def setUp(self):
"""
A function run before each unit test in this class.
"""
self.Tmin = 350.0
self.Tmax = 1500.0
self.comment = "Comment"
self.arrhenius = [
Arrhenius(
A=(9.3e-14, "cm^3/(molecule*s)"),
n=0.0,
Ea=(4740 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
Arrhenius(
A=(1.4e-9, "cm^3/(molecule*s)"),
n=0.0,
Ea=(11200 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
]
self.kinetics = MultiArrhenius(
arrhenius=self.arrhenius, Tmin=(self.Tmin, "K"), Tmax=(self.Tmax, "K"), comment=self.comment
)
self.single_kinetics = MultiArrhenius(
arrhenius=self.arrhenius[:1], Tmin=(self.Tmin, "K"), Tmax=(self.Tmax, "K"), comment=self.comment
)
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.Tmin = 350.
self.Tmax = 1500.
self.comment = 'Comment'
self.arrhenius = [
Arrhenius(
A=(9.3e-14, "cm^3/(molecule*s)"),
n=0.0,
Ea=(4740 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
Arrhenius(
A=(1.4e-9, "cm^3/(molecule*s)"),
n=0.0,
Ea=(11200 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
]
self.kinetics = MultiArrhenius(
arrhenius=self.arrhenius,
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
)
self.single_kinetics = MultiArrhenius(
arrhenius=self.arrhenius[:1],
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
)
def get_arrhenius_from_param(params, settings, arrh_type='Arrhenius'):
"""
Get Arrhenius object given params and settings
Args:
params (dict) : A dictionary contains the information about
A factor, n, Ea, T0 and multiplier
settings (dict): A dictionary contains the information about
variable units, T and P range, description
arrh_type (str): The type of Arrhenius object to be added,
supporting Arrhenius, MultiArrhenius, and
PdepArrehnius
Returns:
(Arrhenius object): The Arrhenius object generated
"""
args = {}
if 'Tmin' in settings and settings['Tmin']:
args['Tmin'] = (settings['Tmin'], settings['T_unit'])
if 'Tmax' in settings and settings['Tmax']:
args['Tmax'] = (settings['Tmax'], settings['T_unit'])
if 'Pmin' in settings and settings['Pmin']:
args['Pmin'] = (settings['Pmin'], settings['P_unit'])
if 'Pmax' in settings and settings['Pmax']:
args['Pmax'] = (settings['Pmax'], settings['P_unit'])
if 'comment' in settings and settings['comment']:
args['comment'] = settings['comment']
if arrh_type == 'Arrhenius':
args['A'] = (params['A'], settings['A_unit'])
args['n'] = params['n']
args['Ea'] = (params['Ea'], settings['E_unit'])
if 'T0' in params and params['T0']:
args['T0'] = (params['T0'], settings['T_unit'])
if 'uncertainty' in params and params['uncertainty']:
args['uncertainty'] = params['uncertainty']
return Arrhenius(**args)
elif arrh_type == 'MultiArrhenius':
args['arrhenius'] = params['arrhenius']
return MultiArrhenius(**args)
elif arrh_type == 'PdepArrhenius':
args['arrhenius'] = params['arrhenius']
args['pressures'] = (params['pressures'], settings['P_unit'])
if 'highPlimit' and params['highPlimit']:
args['highPlimit'] = params['highPlimit']
return PDepArrhenius(**args)
class TestMultiArrhenius(unittest.TestCase):
"""
Contains unit tests of the :class:`MultiArrhenius` class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.Tmin = 350.
self.Tmax = 1500.
self.comment = 'Comment'
self.arrhenius = [
Arrhenius(
A=(9.3e-14, "cm^3/(molecule*s)"),
n=0.0,
Ea=(4740 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
Arrhenius(
A=(1.4e-9, "cm^3/(molecule*s)"),
n=0.0,
Ea=(11200 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
]
self.kinetics = MultiArrhenius(
arrhenius=self.arrhenius,
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
)
self.single_kinetics = MultiArrhenius(
arrhenius=self.arrhenius[:1],
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
)
def test_arrhenius(self):
"""
Test that the MultiArrhenius A property was properly set.
"""
self.assertEqual(self.kinetics.arrhenius, self.arrhenius)
def test_Tmin(self):
"""
Test that the MultiArrhenius Tmin property was properly set.
