def setUp(self):
"""This method is run once before each test."""
coeffs_low = [4.03055, -0.00214171, 4.90611e-05, -5.99027e-08, 2.38945e-11, -11257.6, 3.5613]
coeffs_high = [-0.307954, 0.0245269, -1.2413e-05, 3.07724e-09, -3.01467e-13, -10693, 22.628]
Tmin = 300.
Tmax = 3000.
Tint = 650.73
E0 = -782292. # J/mol.
comment = "C2H6"
self.nasa = NASA(
polynomials=[
NASAPolynomial(coeffs=coeffs_low, Tmin=(Tmin, "K"), Tmax=(Tint, "K")),
NASAPolynomial(coeffs=coeffs_high, Tmin=(Tint, "K"), Tmax=(Tmax, "K")),
],
Tmin=(Tmin, "K"),
Tmax=(Tmax, "K"),
E0=(E0, "J/mol"),
comment=comment,
)
# Chemkin entries for testing - note that the values are all the same
self.entry1 = """C2H6 C 2H 6 G 300.000 3000.000 650.73 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
self.entry2 = """CH3NO2X G 300.000 3000.000 650.73 1&
C 1 H 3 N 1 O 2 X 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
self.entry3 = """CH3NO2SX G 300.000 3000.000 650.73 1&
def testCantera(self):
"""
Test that a Cantera Species object is created correctly.
"""
from rmgpy.thermo import NASA, NASAPolynomial
import cantera as ct
rmgSpecies = Species(label="Ar", thermo=NASA(polynomials=[NASAPolynomial(coeffs=[2.5,0,0,0,0,-745.375,4.37967], Tmin=(200,'K'), Tmax=(1000,'K')), NASAPolynomial(coeffs=[2.5,0,0,0,0,-745.375,4.37967], Tmin=(1000,'K'), Tmax=(6000,'K'))], Tmin=(200,'K'), Tmax=(6000,'K'), comment="""
Thermo library: primaryThermoLibrary
"""), molecule=[Molecule(SMILES="[Ar]")], transportData=TransportData(shapeIndex=0, epsilon=(1134.93,'J/mol'), sigma=(3.33,'angstrom'), dipoleMoment=(2,'De'), polarizability=(1,'angstrom^3'), rotrelaxcollnum=15.0, comment="""GRI-Mech"""))
rmg_ctSpecies = rmgSpecies.toCantera(useChemkinIdentifier = True)
ctSpecies = ct.Species.fromCti("""species(name=u'Ar',
atoms='Ar:1',
thermo=(NASA([200.00, 1000.00],
[ 2.50000000E+00, 0.00000000E+00, 0.00000000E+00,
0.00000000E+00, 0.00000000E+00, -7.45375000E+02,
4.37967000E+00]),
NASA([1000.00, 6000.00],
[ 2.50000000E+00, 0.00000000E+00, 0.00000000E+00,
0.00000000E+00, 0.00000000E+00, -7.45375000E+02,
4.37967000E+00])),
transport=gas_transport(geom='atom',
diam=3.33,
well_depth=136.501,
dipole=2.0,
polar=1.0,
rot_relax=15.0))""")
self.assertEqual(type(rmg_ctSpecies),type(ctSpecies))
self.assertEqual(rmg_ctSpecies.name, ctSpecies.name)
self.assertEqual(rmg_ctSpecies.composition, ctSpecies.composition)
self.assertEqual(rmg_ctSpecies.size, ctSpecies.size)
self.assertEqual(type(rmg_ctSpecies.thermo), type(ctSpecies.thermo))
self.assertEqual(type(rmg_ctSpecies.transport), type(ctSpecies.transport))
def toRMG(self):
"Returns an RMG object"
polynomials = []
for polynomial_number in [1, 2]:
coeffs = [
float(
getattr(
self,
'coefficient_{j}_{i}'.format(j=coefficient_number,
i=polynomial_number)))
for coefficient_number in range(1, 8)
