Add surface combustion example for regression testing

.github/workflows/CI.yml

@@ -167,7 +167,7 @@ jobs:
         id: regression-execution
         timeout-minutes: 60
         run: |
-          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment;
+          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
           do
             if python-jl rmg.py test/regression/"$regr_test"/input.py; then
               echo "$regr_test" "Executed Successfully"
@@ -242,7 +242,7 @@ jobs:
         run: |
           exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout)
           mkdir -p "test/regression-diff"
-          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment;
+          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
           do
             echo ""
             echo "### Regression test $regr_test:"

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,
 )
+
+