"""
self.assertAlmostEqual(self.kinetics.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the MultiArrhenius Tmax property was properly set.
"""
self.assertAlmostEqual(self.kinetics.Tmax.value_si, self.Tmax, 6)
def test_comment(self):
"""
Test that the MultiArrhenius comment property was properly set.
"""
self.assertEqual(self.kinetics.comment, self.comment)
def test_isTemperatureValid(self):
"""
Test the MultiArrhenius.isTemperatureValid() method.
"""
Tdata = numpy.array(
[200, 400, 600, 800, 1000, 1200, 1400, 1600, 1800, 2000])
validdata = numpy.array(
[False, True, True, True, True, True, True, False, False, False],
numpy.bool)
for T, valid in zip(Tdata, validdata):
valid0 = self.kinetics.isTemperatureValid(T)
self.assertEqual(valid0, valid)
def test_getRateCoefficient(self):
"""
Test the MultiArrhenius.getRateCoefficient() method.
"""
Tlist = numpy.array(
[200, 400, 600, 800, 1000, 1200, 1400, 1600, 1800, 2000])
kexplist = numpy.array([
2.85400e-06, 4.00384e-01, 2.73563e+01, 8.50699e+02, 1.20181e+04,
7.56312e+04, 2.84724e+05, 7.71702e+05, 1.67743e+06, 3.12290e+06
])
for T, kexp in zip(Tlist, kexplist):
kact = self.kinetics.getRateCoefficient(T)
self.assertAlmostEqual(kexp, kact, delta=1e-4 * kexp)
def test_pickle(self):
"""
Test that a MultiArrhenius object can be pickled and unpickled with no loss
of information.
"""
import cPickle
kinetics = cPickle.loads(cPickle.dumps(self.kinetics, -1))
self.assertEqual(len(self.kinetics.arrhenius), len(kinetics.arrhenius))
for arrh0, arrh in zip(self.kinetics.arrhenius, kinetics.arrhenius):
self.assertAlmostEqual(arrh0.A.value, arrh.A.value, delta=1e-18)
self.assertEqual(arrh0.A.units, arrh.A.units)
self.assertAlmostEqual(arrh0.n.value, arrh.n.value, 4)
self.assertAlmostEqual(arrh0.Ea.value, arrh.Ea.value, 4)
self.assertEqual(arrh0.Ea.units, arrh.Ea.units)
self.assertAlmostEqual(arrh0.T0.value, arrh.T0.value, 4)
self.assertEqual(arrh0.T0.units, arrh.T0.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.assertEqual(self.kinetics.comment, kinetics.comment)
def test_repr(self):
"""
Test that a MultiArrhenius object can be reconstructed from its repr()
output with no loss of information.
"""
kinetics = None
exec('kinetics = {0!r}'.format(self.kinetics))
self.assertEqual(len(self.kinetics.arrhenius), len(kinetics.arrhenius))
for arrh0, arrh in zip(self.kinetics.arrhenius, kinetics.arrhenius):
self.assertAlmostEqual(arrh0.A.value, arrh.A.value, delta=1e-18)
self.assertEqual(arrh0.A.units, arrh.A.units)
self.assertAlmostEqual(arrh0.n.value, arrh.n.value, 4)
self.assertAlmostEqual(arrh0.Ea.value, arrh.Ea.value, 4)
self.assertEqual(arrh0.Ea.units, arrh.Ea.units)
self.assertAlmostEqual(arrh0.T0.value, arrh.T0.value, 4)
self.assertEqual(arrh0.T0.units, arrh.T0.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.assertEqual(self.kinetics.comment, kinetics.comment)
def test_toArrhenius(self):
"""
Test that we can convert to an Arrhenius
"""
answer = self.single_kinetics.arrhenius[0]
fitted = self.single_kinetics.toArrhenius()
self.assertAlmostEqual(fitted.A.value_si, answer.A.value_si, delta=1e0)
self.assertAlmostEqual(fitted.n.value_si, answer.n.value_si, 1, 4)
self.assertAlmostEqual(fitted.Ea.value_si, answer.Ea.value_si, 2)
self.assertAlmostEqual(fitted.T0.value_si, answer.T0.value_si, 4)
def test_toArrheniusTrange(self):
"""
Test the toArrhenius temperature range is set correctly.
