RMG-database v2.1.9 release

ReactionMechanismGenerator · May 15, 2018 · 68b5ec3 · 68b5ec3
2 parents 7ca5cca + 28e7df3
commit 68b5ec3
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diff --git a/input/forbiddenStructures.py b/input/forbiddenStructures.py
@@ -53,7 +53,7 @@
 
 entry(
     label = "C_quintet",
-    group = 
+    molecule =
 """
 1 C u4 p0
 """,
@@ -483,9 +483,9 @@
 
 entry(
     label = "CO_birad",
-    group =
+    species =
 """
-multiplicity [3]
+multiplicity 3
 1 C u2 p0 c0 {2,D}
 2 O u0 p2 c0 {1,D}
 """,
@@ -501,9 +501,9 @@
 
 entry(
     label = "CS_birad",
-    group =
+    species =
 """
-multiplicity [3]
+multiplicity 3
 1 C u2 p0 c0 {2,D}
 2 S u0 p2 c0 {1,D}
 """,
@@ -519,15 +519,142 @@
 
 entry(
     label = "[N][N]",
-    group =
+    species =
 """
-multiplicity [5]
-1 N u2 p0 c0 {2,S}
-2 N u2 p0 c0 {1,S}
+multiplicity 5
+1 N u2 p1 c0 {2,S}
+2 N u2 p1 c0 {1,S}
 """,
     shortDesc = u"""""",
     longDesc =
 u"""
 N#N can be excited to [N]=[N], but we shouldn't allow it to reach [N][N]
 """,
 )
+
+entry(
+    label = "SOO2",
+    species =
+"""
+multiplicity 3
+1 S u0 p2 c0 {2,S} {3,S}
+2 O u0 p2 c0 {1,S} {4,S}
+3 O u1 p2 c0 {1,S}
+4 O u1 p2 c0 {2,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+The SO--O2 complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable SO--OO bond length),
+yet it is predicted by RMG, e.g, by R_Recombination of [S][O] and [O][O].
+
+Another resonance structure of it which is forbidden as well via this entry is:
+multiplicity 3
+1 S u1 p1 c0 {2,S} {3,D}
+2 O u0 p2 c0 {1,S} {4,S}
+3 O u0 p2 c0 {1,D}
+4 O u1 p2 c0 {2,S}
+""",
+)
+
+entry(
+    label = "SO2O2",
+    species =
+"""
+multiplicity 3
+1 S u0 p1 c0 {2,S} {3,S} {4,D}
+2 O u0 p2 c0 {1,S} {5,S}
+3 O u1 p2 c0 {1,S}
+4 O u0 p2 c0 {1,D}
+5 O u1 p2 c0 {2,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+The SO2--O2 complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable O2S--OO bond length),
+yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of O=S=O and [O][O].
+Also, it is described as a TS in doi: 10.1021/jp067499p (Fig. 1 structure 5, Fig. 2)
+
+Another resonance structure of it which is forbidden as well via this entry is:
+multiplicity 3
+1 S u1 p0 c0 {2,S} {3,D} {4,D}
+2 O u0 p2 c0 {1,S} {5,S}
+3 O u0 p2 c0 {1,D}
+4 O u0 p2 c0 {1,D}
+5 O u1 p2 c0 {2,S}
+""",
+)
+
+entry(
+    label = "S2O2",
+    species =
+"""
+multiplicity 3
+1 O u0 p2 c0 {2,S} {3,S}
+2 S u0 p2 c0 {1,S} {4,S}
+3 O u1 p2 c0 {1,S}
+4 S u1 p2 c0 {2,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+The S2--O2 complex isn't a sable species (has an imaginary frequency),
+yet it is predicted by RMG, e.g, by R_Recombination of [S][S] and [O][O].
+
+Another resonance structure of it which is forbidden as well via this entry is:
+multiplicity 3
+1 O u0 p2 c0 {2,S} {3,S}
+2 S u1 p1 c0 {1,S} {4,D}
+3 O u1 p2 c0 {1,S}
+4 S u0 p2 c0 {2,D}
+""",
+)
+
+entry(
+    label = "N2SH",
+    species =
+"""
+multiplicity 2
+1 N u0 p0 c+1 {2,D} {3,D}
+2 S u1 p1 c0 {1,D} {4,S}
+3 N u0 p2 c-1 {1,D}
+4 H u0 p0 c0 {2,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+The S2--SH complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable NN--SH bond length),
+yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of [SH] to N#N.
+
+Other resonance structures of it which are forbidden as well via this entry are:
+multiplicity 2
+1 N u0 p1 c0 {2,S} {3,D}
+2 S u0 p2 c0 {1,S} {4,S}
+3 N u1 p1 c0 {1,D}
+4 H u0 p0 c0 {2,S}
+
+multiplicity 2
+1 N u1 p0 c+1 {2,S} {3,D}
+2 S u0 p2 c0 {1,S} {4,S}
+3 N u0 p2 c-1 {1,D}
+4 H u0 p0 c0 {2,S}
+""",
+)
+
+entry(
+    label = "SO3(T)",
+    species =
+"""
+multiplicity 3
+1 O u0 p2 c0 {2,D}
+2 S u1 p0 c0 {1,D} {3,D} {4,S}
+3 O u0 p2 c0 {2,D}
+4 O u1 p2 c0 {2,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+The geometry of SO3(T) could not be stabilized at either B3LYP/6-311G(2d,d,p) nor M06-2x
+without getting negative frequency/ies.
+""",
+)
diff --git a/input/kinetics/families/1,4_Linear_birad_scission/groups.py b/input/kinetics/families/1,4_Linear_birad_scission/groups.py
@@ -37,40 +37,3 @@
 L1: RJJ
 """
 )
-
-
-forbidden(
-    label = "N2O2a",
-    group =
-"""
-multiplicity [3]
-1 *3 O u0 p2 c0 {2,S} {3,S}
-2 *2 N u0 p1 c0 {1,S} {4,D}
-3 *4 O u1 p2 c0 {1,S}
-4 *1 N u1 p1 c0 {2,D}
-""",
-    shortDesc = u"""""",
-    longDesc =
-u"""
-N2O2 reacts in this family to form a singlet O2 (O=O)
-See RMG-Py issue #1020
-""",
-)
-
-forbidden(
-    label = "N2O2b",
-    group =
-"""
-multiplicity [3]
-1 *2 O u0 p2 c0 {2,S} {3,S}
-2 *3 N u0 p1 c0 {1,S} {4,D}
-3 *1 O u1 p2 c0 {1,S}
-4 *4 N u1 p1 c0 {2,D}
-""",
-    shortDesc = u"""""",
-    longDesc =
-u"""
-Same as above, inverse atom labeling
-""",
-)
-
diff --git a/input/kinetics/families/Birad_R_Recombination/training/reactions.py b/input/kinetics/families/Birad_R_Recombination/training/reactions.py
@@ -14,10 +14,9 @@
     degeneracy = 1,
     kinetics = Arrhenius(A=(1.42e+16, 'cm^3/(mol*s)'), n=-0.75, Ea=(1226, 'cal/mol'), T0=(1, 'K')),
     rank = 3,
-    shortDesc = u"""Training reaction from kinetics library: SOxNOx""",
+    shortDesc = u"""Training reaction from kinetics library: primaryNitrogenLibrary""",
     longDesc = 
 u"""
-Part of the "NOx" subset
 T range: 500-3000 K
 calculations done at the B3LYP/6-311D(d,p)//B3LYP/6-311D(d,p) level of theory
 D. Chakraborty, C.C. Hsu, M.C. Lin, J. Chem. Phys., 1998, 109, 8887, doi: 10.1063/1.477560
@@ -32,7 +31,7 @@
     degeneracy = 1,
     kinetics = Arrhenius(A=(1.3e+14, 'cm^3/(mol*s)'), n=0.24, Ea=(0, 'cal/mol'), T0=(1, 'K'), Tmin = (300, 'K'), Tmax = (800, 'K')),
     rank = 1,
-    shortDesc = u"""Training reaction from kinetics library: SOxNOx""",
+    shortDesc = u"""Training reaction from kinetics library: N-S_interactions""",
     longDesc = 
 u"""
 A. Goumri, D.D. Shao, P. Marshall, J. Chem. Phys., 2004, 121, 9999, doi: 10.1063/1.1806419
@@ -54,7 +53,7 @@
 #   degeneracy = 1,
 #   kinetics = Arrhenius(A=(2.01e+19, 's^-1'), n=-1.07, Ea=(28377, 'cal/mol'), T0=(1, 'K'), Tmin = (200, 'K'), Tmax = (2000, 'K')),
 #   rank = 2,
-#   shortDesc = u"""Training reaction from kinetics library: SOx""",
+#   shortDesc = u"""Training reaction from kinetics library: primarySulfurLibrary""",
 #   longDesc =
 #u"""
 #T range: 200-2000 K
@@ -71,7 +70,7 @@
    degeneracy = 1,
    kinetics = Arrhenius(A=(3.98e+14, 's^-1'), n=0, Ea=(71700, 'cal/mol'), T0=(1, 'K'), Tmin = (1350, 'K'), Tmax = (2100, 'K')),
    rank = 1,
-   shortDesc = u"""Training reaction from kinetics library: SOx""",
+   shortDesc = u"""Training reaction from kinetics library: primarySulfurLibrary""",
    longDesc =
 u"""
 T range: 1350-2100 K

