Merge pull request #83 from mliu49/sulfur

Changes to database for DTBS model

Author: connie

.travis.yml

@@ -27,7 +27,7 @@ before_install:
 
 install:
   - conda env create
-  - source activate rmg
+  - source activate rmg_env
   - make
 
 script:

input/kinetics/families/SubstitutionS/groups.py

@@ -4781,7 +4781,7 @@
     label = "Y_1centerbirad",
     group = 
 """
-1 *3 [Cs,Cd,O] u2
+1 *3 [Cs,Cd,O,S] u2
 """,
     kinetics = None,
 )
@@ -4912,8 +4912,7 @@
     label = "SJ",
     group = 
 """
-1 *3 S u1 {2,S}
-2    R u0 {1,S}
+1 *3 S u1
 """,
     kinetics = None,
 )
@@ -5380,9 +5379,6 @@
             L4: O_rad/NonDeC
             L4: O_rad/NonDeO
             L4: O_rad/OneDe
-    L2: Y_1centerbirad
-        L3: O_atom_triplet
-        L3: CH2_triplet
     L2: SJ
         L3: SsJ
             L4: SsJ-H

input/kinetics/families/intra_substitutionCS_cyclization/groups.py

@@ -90,11 +90,10 @@
 
 entry(
     index = 4,
-    label = "S-R",
+    label = "S",
     group = 
 """
-1 *2 S u0 {2,S}
-2    R u0 {1,S}
+1 *2 S u0
 """,
     kinetics = None,
 )
@@ -2177,6 +2176,17 @@
     kinetics = None,
 )
 
+entry(
+    index = 167,
+    label = "S-SJ",
+    group = 
+"""
+1 *2 S  u0 {2,S}
+2    S  u1 {1,S}
+""",
+    kinetics = None,
+)
+
 tree(
 """
 L1: XSYJ
@@ -2346,10 +2356,11 @@
     L2: Cds
     L2: Ct 
    
-L1: S-R
+L1: S
     L2: S-H
     L2: S-Cs
     L2: S-Ss
+    L2: S-SJ
 """
 )
 

input/kinetics/families/intra_substitutionCS_cyclization/rules.py

@@ -8,7 +8,7 @@
 """
 entry(
     index = 1,
-    label = "XSYJ;YJ;C;S-R",
+    label = "XSYJ;YJ;C;S",
     kinetics = ArrheniusEP(
         A = (1e+12, 's^-1'),
         n = 0,

input/kinetics/libraries/Sulfur/DTBS/dictionary.txt

@@ -0,0 +1,55 @@
+S2JJ
+multiplicity 3
+1 S u1 p2 c0 {2,S}
+2 S u1 p2 c0 {1,S}
+
+S2
+1 S u0 p2 c0 {2,D}
+2 S u0 p2 c0 {1,D}
+
+HSJ
+multiplicity 2
+1 S u1 p2 c0 {2,S}
+2 H u0 p0 c0 {1,S}
+
+HSSH
+1 S u0 p2 c0 {2,S} {3,S}
+2 S u0 p2 c0 {1,S} {4,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {2,S}
+
+C4H9SJ
+multiplicity 2
+1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
+2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
+3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
+4 C u0 p0 c0 {1,S} {12,S} {13,S} {14,S}
+5 S u1 p2 c0 {1,S}
+6 H u0 p0 c0 {2,S}
+7 H u0 p0 c0 {2,S}
+8 H u0 p0 c0 {2,S}
+9 H u0 p0 c0 {3,S}
+10 H u0 p0 c0 {3,S}
+11 H u0 p0 c0 {3,S}
+12 H u0 p0 c0 {4,S}
+13 H u0 p0 c0 {4,S}
+14 H u0 p0 c0 {4,S}
+
+C4H8JSH
+multiplicity 2
+1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
+2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
+3 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
+4 C u1 p0 c0 {1,S} {12,S} {13,S}
+5 S u0 p2 c0 {1,S} {14,S}
+6 H u0 p0 c0 {2,S}
+7 H u0 p0 c0 {2,S}
+8 H u0 p0 c0 {2,S}
+9 H u0 p0 c0 {3,S}
+10 H u0 p0 c0 {3,S}
+11 H u0 p0 c0 {3,S}
+12 H u0 p0 c0 {4,S}
+13 H u0 p0 c0 {4,S}
+14 H u0 p0 c0 {5,S}
+
+

input/kinetics/libraries/Sulfur/DTBS/reactions.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Sulfur/DTBS"
+shortDesc = u"Di-tert-butyl Sulfide Seed Mechanism"
+longDesc = u"""
+Sulfur library originally created by Caleb Class in RMG-Java.
+Source of kinetics is unclear, although most likely from his quantum calculations.
+"""
+entry(
+    index = 1,
+    label = "S2 <=> S2JJ",
+    degeneracy = 1,
+    kinetics = Arrhenius(A=(2.1e+10, 's^-1'), n=1, Ea=(0, 'kcal/mol'), T0=(1, 'K')),
+)
+
+entry(
+    index = 2,
+    label = "C4H8JSH <=> C4H9SJ",
+    degeneracy = 1,
+    kinetics = Arrhenius(A=(3760, 's^-1'), n=2.4, Ea=(12.28, 'kcal/mol'), T0=(1, 'K')),
+)
+
+entry(
+    index = 3,
+    label = "HSJ + HSJ <=> HSSH",
+    degeneracy = 1,
+    kinetics = ThirdBody(
+        arrheniusLow = Arrhenius(A=(8.7e+18, 'cm^6/(mol^2*s)'), n=-0.76, Ea=(0, 'kJ/mol'), T0=(1, 'K')),
+        efficiencies = {},
+    ),
+)
+