RMG-database v2.4.0 release

ReactionMechanismGenerator · Jun 14, 2019 · 08b8214 · 08b8214
2 parents f7a868c + 5c287c2
commit 08b8214
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diff --git a/.gitignore b/.gitignore
@@ -9,10 +9,13 @@
 .pydevproject
 .settings/*
 
+# PyCharm project files
+.idea/*
+
 # C-Compiled scripts
 *.pyc
 
 *.ipynb_checkpoints
 
 # evaluate kinetics folder stuff
-testing/eval/*
+testing/eval/*
diff --git a/families/images/1+2_Cycloaddition.png b/families/images/1+2_Cycloaddition.png
diff --git a/families/images/1,2-Birad_to_alkene.png b/families/images/1,2-Birad_to_alkene.png
diff --git a/families/images/1,2_Insertion_CO.png b/families/images/1,2_Insertion_CO.png
diff --git a/families/images/1,2_Insertion_carbene.png b/families/images/1,2_Insertion_carbene.png
diff --git a/families/images/1,2_NH3_elimination.png b/families/images/1,2_NH3_elimination.png
diff --git a/families/images/1,2_shiftC.png b/families/images/1,2_shiftC.png
diff --git a/families/images/1,2_shiftS.png b/families/images/1,2_shiftS.png
diff --git a/families/images/1,3_Insertion_CO2.png b/families/images/1,3_Insertion_CO2.png
diff --git a/families/images/1,3_Insertion_ROR.png b/families/images/1,3_Insertion_ROR.png
diff --git a/families/images/1,3_Insertion_RSR.png b/families/images/1,3_Insertion_RSR.png
diff --git a/families/images/1,3_NH3_elimination.png b/families/images/1,3_NH3_elimination.png
diff --git a/families/images/1,4_Cyclic_birad_scission.png b/families/images/1,4_Cyclic_birad_scission.png
diff --git a/families/images/1,4_Linear_birad_scission.png b/families/images/1,4_Linear_birad_scission.png
diff --git a/families/images/2+2_cycloaddition_CCO.png b/families/images/2+2_cycloaddition_CCO.png
diff --git a/families/images/2+2_cycloaddition_CO.png b/families/images/2+2_cycloaddition_CO.png
diff --git a/families/images/2+2_cycloaddition_CS.png b/families/images/2+2_cycloaddition_CS.png
diff --git a/families/images/2+2_cycloaddition_Cd.png b/families/images/2+2_cycloaddition_Cd.png
diff --git a/families/images/6_membered_central_C-C_shift.png b/families/images/6_membered_central_C-C_shift.png
diff --git a/families/images/Baeyer-Villiger_step1_cat.png b/families/images/Baeyer-Villiger_step1_cat.png
diff --git a/families/images/Baeyer-Villiger_step2.png b/families/images/Baeyer-Villiger_step2.png
diff --git a/families/images/Baeyer-Villiger_step2_cat.png b/families/images/Baeyer-Villiger_step2_cat.png
diff --git a/families/images/Bimolec_Hydroperoxide_Decomposition.png b/families/images/Bimolec_Hydroperoxide_Decomposition.png
diff --git a/families/images/Birad_R_Recombination.png b/families/images/Birad_R_Recombination.png
diff --git a/families/images/Birad_recombination.png b/families/images/Birad_recombination.png
diff --git a/families/images/CO_Disproportionation.png b/families/images/CO_Disproportionation.png
diff --git a/families/images/Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH.png b/families/images/Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH.png
diff --git a/families/images/Cyclic_Ether_Formation.png b/families/images/Cyclic_Ether_Formation.png
diff --git a/families/images/Cyclic_Thioether_Formation.png b/families/images/Cyclic_Thioether_Formation.png
diff --git a/families/images/Cyclopentadiene_scission.png b/families/images/Cyclopentadiene_scission.png
diff --git a/families/images/Diels_alder_addition.png b/families/images/Diels_alder_addition.png
diff --git a/families/images/Disproportionation.png b/families/images/Disproportionation.png
diff --git a/families/images/HO2_Elimination_from_PeroxyRadical.png b/families/images/HO2_Elimination_from_PeroxyRadical.png
diff --git a/families/images/H_Abstraction.png b/families/images/H_Abstraction.png
diff --git a/families/images/Intra_2+2_cycloaddition_Cd.png b/families/images/Intra_2+2_cycloaddition_Cd.png
diff --git a/families/images/Intra_5_membered_conjugated_C=C_C=C_addition.png b/families/images/Intra_5_membered_conjugated_C=C_C=C_addition.png
diff --git a/families/images/Intra_Diels_alder_monocyclic.png b/families/images/Intra_Diels_alder_monocyclic.png
diff --git a/families/images/Intra_Disproportionation.png b/families/images/Intra_Disproportionation.png
diff --git a/families/images/Intra_RH_Add_Endocyclic.png b/families/images/Intra_RH_Add_Endocyclic.png