]
polynomial = NASAPolynomial(
coeffs=coeffs,
Tmin=float(
getattr(
self,
'lower_temp_bound_{i}'.format(i=polynomial_number))),
Tmax=float(
getattr(
self,
'upper_temp_bound_{i}'.format(i=polynomial_number))),
E0=None,
comment='')
polynomials.append(polynomial)
rmg_object = NASA(polynomials=polynomials,
Tmin=polynomials[0].Tmin,
Tmax=polynomials[1].Tmin)
return rmg_object
def test_species_requires_refinement():
"""Test whether a species thermo requires refinement"""
t3 = run_minimal()
spc_1 = Species(smiles='C')
spc_1.thermo = NASA()
spc_1.thermo.comment = 'Thermo group additivity estimation: group(O2s-(Cds-Cd)H) + missing(O2d-CO) + ' \
'missing(O2d-CO) + group(Cds-Cds(Cds-O2d)O2s) + group(Cds-O2d(Cds-Cds)(Cds-Cds)) + ' \
'group(Cd-Cd(CO)H) + group(Cd-Cd(CO)H) + group(Cds-O2d(Cds-Cds)H) + group(Cds-CdsHH)'
spc_2 = Species(smiles='C')
spc_2.thermo = NASA()
spc_2.thermo.comment = 'Thermo library: primaryThermoLibrary + radical(HOOj)'
spc_3 = Species(smiles='C')
spc_3.thermo = NASA()
spc_3.thermo.comment = 'Thermo library: primaryThermoLibrary'
assert t3.species_requires_refinement(spc_1) is True
assert t3.species_requires_refinement(spc_2) is True
assert t3.species_requires_refinement(spc_3) is False
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.wilhoit = Wilhoit(
Cp0=(4.0 * constants.R, "J/(mol*K)"),
CpInf=(21.5 * constants.R, "J/(mol*K)"),
a0=0.0977518,
a1=-16.3067,
a2=26.2524,
a3=-12.6785,
B=(1068.68, "K"),
H0=(-94.088 * constants.R, "kJ/mol"),
S0=(-118.46 * constants.R, "J/(mol*K)"),
Tmin=(10, "K"),
Tmax=(3000, "K"),
comment='C2H6',
)
self.nasa = NASA(
polynomials=[
NASAPolynomial(coeffs=[
4.03055, -0.00214171, 4.90611e-05, -5.99027e-08,
2.38945e-11, -11257.6, 3.5613
],
Tmin=(10, "K"),
Tmax=(650.73, "K")),
NASAPolynomial(coeffs=[
-0.307954, 0.0245269, -1.2413e-05, 3.07724e-09,
-3.01467e-13, -10693, 22.628
],
Tmin=(650.73, "K"),
Tmax=(3000, "K")),
],
Tmin=(10, "K"),
Tmax=(3000, "K"),
E0=(-93.6077, 'kJ/mol'),
Cp0=(4.0 * constants.R, "J/(mol*K)"),
CpInf=(21.5 * constants.R, "J/(mol*K)"),
comment='C2H6',
)
self.thermodata = ThermoData(
Tdata=([300, 400, 500, 600, 800, 1000, 1500], "K"),
Cpdata=(numpy.array([
6.38268, 7.80327, 9.22175, 10.5528, 12.8323, 14.6013, 17.40890
]) * constants.R, "J/(mol*K)"),
H298=(-81.7, "kJ/mol"),
S298=(27.5727 * constants.R, "J/(mol*K)"),
Cp0=(4.0 * constants.R, "J/(mol*K)"),
CpInf=(21.5 * constants.R, "J/(mol*K)"),
Tmin=(10, "K"),
Tmax=(3000, "K"),
E0=(-93.6077, 'kJ/mol'),
comment='C2H6',
)
class TestThermoReadWrite(unittest.TestCase):
def setUp(self):
"""This method is run once before each test."""
coeffs_low = [
4.03055, -0.00214171, 4.90611e-05, -5.99027e-08, 2.38945e-11,
-11257.6, 3.5613
]
coeffs_high = [
-0.307954, 0.0245269, -1.2413e-05, 3.07724e-09, -3.01467e-13,
-10693, 22.628
]
Tmin = 300.
Tmax = 3000.
