def setUp(self): """ A function run before each unit test in this class. """ self.arrheniusHigh = Arrhenius( A = (1.39e+16,"cm^3/(mol*s)"), n = -0.534, Ea = (2.243,"kJ/mol"), T0 = (1,"K"), ) self.arrheniusLow = Arrhenius( A = (2.62e+33,"cm^6/(mol^2*s)"), n = -4.76, Ea = (10.21,"kJ/mol"), T0 = (1,"K"), ) self.efficiencies = {"C": 3, "C(=O)=O": 2, "CC": 3, "O": 6, "[Ar]": 0.7, "[C]=O": 1.5, "[H][H]": 2} self.Tmin = 300. self.Tmax = 2000. self.Pmin = 0.01 self.Pmax = 100. self.comment = """H + CH3 -> CH4""" self.lindemann = Lindemann( arrheniusHigh = self.arrheniusHigh, arrheniusLow = self.arrheniusLow, Tmin = (self.Tmin,"K"), Tmax = (self.Tmax,"K"), Pmin = (self.Pmin,"bar"), Pmax = (self.Pmax,"bar"), efficiencies = self.efficiencies, comment = self.comment, )
def setUp(self): """ A function run before each unit test in this class. """ self.arrheniusHigh = Arrhenius( A=(1.39e+16, "cm^3/(mol*s)"), n=-0.534, Ea=(2.243, "kJ/mol"), T0=(1, "K"), ) self.arrheniusLow = Arrhenius( A=(2.62e+33, "cm^6/(mol^2*s)"), n=-4.76, Ea=(10.21, "kJ/mol"), T0=(1, "K"), ) self.efficiencies = { "C": 3, "C(=O)=O": 2, "CC": 3, "O": 6, "[Ar]": 0.7, "[C]=O": 1.5, "[H][H]": 2 } self.Tmin = 300. self.Tmax = 2000. self.Pmin = 0.01 self.Pmax = 100. self.comment = """H + CH3 -> CH4""" self.lindemann = Lindemann( arrheniusHigh=self.arrheniusHigh, arrheniusLow=self.arrheniusLow, Tmin=(self.Tmin, "K"), Tmax=(self.Tmax, "K"), Pmin=(self.Pmin, "bar"), Pmax=(self.Pmax, "bar"), efficiencies=self.efficiencies, comment=self.comment, )
class TestLindemann(unittest.TestCase): """ Contains unit tests of the Lindemann class. """ def setUp(self): """ A function run before each unit test in this class. """ self.arrheniusHigh = Arrhenius( A=(1.39e+16, "cm^3/(mol*s)"), n=-0.534, Ea=(2.243, "kJ/mol"), T0=(1, "K"), ) self.arrheniusLow = Arrhenius( A=(2.62e+33, "cm^6/(mol^2*s)"), n=-4.76, Ea=(10.21, "kJ/mol"), T0=(1, "K"), ) self.efficiencies = { "C": 3, "C(=O)=O": 2, "CC": 3, "O": 6, "[Ar]": 0.7, "[C]=O": 1.5, "[H][H]": 2 } self.Tmin = 300. self.Tmax = 2000. self.Pmin = 0.01 self.Pmax = 100. self.comment = """H + CH3 -> CH4""" self.lindemann = Lindemann( arrheniusHigh=self.arrheniusHigh, arrheniusLow=self.arrheniusLow, Tmin=(self.Tmin, "K"), Tmax=(self.Tmax, "K"), Pmin=(self.Pmin, "bar"), Pmax=(self.Pmax, "bar"), efficiencies=self.efficiencies, comment=self.comment, ) def test_arrheniusHigh(self): """ Test that the Lindemann arrheniusHigh property was properly set. """ self.assertTrue(self.lindemann.arrheniusHigh is self.arrheniusHigh) def test_arrheniusLow(self): """ Test that the Lindemann arrheniusLow property was properly set. """ self.assertTrue(self.lindemann.arrheniusLow is self.arrheniusLow) def test_Tmin(self): """ Test that the Lindemann Tmin property was properly set. """ self.assertAlmostEqual(self.lindemann.Tmin.value_si, self.Tmin, 6) def test_Tmax(self): """ Test that the Lindemann Tmax property was properly set. """ self.assertAlmostEqual(self.lindemann.Tmax.value_si, self.Tmax, 6) def test_Pmin(self): """ Test that the Lindemann Pmin property was properly set. """ self.assertAlmostEqual(self.lindemann.Pmin.value_si * 1e-5, self.Pmin, 6) def test_Pmax(self): """ Test that the Lindemann Pmax property was properly set. """ self.assertAlmostEqual(self.lindemann.Pmax.value_si * 1e-5, self.Pmax, 6) def test_comment(self): """ Test that the Lindemann comment property was properly set. """ self.assertEqual(self.lindemann.comment, self.comment) def test_isPressureDependent(self): """ Test the Lindemann.isPressureDependent() method. """ self.assertTrue(self.lindemann.isPressureDependent()) def test_getRateCoefficient(self): """ Test the Lindemann.getRateCoefficient() method. """ Tlist = numpy.array([300, 500, 1000, 1500]) Plist = numpy.array([1e4, 1e5, 1e6]) Kexp = numpy.array([ [1.38023e+08, 2.45661e+08, 2.66439e+08], [6.09146e+07, 2.12349e+08, 2.82604e+08], [4.75671e+06, 4.09594e+07, 1.71441e+08], [7.03616e+05, 6.85062e+06, 5.42111e+07], ]) for t in range(Tlist.shape[0]): for p in range(Plist.shape[0]): Kact = self.lindemann.getRateCoefficient(Tlist[t], Plist[p]) self.assertAlmostEqual(Kact, Kexp[t, p], delta=1e-4 * Kexp[t, p]) def test_pickle(self): """ Test that a Lindemann object can be pickled and unpickled with no loss of information. """ import cPickle lindemann = cPickle.loads(cPickle.dumps(self.lindemann, -1)) self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value, lindemann.arrheniusHigh.