diff --git a/input/kinetics/families/1,2_shiftS/groups.py b/input/kinetics/families/1,2_shiftS/groups.py index 6f3f52a61a..8e0543623e 100644 --- a/input/kinetics/families/1,2_shiftS/groups.py +++ b/input/kinetics/families/1,2_shiftS/groups.py @@ -18,6 +18,8 @@ ['LOSE_RADICAL', '*3', '1'], ]) +boundaryAtoms = ["*1", "*3"] + entry( index = 1, label = "XSYJ", diff --git a/input/kinetics/families/Birad_recombination/groups.py b/input/kinetics/families/Birad_recombination/groups.py index d0e33aafca..1e11688c41 100644 --- a/input/kinetics/families/Birad_recombination/groups.py +++ b/input/kinetics/families/Birad_recombination/groups.py @@ -24,6 +24,8 @@ kinetics = None, ) +boundaryAtoms = ["*1", "*2"] + entry( index = 2, label = "Y_rad_out", diff --git a/input/kinetics/families/Cyclic_Ether_Formation/groups.py b/input/kinetics/families/Cyclic_Ether_Formation/groups.py index e6498f4bde..a434656640 100644 --- a/input/kinetics/families/Cyclic_Ether_Formation/groups.py +++ b/input/kinetics/families/Cyclic_Ether_Formation/groups.py @@ -18,6 +18,8 @@ ['LOSE_RADICAL', '*1', '1'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "RnOO", diff --git a/input/kinetics/families/Cyclic_Ether_Formation/groups_OLD.py b/input/kinetics/families/Cyclic_Ether_Formation/groups_OLD.py new file mode 100644 index 0000000000..8af8777388 --- /dev/null +++ b/input/kinetics/families/Cyclic_Ether_Formation/groups_OLD.py @@ -0,0 +1,1319 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Cyclic_Ether_Formation/groups" +shortDesc = u"" +longDesc = u""" + +""" + +template(reactants=["RnOO"], products=["RO", "OR"], ownReverse=False) + +reverse = "OH+CyclicEther_Form_Alkyl-hydroperoxyl" + +recipe(actions=[ + ['BREAK_BOND', '*2', 'S', '*3'], + ['FORM_BOND', '*1', 'S', '*2'], + ['GAIN_RADICAL', '*3', '1'], + ['LOSE_RADICAL', '*1', '1'], +]) + +entry( + index = 1, + label = "RnOO", + group = "OR{R2OO, R3OO, R4OO, R5OO}", + kinetics = None, +) + +entry( + index = 2, + label = "Y_rad_intra", + group = +""" +1 *1 R!H u1 +""", + kinetics = None, +) + +entry( + index = 3, + label = "R2OO", + group = "OR{R2OOH, R2OOR, R2OOJ}", + kinetics = None, +) + +entry( + index = 4, + label = "R2OOJ", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u1 {3,S} +""", + kinetics = None, +) + +entry( + index = 5, + label = "R2OOJ_S", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u1 {3,S} +""", + kinetics = None, +) + +entry( + index = 6, + label = "R2OOH", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 7, + label = "R2OOH_S", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 5, + label = "R2OOH_SCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 CO u0 {1,S} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 6, + label = "R2OOH_D", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 7, + label = "R2OOR", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 R!H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 8, + label = "R2OOR_S", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 R!H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 9, + label = "R2OOR_SCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 CO u0 {1,S} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 R!H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 10, + label = "R2OOR_D", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *2 O u0 {2,S} {4,S} +4 *3 O u0 {3,S} {5,S} +5 R!H u0 {4,S} +""", + kinetics = None, +) + +entry( + index = 14, + label = "R3OO", + group = "OR{R3OOH, R3OOR, R3OOJ}", + kinetics = None, +) + +entry( + index = 15, + label = "R3OOJ", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u1 {4,S} +""", + kinetics = None, +) + +entry( + index = 16, + label = "R3OOH", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 17, + label = "R3OOH_SS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *5 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 13, + label = "R3OOH_SSCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *5 CO u0 {2,S} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 14, + label = "R3OOH_SD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *5 Cd u0 {2,D} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 15, + label = "R3OOH_DS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *5 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 16, + label = "R3OOR", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 R!H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 17, + label = "R3OOR_SS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *5 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 R!H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 18, + label = "R3OOR_SSCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *5 CO u0 {2,S} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 R!H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 19, + label = "R3OOR_SD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *5 Cd u0 {2,D} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 