def test_species_atomic_nasa_polynomial(self): """ Test loading a atom with NASA polynomials """ label0 = "H(1)" kwargs = { "structure": SMILES('[H]'), "thermo": NASA(polynomials=[ NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683], Tmin=(200, 'K'), Tmax=(1000, 'K')), NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683], Tmin=(1000, 'K'), Tmax=(6000, 'K')) ], Tmin=(200, 'K'), Tmax=(6000, 'K'), comment="""Thermo library: FFCM1(-)"""), "energyTransferModel": SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'), T0=(300, 'K'), n=0.85) } spc0 = species(label0, **kwargs) self.assertEqual(spc0.label, label0) self.assertEqual(spc0.smiles, '[H]') self.assertTrue(spc0.has_statmech()) self.assertEqual(spc0.thermo, kwargs['thermo'])
def setUp(self): """ A function run before each unit test in this class. """ self.coeffs_low = [ 4.03055, -0.00214171, 4.90611e-05, -5.99027e-08, 2.38945e-11, -11257.6, 3.5613 ] self.coeffs_high = [ -0.307954, 0.0245269, -1.2413e-05, 3.07724e-09, -3.01467e-13, -10693, 22.628 ] self.Tmin = 300. self.Tmax = 3000. self.Tint = 650.73 self.E0 = -782292. # J/mol. self.comment = "C2H6" self.nasa = NASA( polynomials=[ NASAPolynomial(coeffs=self.coeffs_low, Tmin=(self.Tmin, "K"), Tmax=(self.Tint, "K")), NASAPolynomial(coeffs=self.coeffs_high, Tmin=(self.Tint, "K"), Tmax=(self.Tmax, "K")), ], Tmin=(self.Tmin, "K"), Tmax=(self.Tmax, "K"), E0=(self.E0, "J/mol"), comment=self.comment, )
def test_species_polyatomic_nasa_polynomial(self): """ Test loading a species with NASA polynomials """ label0 = "benzyl" kwargs = { "structure": SMILES('[c]1ccccc1'), "thermo": NASA(polynomials=[ NASAPolynomial(coeffs=[ 2.78632, 0.00784632, 7.97887e-05, -1.11617e-07, 4.39429e-11, 39695, 11.5114 ], Tmin=(100, 'K'), Tmax=(943.73, 'K')), NASAPolynomial(coeffs=[ 13.2455, 0.0115667, -2.49996e-06, 4.66496e-10, -4.12376e-14, 35581.1, -49.6793 ], Tmin=(943.73, 'K'), Tmax=(5000, 'K')) ], Tmin=(100, 'K'), Tmax=(5000, 'K'), comment="""Thermo library: Fulvene_H + radical(CbJ)"""), "energyTransferModel": SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'), T0=(300, 'K'), n=0.85) } spc0 = species(label0, **kwargs) self.assertEqual(spc0.label, label0) self.assertTrue(spc0.has_statmech()) self.assertEqual(spc0.thermo, kwargs['thermo'])
def test_correct_entropy(self): """ Tests that correctEntropy effectively makes the isotopomer have the same thermo as isotopeless with the change in entropy corresponding to the symmetry difference. This example compares propane to a asymmetrically labeled propane. """ from rmgpy.thermo.nasa import NASA, NASAPolynomial from copy import deepcopy from rmgpy import constants propanei = Species().from_adjacency_list(""" 1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} 2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S} 3 C u0 p0 c0 i13 {2,S} {9,S} {10,S} {11,S} 4 H u0 p0 c0 {1,S} 5 H u0 p0 c0 {1,S} 6 H u0 p0 c0 {1,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {2,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {3,S} 11 H u0 p0 c0 {3,S} """) propane = Species().from_adjacency_list(""" 1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} 