def setUp(self): """ A function run before each unit test in this class. """ self.nC4H10O = Species( label = 'n-C4H10O', conformer = Conformer( E0 = (-317.807,'kJ/mol'), modes = [ IdealGasTranslation(mass=(74.07,"g/mol")), NonlinearRotor(inertia=([41.5091,215.751,233.258],"amu*angstrom^2"), symmetry=1), HarmonicOscillator(frequencies=([240.915,341.933,500.066,728.41,809.987,833.93,926.308,948.571,1009.3,1031.46,1076,1118.4,1184.66,1251.36,1314.36,1321.42,1381.17,1396.5,1400.54,1448.08,1480.18,1485.34,1492.24,1494.99,1586.16,2949.01,2963.03,2986.19,2988.1,2995.27,3026.03,3049.05,3053.47,3054.83,3778.88],"cm^-1")), HinderedRotor(inertia=(0.854054,"amu*angstrom^2"), symmetry=1, fourier=([[0.25183,-1.37378,-2.8379,0.0305112,0.0028088], [0.458307,0.542121,-0.599366,-0.00283925,0.0398529]],"kJ/mol")), HinderedRotor(inertia=(8.79408,"amu*angstrom^2"), symmetry=1, fourier=([[0.26871,-0.59533,-8.15002,-0.294325,-0.145357], [1.1884,0.99479,-0.940416,-0.186538,0.0309834]],"kJ/mol")), HinderedRotor(inertia=(7.88153,"amu*angstrom^2"), symmetry=1, fourier=([[-4.67373,2.03735,-6.25993,-0.27325,-0.048748], [-0.982845,1.76637,-1.57619,0.474364,-0.000681718]],"kJ/mol")), HinderedRotor(inertia=(2.81525,"amu*angstrom^2"), symmetry=3, barrier=(2.96807,"kcal/mol")), ], spinMultiplicity = 1, opticalIsomers = 1, ), molecularWeight = (74.07,"g/mol"), transportData=TransportData(sigma=(5.94, 'angstrom'), epsilon=(559, 'K')), energyTransferModel = SingleExponentialDown(alpha0=(447.5*0.011962,"kJ/mol"), T0=(300,"K"), n=0.85), ) self.nC4H8 = Species( label = 'n-C4H8', conformer = Conformer( E0 = (-17.8832,'kJ/mol'), modes = [ IdealGasTranslation(mass=(56.06,"g/mol")), NonlinearRotor(inertia=([22.2748,122.4,125.198],"amu*angstrom^2"), symmetry=1), HarmonicOscillator(frequencies=([308.537,418.67,636.246,788.665,848.906,936.762,979.97,1009.48,1024.22,1082.96,1186.38,1277.55,1307.65,1332.87,1396.67,1439.09,1469.71,1484.45,1493.19,1691.49,2972.12,2994.31,3018.48,3056.87,3062.76,3079.38,3093.54,3174.52],"cm^-1")), HinderedRotor(inertia=(5.28338,"amu*angstrom^2"), symmetry=1, fourier=([[-0.579364,-0.28241,-4.46469,0.143368,0.126756], [1.01804,-0.494628,-0.00318651,-0.245289,0.193728]],"kJ/mol")), HinderedRotor(inertia=(2.60818,"amu*angstrom^2"), symmetry=3, fourier=([[0.0400372,0.0301986,-6.4787,-0.0248675,-0.0324753], [0.0312541,0.0538,-0.493785,0.0965968,0.125292]],"kJ/mol")), ], spinMultiplicity = 1, opticalIsomers = 1, ), ) self.H2O = Species( label = 'H2O', conformer = Conformer( E0 = (-269.598,'kJ/mol'), modes = [ IdealGasTranslation(mass=(18.01,"g/mol")), NonlinearRotor(inertia=([0.630578,1.15529,1.78586],"amu*angstrom^2"), symmetry=2), HarmonicOscillator(frequencies=([1622.09,3771.85,3867.85],"cm^-1")), ], spinMultiplicity = 1, opticalIsomers = 1, ), ) self.configuration = Configuration(self.nC4H8, self.H2O)