R!H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 20, + label = "R3OOR_DS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *5 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *2 O u0 {3,S} {5,S} +5 *3 O u0 {4,S} {6,S} +6 R!H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 26, + label = "R4OO", + group = "OR{R4OOH, R4OOR, R4OOJ}", + kinetics = None, +) + +entry( + index = 27, + label = "R4OOJ", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *6 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]} +4 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {3,[S,D]} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u1 {5,S} +""", + kinetics = None, +) + +entry( + index = 28, + label = "R4OOH", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *6 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]} +4 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {3,[S,D]} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 29, + label = "R4OOH_SSS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *5 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 23, + label = "R4OOH_SSSCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs] u0 {2,S} {4,S} +4 *5 CO u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 24, + label = "R4OOH_SSD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *5 Cd u0 {3,D} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 25, + label = "R4OOH_SDS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *6 Cd u0 {2,D} {4,S} +4 *5 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 26, + label = "R4OOH_DSS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *5 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 27, + label = "R4OOH_DSD", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *5 Cd u0 {3,D} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 28, + label = "R4OOR", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *6 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]} +4 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {3,[S,D]} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 R!H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 29, + label = "R4OOR_SSS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *5 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 R!H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 30, + label = "R4OOR_SSSCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs] u0 {2,S} {4,S} +4 *5 CO u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 R!H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 31, + label = "R4OOR_SSD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *5 Cd u0 {3,D} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 R!H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 32, + label = "R4OOR_SDS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *6 Cd u0 {2,D} {4,S} +4 *5 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 R!H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 33, + label = "R4OOR_DSS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *5 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 R!H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 34, + label = "R4OOR_DSD", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *5 Cd u0 {3,D} {5,S} +5 *2 O u0 {4,S} {6,S} +6 *3 O u0 {5,S} {7,S} +7 R!H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 42, + label = "R5OO", + group = "OR{R5OOH, R5OOR, R5OOJ}", + kinetics = None, +) + +entry( + index = 43, + label = "R5OOJ", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *6 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]} +4 *7 [CO,Cd,Cs,Sid,Sis,N] u0 {3,[S,D]} {5,[S,D]} +5 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {4,[S,D]} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u1 {6,S} +""", + kinetics = None, +) + +entry( + index = 44, + label = "R5OOH", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *6 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]} +4 *7 [CO,Cd,Cs,Sid,Sis,N] u0 {3,[S,D]} {5,[S,D]} +5 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {4,[S,D]} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 45, + label = "R5OOH_SSSS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *7 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 37, + label = "R5OOH_SSSSCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs] u0 {2,S} {4,S} +4 *7 [Cd,Cs] u0 {3,S} {5,S} +5 *5 CO u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 38, + label = "R5OOH_SSSD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *7 Cd u0 {3,S} {5,D} +5 *5 Cd u0 {4,D} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 39, + label = "R5OOH_SSDS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *7 Cd u0 {3,D} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 40, + label = "R5OOH_SDSS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *6 Cd u0 {2,D} {4,S} +4 *7 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 41, + label = "R5OOH_DSSS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *7 