Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Enable fitting and reversing of negative reaction rates. #1834

Merged
merged 5 commits into from
Dec 6, 2019
Merged

Enable fitting and reversing of negative reaction rates. #1834

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
0d9046a
Added test_generate_reverse_rate_coefficient to MultiPDepArrhenius
rwest Nov 30, 2019
c49521f
Switch from numpy to scipy for linalg.lstsq
rwest Dec 1, 2019
8a010f6
Allow Arrhenius fitting of negative rates.
rwest Dec 1, 2019
b0d62f5
Revert "Switch from numpy to scipy for linalg.lstsq"
rwest Dec 1, 2019
523cf48
Added test for Arrhenius.fit_to_data on negative rates.
rwest Dec 1, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 10 additions & 1 deletion rmgpy/kinetics/arrhenius.pyx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -152,6 +152,15 @@ cdef class Arrhenius(KineticsModel):
data.
"""
import scipy.stats
if not all(np.isfinite(klist)):
raise ValueError("Rates must all be finite, not inf or NaN")
if any(klist<0):
if not all(klist<0):
raise ValueError("Rates must all be positive or all be negative.")
rate_sign_multiplier = -1
klist = -1 * klist
else:
rate_sign_multiplier = 1

assert len(Tlist) == len(klist), "length of temperatures and rates must be the same"
if len(Tlist) < 3 + three_params:
Expand Down Expand Up @@ -181,7 +190,7 @@ cdef class Arrhenius(KineticsModel):
x = np.array([x[0], 0, x[1]])
cov = np.array([[cov[0, 0], 0, cov[0, 1]], [0, 0, 0], [cov[1, 0], 0, cov[1, 1]]])

self.A = (exp(x[0]), kunits)
self.A = (rate_sign_multiplier * exp(x[0]), kunits)
self.n = x[1]
self.Ea = (x[2] * 0.001, "kJ/mol")
self.T0 = (T0, "K")
Expand Down
48 changes: 48 additions & 0 deletions rmgpy/kinetics/arrheniusTest.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -158,6 +158,21 @@ def test_fit_to_data(self):
self.assertAlmostEqual(arrhenius.Ea.value_si, self.arrhenius.Ea.value_si, 2)
self.assertAlmostEqual(arrhenius.T0.value_si, self.arrhenius.T0.value_si, 4)

def test_fit_to_negative_data(self):
"""
Test the Arrhenius.fit_to_data() method on negative rates
"""
Tdata = np.array([300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500])
kdata = np.array([-1 * self.arrhenius.get_rate_coefficient(T) for T in Tdata])
arrhenius = Arrhenius().fit_to_data(Tdata, kdata, kunits="m^3/(mol*s)")
self.assertEqual(float(self.arrhenius.T0.value_si), 1)
for T, k in zip(Tdata, kdata):
self.assertAlmostEqual(k, arrhenius.get_rate_coefficient(T), delta=1e-6 * abs(k))
self.assertAlmostEqual(arrhenius.A.value_si, -1 * self.arrhenius.A.value_si, delta=1e0)
self.assertAlmostEqual(arrhenius.n.value_si, self.arrhenius.n.value_si, 1, 4)
self.assertAlmostEqual(arrhenius.Ea.value_si, self.arrhenius.Ea.value_si, 2)
self.assertAlmostEqual(arrhenius.T0.value_si, self.arrhenius.T0.value_si, 4)

def test_pickle(self):
"""
Test that an Arrhenius object can be pickled and unpickled with no loss
Expand Down Expand Up @@ -1020,3 +1035,36 @@ def test_change_rate(self):
for T, kexp in zip(Tlist, k0list):
kact = self.kinetics.get_rate_coefficient(T, 1e5)
self.assertAlmostEqual(2 * kexp, kact, delta=1e-6 * kexp)

def test_generate_reverse_rate_coefficient(self):
"""
Test ability to reverse a reaction rate.