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusHigh.A.units, lindemann.arrheniusHigh.A.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value, lindemann.arrheniusHigh.n.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.n.units, lindemann.arrheniusHigh.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value, lindemann.arrheniusHigh.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.Ea.units, lindemann.arrheniusHigh.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value, lindemann.arrheniusHigh.T0.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.T0.units, lindemann.arrheniusHigh.T0.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value, lindemann.arrheniusLow.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusLow.A.units, lindemann.arrheniusLow.A.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value, lindemann.arrheniusLow.n.value, 4) self.assertEqual(self.lindemann.arrheniusLow.n.units, lindemann.arrheniusLow.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value, lindemann.arrheniusLow.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusLow.Ea.units, lindemann.arrheniusLow.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value, lindemann.arrheniusLow.T0.value, 4) self.assertEqual(self.lindemann.arrheniusLow.T0.units, lindemann.arrheniusLow.T0.units) self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value, 4) self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units) self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value, 4) self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units) self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value, 4) self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units) self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value, 4) self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units) efficiencies = {} for mol, eff in self.lindemann.efficiencies.iteritems(): efficiencies[mol.toSMILES()] = eff pickled_efficiencies = {} for mol, eff in lindemann.efficiencies.iteritems(): pickled_efficiencies[mol.toSMILES()] = eff self.assertEqual(efficiencies, pickled_efficiencies) self.assertEqual(self.lindemann.comment, lindemann.comment) def test_repr(self): """ Test that a Lindemann object can be reconstructed from its repr() output with no loss of information. """ lindemann = None exec('lindemann = {0!r}'.format(self.lindemann)) self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value, lindemann.arrheniusHigh.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusHigh.A.units, lindemann.arrheniusHigh.A.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value, lindemann.arrheniusHigh.n.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.n.units, lindemann.arrheniusHigh.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value, lindemann.arrheniusHigh.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.Ea.units, lindemann.arrheniusHigh.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value, lindemann.arrheniusHigh.T0.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.T0.units, lindemann.arrheniusHigh.T0.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value, lindemann.arrheniusLow.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusLow.A.units, lindemann.arrheniusLow.A.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value, lindemann.arrheniusLow.n.value, 4) self.assertEqual(self.lindemann.arrheniusLow.n.units, lindemann.arrheniusLow.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value, lindemann.arrheniusLow.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusLow.Ea.units, lindemann.arrheniusLow.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value, lindemann.arrheniusLow.T0.value, 4) self.assertEqual(self.lindemann.arrheniusLow.T0.units, lindemann.arrheniusLow.T0.units) self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value, 4) self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units) self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value, 4) self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units) self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value, 4) self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units) self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value, 4) self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units) efficiencies = {} for mol, eff in