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 42, + label = "R5OOH_SDSD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *6 Cd u0 {2,D} {4,S} +4 *7 Cd u0 {3,S} {5,D} +5 *5 Cd u0 {4,D} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 43, + label = "R5OOH_DSDS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *7 Cd u0 {3,D} {5,S} +5 *5 Cd u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 44, + label = "R5OOR", + group = +""" +1 *1 [CO,Cd,Cs,Sid,Sis,N] u1 {2,[S,D]} +2 *4 [CO,Cd,Cs,Sid,Sis,N] u0 {1,[S,D]} {3,[S,D]} +3 *6 [CO,Cd,Cs,Sid,Sis,N] u0 {2,[S,D]} {4,[S,D]} +4 *7 [CO,Cd,Cs,Sid,Sis,N] u0 {3,[S,D]} {5,[S,D]} +5 *5 [CO,Cd,Cs,Sid,Sis,N] u0 {4,[S,D]} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 45, + label = "R5OOR_SSSS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *7 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 46, + label = "R5OOR_SSSSCO", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs] u0 {2,S} {4,S} +4 *7 [Cd,Cs] u0 {3,S} {5,S} +5 *5 CO u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 47, + label = "R5OOR_SSSD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *7 Cd u0 {3,S} {5,D} +5 *5 Cd u0 {4,D} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 48, + label = "R5OOR_SSDS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 [Cd,Cs] u0 {1,S} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *7 Cd u0 {3,D} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 49, + label = "R5OOR_SDSS", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *6 Cd u0 {2,D} {4,S} +4 *7 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 50, + label = "R5OOR_DSSS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 [Cd,Cs,CO] u0 {2,S} {4,S} +4 *7 [Cd,Cs,CO] u0 {3,S} {5,S} +5 *5 [Cd,Cs,CO] u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 51, + label = "R5OOR_SDSD", + group = +""" +1 *1 [Cd,Cs] u1 {2,S} +2 *4 Cd u0 {1,S} {3,D} +3 *6 Cd u0 {2,D} {4,S} +4 *7 Cd u0 {3,S} {5,D} +5 *5 Cd u0 {4,D} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 52, + label = "R5OOR_DSDS", + group = +""" +1 *1 Cd u1 {2,D} +2 *4 Cd u0 {1,D} {3,S} +3 *6 Cd u0 {2,S} {4,D} +4 *7 Cd u0 {3,D} {5,S} +5 *5 Cd u0 {4,S} {6,S} +6 *2 O u0 {5,S} {7,S} +7 *3 O u0 {6,S} {8,S} +8 R!H u0 {7,S} +""", + kinetics = None, +) + +entry( + index = 53, + label = "Cd_rad_in", + group = +""" +1 *1 C u1 {2,D} {3,S} +2 *4 C u0 {1,D} +3 R u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 54, + label = "Cd_pri_rad_in", + group = +""" +1 *1 C u1 {2,D} {3,S} +2 *4 C u0 {1,D} +3 H u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 55, + label = "Cd_sec_rad_in", + group = +""" +1 *1 C u1 {2,D} {3,S} +2 *4 C u0 {1,D} +3 R!H u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 56, + label = "Cd_rad_in/NonDeC", + group = +""" +1 *1 C u1 {2,D} {3,S} +2 *4 C u0 {1,D} +3 Cs u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 57, + label = "Cd_rad_in/NonDeO", + group = +""" +1 *1 C u1 {2,D} {3,S} +2 *4 C u0 {1,D} +3 O u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 75, + label = "Cd_rad_in/NonDeN", + group = +""" +1 *1 C u1 {2,D} {3,S} +2 *4 C u0 {1,D} +3 N3s u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 58, + label = "Cd_rad_in/OneDe", + group = +""" +1 *1 C u1 {2,D} {3,S} +2 *4 C u0 {1,D} +3 [Cd,Ct,Cb,CO] u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 59, + label = "Cd_rad_out", + group = +""" +1 *1 C u1 {2,S} {3,D} +2 *4 C u0 {1,S} +3 Cd u0 {1,D} +""", + kinetics = None, +) + +entry( + index = 60, + label = "Cs_rad_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 *4 C u0 {1,S} +3 R u0 {1,S} +4 R u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 61, + label = "C_pri_rad_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 H u0 {1,S} +3 H u0 {1,S} +4 *4 C u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 62, + label = "C_sec_rad_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 H u0 {1,S} +3 *4 C u0 {1,S} +4 R!H u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 63, + label = "C_rad/H/NonDeC_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 H u0 {1,S} +3 *4 C u0 {1,S} +4 Cs u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 64, + label = "C_rad/H/NonDeO_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 H u0 {1,S} +3 *4 C u0 {1,S} +4 O u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 76, + label = "C_rad/H/NonDeN_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 H u0 {1,S} +3 *4 C u0 {1,S} +4 N3s u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 65, + label = "C_rad/H/OneDe_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 H u0 {1,S} +3 [Cd,Ct,Cb,CO] u0 {1,S} +4 *4 C u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 66, + label = "C_ter_rad_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 *4 C u0 {1,S} +3 R!H u0 {1,S} +4 R!H u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 67, + label = "C_rad/NonDeC_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 *4 C u0 {1,S} +3 [Cs,O] u0 {1,S} +4 [Cs,O] u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 68, + label = "C_rad/Cs3_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 *4 C u0 {1,S} +3 Cs u0 {1,S} +4 Cs u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 69, + label = "C_rad/NDMustO_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 *4 C u0 {1,S} +3 O u0 {1,S} +4 [Cs,O] u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 70, + label = "C_rad/OneDe_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 [Cd,Ct,Cb,CO] u0 {1,S} +3 *4 C u0 {1,S} +4 [Cs,O] u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 71, + label = "C_rad/Cs2_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 [Cd,Ct,Cb,CO] u0 {1,S} +3 *4 C u0 {1,S} +4 Cs u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 72, + label = "C_rad/ODMustO_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 [Cd,Ct,Cb,CO] u0 {1,S} +3 *4 C u0 {1,S} +4 O u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 73, + label = "C_rad/TwoDe_intra", + group = +""" +1 *1 C u1 {2,S} {3,S} {4,S} +2 [Cd,Ct,Cb,CO] u0 {1,S} +3 [Cd,Ct,Cb,CO] u0 {1,S} +4 *4 C u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 74, + label = "N_rad", + group = +""" +1 *1 N u1 +""", + kinetics = None, +) + +tree( +""" +L1: RnOO + L2: R2OO + L3: R2OOJ + L4: R2OOJ_S + L3: R2OOH + L4: R2OOH_S + L4: R2OOH_SCO + L4: R2OOH_D + L3: R2OOR + L4: R2OOR_S + L4: R2OOR_SCO + L4: R2OOR_D + L2: R3OO + L3: R3OOJ + L3: R3OOH + L4: R3OOH_SS + L5: R3OOH_SSCO + L4: R3OOH_SD + L4: R3OOH_DS + L3: R3OOR + L4: R3OOR_SS + L5: R3OOR_SSCO + L4: R3OOR_SD + L4: R3OOR_DS + L2: R4OO + L3: R4OOJ + L3: R4OOH + L4: R4OOH_SSS + L5: R4OOH_SSSCO + L4: R4OOH_SSD + L4: R4OOH_SDS + L4: R4OOH_DSS + L4: R4OOH_DSD + L3: R4OOR + L4: R4OOR_SSS + L5: R4OOR_SSSCO + L4: R4OOR_SSD + L4: R4OOR_SDS + L4: R4OOR_DSS + L4: R4OOR_DSD + L2: R5OO + L3: R5OOJ + L3: R5OOH + L4: R5OOH_SSSS + L5: R5OOH_SSSSCO + L4: R5OOH_SSSD + L4: R5OOH_SSDS + L4: R5OOH_SDSS + L4: R5OOH_DSSS + L4: R5OOH_SDSD + L4: R5OOH_DSDS + L3: R5OOR + L4: R5OOR_SSSS + L5: R5OOR_SSSSCO + L4: R5OOR_SSSD + L4: R5OOR_SSDS + L4: R5OOR_SDSS + L4: R5OOR_DSSS + L4: R5OOR_SDSD + L4: R5OOR_DSDS +L1: Y_rad_intra + L2: Cd_rad_in + L3: Cd_pri_rad_in + L3: Cd_sec_rad_in + L4: Cd_rad_in/NonDeC + L4: Cd_rad_in/NonDeO + L4: Cd_rad_in/NonDeN + L4: Cd_rad_in/OneDe + L2: Cd_rad_out + L2: Cs_rad_intra + L3: C_pri_rad_intra + L3: C_sec_rad_intra + L4: C_rad/H/NonDeC_intra + L4: C_rad/H/NonDeO_intra + L4: C_rad/H/NonDeN_intra + L4: C_rad/H/OneDe_intra + L3: C_ter_rad_intra + L4: C_rad/NonDeC_intra + L5: C_rad/Cs3_intra + L5: C_rad/NDMustO_intra + L4: C_rad/OneDe_intra + L5: C_rad/Cs2_intra + L5: C_rad/ODMustO_intra + L4: C_rad/TwoDe_intra + L2: N_rad +""" +) + diff --git a/input/kinetics/families/Cyclic_Ether_Formation/rules_old.py b/input/kinetics/families/Cyclic_Ether_Formation/rules_old.py new file mode 100644 index 0000000000..bc48831eda --- /dev/null +++ b/input/kinetics/families/Cyclic_Ether_Formation/rules_old.py @@ -0,0 +1,577 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Cyclic_Ether_Formation/rules" +shortDesc = u"" +longDesc = u""" + +""" +entry( + index = 812, + label = "RnOO;Y_rad_intra", + kinetics = ArrheniusEP( + A = (1e+11, 's^-1'), + n = 0, + alpha = 0, + E0 = (10, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 0, +) + +entry( + index = 813, + label = "R2OOH_S;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (3.98e+12, 's^-1', '*|/', 1.2), + n = 0, + alpha = (1.3, '', '+|-', 0.3), + E0 = (37, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 813, + label = "R2OOR_S;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (3.98e+12, 's^-1', '*|/', 1.2), + n = 0, + alpha = (1.3, '', '+|-', 0.3), + E0 = (37, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 814, + label = "R2OOH_S;C_sec_rad_intra", + kinetics = ArrheniusEP( + A = (1.38e+12, 's^-1', '*|/', 1.2), + n = 0, + alpha = (1.3, '', '+|-', 0.3), + E0 = (37, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 814, + label = "R2OOR_S;C_sec_rad_intra", + kinetics = ArrheniusEP( + A = (1.38e+12, 's^-1', '*|/', 1.2), + n = 0, + alpha = (1.3, '', '+|-', 0.3), + E0 = (37, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 815, + label = "R2OOR_S;C_ter_rad_intra", + kinetics = ArrheniusEP( + A = (3.09e+12, 's^-1', '*|/', 1.2), + n = 0, + alpha = (1.3, '', '+|-', 0.3), + E0 = (37, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 815, + label = "R2OOH_S;C_ter_rad_intra", + kinetics = ArrheniusEP( + A = (3.09e+12, 's^-1', '*|/', 1.2), + n = 0, + alpha = (1.3, '', '+|-', 0.3), + E0 = (37, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 816, + label = "R3OOH_SS;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (4.47e+11, 's^-1', '*|/', 1.74), + n = 0, + alpha = (1, '', '+|-', 0.1), + E0 = (38.2, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 816, + label = "R3OOR_SS;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (4.47e+11, 's^-1', '*|/', 1.74), + n = 0, + alpha = (1, '', '+|-', 