def setUp(self): """ A function run before each unit test in this class. """ self.nC4H10O = Species( label='n-C4H10O', conformer=Conformer( E0=(-317.807, 'kJ/mol'), modes=[ IdealGasTranslation(mass=(74.07, "g/mol")), NonlinearRotor(inertia=([41.5091, 215.751, 233.258], "amu*angstrom^2"), symmetry=1), HarmonicOscillator(frequencies=([ 240.915, 341.933, 500.066, 728.41, 809.987, 833.93, 926.308, 948.571, 1009.3, 1031.46, 1076, 1118.4, 1184.66, 1251.36, 1314.36, 1321.42, 1381.17, 1396.5, 1400.54, 1448.08, 1480.18, 1485.34, 1492.24, 1494.99, 1586.16, 2949.01, 2963.03, 2986.19, 2988.1, 2995.27, 3026.03, 3049.05, 3053.47, 3054.83, 3778.88 ], "cm^-1")), HinderedRotor(inertia=(0.854054, "amu*angstrom^2"), symmetry=1, fourier=([[ 0.25183, -1.37378, -2.8379, 0.0305112, 0.0028088 ], [ 0.458307, 0.542121, -0.599366, -0.00283925, 0.0398529 ]], "kJ/mol")), HinderedRotor( inertia=(8.79408, "amu*angstrom^2"), symmetry=1, fourier=([[ 0.26871, -0.59533, -8.15002, -0.294325, -0.145357 ], [1.1884, 0.99479, -0.940416, -0.186538, 0.0309834]], "kJ/mol")), HinderedRotor(inertia=(7.88153, "amu*angstrom^2"), symmetry=1, fourier=([[ -4.67373, 2.03735, -6.25993, -0.27325, -0.048748 ], [ -0.982845, 1.76637, -1.57619, 0.474364, -0.000681718 ]], "kJ/mol")), HinderedRotor(inertia=(2.81525, "amu*angstrom^2"), symmetry=3, barrier=(2.96807, "kcal/mol")), ], spin_multiplicity=1, optical_isomers=1, ), molecular_weight=(74.07, "g/mol"), transport_data=TransportData(sigma=(5.94, 'angstrom'), epsilon=(559, 'K')), energy_transfer_model=SingleExponentialDown( alpha0=(447.5 * 0.011962, "kJ/mol"), T0=(300, "K"), n=0.85), ) self.nC4H8 = Species( label='n-C4H8', conformer=Conformer( E0=(-17.8832, 'kJ/mol'), modes=[ IdealGasTranslation(mass=(56.06, "g/mol")), NonlinearRotor(inertia=([22.2748, 122.4, 125.198], "amu*angstrom^2"), symmetry=1), HarmonicOscillator(frequencies=([ 308.537, 418.67, 636.246, 788.665, 848.906, 936.762, 979.97, 1009.48, 1024.22, 1082.96, 1186.38, 1277.55, 1307.65, 1332.87, 1396.67, 1439.09, 1469.71, 1484.45, 1493.19, 1691.49, 2972.12, 2994.31, 3018.48, 3056.87, 3062.76, 3079.38, 3093.54, 3174.52 ], "cm^-1")), HinderedRotor(inertia=(5.28338, "amu*angstrom^2"), symmetry=1, fourier=([[ -0.579364, -0.28241, -4.46469, 0.143368, 0.126756 ], [ 1.01804, -0.494628, -0.00318651, -0.245289, 0.193728 ]], "kJ/mol")), HinderedRotor( inertia=(2.60818, "amu*angstrom^2"), symmetry=3, fourier=([[ 0.0400372, 0.0301986, -6.4787, -0.0248675, -0.0324753 ], [0.0312541, 0.0538, -0.493785, 0.0965968, 0.125292]], "kJ/mol")), ], spin_multiplicity=1, optical_isomers=1, ), ) self.H2O = Species( label='H2O', conformer=Conformer( E0=(-269.598, 'kJ/mol'), modes=[ IdealGasTranslation(mass=(18.01, "g/mol")), NonlinearRotor(inertia=([0.630578, 1.15529, 1.78586], "amu*angstrom^2"), symmetry=2), HarmonicOscillator( frequencies=([1622.09, 3771.85, 3867.85], "cm^-1")), ], spin_multiplicity=1, optical_isomers=1, ), ) self.N2 = Species( label='N2', molecular_weight=(28.04, "g/mol"), transport_data=TransportData(sigma=(3.41, "angstrom"), epsilon=(124, "K")), energy_transfer_model=None, ) self.TS = TransitionState( label='TS', conformer=Conformer( E0=(-42.4373, "kJ/mol"), modes=[ IdealGasTranslation(mass=(74.07, "g/mol")), NonlinearRotor(inertia=([40.518, 232.666, 246.092], "u*angstrom**2"), symmetry=1, quantum=False), HarmonicOscillator(frequencies=([ 134.289, 302.326, 351.792, 407.986, 443.419, 583.988, 699.001, 766.1, 777.969, 829.671, 949.753, 994.731, 1013.59, 1073.98, 1103.79, 1171.89, 1225.91, 1280.67, 1335.08, 1373.9, 1392.32, 1417.43, 1469.51, 1481.61, 1490.16, 1503.73, 1573.16, 2972.85, 2984.3, 3003.67, 3045.78, 3051.77, 3082.37, 3090.44, 3190.73, 3708.52 ], "kayser")), HinderedRotor(inertia=(2.68206, "amu*angstrom^2"), symmetry=3, barrier=(3.35244, "kcal/mol")), HinderedRotor(inertia=(9.77669, "amu*angstrom^2"), symmetry=1, fourier=([[ 