"""
answer = self.single_kinetics.arrhenius[0]
fitted = self.single_kinetics.toArrhenius(Tmin=800, Tmax=1200)
self.assertAlmostEqual(fitted.Tmin.value_si, 800.0)
self.assertAlmostEqual(fitted.Tmax.value_si, 1200.0)
for T in [800, 1000, 1200]:
self.assertAlmostEqual(
fitted.getRateCoefficient(T) / answer.getRateCoefficient(T),
1.0)
def test_toArrheniusMultiple(self):
"""
Test the toArrhenius fitting multiple kinetics over a small range, see if we're within 5% at a few points
"""
answer = self.kinetics
fitted = self.kinetics.toArrhenius(Tmin=800, Tmax=1200)
self.assertAlmostEqual(fitted.Tmin.value_si, 800.0)
self.assertAlmostEqual(fitted.Tmax.value_si, 1200.0)
for T in [800, 1000, 1200]:
self.assertAlmostEqual(fitted.getRateCoefficient(T) /
answer.getRateCoefficient(T),
1.0,
delta=0.05)
def test_changeRate(self):
"""
Test the MultiArrhenius.changeRate() method.
"""
Tlist = numpy.array([
300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400,
1500
])
k0list = numpy.array(
[self.kinetics.getRateCoefficient(T) for T in Tlist])
self.kinetics.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.kinetics.getRateCoefficient(T)
self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)
def test_process_duplicate_reactions(self):
"""
Test that duplicate reactions are handled correctly when
loading a Chemkin file.
"""
s1 = Species().from_smiles('CC')
s2 = Species().from_smiles('[CH3]')
s3 = Species().from_smiles('[OH]')
s4 = Species().from_smiles('C[CH2]')
s5 = Species().from_smiles('O')
r1 = Reaction(reactants=[s1],
products=[s2, s2],
duplicate=False,
kinetics=Arrhenius())
r2 = Reaction(reactants=[s1, s3],
products=[s4, s5],
duplicate=True,
kinetics=Arrhenius())
r3 = Reaction(reactants=[s1, s3],
products=[s4, s5],
duplicate=True,
kinetics=Arrhenius())
r4 = Reaction(reactants=[s1, s3],
products=[s4, s5],
duplicate=False,
kinetics=Arrhenius())
r5 = LibraryReaction(reactants=[s1, s3],
products=[s4, s5],
duplicate=True,
kinetics=Arrhenius(),
library='lib1')
r6 = LibraryReaction(reactants=[s1, s3],
products=[s4, s5],
duplicate=True,
kinetics=Arrhenius(),
library='lib2')
r7 = LibraryReaction(reactants=[s1, s3],
products=[s4, s5],
duplicate=True,
kinetics=Chebyshev(),
library='lib1')
r8 = LibraryReaction(reactants=[s1, s3],
products=[s4, s5],
duplicate=True,
kinetics=Arrhenius(),
library='lib1')
r9 = LibraryReaction(
reactants=[s1, s3],
products=[s4, s5],
duplicate=False,
kinetics=MultiArrhenius(
arrhenius=[Arrhenius(), Arrhenius()]),
library='lib1')
reaction_list_with_duplicate = [r1, r2, r3]
reaction_list_with_duplicate2 = [r1, r2, r3]
reaction_list_unmarked_duplicate = [r1, r2, r4]
reaction_list_unequal_libraries = [r1, r5, r6]
reaction_list_mixed_kinetics = [r1, r5, r7]
reaction_list_mergeable = [r1, r5, r8]
reaction_list_merged = [r1, r9]
# Test that duplicates are not removed for non-library reactions
_process_duplicate_reactions(reaction_list_with_duplicate)
self.assertEqual(reaction_list_with_duplicate,
reaction_list_with_duplicate2)
# Test that unmarked duplicate reactions are detected if both
# reactions are p-dep or p-indep
self.assertRaisesRegexp(ChemkinError,
'Encountered unmarked duplicate reaction',
_process_duplicate_reactions,
reaction_list_unmarked_duplicate)
# Test that unequal libraries are recognized
self.assertRaisesRegexp(ChemkinError, 'from different libraries',
_process_duplicate_reactions,
reaction_list_unequal_libraries)
# Test that an error is raised for reactions with kinetics
# that cannot be merged
self.assertRaisesRegexp(ChemkinError,
'Mixed kinetics for duplicate reaction',
_process_duplicate_reactions,
reaction_list_mixed_kinetics)
