added rmg halogens example of 2btp/CF3Br in CH4 flames

Author: davidfarinajr

examples/rmg/halogens/2-BTP/input.py

@@ -0,0 +1,131 @@
+# Example input file for 2-BTP/CF3Br in methane flames
+
+database(
+    thermoLibraries = ['primaryThermoLibrary', 'DFT_QCI_thermo', 'thermo_DFT_CCSDTF12_BAC',
+                    'halogens', 'CHOBr_G4','CHOF_G4','CHOFBr_G4', '2-BTP', '2-BTP_G4', 'Fluorine',
+                    'CBS_QB3_1dHR','NISTThermoLibrary','JetSurF2.0'],
+    #reactionLibraries = ['2-BTP/seed'], #optional: use NISTs 2-BTP kinetics library as seed or reaction library
+    reactionLibraries = [],
+    seedMechanisms = ['FFCM1(-)'], #optional: use FFCM1(-) kinetics library as seed for methane combustion
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['default','halogens'], # load both the `default` and `halogens` recommended kinetics families
+    kineticsEstimator = 'rate rules',
+)
+
+species(
+    label = "2-BTP",
+    reactive = True,
+    structure = SMILES("FC(F)(F)C(Br)=C")
+)
+
+species(
+    label = "CF3Br",
+    reactive = True,
+    structure = SMILES("FC(F)(F)Br")
+)
+
+species(
+    label = 'CH4',
+    reactive = True,
+    structure = SMILES('C')
+)
+
+species(
+    label = "O2",
+    reactive = True,
+    structure = adjacencyList(
+    """
+    multiplicity 3
+    1 O u1 p2 c0 {2,S}
+    2 O u1 p2 c0 {1,S}
+""" 
+))
+
+species(
+    label = "N2",
+    reactive = False,
+    structure = adjacencyList(
+    """
+    1 N u0 p1 c0 {2,T}
+    2 N u0 p1 c0 {1,T}
+    """
+))
+
+# reactor for 2-BTP in methane flame
+simpleReactor(
+        temperature=[(1000,'K'),(2200,'K')],
+        pressure=(1.0,'bar'),
+        nSims=24,
+        initialMoleFractions={
+        "2-BTP": [0.0,0.04],
+        "CH4" : [0.05,0.15],
+        "O2": 0.21,
+        "N2": 0.78,
+        },
+        terminationConversion={
+        'CH4': 0.99,
+        },
+        terminationTime=(1,'s'),
+        )
+
+# pressue dependence is not yet implemented for halogen chemistry
+# pressureDependence(
+#     method='modified strong collision',
+#     maximumGrainSize=(0.5,'kcal/mol'),
+#     minimumNumberOfGrains=250,
+#     temperatures=(300,2200,'K',8),
+#     pressures=(0.01,100,'bar',5),
+#     interpolation=('Chebyshev', 6, 4),
+# )
+
+
+simulator(
+    atol = 1e-16,
+    rtol = 1e-08,
+    sens_atol = 1e-06,
+    sens_rtol = 0.0001,
+)
+
+model(
+    toleranceMoveToCore = 0.25,
+    toleranceInterruptSimulation = 1,
+    maximumEdgeSpecies = 5e5,
+    filterReactions = True,
+    filterThreshold = 5e8,
+    minCoreSizeForPrune=400,
+    minSpeciesExistIterationsForPrune=4,
+)
+
+
+# model(
+#     toleranceMoveToCore=1,
+#     toleranceInterruptSimulation=1e8,
+#     toleranceKeepInEdge=0.05,
+#     maximumEdgeSpecies=200000,
+#     minCoreSizeForPrune=50,
+#     minSpeciesExistIterationsForPrune=2,
+#     filterReactions = True,
+#     filterThreshold=5e8
+#     )
+
+generatedSpeciesConstraints(
+    allowed=['input species','seed mechanisms','reaction libraries'],
+    maximumCarbonAtoms=12,
+    maximumOxygenAtoms=6,
+    # maximumHeavyAtoms=24,
+    maximumRadicalElectrons=2,
+    maximumSingletCarbenes=1,
+    maximumCarbeneRadicals=0,
+    allowSingletO2 = False,
+)
+
+options(
+    units = "si",
+    saveRestartPeriod = None,
+    generateOutputHTML = True,
+    generatePlots = False,
+    saveSimulationProfiles = True,
+    saveEdgeSpecies = False,
+    keepIrreversible = True,
+    verboseComments = False,
+)