Add regression test for RMS reactor

.github/workflows/CI.yml

@@ -119,7 +119,7 @@ jobs:
       - name: Regression Tests - Execution
         timeout-minutes: 60
         run: |
-          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal;
+          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat;
           do
             if python-jl rmg.py test/regression/"$regr_test"/input.py; then
               echo "$regr_test" "Executed Successfully"
@@ -190,7 +190,7 @@ jobs:
         env:
           REFERENCE: stable_regression_results
         run: |
-          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal;
+          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat;
           do
             # Memory Usage and Execution Time
             echo 'Execution time for Reference:'

rmgpy/rmg/input.py

@@ -836,7 +836,7 @@ def constant_T_V_liquid_reactor(temperature,
     termination = []
     if terminationConversion is not None:
         for spec, conv in terminationConversion.items():
-            termination.append(TerminationConversion(species_dict[spec], conv))
+            termination.append((species_dict[spec], conv))
     if terminationTime is not None:
         termination.append(TerminationTime(Quantity(terminationTime)))
     if terminationRateRatio is not None:

rmgpy/rmg/reactors.py

@@ -441,8 +441,8 @@ def generate_reactor(self, phase_system):
             inter,pinter = rms.ReactiveInternalInterfaceConstantTPhi(domainliq,domaincat,Main.eval("using ReactionMechanismSimulator; Vector{ElementaryReaction}()"),self.initial_conditions["liquid"]["T"],self.initial_conditions["surface"]["A"])
         else:
             inter,pinter = rms.ReactiveInternalInterfaceConstantTPhi(domainliq,domaincat,interface.reactions,self.initial_conditions["liquid"]["T"],self.initial_conditions["surface"]["A"])
-        react,y0,p = rms.Reactor((domainliq,domaincat), (y0liq,y0cat), (0.0, self.tf), [inter], p=(pliq,pcat,pinter))
-        return react, (domainliq,domaincat), [inter], p
+        react,y0,p = rms.Reactor((domainliq,domaincat), (y0liq,y0cat), (0.0, self.tf), (inter,), (pliq,pcat,pinter))
+        return react, (domainliq,domaincat), (inter,), p
 
 class ConstantTVLiquidReactor(Reactor):
     def __init__(self, core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species=[],

test/regression/RMS_CSTR_liquid_oxidation/input.py

@@ -0,0 +1,66 @@
+# Test liquid-phase simulation with reaction filtering and flux pruning
+# Also test adding multiple species in each iteration and imposing species constraints.
+
+database(
+    thermoLibraries=['primaryThermoLibrary'],
+    reactionLibraries=[],
+    seedMechanisms=[],
+    kineticsDepositories='default',
+    kineticsFamilies=['default', 'liquid_peroxide'],
+    kineticsEstimator='rate rules',
+)
+
+generatedSpeciesConstraints(
+    allowed=['input species'],
+    maximumRadicalElectrons=1,
+    maximumCarbonAtoms=5,
+    maximumOxygenAtoms=4,
+)
+
+species(
+    label='oxygen',
+    reactive=True,
+    structure=SMILES('[O][O]')
+)
+
+species(
+    label='pentane',
+    reactive=True,
+    structure=SMILES('CCCCC'),
+)
+
+constantTVLiquidReactor(
+    temperature=(600, 'K'),
+    initialConcentrations={
+        'pentane': (3.0e-3, 'mol/cm^3'),
+        'oxygen': (1.0e-4, 'mol/cm^3'),
+    },
+    residenceTime=(20, 's'),
+    terminationConversion={'pentane': 0.3},
+    terminationTime=(1000, 's'),
+)
+
+solvation(
+    solvent='pentane'
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceMoveToCore=0.01,
+    toleranceKeepInEdge=0.001,
+    toleranceInterruptSimulation=1e8,
+    maximumEdgeSpecies=10000,
+    minCoreSizeForPrune=10,
+    minSpeciesExistIterationsForPrune=2,
+    maxNumObjsPerIter=3,
+    filterReactions=True,
+    maxNumSpecies=35,
+)
+
+options(
+    saveEdgeSpecies=True,
+)

test/regression/RMS_CSTR_liquid_oxidation/regression_input.py

@@ -0,0 +1,25 @@
+options(
+    title='RMS_CSTR_liquid_oxidation',
+    tolerance=0.1
+)
+
+observable(
+    label='pentane',
+    structure=SMILES('CCCCC')
+)
+
+species(
+    label='oxygen',
+    structure=SMILES('[O][O]'),
+)
+
+reactorSetups(
+    reactorTypes=['IdealGasReactor'],
+    terminationTimes=([1e3], 's'),
+    initialMoleFractionsList=[{
+        'pentane': 0.9,
+        'oxygen': 0.1,
+    }],
+    temperatures=([600], 'K'),
+    pressures=([1.0], 'bar'),
+)