# Test that duplicate library reactions are merged successfully
_process_duplicate_reactions(reaction_list_mergeable)
self.assertEqual(len(reaction_list_mergeable),
len(reaction_list_merged))
self.assertEqual(reaction_list_mergeable[0], reaction_list_merged[0])
rtest = reaction_list_mergeable[1]
rtrue = reaction_list_merged[1]
self.assertEqual(rtest.reactants, rtrue.reactants)
self.assertEqual(rtest.products, rtrue.products)
self.assertEqual(rtest.duplicate, rtrue.duplicate)
self.assertEqual(rtest.library, rtrue.library)
self.assertTrue(isinstance(rtest.kinetics, MultiArrhenius))
self.assertTrue(
all(isinstance(k, Arrhenius) for k in rtest.kinetics.arrhenius))
class TestMultiArrhenius(unittest.TestCase):
"""
Contains unit tests of the :class:`MultiArrhenius` class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.Tmin = 350.0
self.Tmax = 1500.0
self.comment = ""
self.arrhenius = [
Arrhenius(
A=(9.3e-14, "cm^3/(molecule*s)"),
n=0.0,
Ea=(4740 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
Arrhenius(
A=(1.4e-9, "cm^3/(molecule*s)"),
n=0.0,
Ea=(11200 * constants.R * 0.001, "kJ/mol"),
T0=(1, "K"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
),
]
self.kinetics = MultiArrhenius(
arrhenius=self.arrhenius, Tmin=(self.Tmin, "K"), Tmax=(self.Tmax, "K"), comment=self.comment
)
def test_arrhenius(self):
"""
Test that the MultiArrhenius A property was properly set.
"""
self.assertEqual(self.kinetics.arrhenius, self.arrhenius)
def test_Tmin(self):
"""
Test that the MultiArrhenius Tmin property was properly set.
"""
self.assertAlmostEqual(self.kinetics.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the MultiArrhenius Tmax property was properly set.
"""
self.assertAlmostEqual(self.kinetics.Tmax.value_si, self.Tmax, 6)
def test_comment(self):
"""
Test that the MultiArrhenius comment property was properly set.
"""
self.assertEqual(self.kinetics.comment, self.comment)
def test_isTemperatureValid(self):
"""
Test the MultiArrhenius.isTemperatureValid() method.
"""
Tdata = numpy.array([200, 400, 600, 800, 1000, 1200, 1400, 1600, 1800, 2000])
validdata = numpy.array([False, True, True, True, True, True, True, False, False, False], numpy.bool)
for T, valid in zip(Tdata, validdata):
valid0 = self.kinetics.isTemperatureValid(T)
self.assertEqual(valid0, valid)
def test_getRateCoefficient(self):
"""
Test the MultiArrhenius.getRateCoefficient() method.
"""
Tlist = numpy.array([200, 400, 600, 800, 1000, 1200, 1400, 1600, 1800, 2000])
kexplist = numpy.array(
[
2.85400e-06,
4.00384e-01,
2.73563e01,
8.50699e02,
1.20181e04,
7.56312e04,
2.84724e05,
7.71702e05,
1.67743e06,
3.12290e06,
]
)
for T, kexp in zip(Tlist, kexplist):
kact = self.kinetics.getRateCoefficient(T)
self.assertAlmostEqual(kexp, kact, delta=1e-4 * kexp)
def test_pickle(self):
"""
Test that a MultiArrhenius object can be pickled and unpickled with no loss
of information.
"""
import cPickle
kinetics = cPickle.loads(cPickle.dumps(self.kinetics))
self.assertEqual(len(self.kinetics.arrhenius), len(kinetics.arrhenius))
for arrh0, arrh in zip(self.kinetics.arrhenius, kinetics.arrhenius):
self.assertAlmostEqual(arrh0.A.value, arrh.A.value, delta=1e-18)
self.assertEqual(arrh0.A.units, arrh.A.units)
self.assertAlmostEqual(arrh0.n.value, arrh.n.value, 4)
self.assertAlmostEqual(arrh0.Ea.value, arrh.Ea.value, 4)
self.assertEqual(arrh0.Ea.units, arrh.Ea.units)
self.assertAlmostEqual(arrh0.T0.value, arrh.T0.value, 4)
self.assertEqual(arrh0.T0.units, arrh.T0.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.assertEqual(self.kinetics.comment, kinetics.comment)
def test_repr(self):
"""
Test that a MultiArrhenius object can be reconstructed from its repr()
output with no loss of information.