self.lindemann.efficiencies.iteritems(): efficiencies[mol.toSMILES()] = eff pickled_efficiencies = {} for mol, eff in lindemann.efficiencies.iteritems(): pickled_efficiencies[mol.toSMILES()] = eff self.assertEqual(efficiencies, pickled_efficiencies) self.assertEqual(self.lindemann.comment, lindemann.comment) def test_changeRate(self): """ Test the Lindemann.changeRate() method. """ Tlist = numpy.array([ 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 ]) k0list = numpy.array( [self.lindemann.getRateCoefficient(T, 1e5) for T in Tlist]) self.lindemann.changeRate(2) for T, kexp in zip(Tlist, k0list): kact = self.lindemann.getRateCoefficient(T, 1e5) self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)
class TestLindemann(unittest.TestCase): """ Contains unit tests of the Lindemann class. """ def setUp(self): """ A function run before each unit test in this class. """ self.arrheniusHigh = Arrhenius( A = (1.39e+16,"cm^3/(mol*s)"), n = -0.534, Ea = (2.243,"kJ/mol"), T0 = (1,"K"), ) self.arrheniusLow = Arrhenius( A = (2.62e+33,"cm^6/(mol^2*s)"), n = -4.76, Ea = (10.21,"kJ/mol"), T0 = (1,"K"), ) self.efficiencies = {"C": 3, "C(=O)=O": 2, "CC": 3, "O": 6, "[Ar]": 0.7, "[C]=O": 1.5, "[H][H]": 2} self.Tmin = 300. self.Tmax = 2000. self.Pmin = 0.01 self.Pmax = 100. self.comment = """H + CH3 -> CH4""" self.lindemann = Lindemann( arrheniusHigh = self.arrheniusHigh, arrheniusLow = self.arrheniusLow, Tmin = (self.Tmin,"K"), Tmax = (self.Tmax,"K"), Pmin = (self.Pmin,"bar"), Pmax = (self.Pmax,"bar"), efficiencies = self.efficiencies, comment = self.comment, ) def test_arrheniusHigh(self): """ Test that the Lindemann arrheniusHigh property was properly set. """ self.assertTrue(self.lindemann.arrheniusHigh is self.arrheniusHigh) def test_arrheniusLow(self): """ Test that the Lindemann arrheniusLow property was properly set. """ self.assertTrue(self.lindemann.arrheniusLow is self.arrheniusLow) def test_Tmin(self): """ Test that the Lindemann Tmin property was properly set. """ self.assertAlmostEqual(self.lindemann.Tmin.value_si, self.Tmin, 6) def test_Tmax(self): """ Test that the Lindemann Tmax property was properly set. """ self.assertAlmostEqual(self.lindemann.Tmax.value_si, self.Tmax, 6) def test_Pmin(self): """ Test that the Lindemann Pmin property was properly set. """ self.assertAlmostEqual(self.lindemann.Pmin.value_si*1e-5, self.Pmin, 6) def test_Pmax(self): """ Test that the Lindemann Pmax property was properly set. """ self.assertAlmostEqual(self.lindemann.Pmax.value_si*1e-5, self.Pmax, 6) def test_comment(self): """ Test that the Lindemann comment property was properly set. """ self.assertEqual(self.lindemann.comment, self.comment) def test_isPressureDependent(self): """ Test the Lindemann.isPressureDependent() method. """ self.assertTrue(self.lindemann.isPressureDependent()) def test_getRateCoefficient(self): """ Test the Lindemann.getRateCoefficient() method. """ Tlist = numpy.array([300,500,1000,1500]) Plist = numpy.array([1e4,1e5,1e6]) Kexp = numpy.array([ [1.38023e+08, 2.45661e+08, 2.66439e+08], [6.09146e+07, 2.12349e+08, 2.82604e+08], [4.75671e+06, 4.09594e+07, 1.71441e+08], [7.03616e+05, 6.85062e+06, 5.42111e+07], ]) for t in range(Tlist.shape[0]): for p in range(Plist.shape[0]): Kact = self.lindemann.getRateCoefficient(Tlist[t], Plist[p]) self.assertAlmostEqual(Kact, Kexp[t,p], delta=1e-4*Kexp[t,p]) def test_pickle(self): """ Test that a Lindemann object can be pickled and unpickled with no loss of information. """ import cPickle lindemann = cPickle.loads(cPickle.dumps(self.lindemann,-1)) self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value, lindemann.arrheniusHigh.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusHigh.A.units, lindemann.arrheniusHigh.A.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value, lindemann.arrheniusHigh.n.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.n.units, lindemann.arrheniusHigh.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value, lindemann.arrheniusHigh.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.Ea.units, lindemann.arrheniusHigh.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value, lindemann.arrheniusHigh.T0.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.T0.units, lindemann.arrheniusHigh.T0.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value, lindemann.arrheniusLow.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusLow.A.units, lindemann.arrheniusLow.A.