diff --git a/families/images/Intra_RH_Add_Exocyclic.png b/families/images/Intra_RH_Add_Exocyclic.png
diff --git a/families/images/Intra_R_Add_Endocyclic.png b/families/images/Intra_R_Add_Endocyclic.png
diff --git a/families/images/Intra_R_Add_ExoTetCyclic.png b/families/images/Intra_R_Add_ExoTetCyclic.png
diff --git a/families/images/Intra_R_Add_Exo_scission.png b/families/images/Intra_R_Add_Exo_scission.png
diff --git a/families/images/Intra_R_Add_Exocyclic.png b/families/images/Intra_R_Add_Exocyclic.png
diff --git a/families/images/Intra_Retro_Diels_alder_bicyclic.png b/families/images/Intra_Retro_Diels_alder_bicyclic.png
diff --git a/families/images/Intra_ene_reaction.png b/families/images/Intra_ene_reaction.png
diff --git a/families/images/Korcek_step1.png b/families/images/Korcek_step1.png
diff --git a/families/images/Korcek_step1_cat.png b/families/images/Korcek_step1_cat.png
diff --git a/families/images/Korcek_step2.png b/families/images/Korcek_step2.png
diff --git a/families/images/Peroxyl_Disproportionation.png b/families/images/Peroxyl_Disproportionation.png
diff --git a/families/images/Peroxyl_Termination.png b/families/images/Peroxyl_Termination.png
diff --git a/families/images/R_Addition_COm.png b/families/images/R_Addition_COm.png
diff --git a/families/images/R_Addition_CSm.png b/families/images/R_Addition_CSm.png
diff --git a/families/images/R_Addition_MultipleBond.png b/families/images/R_Addition_MultipleBond.png
diff --git a/families/images/R_Recombination.png b/families/images/R_Recombination.png
diff --git a/families/images/Singlet_Carbene_Intra_Disproportionation.png b/families/images/Singlet_Carbene_Intra_Disproportionation.png
diff --git a/families/images/Singlet_Val6_to_triplet.png b/families/images/Singlet_Val6_to_triplet.png
diff --git a/families/images/SubstitutionS.png b/families/images/SubstitutionS.png
diff --git a/families/images/Substitution_O.png b/families/images/Substitution_O.png
diff --git a/families/images/Surface_Abstraction.png b/families/images/Surface_Abstraction.png
diff --git a/families/images/Surface_Adsorption_Bidentate.png b/families/images/Surface_Adsorption_Bidentate.png
diff --git a/families/images/Surface_Adsorption_Dissociative.png b/families/images/Surface_Adsorption_Dissociative.png
diff --git a/families/images/Surface_Adsorption_Double.png b/families/images/Surface_Adsorption_Double.png
diff --git a/families/images/Surface_Adsorption_Single.png b/families/images/Surface_Adsorption_Single.png
diff --git a/families/images/Surface_Adsorption_vdW.png b/families/images/Surface_Adsorption_vdW.png
diff --git a/families/images/Surface_Bidentate_Dissociation.png b/families/images/Surface_Bidentate_Dissociation.png
diff --git a/families/images/Surface_Dissociation.png b/families/images/Surface_Dissociation.png
diff --git a/families/images/Surface_Dissociation_vdW.png b/families/images/Surface_Dissociation_vdW.png
diff --git a/families/images/Surface_Recombination.png b/families/images/Surface_Recombination.png
diff --git a/families/images/intra_H_migration.png b/families/images/intra_H_migration.png
diff --git a/families/images/intra_NO2_ONO_conversion.png b/families/images/intra_NO2_ONO_conversion.png
diff --git a/families/images/intra_OH_migration.png b/families/images/intra_OH_migration.png
diff --git a/families/images/intra_substitutionCS_cyclization.png b/families/images/intra_substitutionCS_cyclization.png
diff --git a/families/images/intra_substitutionCS_isomerization.png b/families/images/intra_substitutionCS_isomerization.png
diff --git a/families/images/intra_substitutionS_cyclization.png b/families/images/intra_substitutionS_cyclization.png
diff --git a/families/images/intra_substitutionS_isomerization.png b/families/images/intra_substitutionS_isomerization.png
diff --git a/families/images/ketoenol.png b/families/images/ketoenol.png
diff --git a/families/images/lone_electron_pair_bond.png b/families/images/lone_electron_pair_bond.png
diff --git a/families/rmg_reaction_families.cdx b/families/rmg_reaction_families.cdx
diff --git a/families/rmg_reaction_families.pdf b/families/rmg_reaction_families.pdf
diff --git a/input/forbiddenStructures.py b/input/forbiddenStructures.py
@@ -190,6 +190,20 @@
 """,
 )
 