"""
kinetics = None
exec("kinetics = {0!r}".format(self.kinetics))
self.assertEqual(len(self.kinetics.arrhenius), len(kinetics.arrhenius))
for arrh0, arrh in zip(self.kinetics.arrhenius, kinetics.arrhenius):
self.assertAlmostEqual(arrh0.A.value, arrh.A.value, delta=1e-18)
self.assertEqual(arrh0.A.units, arrh.A.units)
self.assertAlmostEqual(arrh0.n.value, arrh.n.value, 4)
self.assertAlmostEqual(arrh0.Ea.value, arrh.Ea.value, 4)
self.assertEqual(arrh0.Ea.units, arrh.Ea.units)
self.assertAlmostEqual(arrh0.T0.value, arrh.T0.value, 4)
self.assertEqual(arrh0.T0.units, arrh.T0.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.assertEqual(self.kinetics.comment, kinetics.comment)
class TestMultiArrhenius(unittest.TestCase):
"""
Contains unit tests of the :class:`MultiArrhenius` class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.Tmin = 350.
self.Tmax = 1500.
self.comment = 'Comment'
self.arrhenius = [
Arrhenius(
A = (9.3e-14,"cm^3/(molecule*s)"),
n = 0.0,
Ea = (4740*constants.R*0.001,"kJ/mol"),
T0 = (1,"K"),
Tmin = (self.Tmin,"K"),
Tmax = (self.Tmax,"K"),
comment = self.comment,
),
Arrhenius(
A = (1.4e-9,"cm^3/(molecule*s)"),
n = 0.0,
Ea = (11200*constants.R*0.001,"kJ/mol"),
T0 = (1,"K"),
Tmin = (self.Tmin,"K"),
Tmax = (self.Tmax,"K"),
comment = self.comment,
),
]
self.kinetics = MultiArrhenius(
arrhenius = self.arrhenius,
Tmin = (self.Tmin,"K"),
Tmax = (self.Tmax,"K"),
comment = self.comment,
)
self.single_kinetics = MultiArrhenius(
arrhenius = self.arrhenius[:1],
Tmin = (self.Tmin,"K"),
Tmax = (self.Tmax,"K"),
comment = self.comment,
)
def test_arrhenius(self):
"""
Test that the MultiArrhenius A property was properly set.
"""
self.assertEqual(self.kinetics.arrhenius, self.arrhenius)
def test_Tmin(self):
"""
Test that the MultiArrhenius Tmin property was properly set.
"""
self.assertAlmostEqual(self.kinetics.Tmin.value_si, self.Tmin, 6)
def test_Tmax(self):
"""
Test that the MultiArrhenius Tmax property was properly set.
"""
self.assertAlmostEqual(self.kinetics.Tmax.value_si, self.Tmax, 6)
def test_comment(self):
"""
Test that the MultiArrhenius comment property was properly set.
"""
self.assertEqual(self.kinetics.comment, self.comment)
def test_isTemperatureValid(self):
"""
Test the MultiArrhenius.isTemperatureValid() method.
"""
Tdata = numpy.array([200,400,600,800,1000,1200,1400,1600,1800,2000])
validdata = numpy.array([False,True,True,True,True,True,True,False,False,False], numpy.bool)
for T, valid in zip(Tdata, validdata):
valid0 = self.kinetics.isTemperatureValid(T)
self.assertEqual(valid0, valid)
def test_getRateCoefficient(self):
"""
Test the MultiArrhenius.getRateCoefficient() method.
"""
Tlist = numpy.array([200,400,600,800,1000,1200,1400,1600,1800,2000])
kexplist = numpy.array([2.85400e-06, 4.00384e-01, 2.73563e+01, 8.50699e+02, 1.20181e+04, 7.56312e+04, 2.84724e+05, 7.71702e+05, 1.67743e+06, 3.12290e+06])
for T, kexp in zip(Tlist, kexplist):
kact = self.kinetics.getRateCoefficient(T)
self.assertAlmostEqual(kexp, kact, delta=1e-4*kexp)
def test_pickle(self):
"""
Test that a MultiArrhenius object can be pickled and unpickled with no loss
of information.
