add input files for surface combustion test and example

ReactionMechanismGenerator · Feb 2, 2024 · 51f4914 · 51f4914
1 parent 6976fb4
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diff --git a/examples/rmg/minimal_surface/input.py b/examples/rmg/minimal_surface/input.py
@@ -1,67 +1,123 @@
 # Data sources
 database(
-    thermoLibraries = ['primaryThermoLibrary'],
-    reactionLibraries = [],
+    thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'], # 'surfaceThermoPt' is the default. Thermo data is derived using bindingEnergies for other metals 
+    reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006_adjusted', False)], # when Ni is used change the library to Surface/Deutschmann_Ni 
     seedMechanisms = [],
     kineticsDepositories = ['training'],
-    kineticsFamilies = 'default',
+    kineticsFamilies = ['surface', 'default'],
     kineticsEstimator = 'rate rules',
 )
-
-# List of species
+catalystProperties(
+    bindingEnergies = {
+        'H': (-2.75368,'eV/molecule'),
+        'C': (-7.02516,'eV/molecule'),
+        'N': (-4.63225,'eV/molecule'),
+        'O': (-3.81153,'eV/molecule'),
+    },
+    surfaceSiteDensity=(2.483e-9, 'mol/cm^2'),
+    coverageDependence=False
+)
 species(
-    label='ethane',
+    label='CH4',
     reactive=True,
-    structure=SMILES("CC"),
+    structure=SMILES("C"),
 )
-
-# Reaction systems
-simpleReactor(
-    temperature=(1350,'K'),
-    pressure=(1.0,'bar'),
-    initialMoleFractions={
-        "ethane": 1.0,
-    },
-    terminationConversion={
-        'ethane': 0.9,
-    },
-    terminationTime=(1e6,'s'),
+species(
+   label='O2',
+   reactive=True,
+   structure=adjacencyList(
+       """
+1 O u1 p2 c0 {2,S}
+2 O u1 p2 c0 {1,S}
+"""),
 )
-
-simpleReactor(
-    temperature=(1000,'K'),
-    pressure=(1.0,'bar'),
-    initialMoleFractions={
-        "ethane": 1.0,
+species(
+    label='N2',
+    reactive=False,
+    structure=SMILES("N#N"),
+)
+species(
+    label='X',
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+# added for training
+species(
+    label='CO2X',
+    reactive=True,
+    structure=adjacencyList(
+    """
+    1 O u0 p2 c0 {3,D}
+    2 O u0 p2 c0 {3,D}
+    3 C u0 p0 c0 {1,D} {2,D}
+    4 X u0 p0 c0
+    """),
+)
+species(
+    label='COX',
+    reactive=True,
+    structure=adjacencyList(
+    """
+    1 O u0 p2 c0 {2,D}
+    2 C u0 p0 c0 {1,D} {3,D}
+    3 X u0 p0 c0 {2,D}
+    """),
+)
+species(
+    label='OX',
+    reactive=True,
+    structure=adjacencyList(
+    """
+    1 O u0 p2 c0 {2,D}
+    2 X u0 p0 c0 {1,D}
+    """),
+)
+# If you would like to forbid the bidentate form of absorbed CO2 from your model,
+# use the following `CO2_bidentate` forbidden structure
+# forbidden(
+#     label='CO2_bidentate',
+#     structure=SMILES("O=C(*)O*"),
+# )
+#----------
+# Reaction systems
+surfaceReactor(
+    temperature=(1000, 'K'),
+    initialPressure=(1.0, 'bar'),
+    initialGasMoleFractions={
+        "CH4": 0.15,
+        "O2": 0.15,
+        "N2": 0.7,
     },
-    terminationConversion={
-        'ethane': 0.9,
+    initialSurfaceCoverages={
+        "X": 1.0,
     },
-    terminationTime=(1e6,'s'),
+    surfaceVolumeRatio=(1.e5, 'm^-1'),
+    terminationConversion = { "CH4": 0.95,},
+    terminationTime=(0.1, 's'),
+    terminationRateRatio=0.01,
 )
-
-
-
 simulator(
-    atol=1e-16,
-    rtol=1e-8,
+    atol=1e-18,
+    rtol=1e-12,
 )
-
 model(
     toleranceKeepInEdge=0.0,
-    toleranceMoveToCore=100.0,
-    toleranceInterruptSimulation=100.0,
+    toleranceMoveToCore=1e-1,
+    toleranceInterruptSimulation=0.1,
     maximumEdgeSpecies=100000,
-    toleranceMoveEdgeReactionToSurface=1.0,
-    toleranceMoveSurfaceReactionToCore=2.0,
-    toleranceMoveSurfaceSpeciesToCore=.001,
-    dynamicsTimeScale=(1.0e-10,'sec'),
 )
-
 options(
     units='si',
-    generateOutputHTML=True,
-    generatePlots=False,
-    saveEdgeSpecies=True,
-    saveSimulationProfiles=True,
+    generateOutputHTML=False,
+    generatePlots=False, # Enable to make plots of core and edge size etc. But takes a lot of the total runtime!