2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S} 3 C u0 p0 c0 {2,S} {9,S} {10,S} {11,S} 4 H u0 p0 c0 {1,S} 5 H u0 p0 c0 {1,S} 6 H u0 p0 c0 {1,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {2,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {3,S} 11 H u0 p0 c0 {3,S} """) # get thermo of propane original_thermo = NASA(polynomials=[NASAPolynomial( coeffs=[1.10564, 0.0315339, -1.48274e-05, 3.39621e-09, -2.97953e-13, -14351.9, 18.775], Tmin=(100, 'K'), Tmax=(3370.6, 'K')), NASAPolynomial( coeffs=[-1.45473, 0.0241202, -6.87667e-06, 9.03634e-10, -4.48389e-14, -6688.59, 43.0459], Tmin=(3370.6, 'K'), Tmax=(5000, 'K'))], Tmin=(100, 'K'), Tmax=(5000, 'K'), comment="""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R)""") propane.thermo = deepcopy(original_thermo) propanei.thermo = deepcopy(original_thermo) correct_entropy(propanei, propane) self.assertAlmostEqual(propane.get_enthalpy(298), propanei.get_enthalpy(298)) self.assertAlmostEqual(propanei.get_entropy(298) - propane.get_entropy(298), constants.R * np.log(2))
def test_generate_isotopomers(self): """ Test that the generation of isotopomers with N isotopes works. """ from rmgpy.thermo.nasa import NASAPolynomial, NASA spc = Species().from_smiles('CC') polynomial = NASAPolynomial(coeffs=[1., 1., 1., 1., 1., 1., 1.], Tmin=(200, 'K'), Tmax=(1600, 'K'), E0=(1., 'kJ/mol'), comment='made up thermo') spc.thermo = NASA(polynomials=[polynomial], Tmin=(200, 'K'), Tmax=(1600, 'K'), E0=(1., 'kJ/mol'), comment='made up thermo') spcs = generate_isotopomers(spc, 0) self.assertEquals(len(spcs), 0) spcs = generate_isotopomers(spc) self.assertEquals(len(spcs), 1) spcs = generate_isotopomers(spc, 2) self.assertEquals(len(spcs), 2) spcs = generate_isotopomers(spc, 3) self.assertEquals(len(spcs), 2)
def setUp(self): """ A function run before each unit test in this class. """ octyl_pri = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[-0.772759,0.093255,-5.84447e-05,1.8557e-08,-2.37127e-12,-3926.9,37.6131], Tmin=(298,'K'), Tmax=(1390,'K')), NASAPolynomial(coeffs=[25.051,0.036948,-1.25765e-05,1.94628e-09,-1.12669e-13,-13330.1,-102.557], Tmin=(1390,'K'), Tmax=(5000,'K')) ], Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(577.856,'J/(mol*K)'), comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCC")]) octyl_sec = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[-0.304233,0.0880077,-4.90743e-05,1.21858e-08,-8.87773e-13,-5237.93,36.6583], Tmin=(298,'K'), Tmax=(1383,'K')), NASAPolynomial(coeffs=[24.9044,0.0366394,-1.2385e-05,1.90835e-09,-1.10161e-13,-14713.5,-101.345], Tmin=(1383,'K'), Tmax=(5000,'K')) ], Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(577.856,'J/(mol*K)'), comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="CC[CH]CCCCC")]) ethane = Species(label="", thermo=ThermoData( Tdata=([300,400,500,600,800,1000,1500],'K'), Cpdata=([10.294,12.643,14.933,16.932,20.033,22.438,26.281],'cal/(mol*K)'), H298=(12.549,'kcal/mol'), S298=(52.379,'cal/(mol*K)'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(133.032,'J/(mol*K)'), comment="""Thermo library: CH"""), molecule=[Molecule(SMILES="C=C")]) decyl = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[-1.31358,0.117973,-7.51843e-05,2.43331e-08,-3.17523e-12,-9689.68,43.501], Tmin=(298,'K'), Tmax=(1390,'K')), NASAPolynomial(coeffs=[31.5697,0.0455818,-1.54995e-05,2.39711e-09,-1.3871e-13,-21573.8,-134.709], Tmin=(1390,'K'), Tmax=(5000,'K')) ], Tmin=(298,'K'), Tmax=(5000,'K'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(719.202,'J/(mol*K)'), comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCCCC")]) self.database = SolvationDatabase() self.database.load(os.path.join(settings['database.directory'], 'solvation')) self.solvent = 'octane' diffusionLimiter.enable(self.database.getSolventData(self.solvent), self.database) self.T = 298 self.uni_reaction = Reaction(reactants=[octyl_pri], products=[octyl_sec]) self.uni_reaction.kinetics = Arrhenius(A=(2.0, '1/s'), n=0, Ea=(0,'kJ/mol')) self.bi_uni_reaction = Reaction(reactants=[octyl_pri, ethane], products=[decyl]) self.bi_uni_reaction.kinetics = Arrhenius(A=(1.0E-22, 'cm^3/molecule/s'), n=0, Ea=(0,'kJ/mol')) self.intrinsic_rates = { self.uni_reaction: self.uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5), self.bi_uni_reaction: self.bi_uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5), }
def setUp(self): """ A function run before each unit test in this class. """ octyl_pri = Species( label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[ -0.772759, 0.093255, -5.84447e-05, 1.8557e-08, -2.37127e-12, -3926.9, 37.6131 ], Tmin=(298, 'K'), Tmax=(1390, 'K')), NASAPolynomial(coeffs=[ 25.051, 0.036948, -1.25765e-05, 1.94628e-09, -1.12669e-13, -13330.1, -102.557 ], Tmin=(1390, 'K'), Tmax=(5000, 'K')) ], Tmin=(298, 'K'), Tmax=(5000, 'K'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(577.856, 'J/(mol*K)'), comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCC")]) octyl_sec = Species( label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[ -0.304233, 0.0880077, -4.90743e-05, 1.21858e-08, -8.87773e-13, -5237.93, 36.6583 ], Tmin=(298, 'K'), Tmax=(1383, 'K')), NASAPolynomial(coeffs=[ 24.9044, 0.0366394, -1.2385e-05, 1.90835e-09, -1.10161e-13, -14713.5, -101.345 ], Tmin=(1383, 'K'), Tmax=(5000, 'K')) ], Tmin=(298, 'K'), Tmax=(5000, 'K'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(577.856, 'J/(mol*K)'), comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="CC[CH]CCCCC")]) ethane = Species(label="", thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), Cpdata=([ 10.294, 12.643, 14.933, 16.932, 20.033, 22.438, 26.281 ], 'cal/(mol*K)'), H298=(12.549, 'kcal/mol'), S298=(52.379, 'cal/(mol*K)'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(133.032, 'J/(mol*K)'), comment="""Thermo library: CH"""), molecule=[Molecule(SMILES="C=C")]) decyl = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[ -1.31358, 0.117973, -7.51843e-05, 2.43331e-08, -3.17523e-12, -9689.68, 43.501 ], Tmin=(298, 'K'), Tmax=(1390, 'K')), NASAPolynomial(coeffs=[ 31.5697, 0.0455818, -1.54995e-05, 2.39711e-09, -1.3871e-13, -21573.8, -134.709 ], Tmin=(1390, 'K'), Tmax=(5000, 'K')) ], Tmin=(298, 'K'), Tmax=(5000, 'K'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(719.202, 'J/(mol*K)'), comment="""Thermo library: JetSurF0.2"""), molecule=[Molecule(SMILES="[CH2]CCCCCCCCC")]) acetone = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[ 3.75568, 0.0264934, -6.55661e-05, 1.94971e-07, -1.82059e-10, -27905.3, 9.0162 ], Tmin=(10, 'K'), Tmax=(422.477, 'K')), NASAPolynomial(coeffs=[ 0.701289, 0.0344988, -1.9736e-05, 5.48052e-09, -5.92612e-13, -27460.6, 23.329 ], Tmin=(422.477, 'K'), Tmax=(3000, 'K')) ], Tmin=(10, 'K'), Tmax=(3000, 'K'), E0=(-232.025, 'kJ/mol'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(232.805, 'J/(mol*K)')), molecule=[Molecule(SMILES="CC(=O)C")]) peracetic_acid = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[ 3.81786, 0.016419, 3.32204e-05, -8.98403e-08, 6.63474e-11, -42057.8, 9.65245 ], Tmin=(10, 'K'), Tmax=(354.579, 'K')), NASAPolynomial(coeffs=[ 2.75993, 0.0283534, -1.72659e-05, 5.08158e-09, -5.77773e-13, -41982.8, 13.6595 ], Tmin=(354.579, 'K'), Tmax=(3000, 'K')) ], Tmin=(10, 'K'), Tmax=(3000, 'K'), E0=(-349.698, 'kJ/mol'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(199.547, 'J/(mol*K)')), molecule=[Molecule(SMILES="CC(=O)OO")]) acetic_acid = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[ 3.97665, 0.00159915, 8.5542e-05, -1.76486e-07, 1.20201e-10, -53911.5, 8.99309 ], Tmin=(10, 'K'), Tmax=(375.616, 'K')), NASAPolynomial(coeffs=[ 1.57088, 0.0272146, -1.67357e-05, 5.01453e-09, -5.82273e-13, -53730.7, 18.2442 ], Tmin=(375.616, 'K'), Tmax=(3000, 'K')) ], Tmin=(10, 'K'), Tmax=(3000, 'K'), E0=(-448.245, 'kJ/mol'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(182.918, 'J/(mol*K)')), molecule=[Molecule(SMILES="CC(=O)O")]) criegee = Species(label="", thermo=NASA(polynomials=[ NASAPolynomial(coeffs=[ 3.23876, 0.0679583, -3.35611e-05, 7.91519e-10, 3.13038e-12, -77986, 13.6438 ], Tmin=(10, 'K'), Tmax=(1053.46, 'K')), NASAPolynomial(coeffs=[ 9.84525, 0.0536795, -2.86165e-05, 7.39945e-09, -7.48482e-13, -79977.6, -21.4187 ], Tmin=(1053.46, 'K'), Tmax=(3000, 'K')) ], Tmin=(10, 'K'), Tmax=(3000, 'K'), E0=(-648.47, 'kJ/mol'), Cp0=(33.2579, 'J/(mol*K)'), CpInf=(457.296, 'J/(mol*K)')), molecule=[Molecule(SMILES="CC(=O)OOC(C)(O)C")]) self.database = SolvationDatabase() self.database.load( os.path.join(settings['database.directory'], 'solvation')) self.solvent = 'octane' diffusionLimiter.enable(self.database.getSolventData(self.solvent), self.database) self.T = 298 self.uni_reaction = Reaction(reactants=[octyl_pri], products=[octyl_sec]) self.uni_reaction.kinetics = Arrhenius(A=(2.0, '1/s'), n=0, Ea=(0, 'kJ/mol')) self.bi_uni_reaction = Reaction(reactants=[octyl_pri, ethane], products=[decyl]) self.bi_uni_reaction.kinetics = Arrhenius(A=(1.0E-22, 'cm^3/molecule/s'), n=0, Ea=(0, 'kJ/mol')) self.tri_bi_reaction = Reaction( reactants=[acetone, peracetic_acid, acetic_acid], products=[criegee, acetic_acid]) self.tri_bi_reaction.kinetics = Arrhenius(A=(1.07543e-11, 'cm^6/(mol^2*s)'), n=5.47295, Ea=(-38.5379, 'kJ/mol')) self.intrinsic_rates = { self.uni_reaction: self.uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5), self.bi_uni_reaction: self.bi_uni_reaction.kinetics.getRateCoefficient(self.T, P=100e5), self.tri_bi_reaction: self.tri_bi_reaction.kinetics.getRateCoefficient(self.T, P=100e5), }