Tint = 650.73
E0 = -782292. # J/mol.
comment = "C2H6"
self.nasa = NASA(
polynomials=[
NASAPolynomial(coeffs=coeffs_low,
Tmin=(Tmin, "K"),
Tmax=(Tint, "K")),
NASAPolynomial(coeffs=coeffs_high,
Tmin=(Tint, "K"),
Tmax=(Tmax, "K")),
],
Tmin=(Tmin, "K"),
Tmax=(Tmax, "K"),
E0=(E0, "J/mol"),
comment=comment,
)
# Chemkin entries for testing - note that the values are all the same
self.entry1 = """C2H6 C 2H 6 G 300.000 3000.000 650.73 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
self.entry2 = """CH3NO2X G 300.000 3000.000 650.73 1&
C 1 H 3 N 1 O 2 X 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
self.entry3 = """CH3NO2SX G 300.000 3000.000 650.73 1&
C 1 H 3 N 1 O 2 S 1 X 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
def test_write_thermo_block(self):
"""Test that we can write a normal thermo block"""
species = Species(smiles='CC')
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry1)
def test_read_thermo_block(self):
"""Test that we can read a normal thermo block"""
species, thermo, formula = read_thermo_entry(self.entry1)
self.assertEqual(species, 'C2H6')
self.assertEqual(formula, {'H': 6, 'C': 2})
self.assertTrue(self.nasa.is_identical_to(thermo))
def test_write_thermo_block_5_elem(self):
"""Test that we can write a thermo block for a species with 5 elements"""
species = Species().from_adjacency_list("""
1 O u0 p3 c-1 {3,S}
2 O u0 p2 c0 {3,D}
3 N u0 p0 c+1 {1,S} {2,D} {4,S}
4 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S}
5 H u0 p0 c0 {4,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 X u0 p0 c0
""")
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry2)
def test_read_thermo_block_5_elem(self):
"""Test that we can read a thermo block with 5 elements"""
species, thermo, formula = read_thermo_entry(self.entry2)
self.assertEqual(species, 'CH3NO2X')
self.assertEqual(formula, {'X': 1, 'C': 1, 'O': 2, 'H': 3, 'N': 1})
self.assertTrue(self.nasa.is_identical_to(thermo))
def test_write_thermo_block_6_elem(self):
"""Test that we can write a thermo block for a species with 6 elements"""
species = Species().from_adjacency_list("""
1 O u0 p3 c-1 {2,S}
2 N u0 p0 c+1 {1,S} {3,D} {4,S}
3 O u0 p2 c0 {2,D}
4 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S}
5 S u0 p2 c0 {4,S} {8,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {5,S}
9 X u0 p0 c0
""")
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry3)
def test_read_thermo_block_6_elem(self):
"""Test that we can read a thermo block with 6 elements"""
species, thermo, formula = read_thermo_entry(self.entry3)
self.assertEqual(species, 'CH3NO2SX')
self.assertEqual(formula, {
'X': 1,
'C': 1,
'O': 2,
'H': 3,
'N': 1,
'S': 1
})
self.assertTrue(self.nasa.is_identical_to(thermo))
def testParseThermoComments(self):
"""
Test that the ThermoDatabase.extractSourceFromComments function works properly
on various thermo comments.
"""
from rmgpy.thermo import NASA, NASAPolynomial
# Pure group additivity thermo
propane = Species(
index=3,
label="Propane",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
3.05257, 0.0125099, 3.79386e-05, -5.12022e-08,
1.87065e-11, -14454.2, 10.0672
],
Tmin=(100, 'K'),
Tmax=(986.57, 'K')),
NASAPolynomial(coeffs=[
5.91316, 0.0218763, -8.17661e-06, 1.49855e-09,
-1.05991e-13, -16038.9, -8.86555
],
Tmin=(986.57, '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)"""
),
molecule=[Molecule(SMILES="CCC")])
source = self.database.extractSourceFromComments(propane)
self.assertTrue(
'GAV' in source,
'Should have found that propane thermo source is GAV.')
