0 r0 {3,D} +5 R!H ux {1,[S,D,T,B,Q]} +6 R!H ux {1,[S,D,T,B,Q]} """, kinetics = None, ) entry( - index = 56, - label = "Cs_Cb", + index = 6, + label = "Root_N-2CbCdCsHNSSidSis->H", group = """ -1 *3 Cs u0 c0 {2,S} {3,S} {4,S} {5,S} -2 *4 Cb u0 c0 {1,S} -3 H u0 {1,S} -4 H u0 {1,S} -5 H u0 {1,S} +1 *3 [H,Cs,Cd,Cb,Sis,Sid,N,S] u0 c0 {2,S} +2 *4 Cs u0 c0 {1,S} +3 *2 [Cdd,O2d,S2d] u0 {4,D} +4 *1 [Cdd,O2d,S2d] u0 {3,D} """, kinetics = None, ) tree( """ -L1: CO2_CS2 - L2: CO2 - L3: CO2_Od - L3: CO2_Cdd - L2: CS2 - L3: CS2_Sd - L3: CS2_Cdd -L1: RR' - L2: R_H - L3: H2 - L3: Cb_H - L3: Cd_H - L4: Cd_pri - L4: Cd_sec - L5: Cd/H/NonDeC - L5: Cd/H/NonDeO - L5: Cd/H/OneDe - L3: Cs_H - L4: C_methane - L4: C_pri - L5: C_pri/NonDeC - L5: C_pri/NonDeO - L5: C_pri/NonDeS - L5: C_pri/De - L4: C_sec - L5: C/H2/NonDeC - L5: C/H2/NonDeO - L6: C/H2/CsO - L6: C/H2/O2 - L5: C/H2/NonDeS - L6: C/H2/CsS - L6: C/H2/S2 - L5: C/H2/OneDe - L6: C/H2/OneDeC - L6: C/H2/OneDeO - L5: C/H2/TwoDe - L4: C_ter - L5: C/H/NonDeC - L6: C/H/Cs3 - L6: C/H/NDMustO - L5: C/H/OneDe - L6: C/H/Cs2 - L6: C/H/ODMustO - L5: C/H/TwoDe - L6: C/H/Cs - L6: C/H/TDMustO - L5: C/H/ThreeDe - L2: R_R' - L3: Cs_Cs - L4: C_methyl_C_methyl - L4: C_methyl_C_pri - L4: C_methyl_C_sec - L4: C_methyl_C_ter - L3: Cs_Cd - L4: C_methyl_Cd_pri - L4: C_methyl_Cd_sec - L3: Cs_Cb +L1: Root + L2: Root_2CbCdCsHNSSidSis->H + L3: Root_2CbCdCsHNSSidSis->H_1CbCdCsHNSSidSis->H + L3: Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H + L4: Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R + L5: Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R_Ext-1Cs-R + L2: Root_N-2CbCdCsHNSSidSis->H """ ) diff --git a/input/kinetics/families/1,3_Insertion_CO2/rules.py b/input/kinetics/families/1,3_Insertion_CO2/rules.py index b92c4301b2..549ebb6526 100644 --- a/input/kinetics/families/1,3_Insertion_CO2/rules.py +++ b/input/kinetics/families/1,3_Insertion_CO2/rules.py @@ -2,8 +2,8 @@ # encoding: utf-8 name = "1,3_Insertion_CO2/rules" -shortDesc = u"" -longDesc = u""" +shortDesc = "" +longDesc = """ 572 - 575 Some of the tortional motions in the alkyl part of the transition states are treated as free rotations as they are relatively loose TSs. @@ -12,17 +12,107 @@ presumably matching the top level node. """ entry( - index = 571, - label = "CO2_CS2;RR'", - kinetics = ArrheniusEP( - A = (100000, 'cm^3/(mol*s)'), - n = 2, - alpha = 0, - E0 = (75, 'kcal/mol'), - Tmin = (300, 'K'), - Tmax = (1500, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", + index = 1, + label = "Root", + kinetics = ArrheniusBM(A=(0.000102116,'m^3/(mol*s)'), n=3.29652, w0=(820500,'J/mol'), E0=(305487,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=0.034441443868039615, var=7.910772835870151, Tref=1000.0, N=5, data_mean=0.0, correlation='Root',), comment="""BM rule fitted to 5 training reactions at node Root + Total Standard Deviation in ln(k): 5.725073441582979"""), + rank = 11, + shortDesc = """BM rule fitted to 5 training reactions at node Root +Total Standard Deviation in ln(k): 5.725073441582979""", + longDesc = +""" +BM rule fitted to 5 training reactions at node Root +Total Standard Deviation in ln(k): 5.725073441582979 +""", +) + +entry( + index = 2, + label = "Root_2CbCdCsHNSSidSis->H", + kinetics = ArrheniusBM(A=(0.000175732,'m^3/(mol*s)'), n=3.22799, w0=(839250,'J/mol'), E0=(304727,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=0.09003460388904383, var=3.8152453295400095, Tref=1000.0, N=4, data_mean=0.0, correlation='Root_2CbCdCsHNSSidSis->H',), comment="""BM rule fitted to 4 training reactions at node Root_2CbCdCsHNSSidSis->H + Total Standard Deviation in ln(k): 4.141997058721065"""), + rank = 11, + shortDesc = """BM rule fitted to 4 training reactions at node Root_2CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 4.141997058721065""", + longDesc = +""" +BM rule fitted to 4 training reactions at node Root_2CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 4.141997058721065 +""", +) + +entry( + index = 