Add catalytic combustion example to RMG-tests

tests/rmg/catalytic_combustion/input.py

@@ -0,0 +1,129 @@
+# Catalytic combustion of methane on Pt
+# Tests surface chemistry and linear scaling relations 
+# original example put together by Katrin Blondal from https://github.com/ReactionMechanismGenerator/RMG-tests/pull/71/commits/1191dc1e5ea0485342e6cbf41b992c78ea74ebf0  
+
+
+#Data sources
+database(
+    thermoLibraries=['surfaceThermoPt', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'],
+    reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006', False),('BurkeH2O2inN2',False),('FFCM1(-)',False)],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies =['surface','default'],
+    kineticsEstimator = 'rate rules',
+)
+
+catalystProperties(
+    bindingEnergies = { # For Pd(111) from DFT studies
+                        'H': (-2.70, 'eV/molecule'),
+                        'O': (-3.64, 'eV/molecule'),
+                        'C': (-6.90, 'eV/molecule'),
+                        'N': (-4.70, 'eV/molecule'), #Made up value
+                        }, 
+    surfaceSiteDensity=(2.72e-9, 'mol/cm^2'),
+)
+
+generatedSpeciesConstraints(
+    allowed=['reaction libraries'],
+)
+
+
+# List of species
+species(
+    label='X',
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+
+species(
+    label='CH4',
+    reactive=True,
+    structure=SMILES("[CH4]"),
+)
+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"),
+)
+
+
+#----------
+
+surfaceReactor(
+    temperature=(800,'K'),
+    initialPressure=(1.0, 'bar'),
+    initialGasMoleFractions={
+        "CH4": 0.0500,
+        "O2": 0.1995,
+        "N2": 0.7505,
+    },
+    initialSurfaceCoverages={
+        "X": 1.0,
+    },
+    surfaceVolumeRatio=(1.0e4, 'm^-1'),
+    terminationConversion = { "CH4":0.9,}
+)
+
+surfaceReactor(
+    temperature=(1500,'K'),
+    initialPressure=(1.0, 'bar'),
+    initialGasMoleFractions={
+        "CH4": 0.0500,
+        "O2": 0.1995,
+        "N2": 0.7505,
+    },
+    initialSurfaceCoverages={
+        "X": 1.0,
+    },
+    surfaceVolumeRatio=(1.0e4, 'm^-1'),
+    terminationConversion = { "CH4":0.9,}
+)
+
+
+surfaceReactor(
+    temperature=(1750,'K'),
+    initialPressure=(1.0, 'bar'),
+    initialGasMoleFractions={
+        "CH4": 0.0500,
+        "O2": 0.1995,
+        "N2": 0.7505,
+    },
+    initialSurfaceCoverages={
+        "X": 1.0,
+    },
+    surfaceVolumeRatio=(1.0e4, 'm^-1'),
+    terminationConversion = { "CH4":0.9,}
+)
+
+
+
+simulator(
+    atol=1e-18,
+    rtol=1e-12,
+)
+
+model(
+    toleranceMoveToCore=0.01, 
+    toleranceInterruptSimulation=0.1,
+    maximumEdgeSpecies=100000
+)
+
+options(
+    units='si',
+    saveRestartPeriod=None,
+    generateOutputHTML=True,
+    generatePlots=False,
+    saveEdgeSpecies=True,
+    saveSimulationProfiles=True,
+)
+