0.1), + E0 = (38.2, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 817, + label = "R3OOH_SS;C_sec_rad_intra", + kinetics = ArrheniusEP( + A = (2.04e+11, 's^-1', '*|/', 1.74), + n = 0, + alpha = (1, '', '+|-', 0.1), + E0 = (38.2, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 817, + label = "R3OOR_SS;C_sec_rad_intra", + kinetics = ArrheniusEP( + A = (2.04e+11, 's^-1', '*|/', 1.74), + n = 0, + alpha = (1, '', '+|-', 0.1), + E0 = (38.2, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 818, + label = "R3OOR_SS;C_ter_rad_intra", + kinetics = ArrheniusEP( + A = (3.31e+11, 's^-1', '*|/', 1.74), + n = 0, + alpha = (1, '', '+|-', 0.1), + E0 = (38.2, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 818, + label = "R3OOH_SS;C_ter_rad_intra", + kinetics = ArrheniusEP( + A = (3.31e+11, 's^-1', '*|/', 1.74), + n = 0, + alpha = (1, '', '+|-', 0.1), + E0 = (38.2, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 819, + label = "R4OOR_SSS;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (5.13e+10, 's^-1', '*|/', 1.41), + n = 0, + alpha = 0, + E0 = (14.8, 'kcal/mol', '+|-', 2), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 819, + label = "R4OOH_SSS;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (5.13e+10, 's^-1', '*|/', 1.41), + n = 0, + alpha = 0, + E0 = (14.8, 'kcal/mol', '+|-', 2), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 820, + label = "R4OOR_SSS;C_sec_rad_intra", + kinetics = ArrheniusEP( + A = (3.63e+10, 's^-1', '*|/', 1.41), + n = 0, + alpha = 0, + E0 = (13, 'kcal/mol', '+|-', 2.5), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 820, + label = "R4OOH_SSS;C_sec_rad_intra", + kinetics = ArrheniusEP( + A = (3.63e+10, 's^-1', '*|/', 1.41), + n = 0, + alpha = 0, + E0 = (13, 'kcal/mol', '+|-', 2.5), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 821, + label = "R4OOR_SSS;C_ter_rad_intra", + kinetics = ArrheniusEP( + A = (2.57e+10, 's^-1', '*|/', 1.41), + n = 0, + alpha = 0, + E0 = (11.5, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 821, + label = "R4OOH_SSS;C_ter_rad_intra", + kinetics = ArrheniusEP( + A = (2.57e+10, 's^-1', '*|/', 1.41), + n = 0, + alpha = 0, + E0 = (11.5, 'kcal/mol', '+|-', 3), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 2, + shortDesc = u"""CBS-QB3 and BH&HLYP calculations (Catherina Wijaya & Sumathy Raman). Including treatment of hindered rotor.""", +) + +entry( + index = 822, + label = "R2OOR_S;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (6e+11, 's^-1'), + n = 0, + alpha = 0, + E0 = (22, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 822, + label = "R2OOH_S;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (6e+11, 's^-1'), + n = 0, + alpha = 0, + E0 = (22, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 823, + label = "R3OOR_SS;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (7.5e+10, 's^-1'), + n = 0, + alpha = 0, + E0 = (15.25, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 823, + label = "R3OOH_SS;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (7.5e+10, 's^-1'), + n = 0, + alpha = 0, + E0 = (15.25, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 824, + label = "R4OOR_SSS;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (9.38e+09, 's^-1'), + n = 0, + alpha = 0, + E0 = (7, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 824, + label = "R4OOH_SSS;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (9.38e+09, 's^-1'), + n = 0, + alpha = 0, + E0 = (7, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 825, + label = "R5OOH_SSSS;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.17e+09, 's^-1'), + n = 0, + alpha = 0, + E0 = (1.8, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 825, + label = "R5OOR_SSSS;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.17e+09, 's^-1'), + n = 0, + alpha = 0, + E0 = (1.8, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Curran's [8] estimation in reaction type 19, QOOH = cyclic ether + OH""", +) + +entry( + index = 826, + label = "R5OOR_SSSSCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.27e+08, 's^-1'), + n = 0.77, + alpha = 0, + E0 = (18.73, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""CBS-QB3 Including treatment of hindered rotor (SSM)""", +) + +entry( + index = 826, + label = "R5OOH_SSSSCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.27e+08, 's^-1'), + n = 0.77, + alpha = 0, + E0 = (18.73, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""CBS-QB3 Including treatment of hindered rotor (SSM)""", +) + +entry( + index = 827, + label = "R2OOR_SCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (6.92e+15, 's^-1'), + n = -0.53, + alpha = 0, + E0 = (24.34, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""CBS-QB3 Including treatment for hindered rotor, QTST Calculation (CFG & JWA)""", +) + +entry( + index = 827, + label = "R2OOH_SCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (6.92e+15, 's^-1'), + n = -0.53, + alpha = 0, + E0 = (24.34, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""CBS-QB3 