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value, lindemann.arrheniusLow.n.value, 4) self.assertEqual(self.lindemann.arrheniusLow.n.units, lindemann.arrheniusLow.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value, lindemann.arrheniusLow.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusLow.Ea.units, lindemann.arrheniusLow.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value, lindemann.arrheniusLow.T0.value, 4) self.assertEqual(self.lindemann.arrheniusLow.T0.units, lindemann.arrheniusLow.T0.units) self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value, 4) self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units) self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value, 4) self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units) self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value, 4) self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units) self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value, 4) self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units) efficiencies = {} for mol, eff in self.lindemann.efficiencies.iteritems(): efficiencies[mol.toSMILES()] = eff pickled_efficiencies = {} for mol, eff in lindemann.efficiencies.iteritems(): pickled_efficiencies[mol.toSMILES()] = eff self.assertEqual(efficiencies, pickled_efficiencies) self.assertEqual(self.lindemann.comment, lindemann.comment) def test_repr(self): """ Test that a Lindemann object can be reconstructed from its repr() output with no loss of information. """ lindemann = None exec('lindemann = {0!r}'.format(self.lindemann)) self.assertAlmostEqual(self.lindemann.arrheniusHigh.A.value, lindemann.arrheniusHigh.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusHigh.A.units, lindemann.arrheniusHigh.A.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.n.value, lindemann.arrheniusHigh.n.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.n.units, lindemann.arrheniusHigh.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusHigh.Ea.value, lindemann.arrheniusHigh.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.Ea.units, lindemann.arrheniusHigh.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusHigh.T0.value, lindemann.arrheniusHigh.T0.value, 4) self.assertEqual(self.lindemann.arrheniusHigh.T0.units, lindemann.arrheniusHigh.T0.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.A.value, lindemann.arrheniusLow.A.value, delta=1e0) self.assertEqual(self.lindemann.arrheniusLow.A.units, lindemann.arrheniusLow.A.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.n.value, lindemann.arrheniusLow.n.value, 4) self.assertEqual(self.lindemann.arrheniusLow.n.units, lindemann.arrheniusLow.n.units, 4) self.assertAlmostEqual(self.lindemann.arrheniusLow.Ea.value, lindemann.arrheniusLow.Ea.value, 4) self.assertEqual(self.lindemann.arrheniusLow.Ea.units, lindemann.arrheniusLow.Ea.units) self.assertAlmostEqual(self.lindemann.arrheniusLow.T0.value, lindemann.arrheniusLow.T0.value, 4) self.assertEqual(self.lindemann.arrheniusLow.T0.units, lindemann.arrheniusLow.T0.units) self.assertAlmostEqual(self.lindemann.Tmin.value, lindemann.Tmin.value, 4) self.assertEqual(self.lindemann.Tmin.units, lindemann.Tmin.units) self.assertAlmostEqual(self.lindemann.Tmax.value, lindemann.Tmax.value, 4) self.assertEqual(self.lindemann.Tmax.units, lindemann.Tmax.units) self.assertAlmostEqual(self.lindemann.Pmin.value, lindemann.Pmin.value, 4) self.assertEqual(self.lindemann.Pmin.units, lindemann.Pmin.units) self.assertAlmostEqual(self.lindemann.Pmax.value, lindemann.Pmax.value, 4) self.assertEqual(self.lindemann.Pmax.units, lindemann.Pmax.units) efficiencies = {} for mol, eff in self.lindemann.efficiencies.iteritems(): efficiencies[mol.toSMILES()] = eff pickled_efficiencies = {} for mol, eff in lindemann.efficiencies.iteritems(): pickled_efficiencies[mol.toSMILES()] = eff self.assertEqual(efficiencies, pickled_efficiencies) self.assertEqual(self.lindemann.comment, lindemann.comment) def test_changeRate(self): """ Test the Lindemann.changeRate() method. """ Tlist = numpy.array([300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500]) k0list = numpy.array([self.lindemann.getRateCoefficient(T,1e5) for T in Tlist]) self.lindemann.changeRate(2) for T, kexp in zip(Tlist, k0list): kact = self.lindemann.getRateCoefficient(T,1e5) self.assertAlmostEqual(2*kexp, kact, delta=1e-6*kexp)