self.assertEqual(len(source['GAV']['group']), 2)
self.assertEqual(len(source['GAV']['other']), 1)
self.assertEqual(len(source['GAV']['gauche']), 2)
# Pure library thermo
dipk = Species(index=1,
label="DIPK",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
3.35002, 0.017618, -2.46235e-05, 1.7684e-08,
-4.87962e-12, 35555.7, 5.75335
],
Tmin=(100, 'K'),
Tmax=(888.28, 'K')),
NASAPolynomial(coeffs=[
6.36001, 0.00406378, -1.73509e-06, 5.05949e-10,
-4.49975e-14, 35021, -8.41155
],
Tmin=(888.28, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment="""Thermo library: DIPK"""),
molecule=[Molecule(SMILES="CC(C)C(=O)C(C)C")])
source = self.database.extractSourceFromComments(dipk)
self.assertTrue('Library' in source)
# Mixed library and HBI thermo
dipk_rad = Species(
index=4,
label="R_tert",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
2.90061, 0.0298018, -7.06268e-05, 6.9636e-08, -2.42414e-11,
54431, 5.44492
],
Tmin=(100, 'K'),
Tmax=(882.19, 'K')),
NASAPolynomial(coeffs=[
6.70999, 0.000201027, 6.65617e-07, -7.99543e-11,
4.08721e-15, 54238.6, -9.73662
],
Tmin=(882.19, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment="""Thermo library: DIPK + radical(C2CJCHO)"""),
molecule=[
Molecule(SMILES="C[C](C)C(=O)C(C)C"),
Molecule(SMILES="CC(C)=C([O])C(C)C")
])
source = self.database.extractSourceFromComments(dipk_rad)
self.assertTrue('Library' in source)
self.assertTrue('GAV' in source)
self.assertEqual(len(source['GAV']['radical']), 1)
# Pure QM thermo
cineole = Species(
index=6,
label="Cineole",
thermo=NASA(polynomials=[
NASAPolynomial(coeffs=[
-0.324129, 0.0619667, 9.71008e-05, -1.60598e-07,
6.28285e-11, -38699.9, 29.3686
],
Tmin=(100, 'K'),
Tmax=(985.52, 'K')),
NASAPolynomial(coeffs=[
20.6043, 0.0586913, -2.22152e-05, 4.19949e-09,
-3.06046e-13, -46791, -91.4152
],
Tmin=(985.52, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment="""QM MopacMolPM3 calculation attempt 1"""),
molecule=[Molecule(SMILES="CC12CCC(CC1)C(C)(C)O2")])
source = self.database.extractSourceFromComments(cineole)
self.assertTrue('QM' in source)
# Mixed QM and HBI thermo
cineole_rad = Species(
index=7,
label="CineoleRad",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
-0.2897, 0.0627717, 8.63299e-05, -1.47868e-07,
5.81665e-11, -14017.6, 31.0266
],
Tmin=(100, 'K'),
Tmax=(988.76, 'K')),
NASAPolynomial(coeffs=[
20.4836, 0.0562555, -2.13903e-05, 4.05725e-09,
-2.96023e-13, -21915, -88.1205
],
Tmin=(988.76, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment=
"""QM MopacMolPM3 calculation attempt 1 + radical(Cs_P)"""),
molecule=[Molecule(SMILES="[CH2]C12CCC(CC1)C(C)(C)O2")])
source = self.database.extractSourceFromComments(cineole_rad)
self.assertTrue('QM' in source)
self.assertTrue('GAV' in source)
self.assertEqual(len(source['GAV']['radical']), 1)
# No thermo comments
other = Species(
index=7,
label="CineoleRad",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
-0.2897, 0.0627717, 8.63299e-05, -1.47868e-07,
5.81665e-11, -14017.6, 31.0266
],
Tmin=(100, 'K'),
Tmax=(988.76, 'K')),
NASAPolynomial(coeffs=[
20.4836, 0.0562555, -2.13903e-05, 4.05725e-09,
-2.96023e-13, -21915, -88.1205
],
Tmin=(988.76, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
),
