Adding Nitrogen to RMG-Py

examples/rmg/1,3-hexadiene/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = [],
     kineticsDepositories = ['training'], #  'all', 'default'==['training'], [], 
-    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/TEOS/input.py

@@ -4,7 +4,7 @@
 	reactionLibraries = [],
 	seedMechanisms = [],
 	kineticsDepositories = ['training'],
-	kineticsFamilies = ['!Intra_Disproportionation'],
+	kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
 	kineticsEstimator = 'rate rules',
 )
 

examples/rmg/c3h4/input.py

@@ -1,10 +1,10 @@
 # Data sources
 database(
-	thermoLibraries = ['primaryThermoLibrary', 'GRI-Mech3.0'],
+	thermoLibraries = ['primaryThermoLibrary', 'GRI-Mech3.0-N'],
 	reactionLibraries = [],
-	seedMechanisms = [],
+	seedMechanisms = ['GRI-Mech3.0-N'],
 	kineticsDepositories = ['training'], #  'all', 'default'==['training'], [], 
-	kineticsFamilies = ['!Intra_Disproportionation'],
+	kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
 	kineticsEstimator = 'rate rules',
 )
 

examples/rmg/ch3no2/input.py

@@ -0,0 +1,86 @@
+# Data sources
+database(
+    thermoLibraries = ['KlippensteinH2O2', 'primaryThermoLibrary','DFT_QCI_thermo','CH','CHN','CHO','CHON','CN','NISTThermoLibrary','thermo_DFT_CCSDTF12_BAC','GRI-Mech3.0-N'],
+    reactionLibraries = [('Nitrogen_Dean_and_Bozelli',False)], 
+    seedMechanisms = ['ERC-FoundationFuelv0.9'],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['!Intra_Disproportionation', '!Substitution_O'],
+    kineticsEstimator = 'rate rules',
+)
+
+# Constraints on generated species
+generatedSpeciesConstraints(
+    #maximumCarbonAtoms = 7,
+    #maximumHydrogenAtoms = 8,
+    #maximumOxygenAtoms = 5,
+    maximumNitrogenAtoms = 2,
+    #maximumSiliconAtoms = 0,
+    #maximumSulfurAtoms = 0,
+    #maximumHeavyAtoms = 3,
+    maximumRadicalElectrons = 2,
+)
+
+# List of species
+species(
+    label='CH3NO2',
+    reactive=True,
+        structure=adjacencyList(
+        """
+        1 C 0 0 {2,S} {3,S} {4,S} {5,S}
+        2 H 0 0 {1,S}
+        3 H 0 0 {1,S}
+        4 H 0 0 {1,S}
+        5 N 0 0 {1,S} {6,D} {7,S}
+        6 O 0 2 {5,D}
+        7 O 0 3 {5,S}
+        """),
+)
+
+species(
+    label='O2',
+    reactive=True,
+        structure=adjacencyList(
+        """
+        1 O 1 2 {2,S}
+        2 O 1 2 {1,S}
+        """),
+)
+
+species(
+    label='N2',
+    reactive=True,
+        structure=adjacencyList(
+        """
+        1 N 1 1 {2,T}
+        2 N 1 1 {1,T}
+        """),
+)
+
+# Reaction systems
+
+simpleReactor(
+    temperature=(1500,'K'),
+    pressure=(10.0,'bar'),
+    initialMoleFractions={
+        "CH3NO2": 0.1,
+        "O2": 0.21,
+        "N2": 0.69,
+    },
+    terminationConversion={
+        'CH3NO2': 0.1,
+    },
+)
+
+model(
+    toleranceKeepInEdge=1e-5,
+    toleranceMoveToCore=0.1,
+    toleranceInterruptSimulation=0.1,
+    maximumEdgeSpecies=10000
+)
+
+options(
+    units='si',
+    saveRestartPeriod=None,
+    drawMolecules=False,
+    generatePlots=False,
+)

examples/rmg/diesel/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = [],
     kineticsDepositories = ['training'], #  'all', 'default'==['training'], [], 
-    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/e85/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = ['GRI-Mech3.0'],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/liquid_phase/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = [],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/methylformate/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [('Methylformate',False),('Glarborg/highP',False)],
     seedMechanisms = ['Glarborg/C2'],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/minimal/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = [],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
     kineticsEstimator = 'rate rules',
 )
 

examples/rmg/minimal_sensitivity/input.py

@@ -4,7 +4,7 @@
     reactionLibraries = [],
     seedMechanisms = [],
     kineticsDepositories = ['training'],
-    kineticsFamilies = ['!Intra_Disproportionation'],
+    kineticsFamilies = ['!Intra_Disproportionation','!Substitution_O'],
     kineticsEstimator = 'rate rules',
 )