def read_spc_list_from_yml(yml_file): """ Read the species contained in a yaml file. The function assumes that species are listed under the key "species". It also assumes the molecule contains at least one kind of geom info. Currently only support SMILES and Adjacency list. Args: yml_file (str): The path to the input yml file Return: spc_list (list): A list contains all the species in the file """ content = read_yaml_file(yml_file) if 'species' in content.keys(): content = content['species'] else: logging.error('Invalid yaml file which does not contain species entry') return spc_list = list() for entry in content: spc = Species(label=entry['label']) try: if 'adjlist' in entry.keys(): spc.from_adjacency_list(entry['adjlist']) elif 'smiles' in entry.keys(): spc.from_smiles(entry['smiles']) except: logging.warning('Species %s is not readable' % (entry['label'])) continue if 'multiplicity' in entry.keys(): spc.multiplicity = entry['multiplicity'] spc_list.append(spc) return spc_list
class TestPdep(unittest.TestCase): def setUp(self): """ A method that is 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.nC4H10O.from_smiles('CCCCO') 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.nC4H8.from_smiles('CCC=C') 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.H2O.from_smiles('O') 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.N2.from_smiles('N#N') logging.error('to TS') 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, kinetics=Arrhenius(A=(0.0387, 'm^3/(mol*s)'), n=2.7, Ea=(2.6192e4, 'J/mol'), T0=(1, 'K'))) 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}, ) self.pdepnetwork = deepcopy(self.network) self.pdepnetwork.__class__ = PDepNetwork self.pdepnetwork.source = [self.pdepnetwork.isomers[0].species[0]] self.pdepnetwork.index = 1 self.pdepnetwork.explored = [] def test_energy_filter(self): rxns = self.pdepnetwork.get_energy_filtered_reactions(1000.0, 0.0) self.assertEquals(len(rxns), 1) self.assertEquals(rxns[0], self.pdepnetwork.path_reactions[0]) def test_flux_filter(self): prods = self.pdepnetwork.get_rate_filtered_products( 1000.0, 100000.0, 1.0) self.assertEquals(len(prods), 0)