molecule=[Molecule(SMILES="[CH2]C12CCC(CC1)C(C)(C)O2")])
# Function should complain if there's no thermo comments
self.assertRaises(self.database.extractSourceFromComments(cineole_rad))
# Check a dummy species that has plus and minus thermo group contributions
polycyclic = Species(
index=7,
label="dummy",
thermo=NASA(
polynomials=[
NASAPolynomial(coeffs=[
-0.2897, 0.0627717, 8.63299e-05, -1.47868e-07,
5.81665e-11, -14017.6, 31.0266
],
Tmin=(100, 'K'),
Tmax=(988.76, 'K')),
NASAPolynomial(coeffs=[
20.4836, 0.0562555, -2.13903e-05, 4.05725e-09,
-2.96023e-13, -21915, -88.1205
],
Tmin=(988.76, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment=
"""Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsCsHH) - ring(Benzene)"""
),
molecule=[Molecule(SMILES="[CH2]C12CCC(CC1)C(C)(C)O2")])
source = self.database.extractSourceFromComments(polycyclic)
self.assertTrue('GAV' in source)
self.assertEqual(source['GAV']['ring'][0][1],
-1) # the weight of benzene contribution should be -1
self.assertEqual(
source['GAV']['group'][0][1],
2) # weight of the group(Cs-CsCsHH) conbtribution should be 2
def test_solve_ch3(self):
"""
Test the surface batch reactor with a nondissociative adsorption of CH3
Here we choose a kinetic model consisting of the adsorption reaction
CH3 + X <=> CH3X
We use a sticking coefficient for the rate expression.
"""
ch3 = Species(
molecule=[Molecule().from_smiles("[CH3]")],
thermo=NASA(
polynomials=[
NASAPolynomial(
coeffs=[3.91547, 0.00184155, 3.48741e-06, -3.32746e-09, 8.49953e-13, 16285.6, 0.351743],
Tmin=(100, 'K'), Tmax=(1337.63, 'K')),
NASAPolynomial(
coeffs=[3.54146, 0.00476786, -1.82148e-06, 3.28876e-10, -2.22545e-14, 16224, 1.66032],
Tmin=(1337.63, 'K'), Tmax=(5000, 'K'))],
Tmin=(100, 'K'), Tmax=(5000, 'K'), E0=(135.382, 'kJ/mol'),
comment="""Thermo library: primaryThermoLibrary + radical(CH3)"""
),
molecular_weight=(15.0345, 'amu'),
)
x = Species(
molecule=[Molecule().from_adjacency_list("1 X u0 p0")],
thermo=NASA(polynomials=[NASAPolynomial(coeffs=[0, 0, 0, 0, 0, 0, 0], Tmin=(298, 'K'), Tmax=(1000, 'K')),
NASAPolynomial(coeffs=[0, 0, 0, 0, 0, 0, 0], Tmin=(1000, 'K'), Tmax=(2000, 'K'))],
Tmin=(298, 'K'), Tmax=(2000, 'K'), E0=(-6.19426, 'kJ/mol'),
comment="""Thermo library: surfaceThermo""")
)
ch3x = Species(
molecule=[Molecule().from_adjacency_list("1 H u0 p0 {2,S} \n 2 X u0 p0 {1,S}")],
thermo=NASA(
polynomials=[
NASAPolynomial(
coeffs=[-0.552219, 0.026442, -3.55617e-05, 2.60044e-08, -7.52707e-12, -4433.47, 0.692144],
Tmin=(298, 'K'), Tmax=(1000, 'K')),
NASAPolynomial(
coeffs=[3.62557, 0.00739512, -2.43797e-06, 1.86159e-10, 3.6485e-14, -5187.22, -18.9668],
Tmin=(1000, 'K'), Tmax=(2000, 'K'))],
Tmin=(298, 'K'), Tmax=(2000, 'K'), E0=(-39.1285, 'kJ/mol'),
comment="""Thermo library: surfaceThermo""")
)
rxn1 = Reaction(reactants=[ch3, x],
products=[ch3x],
kinetics=StickingCoefficient(
A=0.1, n=0, Ea=(0, 'kcal/mol'), T0=(1, 'K'), Tmin=(200, 'K'), Tmax=(3000, 'K'),
comment="""Exact match found for rate rule (Adsorbate;VacantSite)"""
)
# kinetics=SurfaceArrhenius(A=(2.7e10, 'cm^3/(mol*s)'),
# n=0.5,
# Ea=(5.0, 'kJ/mol'),
# T0=(1.0, 'K'))
)
core_species = [ch3, x, ch3x]
edge_species = []
core_reactions = [rxn1]
edge_reactions = []
T = 800.