Including treatment for hindered rotor, QTST Calculation (CFG & JWA)""", +) + +entry( + index = 828, + label = "R4OOR_SSSCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.27e+08, 's^-1'), + n = 0.77, + alpha = 0, + E0 = (18.73, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 0, + shortDesc = u"""Estimate (Same as 5 memebered ring)""", +) + +entry( + index = 828, + label = "R4OOH_SSSCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.27e+08, 's^-1'), + n = 0.77, + alpha = 0, + E0 = (18.73, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 0, + shortDesc = u"""Estimate (Same as 5 memebered ring)""", +) + +entry( + index = 829, + label = "R3OOH_SSCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.27e+08, 's^-1'), + n = 0.77, + alpha = 0, + E0 = (18.73, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 0, + shortDesc = u"""Estimate (Same as 5 memebered ring)""", +) + +entry( + index = 829, + label = "R3OOR_SSCO;Cs_rad_intra", + kinetics = ArrheniusEP( + A = (1.27e+08, 's^-1'), + n = 0.77, + alpha = 0, + E0 = (18.73, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 0, + shortDesc = u"""Estimate (Same as 5 memebered ring)""", +) + +entry( + index = 830, + label = "R2OOJ_S;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (1.62e+09, 's^-1'), + n = 1.1, + alpha = 0, + E0 = (31.9, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""AG Vandeputte, BMK/cbsb7""", +) + +entry( + index = 831, + label = "R2OOJ_S;C_pri_rad_intra", + kinetics = ArrheniusEP( + A = (1.61e+09, 's^-1'), + n = 1.09, + alpha = 0, + E0 = (29.9, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""AG Vandeputte, BMK/cbsb7""", +) + +entry( + index = 832, + label = "R2OOJ_S;C_rad/H/NonDeC_intra", + kinetics = ArrheniusEP( + A = (3.27e+09, 's^-1'), + n = 1.06, + alpha = 0, + E0 = (31, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""AG Vandeputte, BMK/cbsb7""", +) + diff --git a/input/kinetics/families/Intra_Disproportionation/groups.py b/input/kinetics/families/Intra_Disproportionation/groups.py index 8f33a6dbc1..184a6bf9e9 100644 --- a/input/kinetics/families/Intra_Disproportionation/groups.py +++ b/input/kinetics/families/Intra_Disproportionation/groups.py @@ -19,6 +19,8 @@ ['LOSE_RADICAL', '*3', '1'], ]) +boundaryAtoms = ["*1", "*3"] + entry( index = 1, label = "Rn", diff --git a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py index fbdad18e22..aa2ffbb751 100644 --- a/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py +++ b/input/kinetics/families/Intra_RH_Add_Endocyclic/groups.py @@ -18,6 +18,8 @@ ['CHANGE_BOND', '*2', '-1', '*3'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "Rn", diff --git a/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py b/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py index 56b4ba6cc3..ffbaebd0a4 100644 --- a/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py +++ b/input/kinetics/families/Intra_RH_Add_Exocyclic/groups.py @@ -18,6 +18,8 @@ ['CHANGE_BOND', '*2', -1, '*3'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "Rn", diff --git a/input/kinetics/families/Intra_R_Add_Endocyclic/groups.py b/input/kinetics/families/Intra_R_Add_Endocyclic/groups.py index e5fbd9bcda..f28c43047d 100644 --- a/input/kinetics/families/Intra_R_Add_Endocyclic/groups.py +++ b/input/kinetics/families/Intra_R_Add_Endocyclic/groups.py @@ -18,6 +18,8 @@ ['LOSE_RADICAL', '*1', '1'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "Rn", diff --git a/input/kinetics/families/Intra_R_Add_ExoTetCyclic/groups.py b/input/kinetics/families/Intra_R_Add_ExoTetCyclic/groups.py index b6c87ac635..abd6f77047 100644 --- a/input/kinetics/families/Intra_R_Add_ExoTetCyclic/groups.py +++ b/input/kinetics/families/Intra_R_Add_ExoTetCyclic/groups.py @@ -18,6 +18,8 @@ ['GAIN_RADICAL', '*3', '1'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "R1_rad_R2_R3", diff --git a/input/kinetics/families/Intra_R_Add_Exocyclic/groups.py b/input/kinetics/families/Intra_R_Add_Exocyclic/groups.py index c70edd3085..c481419cb1 100644 --- a/input/kinetics/families/Intra_R_Add_Exocyclic/groups.py +++ b/input/kinetics/families/Intra_R_Add_Exocyclic/groups.py @@ -18,6 +18,8 @@ ['GAIN_RADICAL', '*3', '1'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "Rn", diff --git a/input/kinetics/families/intra_H_migration/groups.py b/input/kinetics/families/intra_H_migration/groups.py index f87d91890e..5466b97ee0 100644 --- a/input/kinetics/families/intra_H_migration/groups.py +++ b/input/kinetics/families/intra_H_migration/groups.py @@ -16,6 +16,8 @@ ['LOSE_RADICAL', '*1', '1'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "RnH", diff --git a/input/kinetics/families/intra_H_migration/groupsTest.py b/input/kinetics/families/intra_H_migration/groupsTest.py new file mode 100644 index 0000000000..37f2cc012a --- /dev/null +++ b/input/kinetics/families/intra_H_migration/groupsTest.py @@ -0,0 +1,427 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "intra_H_migration/groups" +shortDesc = u"" +longDesc = u""" + +""" + +template(reactants=["RnH"], products=["RnH"], ownReverse=True) + +recipe(actions=[ + ['BREAK_BOND', '*2', 1, '*3'], + ['FORM_BOND', '*1', 1, '*3'], + ['GAIN_RADICAL', '*2', '1'], + ['LOSE_RADICAL', '*1', '1'], +]) + +entry( + index = 1, + label = "RnH", + group = "OR{R2Hall, R3Hall, R4Hall, R5Hall, R6Hall, R7Hall}", + kinetics = None, +) + +entry( + index = 2, + label = "Y_rad_out", + group = +""" +1 *1 R!H u1 +""", + kinetics = None, +) + +entry( + index = 3, + label = "XH_out", + group = +""" +1 *2 R!H u0 {2,S} +2 *3 H u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 74, + label = "R5Hall", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *5 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *2 R!H u0 {4,[S,D,T,B]} {6,S} +6 *3 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 75, + label = "R5HJ_1", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u1 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u0 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *5 R!H u0 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *2 R!H u0 {4,[S,D,T,B]} {6,S} +6 *3 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 76, + label = "R5HJ_2", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u0 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u1 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *5 R!H u0 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *2 R!H u0 {4,[S,D,T,B]} {6,S} +6 *3 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 77, + label = "R5HJ_3", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u0 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u0 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *5 R!H u1 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *2 R!H u0 {4,[S,D,T,B]} {6,S} +6 *3 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 78, + label = "R5H", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u0 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u0 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *5 R!H u0 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *2 R!H u0 {4,[S,D,T,B]} {6,S} +6 *3 H u0 {5,S} +""", + kinetics = None, +) + +entry( + index = 131, + label = "R6Hall", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *7 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *5 R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} +6 *2 R!H u0 {5,[S,D,T,B]} {7,S} +7 *3 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 132, + label = "R6HJ_1", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u1 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u0 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *7 R!H u0 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *5 R!H u0 {4,[S,D,T,B]} {6,[S,D,T,B]} +6 *2 R!H u0 {5,[S,D,T,B]} {7,S} +7 *3 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 133, + label = "R6HJ_2", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u0 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u1 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *7 R!H u0 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *5 R!H u0 {4,[S,D,T,B]} {6,[S,D,T,B]} +6 *2 R!H u0 {5,[S,D,T,B]} {7,S} +7 *3 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 134, + label = "R6HJ_3", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u0 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u0 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *7 R!H u1 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *5 R!H u0 {4,[S,D,T,B]} {6,[S,D,T,B]} +6 *2 R!H u0 {5,[S,D,T,B]} {7,S} +7 *3 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 135, + label = "R6HJ_4", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u0 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u0 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *7 R!H u0 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *5 R!H u1 {4,[S,D,T,B]} {6,[S,D,T,B]} +6 *2 R!H u0 {5,[S,D,T,B]} {7,S} +7 *3 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 136, + label = "R6H", + group = +""" +1 *1 R!H u1 {2,[S,D,T,B]} +2 *4 R!H u0 {1,[S,D,T,B]} {3,[S,D,T,B]} +3 *6 R!H u0 {2,[S,D,T,B]} {4,[S,D,T,B]} +4 *7 R!H u0 {3,[S,D,T,B]} {5,[S,D,T,B]} +5 *5 R!H u0 {4,[S,D,T,B]} {6,[S,D,T,B]} +6 *2 R!H u0 {5,[S,D,T,B]} {7,S} +7 *3 H u0 {6,S} +""", + kinetics = None, +) + +entry( + index = 188, + label = "O_rad_out", + group = +""" +1 *1 O u1 +""", + kinetics = None, +) + +entry( + index = 190, + label = "Cd_rad_out", + group = +""" +1 *1 Cd u1 +""", + kinetics = None, +) + +entry( + index = 199, + label = "C_rad_out_single", + group = +""" +1 *1 C u1 {2,S} {3,S} +2 R u0 {1,S} +3 R u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 219, + label = "O_H_out", + group = +""" +1 *2 O u0 {2,S} +2 *3 H u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 223, + label = "Cd_H_out_double", + group = +""" +1 *2 Cd u0 {2,S} {3,D} +2 *3 H u0 {1,S} +3 [Cd,Cdd,O] u0 {1,D} +""", + kinetics = None, +) + +entry( + index = 226, + label = "Cd_H_out_single", + group = +""" +1 *2 Cd u0 {2,S} {3,S} +2 *3 H u0 {1,S} +3 R u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 230, + label = "Cs_H_out", + group = +""" +1 *2 Cs u0 {2,S} {3,S} {4,S} +2 *3 H u0 {1,S} +3 R u0 {1,S} +4 R u0 {1,S} +""", + kinetics = None, +) + +tree( +""" +L1: RnH + L2: R5Hall + L3: R5HJ_1 + L3: R5HJ_2 + L3: R5HJ_3 + L3: R5H + L2: R6Hall + L3: R6HJ_1 + L3: R6HJ_2 + L3: R6HJ_3 + L3: R6HJ_4 + L3: R6H +L1: Y_rad_out + L2: O_rad_out + L2: Cd_rad_out + L2: C_rad_out_single +L1: XH_out + L2: O_H_out + L2: Cd_H_out_double + L2: Cd_H_out_single + L2: Cs_H_out +""" +) + +forbidden( + label = "[CH2]C1=CC(C)CC=C1_1", + group = +""" +1 *5 C u0 {2,S} {3,S} {8,S} +2 *2 C u0 {1,S} {9,S} +3 C u0 {1,S} {4,S} +4 C u0 {3,S} {5,D} +5 C u0 {4,D} {6,S} +6 *4 C u0 {5,S} {7,S} {8,D} +7 *1 C u1 {6,S} +8 *6 C u0 {1,S} {6,D} +9 *3 H u0 {2,S} +""", + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +forbidden( + label = "[CH2]C1=CC(C)CC=C1_2", + group = +""" +1 *5 C u0 {2,S} {3,S} {8,S} +2 C u0 {1,S} +3 *2 C u0 {1,S} {4,S} {9,S} +4 C u0 {3,S} {5,D} +5 C u0 {4,D} {6,S} +6 *4 C u0 {5,S} {7,S} {8,D} +7 *1 C u1 {6,S} +8 *6 C u0 {1,S} {6,D} +9 *3 H u0 {3,S} +""", + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +forbidden( + label = "[CH2]C1=CC(C)CC=C1_3", + group = +""" +1 C u0 {2,S} {3,S} {8,S} +2 C u0 {1,S} +3 *2 C u0 {1,S} {4,S} {9,S} +4 *5 C u0 {3,S} {5,D} +5 *6 C u0 {4,D} {6,S} +6 *4 C u0 {5,S} {7,S} {8,D} +7 *1 C u1 {6,S} +8 C u0 {1,S} {6,D} +9 *3 H u0 {3,S} +""", + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +forbidden( + label = "bridged56_1243", + group = +""" +1 *1 C u1 {2,S} {6,S} +2 *4 C u0 {1,S} {3,S} {7,S} +3 *2 C u0 {2,S} {4,S} {8,S} +4 *5 C u0 {3,S} {5,S} +5 C u0 {4,S} {6,S} {7,S} +6 C u0 {1,S} {5,S} +7 C u0 {2,S} {5,S} +8 *3 H u0 {3,S} +""", + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +forbidden( + label = "bridged56_1254", + group = +""" +1 *1 C u1 {2,S} {6,S} +2 *4 C u0 {1,S} {3,S} {7,S} +3 C u0 {2,S} {4,S} +4 *2 C u0 {3,S} {5,S} {8,S} +5 *5 C u0 {4,S} {6,S} {7,S} +6 C u0 {1,S} {5,S} +7 C u0 {2,S} {5,S} +8 *3 H u0 {4,S} +""", + shortDesc = u"""""", + longDesc = +u""" + +""", +) + + diff --git a/input/kinetics/families/intra_H_migration/rulesTest.py b/input/kinetics/families/intra_H_migration/rulesTest.py new file mode 100644 index 0000000000..d5c3b402c6 --- /dev/null +++ b/input/kinetics/families/intra_H_migration/rulesTest.py @@ -0,0 +1,44 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "intra_H_migration/rules" +shortDesc = u"" +longDesc = u""" + +""" +entry( + index = 614, + label = "RnH;Y_rad_out;XH_out", + kinetics = ArrheniusEP( + A = (1e+10, 's^-1'), + n = 0, + alpha = 0, + E0 = (25, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 0, + shortDesc = u"""default""", +) + +entry( + index = 615, + label = "R2H_S;C_rad_out_single;Cs_H_out", + kinetics = ArrheniusEP( + A = (5.48e+08, 's^-1'), + n = 1.62, + alpha = 0, + E0 = (38.76, 'kcal/mol'), + Tmin = (300, 'K'), + Tmax = (1500, 'K'), + ), + rank = 5, + shortDesc = u"""Currans's estimation [5] in his reaction type 5.""", + longDesc = +u""" +[5] Curran, H.J.; Gaffuri, P.; Pit z, W.J.; Westbrook, C.K. Combust. Flame 1998, 114, 149. +Currans's estimation in his reaction type 5. C7H15 + +Checked by Paul Green. +""", +) diff --git a/input/kinetics/families/intra_OH_migration/groups.py b/input/kinetics/families/intra_OH_migration/groups.py index d61731c8f7..a8a08302e9 100644 --- a/input/kinetics/families/intra_OH_migration/groups.py +++ b/input/kinetics/families/intra_OH_migration/groups.py @@ -18,6 +18,8 @@ ['LOSE_RADICAL', '*1', '1'], ]) +boundaryAtoms = ["*1", "*2"] + entry( index = 1, label = "RnOOH", diff --git a/input/kinetics/families/intra_substitutionCS_cyclization/groups.py b/input/kinetics/families/intra_substitutionCS_cyclization/groups.py index b56f5f562d..adae6b1695 100644 --- a/input/kinetics/families/intra_substitutionCS_cyclization/groups.py +++ b/input/kinetics/families/intra_substitutionCS_cyclization/groups.py @@ -18,6 +18,8 @@ ['LOSE_RADICAL', '*3', '1'], ]) +boundaryAtoms = ["*1", "*3"] + entry( index = 1, label = "XSYJ", diff --git a/input/kinetics/families/intra_substitutionCS_isomerization/groups.py b/input/kinetics/families/intra_substitutionCS_isomerization/groups.py index e9bc714ad3..d1a5294e79 100644 --- a/input/kinetics/families/intra_substitutionCS_isomerization/groups.py +++ b/input/kinetics/families/intra_substitutionCS_isomerization/groups.py @@ -18,6 +18,8 @@ ['LOSE_RADICAL', '*3', '1'], ]) +boundaryAtoms = ["*1", "*3"] + entry( index = 1, label = "XSYJ", diff --git a/input/kinetics/families/ketoenol/groups.py b/input/kinetics/families/ketoenol/groups.py index 4446b9b9a5..c3c25b6343 100644 --- a/input/kinetics/families/ketoenol/groups.py +++ b/input/kinetics/families/ketoenol/groups.py @@ -18,6 +18,8 @@ ['FORM_BOND', '*4', 1, '*1'], ]) +boundaryAtoms = ["*2", "*3"] + entry( index = 19, label = 'R1_doublebond',