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Allow ArrheniusBM Fitting up to 2000K for RMG-database Rate Trees #2243

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Merged
davidfarinajr merged 2 commits into from
Dec 11, 2021
+129 −2
Merged

Allow ArrheniusBM Fitting up to 2000K for RMG-database Rate Trees #2243

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734e253
Add 2000K to the default list of temperatures for fitting
kspieks Dec 9, 2021
008d3eb
Add unit test for ArrheniusBM
kspieks Dec 10, 2021
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2 changes: 1 addition & 1 deletion rmgpy/kinetics/arrhenius.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -591,7 +591,7 @@ cdef class ArrheniusBM(KineticsModel):
assert w0 is not None or recipe is not None, 'either w0 or recipe must be specified'

if Ts is None:
Ts = [300.0, 500.0, 600.0, 700.0, 800.0, 900.0, 1000.0, 1100.0, 1200.0, 1500.0]
Ts = [300.0, 500.0, 600.0, 700.0, 800.0, 900.0, 1000.0, 1100.0, 1200.0, 1500.0, 2000.0]
if w0 is None:
#estimate w0
w0s = get_w0s(recipe, rxns)
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129 changes: 128 additions & 1 deletion rmgpy/kinetics/arrheniusTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,11 @@
import numpy as np

import rmgpy.constants as constants
from rmgpy.kinetics.arrhenius import Arrhenius, ArrheniusEP, PDepArrhenius, MultiArrhenius, MultiPDepArrhenius
from rmgpy.kinetics.arrhenius import Arrhenius, ArrheniusEP, ArrheniusBM, PDepArrhenius, MultiArrhenius, MultiPDepArrhenius
from rmgpy.molecule.molecule import Molecule
from rmgpy.reaction import Reaction
from rmgpy.species import Species
from rmgpy.thermo import NASA, NASAPolynomial


################################################################################
Expand Down Expand Up @@ -404,6 +408,129 @@ def test_change_rate(self):
self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)


################################################################################

class TestArrheniusBM(unittest.TestCase):
"""
Contains unit tests of the :class:`ArrheniusBM` class.
"""

def setUp(self):
"""
A function run before each unit test in this class.
"""
self.A = 8.00037e+12
self.n = 0.391734
self.w0 = 798000
self.E0 = 115905
self.Tmin = 300.
self.Tmax = 2000.
self.comment = 'rxn001084'
self.arrhenius_bm = ArrheniusBM(
A=(self.A, "s^-1"),
n=self.n,
w0=(self.w0, 'J/mol'),
E0=(self.E0, "J/mol"),
Tmin=(self.Tmin, "K"),
Tmax=(self.Tmax, "K"),
comment=self.comment,
)

self.rsmi = 'NC(=NC=O)O'
self.psmi = 'O=CNC(=O)N'
self.arrhenius = Arrhenius(A=(8.00037e+12,'s^-1'),
n=0.391734,
Ea=(94.5149,'kJ/mol'),
T0=(1,'K'),
Tmin=(300,'K'),
Tmax=(2000,'K'),
comment="""Fitted to 50 data points; dA = *|/ 1.18377, dn = +|- 0.0223855, dEa = +|- 0.115431 kJ/mol"""
)

self.r_thermo = NASA(polynomials=[
NASAPolynomial(coeffs=[3.90453,0.0068491,0.000125755,-2.92973e-07,2.12971e-10,-45444.2,10.0669], Tmin=(10,'K'), Tmax=(433.425,'K')),
NASAPolynomial(coeffs=[2.09778,0.0367646,-2.36023e-05,7.24527e-09,-8.51275e-13,-45412,15.8381], Tmin=(433.425,'K'), Tmax=(3000,'K'))],
Tmin=(10,'K'), Tmax=(3000,'K'), E0=(-377.851,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(232.805,'J/(mol*K)'),
comment="""Thermo library: Spiekermann_refining_elementary_reactions"""
)
self.p_thermo = NASA(polynomials=[
NASAPolynomial(coeffs=[3.88423,0.00825528,0.000133399,-3.31802e-07,2.52823e-10,-51045.1,10.3937], Tmin=(10,'K'), Tmax=(428.701,'K')),
NASAPolynomial(coeffs=[2.89294,0.0351772,-2.26349e-05,7.00331e-09,-8.2982e-13,-51122.5,12.4424], Tmin=(428.701,'K'), Tmax=(3000,'K'))],
Tmin=(10,'K'), Tmax=(3000,'K'), E0=(-424.419,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(232.805,'J/(mol*K)'),
comment="""Thermo library: Spiekermann_refining_elementary_reactions"""
)

def test_a_factor(self):
"""
Test that the ArrheniusBM A property was properly set.
"""
self.assertAlmostEqual(self.arrhenius_bm.A.value_si, self.A, delta=1e0)

def test_n(self):
"""
Test that the ArrheniusBM n property was properly set.
"""
self.assertAlmostEqual(self.arrhenius_bm.n.value_si, self.n, 6)

def test_w0(self):
"""
Test that the ArrheniusBM w0 property was properly set.
"""
self.assertAlmostEqual(self.arrhenius_bm.w0.value_si, self.w0, 6)

def test_e0(self):
"""
Test that the ArrheniusBM E0 property was properly set.
"""
self.assertAlmostEqual(self.arrhenius_bm.E0.value_si, self.E0, 6)

def test_temperature_min(self):
"""
Test that the ArrheniusBM Tmin property was properly set.
"""
self.assertAlmostEqual(self.arrhenius_bm.Tmin.value_si, self.Tmin, 6)

def test_temperature_max(self):
"""
Test that the ArrheniusBM Tmax property was properly set.
"""
self.assertAlmostEqual(self.arrhenius_bm.Tmax.value_si, self.Tmax, 6)

def test_is_temperature_valid(self):
"""
Test the ArrheniusBM.is_temperature_valid() method.
"""
Tdata = np.array([200, 400, 600, 800, 1000, 1200, 1400, 1600, 1800, 2000])
validdata = np.array([False, True, True, True, True, True, True, True, True, True], np.bool)
for T, valid in zip(Tdata, validdata):
valid0 = self.arrhenius_bm.is_temperature_valid(T)
self.assertEqual(valid0, valid)

def test_fit_to_data(self):
"""
Test the ArrheniusBM.fit_to_data() method.
"""
reactant = Molecule(smiles=self.rsmi)
product = Molecule(smiles=self.psmi)
reaction = Reaction(reactants=[Species(molecule=[reactant], thermo=self.r_thermo,)],
products=[Species(molecule=[product], thermo=self.p_thermo)],
kinetics=self.arrhenius,
)

arrhenius_bm = ArrheniusBM().fit_to_reactions([reaction], w0=self.w0)
self.assertAlmostEqual(arrhenius_bm.A.value_si, self.arrhenius_bm.A.value_si, delta=1.5e1)
self.assertAlmostEqual(arrhenius_bm.n.value_si, self.arrhenius_bm.n.value_si, 1, 4)
self.assertAlmostEqual(arrhenius_bm.E0.value_si, self.arrhenius_bm.E0.value_si, 1)

def test_get_activation_energy(self):
"""
Test the ArrheniusBM.get_activation_energy() method.
"""
Hrxn = -44000 # J/mol
Ea = self.arrhenius_bm.get_activation_energy(Hrxn)
self.assertAlmostEqual(Ea, 95074, delta=1e1)


################################################################################

class TestPDepArrhenius(unittest.TestCase):
Expand Down