P_initial = 1.0e5
rxn_system = SurfaceReactor(
T, P_initial,
n_sims=1,
initial_gas_mole_fractions={ch3: 1.0},
initial_surface_coverages={x: 1.0},
surface_volume_ratio=(1., 'm^-1'),
surface_site_density=(2.72e-9, 'mol/cm^2'),
termination=[])
# in chemkin, the sites are mostly occupied in about 1e-8 seconds.
rxn_system.initialize_model(core_species, core_reactions, edge_species, edge_reactions)
tlist = np.logspace(-13, -5, 81, dtype=np.float64)
print("Surface site density:", rxn_system.surface_site_density.value_si)
print("rxn1 rate coefficient",
rxn1.get_surface_rate_coefficient(rxn_system.T.value_si, rxn_system.surface_site_density.value_si))
# Integrate to get the solution at each time point
t = []
y = []
reaction_rates = []
species_rates = []
t.append(rxn_system.t)
# You must make a copy of y because it is overwritten by DASSL at
# each call to advance()
y.append(rxn_system.y.copy())
reaction_rates.append(rxn_system.core_reaction_rates.copy())
species_rates.append(rxn_system.core_species_rates.copy())
print("time: ", t)
print("moles:", y)
print("reaction rates:", reaction_rates)
print("species rates:", species_rates)
for t1 in tlist:
rxn_system.advance(t1)
t.append(rxn_system.t)
# You must make a copy of y because it is overwritten by DASSL at
# each call to advance()
y.append(rxn_system.y.copy())
reaction_rates.append(rxn_system.core_reaction_rates.copy())
species_rates.append(rxn_system.core_species_rates.copy())
# Convert the solution vectors to np arrays
t = np.array(t, np.float64)
y = np.array(y, np.float64)
reaction_rates = np.array(reaction_rates, np.float64)
species_rates = np.array(species_rates, np.float64)
V = constants.R * rxn_system.T.value_si * np.sum(y) / rxn_system.P_initial.value_si
# Check that we're computing the species fluxes correctly
for i in range(t.shape[0]):
self.assertAlmostEqual(reaction_rates[i, 0], -species_rates[i, 0],
delta=1e-6 * reaction_rates[i, 0])
self.assertAlmostEqual(reaction_rates[i, 0], -species_rates[i, 1],
delta=1e-6 * reaction_rates[i, 0])
self.assertAlmostEqual(reaction_rates[i, 0], species_rates[i, 2],
delta=1e-6 * reaction_rates[i, 0])
# Check that we've reached equilibrium by the end
self.assertAlmostEqual(reaction_rates[-1, 0], 0.0, delta=1e-2)
class TestThermoReadWrite(unittest.TestCase):
def setUp(self):
"""This method is run once before each test."""
coeffs_low = [
4.03055, -0.00214171, 4.90611e-05, -5.99027e-08, 2.38945e-11,
-11257.6, 3.5613
]
coeffs_high = [
-0.307954, 0.0245269, -1.2413e-05, 3.07724e-09, -3.01467e-13,
-10693, 22.628
]
Tmin = 300.
Tmax = 3000.
Tint = 650.73
E0 = -782292. # J/mol.