3, + label = "Root_N-2CbCdCsHNSSidSis->H", + kinetics = ArrheniusBM(A=(7.3e-05,'m^3/(mol*s)'), n=3.13, w0=(745500,'J/mol'), E0=(457668,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=0.0, var=33.13686319048999, Tref=1000.0, N=1, data_mean=0.0, correlation='Root_N-2CbCdCsHNSSidSis->H',), comment="""BM rule fitted to 1 training reactions at node Root_N-2CbCdCsHNSSidSis->H + Total Standard Deviation in ln(k): 11.540182761524994"""), + rank = 11, + shortDesc = """BM rule fitted to 1 training reactions at node Root_N-2CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 11.540182761524994""", + longDesc = +""" +BM rule fitted to 1 training reactions at node Root_N-2CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 11.540182761524994 +""", +) + +entry( + index = 4, + label = "Root_2CbCdCsHNSSidSis->H_1CbCdCsHNSSidSis->H", + kinetics = ArrheniusBM(A=(1510,'m^3/(mol*s)'), n=1.23, w0=(871500,'J/mol'), E0=(307270,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=0.0, var=33.13686319048999, Tref=1000.0, N=1, data_mean=0.0, correlation='Root_2CbCdCsHNSSidSis->H_1CbCdCsHNSSidSis->H',), comment="""BM rule fitted to 1 training reactions at node Root_2CbCdCsHNSSidSis->H_1CbCdCsHNSSidSis->H + Total Standard Deviation in ln(k): 11.540182761524994"""), + rank = 11, + shortDesc = """BM rule fitted to 1 training reactions at node Root_2CbCdCsHNSSidSis->H_1CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 11.540182761524994""", + longDesc = +""" +BM rule fitted to 1 training reactions at node Root_2CbCdCsHNSSidSis->H_1CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 11.540182761524994 +""", +) + +entry( + index = 5, + label = "Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H", + kinetics = ArrheniusBM(A=(0.00124375,'m^3/(mol*s)'), n=2.93231, w0=(828500,'J/mol'), E0=(310232,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=-0.0075186726087721435, var=1.1062410781291196, Tref=1000.0, N=3, data_mean=0.0, correlation='Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H',), comment="""BM rule fitted to 3 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H + Total Standard Deviation in ln(k): 2.1274313108796026"""), + rank = 11, + shortDesc = """BM rule fitted to 3 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 2.1274313108796026""", + longDesc = +""" +BM rule fitted to 3 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H +Total Standard Deviation in ln(k): 2.1274313108796026 +""", +) + +entry( + index = 6, + label = "Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R", + kinetics = ArrheniusBM(A=(0.00469141,'m^3/(mol*s)'), n=2.69282, w0=(828500,'J/mol'), E0=(309525,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=3.895124125462989e-05, var=2.520758984959268, Tref=1000.0, N=2, data_mean=0.0, correlation='Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R',), comment="""BM rule fitted to 2 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R + Total Standard Deviation in ln(k): 3.1829953545126424"""), + rank = 11, + shortDesc = """BM rule fitted to 2 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R +Total Standard Deviation in ln(k): 3.1829953545126424""", + longDesc = +""" +BM rule fitted to 2 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R +Total Standard Deviation in ln(k): 3.1829953545126424 +""", +) + +entry( + index = 7, + label = "Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R_Ext-1Cs-R", + kinetics = ArrheniusBM(A=(0.106,'m^3/(mol*s)'), n=2.13, w0=(828500,'J/mol'), E0=(307743,'J/mol'), Tmin=(300,'K'), Tmax=(1500,'K'), uncertainty=RateUncertainty(mu=0.0, var=33.13686319048999, Tref=1000.0, N=1, data_mean=0.0, correlation='Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R_Ext-1Cs-R',), comment="""BM rule fitted to 1 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R_Ext-1Cs-R + Total Standard Deviation in ln(k): 11.540182761524994"""), + rank = 11, + shortDesc = """BM rule fitted to 1 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R_Ext-1Cs-R +Total Standard Deviation in ln(k): 11.540182761524994""", + longDesc = +""" +BM rule fitted to 1 training reactions at node Root_2CbCdCsHNSSidSis->H_N-1CbCdCsHNSSidSis->H_Ext-1Cs-R_Ext-1Cs-R +Total Standard Deviation in ln(k): 11.540182761524994 +""", ) diff --git a/input/kinetics/families/1,3_Insertion_CO2/training/reactions.py b/input/kinetics/families/1,3_Insertion_CO2/training/reactions.py index 67eb87dac0..c1cbd038c0 100644 --- a/input/kinetics/families/1,3_Insertion_CO2/training/reactions.py +++ b/input/kinetics/families/1,3_Insertion_CO2/training/reactions.py @@ -2,27 +2,20 @@ # encoding: utf-8 name = "1,3_Insertion_CO2/training" -shortDesc = u"Reaction kinetics used to generate rate rules" -longDesc = u""" +shortDesc = "Reaction kinetics used to generate rate rules" +longDesc = """ 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 = 1, + index = 0, label = "H2 + CO2 <=> CH2O2", degeneracy = 1.0, - kinetics = Arrhenius( - A = (1.51e+09, 'cm^3/(mol*s)'), - n = 1.23, - Ea = (309.198, 'kJ/mol'), - T0 = (1, 'K'), - Tmin = (300, 'K'), - Tmax = (1500, 'K'), - ), + kinetics = Arrhenius(A=(1.51e+09,'cm^3/(mol*s)'), n=1.23, Ea=(309.198,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(1500,'K')), rank = 5, - shortDesc = u"""[87]CBS-QB3 calculations from Sumathi 2003.""", + shortDesc = """[87]CBS-QB3 calculations from Sumathi 2003.""", longDesc = -u""" +""" Degeneracy not recalculated Converted to training reaction from rate rule: CO2_Cdd;H2 @@ -30,81 +23,53 @@ ) entry( - index = 2, + index = 1, label = "CH4 + CO2 <=> C2H4O2", degeneracy = 8.0, - kinetics = Arrhenius( - A = (36240, 'cm^3/(mol*s)'), - n = 2.83, - Ea = (331.373, 'kJ/mol'), - T0 = (1, 'K'), - Tmin = (300, 'K'), - Tmax = (1500, 'K'), - ), + kinetics = Arrhenius(A=(36240,'cm^3/(mol*s)'), n=2.83, Ea=(331.373,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(1500,'K')), rank = 5, - shortDesc = u"""[87]CBS-QB3 calculations from Sumathi 2003.""", + shortDesc = """[87]CBS-QB3 calculations from Sumathi 2003.""", longDesc = -u""" +""" Converted to training reaction from rate rule: CO2_Cdd;C_methane """, ) entry( - index = 3, + index = 2, label = "C2H6 + CO2 <=> C3H6O2", degeneracy = 12.0, - kinetics = Arrhenius( - A = (130800, 'cm^3/(mol*s)'), - n = 2.56, - Ea = (320.494, 'kJ/mol'), - T0 = (1, 'K'), - Tmin = (300, 'K'), - Tmax = (1500, 'K'), - ), + kinetics = Arrhenius(A=(130800,'cm^3/(mol*s)'), n=2.56, Ea=(320.494,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(1500,'K')), rank = 5, - shortDesc = u"""[87]CBS-QB3 calculations from Sumathi 2003.""", + shortDesc = """[87]CBS-QB3 calculations from Sumathi 2003.""", longDesc = -u""" +""" Converted to training reaction from rate rule: CO2_Cdd;C_pri/NonDeC """, ) entry( - index = 4, + index = 3, label = "C3H8 + CO2 <=> C4H8O2", degeneracy = 4.0, - kinetics = Arrhenius( - A = (424000, 'cm^3/(mol*s)'), - n = 2.13, - Ea = (322.168, 'kJ/mol'), - T0 = (1, 'K'), - Tmin = (300, 'K'), - Tmax = (1500, 'K'), - ), + kinetics = Arrhenius(A=(424000,'cm^3/(mol*s)'), n=2.13, Ea=(322.168,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(1500,'K')), rank = 5, - shortDesc = u"""[87]CBS-QB3 calculations from Sumathi 2003.""", + shortDesc = """[87]CBS-QB3 calculations from Sumathi 2003.""", longDesc = -u""" +""" Converted to training reaction from rate rule: CO2_Cdd;C/H2/NonDeC """, ) entry( - index = 5, + index = 4, label = "C3H8-2 + CO2-2 <=> C4H8O2-2", degeneracy = 4.0, - kinetics = Arrhenius( - A = (292, 'cm^3/(mol*s)'), - n = 3.13, - Ea = (493.712, 'kJ/mol'), - T0 = (1, 'K'), - Tmin = (300, 'K'), - Tmax = (1500, 'K'), - ), + kinetics = Arrhenius(A=(292,'cm^3/(mol*s)'), n=3.13, Ea=(493.712,'kJ/mol'), T0=(1,'K'), Tmin=(300,'K'), Tmax=(1500,'K')), rank = 10, - shortDesc = u"""Aaron Vandeputte calculation for methylpropanate using BMK/CBSB7""", + shortDesc = """Aaron Vandeputte calculation for methylpropanate using BMK/CBSB7""", longDesc = -u""" +""" Converted to training reaction from rate rule: CO2_Od;C_methyl_C_pri """, )