test/regression/RMS_constantVIdealGasReactor_superminimal/input.py

@@ -0,0 +1,50 @@
+# Data sources
+database(
+    thermoLibraries = ['primaryThermoLibrary'],
+    reactionLibraries = [],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['H_Abstraction','Disproportionation','R_Recombination',
+                        'Birad_recombination', 'Birad_R_Recombination'],
+    kineticsEstimator = 'rate rules',
+)
+
+# List of species
+species(
+    label='H2',
+    reactive=True,
+    structure=SMILES("[H][H]"),
+)
+species(
+   label='O2',
+   reactive=True,
+   structure=SMILES("[O][O]"),
+)
+
+# Reaction systems
+constantVIdealGasReactor(
+    temperature=(1000,'K'),
+    pressure=(1.0,'bar'),
+    initialMoleFractions={
+        'H2':.67, 'O2':.33,
+    },
+    terminationConversion={
+        'H2': 0.9,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceMoveToCore=0.01,
+    toleranceInterruptSimulation=0.01,
+)
+
+options(
+    units='si',
+    saveEdgeSpecies=True,
+)

test/regression/RMS_constantVIdealGasReactor_superminimal/regression_input.py

@@ -0,0 +1,26 @@
+
+options(
+    title='RMS_constantVIdealGasReactor_superminimal',
+    tolerance=0.1
+)
+
+observable(
+    label='H2',
+    structure=SMILES("[H][H]"),
+)
+
+observable(
+   label='O2',
+   structure=SMILES("[O][O]"),
+)
+
+reactorSetups(
+    reactorTypes=['IdealGasReactor'],
+    terminationTimes=([0.01],'s'),
+    initialMoleFractionsList=[{
+        'H2':.67,
+        'O2':.33,
+    }],
+    temperatures=([1000],'K'),
+    pressures=([1.0],'bar'),
+)

test/regression/RMS_liquidSurface_ch4o2cat/input.py

@@ -0,0 +1,88 @@
+# 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(metal="Pt111")
+
+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="pentane",
+    reactive=False,
+    structure=SMILES("CCCCC"),
+)
+
+species(
+    label="vacantX",
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+
+# Reaction systems
+liquidSurfaceReactor(
+    temperature=(600, "K"),
+    initialConcentrations={
+        "CH4": (1.0e-4, "mol/cm^3"),
+        "O2": (1.0e-4, "mol/cm^3"),
+        "pentane": (3.0e-3, "mol/cm^3"),
+    },
+    initialSurfaceCoverages={
+        "vacantX": 1.0,
+    },
+    surfaceVolumeRatio=(1.0e5, "m^-1"),
+    terminationConversion={
+        "CH4": 0.99,
+    },
+    terminationTime=(0.1, "s"),
+)
+
+solvation(solvent="pentane")
+
+simulator(
+    atol=1e-18,
+    rtol=1e-12,
+)
+
+model(
+    toleranceMoveToCore=0.01,
+    toleranceKeepInEdge=0.001,
+    toleranceInterruptSimulation=1e8,
+    maximumEdgeSpecies=10000,
+    minCoreSizeForPrune=10,
+    minSpeciesExistIterationsForPrune=2,
+    maxNumObjsPerIter=3,
+    maxNumSpecies=35,
+)
+
+options(
+    units="si",
+    saveEdgeSpecies=True,
+)

test/regression/RMS_liquidSurface_ch4o2cat/regression_input.py

@@ -0,0 +1,39 @@
+
+options(
+    title='RMS_liquidSurface_ch4o2cat',
+    tolerance=0.1
+)
+
+
+observable(
+    label='CH4',
+    structure=SMILES("[CH4]"),
+)
+
+observable(
+   label='O2',
+   structure=adjacencyList(
+       """
+1 O u1 p2 c0 {2,S}
+2 O u1 p2 c0 {1,S}
+"""),
+)
+
+species(
+    label='vacantX',
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+
+
+reactorSetups(
+    reactorTypes=['IdealGasReactor'],
+    terminationTimes=([0.01],'s'),
+    initialMoleFractionsList=[{
+        "CH4": 0.1,
+        "O2": 0.2,
+        "vacantX": 1.0,
+    }],
+    temperatures=([600],'K'),
+    pressures=([1.0],'bar'),
+)