"""
import cPickle
kinetics = cPickle.loads(cPickle.dumps(self.kinetics,-1))
self.assertEqual(len(self.kinetics.arrhenius), len(kinetics.arrhenius))
for arrh0, arrh in zip(self.kinetics.arrhenius, kinetics.arrhenius):
self.assertAlmostEqual(arrh0.A.value, arrh.A.value, delta=1e-18)
self.assertEqual(arrh0.A.units, arrh.A.units)
self.assertAlmostEqual(arrh0.n.value, arrh.n.value, 4)
self.assertAlmostEqual(arrh0.Ea.value, arrh.Ea.value, 4)
self.assertEqual(arrh0.Ea.units, arrh.Ea.units)
self.assertAlmostEqual(arrh0.T0.value, arrh.T0.value, 4)
self.assertEqual(arrh0.T0.units, arrh.T0.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.assertEqual(self.kinetics.comment, kinetics.comment)
def test_repr(self):
"""
Test that a MultiArrhenius object can be reconstructed from its repr()
output with no loss of information.
"""
kinetics = None
exec('kinetics = {0!r}'.format(self.kinetics))
self.assertEqual(len(self.kinetics.arrhenius), len(kinetics.arrhenius))
for arrh0, arrh in zip(self.kinetics.arrhenius, kinetics.arrhenius):
self.assertAlmostEqual(arrh0.A.value, arrh.A.value, delta=1e-18)
self.assertEqual(arrh0.A.units, arrh.A.units)
self.assertAlmostEqual(arrh0.n.value, arrh.n.value, 4)
self.assertAlmostEqual(arrh0.Ea.value, arrh.Ea.value, 4)
self.assertEqual(arrh0.Ea.units, arrh.Ea.units)
self.assertAlmostEqual(arrh0.T0.value, arrh.T0.value, 4)
self.assertEqual(arrh0.T0.units, arrh.T0.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.assertEqual(self.kinetics.comment, kinetics.comment)
def test_toArrhenius(self):
"""
Test that we can convert to an Arrhenius
"""
answer = self.single_kinetics.arrhenius[0]
fitted = self.single_kinetics.toArrhenius()
self.assertAlmostEqual(fitted.A.value_si, answer.A.value_si, delta=1e0)
self.assertAlmostEqual(fitted.n.value_si, answer.n.value_si, 1, 4)
self.assertAlmostEqual(fitted.Ea.value_si, answer.Ea.value_si, 2)
self.assertAlmostEqual(fitted.T0.value_si, answer.T0.value_si, 4)
def test_toArrheniusTrange(self):
"""
Test the toArrhenius temperature range is set correctly.
"""
answer = self.single_kinetics.arrhenius[0]
fitted = self.single_kinetics.toArrhenius(Tmin=800, Tmax=1200)
self.assertAlmostEqual(fitted.Tmin.value_si, 800.0)
self.assertAlmostEqual(fitted.Tmax.value_si, 1200.0)
for T in [800,1000,1200]:
self.assertAlmostEqual(fitted.getRateCoefficient(T) / answer.getRateCoefficient(T), 1.0)
def test_toArrheniusMultiple(self):
"""
Test the toArrhenius fitting multiple kinetics over a small range, see if we're within 5% at a few points
"""
answer = self.kinetics
fitted = self.kinetics.toArrhenius(Tmin=800, Tmax=1200)
self.assertAlmostEqual(fitted.Tmin.value_si, 800.0)
self.assertAlmostEqual(fitted.Tmax.value_si, 1200.0)
for T in [800,1000,1200]:
self.assertAlmostEqual(fitted.getRateCoefficient(T) / answer.getRateCoefficient(T), 1.0, delta=0.05)
def test_changeRate(self):
"""
Test the MultiArrhenius.changeRate() method.
"""
Tlist = numpy.array([300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500])
k0list = numpy.array([self.kinetics.getRateCoefficient(T) for T in Tlist])
self.kinetics.changeRate(2)
for T, kexp in zip(Tlist, k0list):
kact = self.kinetics.getRateCoefficient(T)
self.assertAlmostEqual(2*kexp, kact, delta=1e-6*kexp)