diff --git a/input/kinetics/families/H_Abstraction/groups.py b/input/kinetics/families/H_Abstraction/groups.py
@@ -7056,6 +7056,28 @@
     kinetics = None,
 )
 
+entry(
+    index = 442,
+    label = "Cl_rad",
+    group = 
+"""
+1 *3 Cl1s u1
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 443,
+    label = "HCl",
+    group = 
+"""
+1 *1 Cl1s u0 {2,S}
+2 *2 H u0 {1,S}
+""",
+    kinetics = None,
+)
+
+
 tree(
 """
 L1: X_H_or_Xrad_H_Xbirad_H_Xtrirad_H
@@ -7329,6 +7351,7 @@
         L3: N5_H
             L4: N5dc_H
                 L5: N5dc/H/NonDeOO
+	L3: HCl
 L1: Y_rad_birad_trirad_quadrad
     L2: Y_1centerquadrad
         L3: C_quintet
@@ -7584,20 +7607,70 @@
                         L7: N3d_rad/OneDeCdd_O
         L3: N5_rad
             L4: N5dc_rad
+        L3: Cl_rad
 """
 )
 
 forbidden(
-    label = "disprop1",
+    label = "disprop1_base_case",
     group = 
 """
-1 *1 R u0 {2,S} {3,S}
-2    C u1 {1,S}
-3 *2 H u0 {1,S}
+1 *1 R     u0 {2,S} {3,S}
+2    [C,N] u1 {1,S}
+3 *2 H     u0 {1,S}
 """,
     shortDesc = u"""""",
     longDesc = 
 u"""
+Generally, we'd like to forbid `HR[R].` from reacting here (`.` marks a radical), since this is a disprop reaction.
+However, the following specific cases must not be forbidden here: `HO2`, `HSS`, `HOS`, `HSO`
+(since they form the ground state triplets O2, S2, and SO).
+This group forbids `HR[C,N].`, where the radical site isn't O or S
+""",
+)
+
+forbidden(
+    label = "disprop1_OS_rad",
+    group =
+"""
+1 *1 [C,N] u0 {2,S} {3,S}
+2    [O,S] u1 {1,S}
+3 *2 H     u0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+This group forbids `H[C,N][O,S].`, where the radical site is O or S, but the non-rad site isn't
+""",
+)
+
+forbidden(
+    label = "disprop1_hyperS_H",
+    group =
+"""
+1 *1 S u0 p[0,1] {2,S} {3,S}
+2    [O,S] u1    {1,S}
+3 *2 H     u0    {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+This group forbids `H[S p0,1][O,S].`, where hypervalance S is allowed at the H site
+""",
+)
+
+forbidden(
+    label = "disprop1_hyperS_rad",
+    group =
+"""
+1 *1 [O,S] u0        {2,S} {3,S}
+2    S     u1 p[0,1] {1,S}
+3 *2 H     u0        {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+This group forbids `H[O,S][S p0,1].`, where hypervalance S is allowed at the rad site
 """,
 )