+    saveEdgeSpecies=False,
+    saveSimulationProfiles=False,
+)
+generatedSpeciesConstraints(
+    allowed=['input species','reaction libraries'],
+    maximumCarbonAtoms=2, 
+    maximumOxygenAtoms=2,
+    maximumSurfaceSites=2,
 )
+
+
diff --git a/test/regression/minimal_surface/input.py b/test/regression/minimal_surface/input.py
@@ -0,0 +1,123 @@
+# Data sources
+database(
+    thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'], # 'surfaceThermoPt' is the default. Thermo data is derived using bindingEnergies for other metals 
+    reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006_adjusted', False)], # when Ni is used change the library to Surface/Deutschmann_Ni 
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['surface', 'default'],
+    kineticsEstimator = 'rate rules',
+)
+catalystProperties(
+    bindingEnergies = {
+        'H': (-2.75368,'eV/molecule'),
+        'C': (-7.02516,'eV/molecule'),
+        'N': (-4.63225,'eV/molecule'),
+        'O': (-3.81153,'eV/molecule'),
+    },
+    surfaceSiteDensity=(2.483e-9, 'mol/cm^2'),
+    coverageDependence=False
+)
+species(
+    label='CH4',
+    reactive=True,
+    structure=SMILES("C"),
+)
+species(
+   label='O2',
+   reactive=True,
+   structure=adjacencyList(
+       """
+1 O u1 p2 c0 {2,S}
+2 O u1 p2 c0 {1,S}
+"""),
+)
+species(
+    label='N2',
+    reactive=False,
+    structure=SMILES("N#N"),
+)
+species(
+    label='X',
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+# added for training
+species(
+    label='CO2X',
+    reactive=True,
+    structure=adjacencyList(
+    """
+    1 O u0 p2 c0 {3,D}
+    2 O u0 p2 c0 {3,D}
+    3 C u0 p0 c0 {1,D} {2,D}
+    4 X u0 p0 c0
+    """),
+)
+species(
+    label='COX',
+    reactive=True,
+    structure=adjacencyList(
+    """
+    1 O u0 p2 c0 {2,D}
+    2 C u0 p0 c0 {1,D} {3,D}
+    3 X u0 p0 c0 {2,D}
+    """),
+)
+species(
+    label='OX',
+    reactive=True,
+    structure=adjacencyList(
+    """
+    1 O u0 p2 c0 {2,D}
+    2 X u0 p0 c0 {1,D}
+    """),
+)
+# If you would like to forbid the bidentate form of absorbed CO2 from your model,
+# use the following `CO2_bidentate` forbidden structure
+# forbidden(
+#     label='CO2_bidentate',
+#     structure=SMILES("O=C(*)O*"),
+# )
+#----------
+# Reaction systems
+surfaceReactor(
+    temperature=(1000, 'K'),
+    initialPressure=(1.0, 'bar'),
+    initialGasMoleFractions={
+        "CH4": 0.15,
+        "O2": 0.15,
+        "N2": 0.7,
+    },
+    initialSurfaceCoverages={
+        "X": 1.0,
+    },
+    surfaceVolumeRatio=(1.e5, 'm^-1'),
+    terminationConversion = { "CH4": 0.95,},
+    terminationTime=(0.1, 's'),
+    terminationRateRatio=0.01,
+)
+simulator(
+    atol=1e-18,
+    rtol=1e-12,
+)
+model(
+    toleranceKeepInEdge=0.0,
+    toleranceMoveToCore=1e-1,
+    toleranceInterruptSimulation=0.1,
+    maximumEdgeSpecies=100000,
+)
+options(
+    units='si',
+    generateOutputHTML=False,
+    generatePlots=False, # Enable to make plots of core and edge size etc. But takes a lot of the total runtime!
+    saveEdgeSpecies=False,
+    saveSimulationProfiles=False,
+)
+generatedSpeciesConstraints(
+    allowed=['input species','reaction libraries'],
+    maximumCarbonAtoms=2, 
+    maximumOxygenAtoms=2,
+    maximumSurfaceSites=2,
+)
+
+
diff --git a/test/regression/minimal_surface/regression_input.py b/test/regression/minimal_surface/regression_input.py
@@ -0,0 +1,67 @@
+options(
+    title = 'minimal_surface',
+    tolerance = 0.5,
+)
+
+# observables
+observable(
+	label = 'CH4',
+    structure=SMILES('C'),
+)
+
+observable(
+	label = 'O2',
+    structure=SMILES('[O][O]'),
+)
+
+observable(
+	label = 'X',
+    structure=adjacencyList(
+        """
+1 X u0 p0 c0
+"""),
+)
+
+
+# List of species
+species(
+    label='CH4',
+    structure=SMILES("[CH4]"),
+)
+species(
+   label='O2',
+   structure=adjacencyList(
+       """
+1 O u1 p2 c0 {2,S}
+2 O u1 p2 c0 {1,S}
+"""),
+)
+species(
+    label='N2',
+    structure=SMILES("N#N"),
+)
+species(
+	label='X',
+    structure=adjacencyList(
+        """
+1 X u0 p0 c0
+"""),
+)
+
+
+# reactor setups
+reactorSetups(
+    reactorTypes=['IdealGasReactor'],
+    terminationTimes=([1.0], 's'),
+    initialMoleFractionsList=[{
+        'CH4': 0.15,
+        'O2': 0.15,
+        'N2': 0.7,
+    }],
+    initialSurfaceMoleFractionsList=[{
+        'X': 1.0,
+    }],
+
+    temperatures=([1000.0], 'K'),
+    pressures=([1.0], 'bar'),
+)