diff --git a/tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/iteration_1/RMG/input.py b/tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/iteration_1/RMG/input.py index 86c288cb..852c43da 100644 --- a/tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/iteration_1/RMG/input.py +++ b/tests/test_simulate_adapters/data/rmg_simulator_test_ranges_3c/iteration_1/RMG/input.py @@ -1,6 +1,6 @@ database( - thermoLibraries=['primaryThermoLibrary'], - reactionLibraries=[], + thermoLibraries=['primaryThermoLibrary', 'BurkeH2O2', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo', 'Spiekermann_refining_elementary_reactions', 'CurranPentane', 'CBS_QB3_1dHR', 'primaryNS'], + reactionLibraries=['primaryH2O2', 'NOx2018', '2006_Joshi_OH_CO', 'CurranPentane', 'Klippenstein_Glarborg2016', 'C2H4+O_Klipp2017', 'FFCM1(-)', 'C2H2_init', 'Narayanaswamy', 'Mebel_C6H5_C2H2', 'C10H11', 'C12H11_pdep', 'Lai_Hexylbenzene', '1989_Stewart_2CH3_to_C2H5_H', '2001_Tokmakov_H_Toluene_to_CH3_Benzene', '2003_Miller_Propargyl_Recomb_High_P', '2005_Senosiain_OH_C2H2', 'kislovB', 'c-C5H5_CH3_Sharma', 'fascella', '2006_Joshi_OH_CO', '2009_Sharma_C5H5_CH3_highP', '2015_Buras_C2H3_C4H6_highP', 'C3', 'Methylformate', 'C6H5_C4H4_Mebel', 'vinylCPD_H', 'Mebel_Naphthyl', 'Fulvene_H'], transportLibraries=['OneDMinN2', 'PrimaryTransportLibrary', 'NOx2018', 'GRI-Mech'], seedMechanisms=[], kineticsDepositories='default', @@ -14,6 +14,12 @@ structure=SMILES('OC=O'), ) +species( + label='N2', + reactive=False, + structure=SMILES('N#N'), +) + species( label='O2', reactive=True, @@ -21,26 +27,424 @@ ) species( - label='N2', - reactive=False, - structure=SMILES('N#N'), + label='OH', + reactive=True, + structure=SMILES('[OH]'), +) + +species( + label='HO2', + reactive=True, + structure=SMILES('O[O]'), +) + +species( + label='H', + reactive=True, + structure=SMILES('[H]'), +) + +species( + label='H2', + reactive=True, + structure=SMILES('[H][H]'), +) + +species( + label='CH3', + reactive=True, + structure=SMILES('[CH3]'), +) + +species( + label='CO', + reactive=True, + structure=SMILES('[C-]#[O+]'), +) + +species( + label='CO2', + reactive=True, + structure=SMILES('O=C=O'), +) + +species( + label='HOCO', + reactive=True, + structure=SMILES('O[C]=O'), +) + +species( + label='OCHO', + reactive=True, + structure=SMILES('[O]C=O'), +) + +species( + label='CH2O', + reactive=True, + structure=SMILES('C=O'), +) + +species( + label='HCO', + reactive=True, + structure=SMILES('[CH]=O'), +) + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(500.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(1250.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, ) + simpleReactor( - temperature=(1000.0, 'K'), + temperature=(2000.0, 'K'), pressure=(1.0, 'bar'), initialMoleFractions={ 'N2': 3.76, - 'FA': [1.0, 4.0], + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(1.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(10.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, 'O2': 1.0, }, - terminationRateRatio=0.1, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'O2': 1.0, + 'FA': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'N2': 3.76, + 'FA': 2.5, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), + nSims=12, +) + + +simpleReactor( + temperature=(2000.0, 'K'), + pressure=(100.0, 'bar'), + initialMoleFractions={ + 'FA': 4.0, + 'N2': 3.76, + 'O2': 1.0, + }, + terminationTime=(60.0, 's'), nSims=12, ) model( - toleranceMoveToCore=0.01, - toleranceInterruptSimulation=0.01, + toleranceMoveToCore=0.2, + toleranceInterruptSimulation=0.2, filterReactions=True, filterThreshold=100000000.0, maxNumObjsPerIter=1, @@ -49,18 +453,42 @@ simulator(atol=1e-16, rtol=1e-08, sens_atol=1e-06, sens_rtol=0.0001) +pressureDependence( + method='modified strong collision', + maximumGrainSize=(2.0, 'kJ/mol'), + minimumNumberOfGrains=250, + temperatures=(300, 2500, 'K', 10), + pressures=(0.1, 110, 'bar', 10), + interpolation=('Chebyshev', 6, 4), + maximumAtoms=16, +) + options( name='Seed', generateSeedEachIteration=True, saveSeedToDatabase=False, units='si', - generateOutputHTML=False, + generateOutputHTML=True, generatePlots=False, - saveSimulationProfiles=False, + saveSimulationProfiles=True, verboseComments=False, - saveEdgeSpecies=True, + saveEdgeSpecies=False, keepIrreversible=False, trimolecularProductReversible=True, - wallTime='00:00:05:00', + wallTime='00:00:00:00', saveSeedModulus=-1, ) + +generatedSpeciesConstraints( + allowed=['input species', 'seed mechanisms', 'reaction libraries'], + maximumCarbonAtoms=2, + maximumOxygenAtoms=4, + maximumNitrogenAtoms=0, + maximumSiliconAtoms=0, + maximumSulfurAtoms=0, + maximumHeavyAtoms=5, + maximumRadicalElectrons=1, + maximumSingletCarbenes=1, + maximumCarbeneRadicals=0, + allowSingletO2=True, +) diff --git a/tests/test_simulate_adapters/test_rmg_constantTP.py b/tests/test_simulate_adapters/test_rmg_constantTP.py index 82c75df3..58d4cde6 100755 --- a/tests/test_simulate_adapters/test_rmg_constantTP.py +++ b/tests/test_simulate_adapters/test_rmg_constantTP.py @@ -188,6 +188,8 @@ def test_run_sa_via_rmg(): input_dict = read_yaml_file(os.path.join(TEST_DIR_4, 'input.yml')) input_dict['project_directory'] = TEST_DIR_4 t3_object = T3(**input_dict) + t3_object.iteration = 1 + t3_object.set_paths() t3_object.sa_observable = ['FA'] simulate_adapter = RMGConstantTP(t3=t3_object.t3, rmg=t3_object.rmg,