This is a real example from an imported chemkin file.
"""
from rmgpy.species import Species
from rmgpy.molecule import Molecule
from rmgpy.data.kinetics import LibraryReaction
from rmgpy.thermo import NASA, NASAPolynomial
test_reaction = LibraryReaction(reactants=[Species(label="C2H3", thermo=NASA(polynomials=[NASAPolynomial(coeffs=[3.12502,0.00235137,2.36803e-05,-3.35092e-08,1.39444e-11,34524.3,8.81538], Tmin=(200,"K"), Tmax=(1000,"K")), NASAPolynomial(coeffs=[4.37211,0.00746869,-2.64716e-06,4.22753e-10,-2.44958e-14,33805.2,0.428772], Tmin=(1000,"K"), Tmax=(6000,"K"))], Tmin=(200,"K"), Tmax=(6000,"K"), E0=(285.696,"kJ/mol"), Cp0=(33.2579,"J/mol/K"), CpInf=(108.088,"J/mol/K"), comment="""ATcT3E\nC2H3 <g> ATcT ver. 1.122, DHf298 = 296.91 ± 0.33 kJ/mol - fit JAN17"""), molecule=[Molecule(smiles="[CH]=C")], molecular_weight=(27.0452,"amu")),
Species(label="CH2O", thermo=NASA(polynomials=[NASAPolynomial(coeffs=[4.77187,-0.00976266,3.70122e-05,-3.76922e-08,1.31327e-11,-14379.8,0.696586], Tmin=(200,"K"), Tmax=(1000,"K")), NASAPolynomial(coeffs=[2.91333,0.0067004,-2.55521e-06,4.27795e-10,-2.44073e-14,-14462.2,7.43823], Tmin=(1000,"K"), Tmax=(6000,"K"))], Tmin=(200,"K"), Tmax=(6000,"K"), E0=(-119.527,"kJ/mol"), Cp0=(33.2579,"J/mol/K"), CpInf=(83.1447,"J/mol/K"), comment="""ATcT3E\nH2CO <g> ATcT ver. 1.122, DHf298 = -109.188 ± 0.099 kJ/mol - fit JAN17"""), molecule=[Molecule(smiles="C=O")], molecular_weight=(30.026,"amu"))],
products=[Species(label="C2H4", thermo=NASA(polynomials=[NASAPolynomial(coeffs=[3.65151,-0.00535067,5.16486e-05,-6.36869e-08,2.50743e-11,5114.51,5.38561], Tmin=(200,"K"), Tmax=(1000,"K")), NASAPolynomial(coeffs=[4.14446,0.0102648,-3.61247e-06,5.74009e-10,-3.39296e-14,4190.59,-1.14778], Tmin=(1000,"K"), Tmax=(6000,"K"))], Tmin=(200,"K"), Tmax=(6000,"K"), E0=(42.06,"kJ/mol"), Cp0=(33.2579,"J/mol/K"), CpInf=(133.032,"J/mol/K"), comment="""ATcT3E\nC2H4 <g> ATcT ver. 1.122, DHf298 = 52.45 ± 0.13 kJ/mol - fit JAN17"""), molecule=[Molecule(smiles="C=C")], molecular_weight=(28.0532,"amu")),
Species(label="HCO", thermo=NASA(polynomials=[NASAPolynomial(coeffs=[3.97075,-0.00149122,9.54042e-06,-8.8272e-09,2.67645e-12,3842.03,4.4466], Tmin=(200,"K"), Tmax=(1000,"K")), NASAPolynomial(coeffs=[3.85781,0.00264114,-7.44177e-07,1.23313e-10,-8.88959e-15,3616.43,3.92451], Tmin=(1000,"K"), Tmax=(6000,"K"))], Tmin=(200,"K"), Tmax=(6000,"K"), E0=(32.0237,"kJ/mol"), Cp0=(33.2579,"J/mol/K"), CpInf=(58.2013,"J/mol/K"), comment="""HCO <g> ATcT ver. 1.122, DHf298 = 41.803 ± 0.099 kJ/mol - fit JAN17"""), molecule=[Molecule(smiles="[CH]=O")], molecular_weight=(29.018,"amu"))],
kinetics=MultiPDepArrhenius(arrhenius=[PDepArrhenius(pressures=([0.001,0.01,0.1,1,10,100,1000],"atm"),
arrhenius=[Arrhenius(A=(1.1e+07,"cm^3/(mol*s)"), n=1.09, Ea=(1807,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(2.5e+07,"cm^3/(mol*s)"), n=0.993, Ea=(1995,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(2.5e+08,"cm^3/(mol*s)"), n=0.704, Ea=(2596,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(1.4e+10,"cm^3/(mol*s)"), n=0.209, Ea=(3934,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(3.5e+13,"cm^3/(mol*s)"), n=-0.726, Ea=(6944,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(3.3e+14,"cm^3/(mol*s)"), n=-0.866, Ea=(10966,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(17,"cm^3/(mol*s)"), n=3.17, Ea=(9400,"cal/mol"), T0=(1,"K"))]),
PDepArrhenius(pressures=([0.001,0.01,0.1,1,10,100,1000],"atm"),
arrhenius=[Arrhenius(A=(-2.3e+16,"cm^3/(mol*s)"), n=-1.269, Ea=(20617,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(-5.2e+16,"cm^3/(mol*s)"), n=-1.366, Ea=(20805,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(-1.5e+18,"cm^3/(mol*s)"), n=-1.769, Ea=(22524,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(-8.5e+19,"cm^3/(mol*s)"), n=-2.264, Ea=(23862,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(-4.4e+23,"cm^3/(mol*s)"), n=-3.278, Ea=(27795,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(-4.2e+24,"cm^3/(mol*s)"), n=-3.418, Ea=(31817,"cal/mol"), T0=(1,"K")),
Arrhenius(A=(-2.1e+11,"cm^3/(mol*s)"), n=0.618, Ea=(30251,"cal/mol"), T0=(1,"K"))])
]), duplicate=True)
test_reaction.generate_reverse_rate_coefficient()