comment = "C2H6"
self.nasa = NASA(
polynomials=[
NASAPolynomial(coeffs=coeffs_low,
Tmin=(Tmin, "K"),
Tmax=(Tint, "K")),
NASAPolynomial(coeffs=coeffs_high,
Tmin=(Tint, "K"),
Tmax=(Tmax, "K")),
],
Tmin=(Tmin, "K"),
Tmax=(Tmax, "K"),
E0=(E0, "J/mol"),
comment=comment,
)
# Chemkin entries for testing - note that the values are all the same
self.entry1 = """C2H6 C 2H 6 G 300.000 3000.000 650.73 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
self.entry2 = """CH3NO2X G 300.000 3000.000 650.73 1&
C 1 H 3 N 1 O 2 X 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
self.entry3 = """CH3NO2SX G 300.000 3000.000 650.73 1&
C 1 H 3 N 1 O 2 S 1 X 1
-3.07954000E-01 2.45269000E-02-1.24130000E-05 3.07724000E-09-3.01467000E-13 2
-1.06930000E+04 2.26280000E+01 4.03055000E+00-2.14171000E-03 4.90611000E-05 3
-5.99027000E-08 2.38945000E-11-1.12576000E+04 3.56130000E+00 4
"""
def test_write_thermo_block(self):
"""Test that we can write a normal thermo block"""
species = Species(smiles='CC')
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry1)
def test_read_thermo_block(self):
"""Test that we can read a normal thermo block"""
species, thermo, formula = read_thermo_entry(self.entry1)
self.assertEqual(species, 'C2H6')
self.assertEqual(formula, {'H': 6, 'C': 2})
self.assertTrue(self.nasa.is_identical_to(thermo))
def test_write_thermo_block_5_elem(self):
"""Test that we can write a thermo block for a species with 5 elements"""
species = Species().from_adjacency_list("""
1 O u0 p3 c-1 {3,S}
2 O u0 p2 c0 {3,D}
3 N u0 p0 c+1 {1,S} {2,D} {4,S}
4 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S}
5 H u0 p0 c0 {4,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 X u0 p0 c0
""")
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry2)
def test_read_thermo_block_5_elem(self):
"""Test that we can read a thermo block with 5 elements"""
species, thermo, formula = read_thermo_entry(self.entry2)
self.assertEqual(species, 'CH3NO2X')
self.assertEqual(formula, {'X': 1, 'C': 1, 'O': 2, 'H': 3, 'N': 1})
self.assertTrue(self.nasa.is_identical_to(thermo))
def test_write_thermo_block_6_elem(self):
"""Test that we can write a thermo block for a species with 6 elements"""
species = Species().from_adjacency_list("""
1 O u0 p3 c-1 {2,S}
2 N u0 p0 c+1 {1,S} {3,D} {4,S}
3 O u0 p2 c0 {2,D}
4 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S}
5 S u0 p2 c0 {4,S} {8,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {5,S}
9 X u0 p0 c0
""")
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry3)
def test_read_thermo_block_6_elem(self):
"""Test that we can read a thermo block with 6 elements"""
species, thermo, formula = read_thermo_entry(self.entry3)
self.assertEqual(species, 'CH3NO2SX')
self.assertEqual(formula, {
'X': 1,
'C': 1,
'O': 2,
'H': 3,
'N': 1,
'S': 1
})
self.assertTrue(self.nasa.is_identical_to(thermo))
def test_write_bidentate_species(self):
"""Test that species with 2 or more surface sites get proper formatting"""
folder = os.path.join(os.path.dirname(rmgpy.__file__),
'test_data/chemkin/chemkin_py')
chemkin_path = os.path.join(folder, 'surface', 'chem-surface.inp')
dictionary_path = os.path.join(folder, 'surface',
'species_dictionary.txt')
chemkin_save_path = os.path.join(folder, 'surface',
'chem-surface-test.inp')
species, reactions = load_chemkin_file(chemkin_path, dictionary_path)
surface_atom_count = species[3].molecule[0].get_num_atoms('X')
self.assertEqual(surface_atom_count, 3)
save_chemkin_surface_file(chemkin_save_path,
species,
reactions,
verbose=False,
check_for_duplicates=False)
bidentate_test = " CH2OX2(52)/2/ \n"
tridentate_test = " CHOX3(61)/3/ \n"
with open(chemkin_save_path, "r") as f:
for i, line in enumerate(f):
if i == 3:
bidentate_read = line
if i == 4:
tridentate_read = line
self.assertEqual(bidentate_test.strip(), bidentate_read.strip())
self.assertEqual(tridentate_test.strip(), tridentate_read.strip())
os.remove(chemkin_save_path)
