Lithium rebase

.github/workflows/CI.yml

@@ -98,7 +98,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
@@ -208,7 +208,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-core.log"
+            cat "$regr_test-core.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
             echo "<details>"
             if python-jl scripts/checkModels.py \
@@ -225,7 +225,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-edge.log"
+            cat "$regr_test-edge.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
 
             # Check for Regression between Reference and Dynamic (skip superminimal)

input/forbiddenStructures.py

@@ -24,28 +24,28 @@
 
 entry(
     label = "Od_rad",
-    group = 
+    group =
 """
 1 O u1 {2,D}
 2 R ux {1,D}
 """,
     shortDesc = u"""""",
-    longDesc = 
+    longDesc =
 u"""
 
 """,
 )
 
 entry(
     label = "N_birad_triplet_2singleBonds",
-    group = 
+    group =
 """
 1 N u2 p0 {2,S} {3,S}
 2 R ux {1,S}
 3 R ux {1,S}
 """,
     shortDesc = u"""""",
-    longDesc = 
+    longDesc =
 u"""
 
 """,
@@ -58,7 +58,7 @@
 1 C u4 p0
 """,
     shortDesc = u"""""",
-    longDesc = 
+    longDesc =
 u"""
 
 """,
@@ -129,46 +129,46 @@
 
 entry(
     label = "O3",
-    group = 
+    group =
 """
 1 O u[0,1] {2,S}
 2 O u0     {1,S} {3,S}
 3 O u[0,1] {2,S}
 """,
     shortDesc = u"""""",
-    longDesc = 
+    longDesc =
 u"""
 
 """,
 )
 
 entry(
     label = "O4..",
-    group = 
+    group =
 """
 1 O u1 {2,S}
 2 O u0 {1,S} {3,S}
 3 O u0 {2,S} {4,S}
 4 O u1 {3,S}
 """,
     shortDesc = u"""""",
-    longDesc = 
+    longDesc =
 u"""
 
 """,
 )
 
 entry(
     label = "cyclic-C3O",
-    group = 
+    group =
 """
 1 C u0 {2,D} {3,S} {4,S}
 2 O u0 {1,D}
 3 C u0 {1,S} {4,T}
 4 C u0 {1,S} {3,T}
 """,
     shortDesc = u"""""",
-    longDesc = 
+    longDesc =
 u"""
 
 """,
@@ -189,6 +189,23 @@
 """,
 )
 
+
+entry(
+    label = "LiCONSFCl",
+    group =
+"""
+1 Li u0 p0 c0 {2,S}
+2 C ux px c0 {3,[S,D,T]} {1,S}
+3 [O,N,S,F,Cl] ux px c0 {2,[S,D,T]}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+In these species the other atom tends to take most of the charge from the Li
+so it isn't really bonded to C
+""",
+)
+
 entry(
     label = "CO_birad",
     species =
@@ -492,6 +509,20 @@
 """,
 )
 
+entry(
+    label = "LiX",
+    species =
+"""
+1 Li u0 p0 c0 {2,S}
+2 X  u0 p0 c0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Don't allow Li to plate
+""",
+)
+
 entry(
     label = "CO2X2",
     species =