def test_fit_to_data(self): """ Test the PDepArrhenius.fit_to_data() method. """ Tdata = np.array([ 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 ], np.float) Pdata = np.array([1e4, 3e4, 1e5, 3e5, 1e6], np.float) kdata = np.zeros([len(Tdata), len(Pdata)], np.float) for t in range(len(Tdata)): for p in range(len(Pdata)): kdata[t, p] = self.kinetics.get_rate_coefficient( Tdata[t], Pdata[p]) kinetics = PDepArrhenius().fit_to_data(Tdata, Pdata, kdata, kunits="s^-1") for t in range(len(Tdata)): for p in range(len(Pdata)): self.assertAlmostEqual(kinetics.get_rate_coefficient( Tdata[t], Pdata[p]), kdata[t, p], delta=1e-6 * kdata[t, p])
class TestPDepArrhenius(unittest.TestCase): """ Contains unit tests of the :class:`PDepArrhenius` class. """ def setUp(self): """ A function run before each unit test in this class. """ self.arrhenius0 = Arrhenius( A=(1.0e6, "s^-1"), n=1.0, Ea=(10.0, "kJ/mol"), T0=(300.0, "K"), Tmin=(300.0, "K"), Tmax=(2000.0, "K"), comment="""This data is completely made up""", ) self.arrhenius1 = Arrhenius( A=(1.0e12, "s^-1"), n=1.0, Ea=(20.0, "kJ/mol"), T0=(300.0, "K"), Tmin=(300.0, "K"), Tmax=(2000.0, "K"), comment="""This data is completely made up""", ) self.pressures = np.array([0.1, 10.0]) self.arrhenius = [self.arrhenius0, self.arrhenius1] self.Tmin = 300.0 self.Tmax = 2000.0 self.Pmin = 0.1 self.Pmax = 10.0 self.comment = """This data is completely made up""" self.kinetics = PDepArrhenius( pressures=(self.pressures, "bar"), arrhenius=self.arrhenius, Tmin=(self.Tmin, "K"), Tmax=(self.Tmax, "K"), Pmin=(self.Pmin, "bar"), Pmax=(self.Pmax, "bar"), comment=self.comment, ) def test_pressures(self): """ Test that the PDepArrhenius pressures property was properly set. """ self.assertEqual(len(self.kinetics.pressures.value_si), 2) for i in range(2): self.assertAlmostEqual(self.kinetics.pressures.value_si[i] * 1e-5, self.pressures[i], 4) def test_arrhenius(self): """ Test that the PDepArrhenius arrhenius property was properly set. """ self.assertEqual(len(self.kinetics.arrhenius), 2) for i in range(2): self.assertAlmostEqual(self.kinetics.arrhenius[i].A.value, self.arrhenius[i].A.value, delta=1e0) self.assertEqual(self.kinetics.arrhenius[i].A.units, self.arrhenius[i].A.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].n.value, self.arrhenius[i].n.value, 4) self.assertAlmostEqual(self.kinetics.arrhenius[i].Ea.value, self.arrhenius[i].Ea.value, 4) self.assertEqual(self.kinetics.arrhenius[i].Ea.units, self.arrhenius[i].Ea.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].T0.value, self.arrhenius[i].T0.value, 4) self.assertEqual(self.kinetics.arrhenius[i].T0.units, self.arrhenius[i].T0.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].Tmin.value, self.arrhenius[i].Tmin.value, 4) self.assertEqual(self.kinetics.arrhenius[i].Tmin.units, self.arrhenius[i].Tmin.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].Tmax.value, self.arrhenius[i].Tmax.value, 4) self.assertEqual(self.kinetics.arrhenius[i].Tmax.units, self.arrhenius[i].Tmax.units) self.assertEqual(self.kinetics.arrhenius[i].comment, self.arrhenius[i].comment) def test_temperature_min(self): """ Test that the PDepArrhenius Tmin property was properly set. """ self.assertAlmostEqual(self.kinetics.Tmin.value_si, self.Tmin, 6) def test_temperature_max(self): """ Test that the PDepArrhenius Tmax property was properly set. """ self.assertAlmostEqual(self.kinetics.Tmax.value_si, self.Tmax, 6) def test_pressure_min(self): """ Test that the PDepArrhenius Pmin property was properly set. """ self.assertAlmostEqual(self.kinetics.Pmin.value_si * 1e-5, self.Pmin, 6) def test_pressure_max(self): """ Test that the PDepArrhenius Pmax property was properly set. """ self.assertAlmostEqual(self.kinetics.Pmax.value_si * 1e-5, self.Pmax, 6) def test_comment(self): """ Test that the PDepArrhenius comment property was properly set. """ self.assertEqual(self.kinetics.comment, self.comment) def test_is_pressure_dependent(self): """ Test the PDepArrhenius.is_pressure_dependent() method. """ self.assertTrue(self.kinetics.is_pressure_dependent()) def test_get_rate_coefficient(self): """ Test the PDepArrhenius.get_rate_coefficient() method. """ P = 1e4 for T in [ 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 ]: k0 = self.kinetics.get_rate_coefficient(T, P) k1 = self.arrhenius0.get_rate_coefficient(T) self.assertAlmostEqual(k0, k1, delta=1e-6 * k1) P = 1e6 for T in [ 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 ]: k0 = self.kinetics.get_rate_coefficient(T, P) k1 = self.arrhenius1.get_rate_coefficient(T) self.assertAlmostEqual(k0, k1, delta=1e-6 * k1) P = 1e5 for T in [ 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 ]: k0 = self.kinetics.get_rate_coefficient(T, P) k1 = math.sqrt( self.arrhenius0.get_rate_coefficient(T) * self.arrhenius1.get_rate_coefficient(T)) self.assertAlmostEqual(k0, k1, delta=1e-6 * k1) def test_fit_to_data(self): """ Test the PDepArrhenius.fit_to_data() method. """ Tdata = np.array([ 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 ], np.float) Pdata = np.array([1e4, 3e4, 1e5, 3e5, 1e6], np.float) kdata = np.zeros([len(Tdata), len(Pdata)], np.float) for t in range(len(Tdata)): for p in range(len(Pdata)): kdata[t, p] = self.kinetics.get_rate_coefficient( Tdata[t], Pdata[p]) kinetics = PDepArrhenius().fit_to_data(Tdata, Pdata, kdata, kunits="s^-1") for t in range(len(Tdata)): for p in range(len(Pdata)): self.assertAlmostEqual(kinetics.get_rate_coefficient( Tdata[t], Pdata[p]), kdata[t, p], delta=1e-6 * kdata[t, p]) def test_pickle(self): """ Test that a PDepArrhenius object can be successfully pickled and unpickled with no loss of information. """ import pickle kinetics = pickle.loads(pickle.dumps(self.kinetics, -1)) Narrh = 2 self.assertEqual(len(self.kinetics.pressures.value), Narrh) self.assertEqual(len(kinetics.pressures.value), Narrh) self.assertEqual(len(self.kinetics.arrhenius), Narrh) self.assertEqual(len(kinetics.arrhenius), Narrh) for i in range(Narrh): self.assertAlmostEqual(self.kinetics.pressures.value[i], kinetics.pressures.value[i], 4) self.assertAlmostEqual(self.kinetics.arrhenius[i].A.value, kinetics.arrhenius[i].A.value, delta=1e0) self.assertEqual(self.kinetics.arrhenius[i].A.units, kinetics.arrhenius[i].A.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].n.value, kinetics.arrhenius[i].n.value) self.assertAlmostEqual(self.kinetics.arrhenius[i].T0.value, kinetics.arrhenius[i].T0.value, 4) self.assertEqual(self.kinetics.arrhenius[i].T0.units, kinetics.arrhenius[i].T0.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].Ea.value, kinetics.arrhenius[i].Ea.value, 4) self.assertEqual(self.kinetics.arrhenius[i].Ea.units, kinetics.arrhenius[i].Ea.units) self.assertAlmostEqual(self.kinetics.Tmin.value, kinetics.Tmin.value, 4) self.assertEqual(self.kinetics.Tmin.units, kinetics.Tmin.units) self.assertAlmostEqual(self.kinetics.Tmax.value, kinetics.Tmax.value, 4) self.assertEqual(self.kinetics.Tmax.units, kinetics.Tmax.units) self.assertAlmostEqual(self.kinetics.Pmin.value, kinetics.Pmin.value, 4) self.assertEqual(self.kinetics.Pmin.units, kinetics.Pmin.units) self.assertAlmostEqual(self.kinetics.Pmax.value, kinetics.Pmax.value, 4) self.assertEqual(self.kinetics.Pmax.units, kinetics.Pmax.units) self.assertEqual(self.kinetics.comment, kinetics.comment) def test_repr(self): """ Test that a PDepArrhenius object can be successfully reconstructed from its repr() output with no loss of information. """ namespace = {} exec('kinetics = {0!r}'.format(self.kinetics), globals(), namespace) self.assertIn('kinetics', namespace) kinetics = namespace['kinetics'] Narrh = 2 self.assertEqual(len(self.kinetics.pressures.value), Narrh) self.assertEqual(len(kinetics.pressures.value), Narrh) self.assertEqual(len(self.kinetics.arrhenius), Narrh) self.assertEqual(len(kinetics.arrhenius), Narrh) for i in range(Narrh): self.assertAlmostEqual(self.kinetics.pressures.value[i], kinetics.pressures.value[i], 4) self.assertAlmostEqual(self.kinetics.arrhenius[i].A.value, kinetics.arrhenius[i].A.value, delta=1e0) self.assertEqual(self.kinetics.arrhenius[i].A.units, kinetics.arrhenius[i].A.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].n.value, kinetics.arrhenius[i].n.value) self.assertAlmostEqual(self.kinetics.arrhenius[i].T0.value, kinetics.arrhenius[i].T0.value, 4) self.assertEqual(self.kinetics.arrhenius[i].T0.units, kinetics.arrhenius[i].T0.units) self.assertAlmostEqual(self.kinetics.arrhenius[i].Ea.value, kinetics.arrhenius[i].Ea.value, 4) self.assertEqual(self.kinetics.arrhenius[i].Ea.units, kinetics.arrhenius[i].Ea.units) self.assertAlmostEqual(self.kinetics.Tmin.value, kinetics.Tmin.value, 4) self.assertEqual(self.kinetics.Tmin.units, kinetics.Tmin.units) self.assertAlmostEqual(self.kinetics.Tmax.value, kinetics.Tmax.value, 4) self.assertEqual(self.kinetics.Tmax.units, kinetics.Tmax.units) self.assertAlmostEqual(self.kinetics.Pmin.value, kinetics.Pmin.value, 4) self.assertEqual(self.kinetics.Pmin.units, kinetics.Pmin.units) self.assertAlmostEqual(self.kinetics.Pmax.value, kinetics.Pmax.value, 4) self.assertEqual(self.kinetics.Pmax.units, kinetics.Pmax.units) self.assertEqual(self.kinetics.comment, kinetics.comment) def test_change_rate(self): """ Test the PDepArrhenius.change_rate() method. """ Tlist = np.array([ 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 ]) k0list = np.array( [self.kinetics.get_rate_coefficient(T, 1e5) for T in Tlist]) self.kinetics.change_rate(2) for T, kexp in zip(Tlist, k0list): kact = self.kinetics.get_rate_coefficient(T, 1e5) self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)