Merge pull request #206 from ReactionMechanismGenerator/Aromatics_upd…

…ates_2 Aromatics updates 2 (out of 4): Thermo Groups
ReactionMechanismGenerator · Sep 8, 2017 · f4872ba · f4872ba
2 parents 7b3881b + a058352
commit f4872ba
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diff --git a/input/forbiddenStructures.py b/input/forbiddenStructures.py
@@ -319,22 +319,22 @@
 """,
 )
 
-entry(
-    label = "cyclopropyne",
-    group = 
-"""
-1 C u0 {2,T} {3,S}
-2 C u0 {1,T} {3,S}
-3 C u0 {1,S} {2,S} {4,S} {5,S}
-4 H u0 {3,S}
-5 H u0 {3,S}
-""",
-    shortDesc = u"""""",
-    longDesc = 
-u"""
-
-""",
-)
+# entry(
+#     label = "cyclopropyne",
+#     group =
+# """
+# 1 C u0 {2,T} {3,S}
+# 2 C u0 {1,T} {3,S}
+# 3 C u0 {1,S} {2,S} {4,S} {5,S}
+# 4 H u0 {3,S}
+# 5 H u0 {3,S}
+# """,
+#     shortDesc = u"""""",
+#     longDesc =
+# u"""
+#
+# """,
+# )
 
 entry(
     label = "3H-Pyrazol",
@@ -443,3 +443,177 @@
 """,
 )
 
