def setUp(self):
"""
A function run before each unit test in this class.
"""
self.Tmin = 300.
self.Tmax = 2000.
self.Pmin = 0.01
self.Pmax = 100.
self.coeffs = numpy.array([
[11.67723, 0.729281, -0.11984, 0.00882175],
[-1.02669, 0.853639, -0.0323485, -0.027367],
[-0.447011, 0.244144, 0.0559122, -0.0101723],
[-0.128261, 0.0111596, 0.0281176, 0.00604353],
[-0.0117034, -0.0235646, 0.00061009, 0.00401309],
[0.0155433, -0.0136846, -0.00463048, -0.000261353],
])
self.comment = """acetyl + O2 -> acetylperoxy"""
self.chebyshev = Chebyshev(
coeffs=self.coeffs,
kunits="cm^3/(mol*s)",
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
def test_fitToData2(self):
"""
Test the Chebyshev.fitToData() method throws error without enough degrees of freedom.
Here only 3 temperatures are given, but the polynomial desired has 6 parameters.
"""
Tdata = numpy.array([300, 1200, 2000])
Pdata = numpy.array([1e5, 3e5, 1e6, 3e7])
nT = len(Tdata)
nP = len(Pdata)
kdata = numpy.zeros((nT, nP))
for t in range(nT):
for p in range(nP):
kdata[t, p] = self.chebyshev.getRateCoefficient(
Tdata[t], Pdata[p])
with self.assertRaises(KineticsError):
Chebyshev().fitToData(Tdata,
Pdata,
kdata,
kunits="cm^3/(mol*s)",
degreeT=12,
degreeP=8,
Tmin=300,
Tmax=2000,
Pmin=0.1,
Pmax=10.)
def test_fitToData(self):
"""
Test the Chebyshev.fitToData() method.
"""
Tdata = numpy.array([
300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400,
1500, 1600, 1700, 1800, 1900, 2000
])
Pdata = numpy.array([3e3, 1e4, 3e4, 1e5, 3e5, 1e6, 3e7])
nT = len(Tdata)
nP = len(Pdata)
kdata = numpy.zeros((nT, nP))
for t in range(nT):
for p in range(nP):
kdata[t, p] = self.chebyshev.getRateCoefficient(
Tdata[t], Pdata[p]) * 1e6
chebyshev = Chebyshev().fitToData(Tdata,
Pdata,
kdata,
kunits="cm^3/(mol*s)",
degreeT=6,
degreeP=4,
Tmin=300,
Tmax=2000,
Pmin=0.1,
Pmax=10.)
for t in range(nT):
for p in range(nP):
kfit = chebyshev.getRateCoefficient(Tdata[t], Pdata[p]) * 1e6
self.assertAlmostEqual(kfit,
kdata[t, p],
delta=1e-4 * kdata[t, p])
def test_mark_duplicate_reactions(self):
"""Test that we can properly mark duplicate reactions for Chemkin."""
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')
s6 = Species().from_smiles('[H]')
# Try initializing with duplicate=False
reaction_list = [
Reaction(reactants=[s1], products=[s2, s2], duplicate=False, kinetics=Arrhenius()),
Reaction(reactants=[s1], products=[s2, s2], duplicate=False, kinetics=Arrhenius()),
Reaction(reactants=[s1, s3], products=[s4, s5], duplicate=False, kinetics=Arrhenius()),
Reaction(reactants=[s1, s3], products=[s4, s5], duplicate=False, kinetics=Chebyshev()),
Reaction(reactants=[s1], products=[s4, s6], duplicate=False, kinetics=Arrhenius(), reversible=False),
Reaction(reactants=[s1], products=[s4, s6], duplicate=False, kinetics=Arrhenius(), reversible=False),
Reaction(reactants=[s5], products=[s3, s6], duplicate=False, kinetics=Arrhenius(), reversible=False),
Reaction(reactants=[s3, s6], products=[s5], duplicate=False, kinetics=Arrhenius(), reversible=False),
]
expected_flags = [True, True, False, False, True, True, False, False]
mark_duplicate_reactions(reaction_list)
duplicate_flags = [rxn.duplicate for rxn in reaction_list]
self.assertEqual(duplicate_flags, expected_flags)
# Try initializing with duplicate=True
reaction_list = [
Reaction(reactants=[s1], products=[s2, s2], duplicate=True, kinetics=Arrhenius()),
Reaction(reactants=[s1], products=[s2, s2], duplicate=True, kinetics=Arrhenius()),
Reaction(reactants=[s1, s3], products=[s4, s5], duplicate=True, kinetics=Arrhenius()),
Reaction(reactants=[s1, s3], products=[s4, s5], duplicate=True, kinetics=Chebyshev()),
Reaction(reactants=[s1], products=[s4, s6], duplicate=True, kinetics=Arrhenius(), reversible=False),
Reaction(reactants=[s1], products=[s4, s6], duplicate=True, kinetics=Arrhenius(), reversible=False),
Reaction(reactants=[s5], products=[s3, s6], duplicate=True, kinetics=Arrhenius(), reversible=False),
Reaction(reactants=[s3, s6], products=[s5], duplicate=True, kinetics=Arrhenius(), reversible=False),
]
mark_duplicate_reactions(reaction_list)
duplicate_flags = [rxn.duplicate for rxn in reaction_list]
self.assertEqual(duplicate_flags, expected_flags)
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))
def test_is_identical_to(self):
"""
Test the Chebyshev.is_identical_to() method.
"""
# Trivial case, compare to a KineticsModel
from rmgpy.kinetics.model import KineticsModel
self.assertFalse(self.chebyshev.is_identical_to(KineticsModel()))
# Compare to identical Chebyshev
new_chebyshev = Chebyshev(
coeffs=self.coeffs,
kunits="cm^3/(mol*s)",
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
self.assertTrue(self.chebyshev.is_identical_to(new_chebyshev))
# Compare to Chebyshev with different Tmin/Tmax
new_chebyshev = Chebyshev(
coeffs=self.coeffs,
kunits="cm^3/(mol*s)",
Tmin=(200, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
self.assertFalse(self.chebyshev.is_identical_to(new_chebyshev))
new_chebyshev = Chebyshev(
coeffs=self.coeffs,
kunits="cm^3/(mol*s)",
Tmin=(self.Tmin, "K"),
Tmax=(2500, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
self.assertFalse(self.chebyshev.is_identical_to(new_chebyshev))
# Compare to Chebyshev with different degreeT/degreeP
new_chebyshev = Chebyshev(
coeffs=self.coeffs[0:-1, :], # Remove one T dimension
kunits="cm^3/(mol*s)",
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
self.assertFalse(self.chebyshev.is_identical_to(new_chebyshev))
new_chebyshev = Chebyshev(
coeffs=self.coeffs[:, 0:-1], # Remove one P dimension
kunits="cm^3/(mol*s)",
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
self.assertFalse(self.chebyshev.is_identical_to(new_chebyshev))
# Compare to Chebyshev with different units
new_chebyshev = Chebyshev(
coeffs=self.coeffs,
kunits="m^3/(mol*s)",
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
self.assertFalse(self.chebyshev.is_identical_to(new_chebyshev))
# Compare to Chebyshev with slightly different coefficients
new_chebyshev = Chebyshev(
coeffs=np.copy(self.coeffs) * 0.01,
kunits="cm^3/(mol*s)",
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
Pmin=(self.Pmin, "bar"),
Pmax=(self.Pmax, "bar"),
comment=self.comment,
)
self.assertFalse(self.chebyshev.is_identical_to(new_chebyshev))