Added CO2 reduction examples

examples/rmg/CO2RR/input.py

@@ -0,0 +1,166 @@
+# Data sources
+database(
+    thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo', 'electrocatThermo'],
+    reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006_adjusted', False)],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['surface','electrochem'],
+    kineticsEstimator = 'rate rules',
+
+)
+
+catalystProperties(
+    metal = 'Ag111'
+)
+
+# List of species
+species(
+    label='CO2',
+    reactive=True,
+    structure=adjacencyList(
+        """
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,D}
+3 O u0 p2 c0 {2,D}
+"""),
+)
+
+
+species(
+   label='proton',
+   reactive=True,
+   structure=adjacencyList(
+       """
+1 H u0 p0 c+1
+"""),
+)
+
+species(
+    label='vacantX',
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+
+species(
+   label='H',
+   reactive=True,
+   structure=adjacencyList(
+       """
+1 H u1 p0 c0
+"""),
+)
+
+# species(
+#    label='water',
+#    reactive=True,
+#    structure=adjacencyList(
+#        """
+# 1 H u0 p0 c0 {3,S}
+# 2 H u0 p0 c0 {3,S}
+# 3 O u0 p2 c0 {1,S} {2,S}
+# """),
+# )
+
+# species(
+#     label='CO2X2',
+#     reactive=True,
+#     structure=adjacencyList("""
+# 1 O u0 p2 c0 {3,S} {5,S}
+# 2 O u0 p2 c0 {3,D}
+# 3 C u0 p0 c0 {1,S} {2,D} {4,S}
+# 4 X u0 p0 c0 {3,S}
+# 5 X u0 p0 c0 {1,S}
+# """),
+# )
+
+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='CHO2X',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 H u0 p0 c0 {3,S}
+5 X u0 p0 c0 {1,S}
+"""),
+)
+
+# species(
+#     label='HX',
+#     reactive=True,
+#     structure=adjacencyList(
+#         """
+# 1 X u0 {2,S}
+# 2 H u0 p0 c0 {1,S}
+# """),
+# )
+
+liquidSurfaceReactor(
+    temperature=(300,'K'),
+    liqPotential=(0,'V'),
+    surfPotential=(-1.2,'V'),
+    initialConcentrations={
+        # "CO2": (1e-3,'mol/cm^3'),
+        "proton": (1e-3,'mol/m^3'),
+        # "water": (0.055, 'mol/cm^3'),
+    },
+	initialSurfaceCoverages={
+        # "HX": 0.5,
+        # # "CXO2": 0.0,
+        "CHO2X": 1.0,
+        # "vacantX": 1.0,
+    },
+    surfaceVolumeRatio=(1.0e5, 'm^-1'),
+    terminationTime=(1.0,'sec'),
+    # terminationConversion={'CO2': 0.90},
+    # constantSpecies=["proton"],
+ )
+
+solvation(
+	solvent='water'
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceKeepInEdge=1E-16,
+    toleranceMoveToCore=1E-8,
+    toleranceRadMoveToCore=1E-10,
+    toleranceInterruptSimulation=1E10,
+    filterReactions=False,
+    maximumEdgeSpecies=10000,
+    toleranceBranchReactionToCore=1E-8,
+    branchingIndex=0.5,
+    branchingRatioMax=1.0,
+)
+
+options(
+    units='si',
+    generateOutputHTML=True,
+    generatePlots=True,
+    saveEdgeSpecies=True,
+    saveSimulationProfiles=False,
+)
+
+generatedSpeciesConstraints(
+    allowed=['input species','reaction libraries'],
+    maximumSurfaceSites=2,
+    maximumCarbonAtoms=4,
+    maximumOxygenAtoms=4,
+    maximumRadicalElectrons=1,
+)
+