+entry(
+    label = "cyclobutyne",
+    group =
+"""
+1   R!H ux {2,T} {4,[S,D,T]}
+2   R!H ux {1,T} {3,[S,D,T]}
+3   R!H ux {2,[S,D,T]} {4,[S,D,T]}
+4   R!H ux {1,[S,D,T]} {3,[S,D,T]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+""",
+)
+
+entry(
+    label = "s2_3_4_yne_1",
+    group =
+"""
+1   R!H ux {2,[S,D,T,B]} {3,[S,D,T,B]} {4,[S,D,T,B]}
+2   R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} {5,[S,D,T,B]}
+3   R!H ux {1,[S,D,T,B]} {2,[S,D,T,B]}
+4   R!H ux {1,[S,D,T,B]} {5,T}
+5   R!H ux {2,[S,D,T,B]} {4,T}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+""",
+)
+
+entry(
+    label = "s2_4_4_yne_1",
+    group =
+"""
+1   R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} {5,[S,D,T,B]}
+2   R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} {6,[S,D,T,B]}
+3   R!H ux {2,[S,D,T,B]} {4,T}
+4   R!H ux {1,[S,D,T,B]} {3,T}
+5   R!H ux {1,[S,D,T,B]} {6,[S,D,T,B]}
+6   R!H ux {2,[S,D,T,B]} {5,[S,D,T,B]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+""",
+)
+
+entry(
+    label = "s2_4_5_yne_5",
+    group =
+"""
+1   R!H ux {2,[S,D,T,B]} {3,[S,D,T,B]} {5,[S,D,T,B]}
+2   R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {6,[S,D,T,B]}
+3   R!H ux {1,[S,D,T,B]} {4,T}
+4   R!H ux {2,[S,D,T,B]} {3,T}
+5   R!H ux {1,[S,D,T,B]} {7,[S,D,T,B]}
+6   R!H ux {2,[S,D,T,B]} {7,[S,D,T,B]}
+7   R!H ux {5,[S,D,T,B]} {6,[S,D,T,B]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+""",
+)
+
+entry(
+    label = "s2_4_6_yne_6",
+    group =
+"""
+1   R!H ux {2,[S,D,T,B]} {3,[S,D,T,B]} {6,[S,D,T,B]}
+2   R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {5,[S,D,T,B]}
+3   R!H ux {1,[S,D,T,B]} {4,T}
+4   R!H ux {2,[S,D,T,B]} {3,T}
+5   R!H ux {2,[S,D,T,B]} {8,[S,D,T,B]}
+6   R!H ux {1,[S,D,T,B]} {7,[S,D,T,B]}
+7   R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]}
+8   R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+""",
+)
+
+entry(
+    label = "strained_tetracyclic_1",
+    group =
+"""
+1  R!H ux {2,[S,D,T,B]} {9,[S,D,T,B]}
+2  R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]}
+3  R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} {10,[S,D,T,B]}
+4  R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} {9,[S,D,T,B]}
+5  R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]}
+6  R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]}
+7  R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]} {10,[S,D,T,B]}
+8  R!H ux {7,[S,D,T,B]} {9,[S,D,T,B]} {10,[S,D,T,B]}
+9  R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {8,[S,D,T,B]}
+10 R!H ux {3,[S,D,T,B]} {7,[S,D,T,B]} {8,[S,D,T,B]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+For certain unsaturated versions of this strained tetracyclic, RMG finds multiple reverse H-abstraction reactions, causing RMG
+to crash.
+""",
+)
+
+entry(
+    label = "strained_tricyclic_1",
+    group =
+"""
+2  R!H ux {3,[S,D,T,B]} {10,[S,D,T,B]}
+3  R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]}
+4  R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]}
+5  R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} {9,[S,D,T,B]}
+6  R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]} {10,[S,D,T,B]}
+7  R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]}
+8  R!H ux {7,[S,D,T,B]} {9,[S,D,T,B]}
+9  R!H ux {5,[S,D,T,B]} {8,[S,D,T,B]} {10,[S,D,T,B]}
+10 R!H ux {2,[S,D,T,B]} {6,[S,D,T,B]} {9,[S,D,T,B]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+For certain unsaturated versions of this strained tricyclic, RMG's Clar optimization fails, causing RMG
+to crash.
+""",
+)
+
+entry(
+    label = "strained_tricyclic_2",
+    group =
+"""
+1  R!H ux {2,[S,D,T,B]} {10,[S,D,T,B]}
+2  R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]}
+3  R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} {8,[S,D,T,B]}
+4  R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]}
+5  R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} {10,[S,D,T,B]}
+6  R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]}
+7  R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]}
+8  R!H ux {3,[S,D,T,B]} {7,[S,D,T,B]} {9,[S,D,T,B]}
+9  R!H ux {8,[S,D,T,B]} {10,[S,D,T,B]}
+10 R!H ux {1,[S,D,T,B]} {5,[S,D,T,B]} {9,[S,D,T,B]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Certain unsaturated versions of this strained tricyclic cause RMG
+to crash.
+""",
+)
+
+entry(
+    label = "strained_tricyclic_3",
+    group =
+"""
+1  R!H ux {3,[S,D,T,B]} {7,[S,D,T,B]}
+3  R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {10,[S,D,T,B]}
+4  R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]}
+5  R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} {10,[S,D,T,B]}
+6  R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]}
+7  R!H ux {1,[S,D,T,B]} {6,[S,D,T,B]} {8,[S,D,T,B]}
+8  R!H ux {7,[S,D,T,B]} {9,[S,D,T,B]}
+9  R!H ux {8,[S,D,T,B]} {10,[S,D,T,B]}
+10 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} {9,[S,D,T,B]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Certain unsaturated versions of this strained tricyclic cause RMG
+to crash.
+""",
+)
diff --git a/input/thermo/groups/group.py b/input/thermo/groups/group.py
@@ -44845,6 +44845,30 @@
     """,
 )
 
+entry(
+    index = 1932,
+    label = "Cds-(Cds-Os)CbH",
+    group =
+"""
+1 * Cd u0 {2,D} {3,S} {4,S}
+2   Cd u0 {1,D} {5,S}
+3   Cb u0 {1,S}
+4   H  u0 {1,S}
+5   Os u0 {2,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([5.28, 6.83, 7.245, 7.264, 8.226, 9.901, 10.176],'cal/(mol*K)'),
+        H298 = (10.329,'kcal/mol'),
+        S298 = (2.958,'cal/(mol*K)'),
+    ),
+    shortDesc = u"""CBS-QB3""",
+    longDesc =
+u"""
+Fitted to CBS-QB3 calculations for OC=Cc1ccccc1
+""",
+)
+
 tree(
 """
 L1: R
@@ -45053,6 +45077,7 @@
                 L5: Cds-CdsCtH
                     L6: Cds-CdsH(CtN3t)
                 L5: Cds-CdsCbH
+                    L6: Cds-(Cds-Os)CbH
                 L5: Cds-CddCsH
                     L6: Cds-(Cdd-Od)CsH
                     L6: Cds-(Cdd-Sd)CsH