+entry(
+    label = "N-N(S)",
+    species =
+"""
+1 N u0 p2 c0 {2,S}
+2 N u0 p2 c0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+This structure is not a stationary point, and should quickly become N#N
+""",
+)
+
 entry(
     label = "[N][N]",
     species =
@@ -349,3 +363,80 @@
 without getting negative frequency/ies.
 """,
 )
+
+entry(
+    label = "cN3HNH2",
+    species =
+"""
+multiplicity 2
+1 N u0 p1 c0 {2,S} {3,S} {4,S}
+2 N u0 p1 c0 {1,S} {4,S} {5,S}
+3 N u0 p1 c0 {1,S} {6,S} {7,S}
+4 N u1 p1 c0 {1,S} {2,S}
+5 H u0 p0 c0 {2,S}
+6 H u0 p0 c0 {3,S}
+7 H u0 p0 c0 {3,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Geometry could not converge at CBS-QB3
+""",
+)
+
+entry(
+    label = "cN3HN",
+    group =
+"""
+1 N u0     p1 c0 {2,S} {3,S} {5,S}
+2 N u[0,1] p1 c0 {1,S} {3,S}
+3 N u0     p0 c+1 {1,S} {2,S} {4,D}
+4 N u0     p2 c-1 {3,D}
+5 R ux     px cx {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Geometry of the following species in this group could not converge at CBS-QB3
+[N-]=[N+]1[N]N1
+[N-]=[N+]1NN1
+""",
+)
+
+entry(
+    label = "NH3NNH",
+    species =
+"""
+multiplicity 2
+1 N u0 p0 c+1 {2,S} {4,S} {5,S} {6,S}
+2 N u0 p2 c-1 {1,S} {3,S}
+3 N u1 p1 c0 {2,S} {7,S}
+4 H u0 p0 c0 {1,S}
+5 H u0 p0 c0 {1,S}
+6 H u0 p0 c0 {1,S}
+7 H u0 p0 c0 {3,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Geometry could not converge at wB97x-D3/6-311++G(3df,3pd) (alongd ref - xq1488)
+""",
+)
+
+entry(
+    label = "NNHNH",
+    species =
+"""
+multiplicity 2
+1 N u0 p0 c+1 {2,S} {3,D} {5,S}
+2 N u0 p1 c0 {1,S} {4,D}
+3 N u0 p2 c-1 {1,D}
+4 N u1 p1 c0 {2,D}
+5 H u0 p0 c0 {1,S}
+""",
+    shortDesc = u"""""",
+    longDesc =
+u"""
+Geometry could not converge at wB97x-D3/6-311++G(3df,3pd) (alongd ref - xq1492)
+""",
+)
diff --git a/input/kinetics/families/1+2_Cycloaddition/template.cdx b/input/kinetics/families/1+2_Cycloaddition/template.cdx