0.208938, -1.55291, -4.05398, -0.105798, -0.104752 ], [ 2.00518, -0.020767, -0.333595, 0.137791, -0.274578 ]], "kJ/mol")), ], spin_multiplicity=1, optical_isomers=1, ), frequency=(-2038.34, 'cm^-1'), ) self.reaction = Reaction( label='dehydration', reactants=[self.nC4H10O], products=[self.nC4H8, self.H2O], transition_state=self.TS, ) self.network = Network( label='n-butanol', isomers=[Configuration(self.nC4H10O)], reactants=[], products=[Configuration(self.nC4H8, self.H2O)], path_reactions=[self.reaction], bath_gas={self.N2: 1.0}, )
def network(label, isomers=None, reactants=None, products=None, pathReactions=None, bathGas=None): """Load a network from an input file""" global network_dict, species_dict, reaction_dict logging.info('Loading network {0}...'.format(label)) isomers0 = isomers or [] isomers = [] for isomer in isomers0: if isinstance(isomer, (list, tuple)): raise ValueError( 'Only one species can be present in a unimolecular isomer.') isomers.append(species_dict[isomer]) reactants0 = reactants or [] reactants = [] for reactant in reactants0: if not isinstance(reactant, (list, tuple)): reactant = [reactant] reactants.append(sorted([species_dict[spec] for spec in reactant])) if pathReactions is None: # Only add reactions that match reactants and/or isomers path_reactions = [] for rxn in reaction_dict.values(): if not rxn.is_unimolecular(): # this reaction is not pressure dependent continue reactant_is_isomer = len( rxn.reactants) == 1 and rxn.reactants[0] in isomers product_is_isomer = len( rxn.products) == 1 and rxn.products[0] in isomers reactant_is_reactant = any([ frozenset(rxn.reactants) == frozenset(reactant_pair) for reactant_pair in reactants ]) product_is_reactant = any([ frozenset(rxn.products) == frozenset(reactant_pair) for reactant_pair in reactants ]) if reactant_is_isomer or reactant_is_reactant or product_is_isomer or product_is_reactant: path_reactions.append(rxn) logging.debug('Path reactions {} were found for network {}'.format( [rxn.label for rxn in path_reactions], label)) else: path_reactions_0 = pathReactions path_reactions = [] for rxn in path_reactions_0: path_reactions.append(reaction_dict[rxn]) if products is None: # Figure out which configurations are isomers, reactant channels, and product channels products = [] for rxn in path_reactions: # Sort bimolecular configurations so that we always encounter them in the same order # The actual order doesn't matter, as long as it is consistent rxn.reactants.sort() rxn.products.sort() # All reactant configurations not already defined as reactants or # isomers are assumed to be product channels if len(rxn.reactants) == 1 and rxn.reactants[ 0] not in isomers and rxn.reactants not in products: products.append(rxn.reactants) elif len( rxn.reactants ) > 1 and rxn.reactants not in reactants and rxn.reactants not in products: products.append(rxn.reactants) # All product configurations not already defined as reactants or # isomers are assumed to be product channels if len(rxn.products) == 1 and rxn.products[ 0] not in isomers and rxn.products not in products: products.append(rxn.products) elif len( rxn.products ) > 1 and rxn.products not in reactants and rxn.products not in products: products.append(rxn.products) else: products0 = products or [] products = [] for product in products0: if not isinstance(product, (list, tuple)): product = [product] products.append(sorted([species_dict[spec] for spec in product])) isomers = [Configuration(species) for species in isomers] reactants = [Configuration(*species) for species in reactants] products = [Configuration(*species) for species in products] bath_gas_0 = bathGas or {} bath_gas = {} for spec, fraction in bath_gas_0.items(): bath_gas[species_dict[spec]] = fraction network = Network( label=label, isomers=isomers, reactants=reactants, products=products, path_reactions=path_reactions, bath_gas=bath_gas, ) network_dict[label] = network
def network(label, isomers=None, reactants=None, products=None, pathReactions=None, bathGas=None): global networkDict, speciesDict, reactionDict logging.info('Loading network {0}...'.format(label)) isomers0 = isomers or [] isomers = [] for isomer in isomers0: if isinstance(isomer, (list, tuple)): raise ValueError( 'Only one species can be present in a unimolecular isomer.') isomers.append(speciesDict[isomer]) reactants0 = reactants or [] reactants = [] for reactant in reactants0: if not isinstance(reactant, (list, tuple)): reactant = [reactant] reactants.append(sorted([speciesDict[spec] for spec in reactant])) if pathReactions is None: # If not explicitly given, use all reactions in input file pathReactions = reactionDict.values() else: pathReactions0 = pathReactions pathReactions = [] for rxn in pathReactions0: pathReactions.append(reactionDict[rxn]) if products is None: # Figure out which configurations are isomers, reactant channels, and product channels products = [] for rxn in pathReactions: # Sort bimolecular configurations so that we always encounter them in the # same order # The actual order doesn't matter, as long as it is consistent rxn.reactants.sort() rxn.products.sort() # All reactant configurations not already defined as reactants or # isomers are assumed to be product channels if len(rxn.reactants) == 1 and rxn.reactants[ 0] not in isomers and rxn.reactants not in products: products.append(rxn.reactants) elif len( rxn.reactants ) > 1 and rxn.reactants not in reactants and rxn.reactants not in products: products.append(rxn.reactants) # All product configurations not already defined as reactants or # isomers are assumed to be product channels if len(rxn.products) == 1 and rxn.products[ 0] not in isomers and rxn.products not in products: products.append(rxn.products) elif len( rxn.products ) > 1 and rxn.products not in reactants and rxn.products not in products: products.append(rxn.products) else: products0 = products or [] products = [] for product in products0: if not isinstance(product, (list, tuple)): product = [product] products.append(sorted([speciesDict[spec] for spec in product])) isomers = [Configuration(species) for species in isomers] reactants = [Configuration(*species) for species in reactants] products = [Configuration(*species) for species in products] bathGas0 = bathGas or {} bathGas = {} for spec, fraction in bathGas0.items(): bathGas[speciesDict[spec]] = fraction network = Network( label=label, isomers=isomers, reactants=reactants, products=products, pathReactions=pathReactions, bathGas=bathGas, ) networkDict[label] = network