modifed arrbm fit_to_data unit test

Test now compares the fitted rate to the rate it was trained on to make sure they agree.

rmgpy/kinetics/arrheniusTest.py

@@ -41,7 +41,7 @@
 from rmgpy.molecule.molecule import Molecule
 from rmgpy.reaction import Reaction
 from rmgpy.species import Species
-from rmgpy.thermo import NASA, NASAPolynomial
+from rmgpy.thermo import NASA, NASAPolynomial, ThermoData
 
 
 ################################################################################
@@ -460,6 +460,42 @@ def setUp(self):
             comment="""Thermo library: Spiekermann_refining_elementary_reactions"""
             )
 
+        CF2 = Species().from_adjacency_list(
+            """
+            1 F u0 p3 c0 {2,S}
+            2 C u0 p1 c0 {1,S} {3,S}
+            3 F u0 p3 c0 {2,S}
+            """
+        )
+        CF2.thermo = NASA(
+            polynomials=[
+                    NASAPolynomial(coeffs=[2.28591,0.0107608,-1.05382e-05,4.89881e-09,-8.86384e-13,-24340.7,13.1348], Tmin=(298,'K'), Tmax=(1300,'K')), 
+                    NASAPolynomial(coeffs=[5.33121,0.00197748,-9.60248e-07,2.10704e-10,-1.5954e-14,-25190.9,-2.56367], Tmin=(1300,'K'), Tmax=(3000,'K'))
+                ], 
+                Tmin=(298,'K'), Tmax=(3000,'K'), Cp0=(33.2579,'J/mol/K'), CpInf=(58.2013,'J/mol/K'),
+                comment="""Thermo library: halogens"""
+            )
+        C2H6 = Species(smiles="CC")
+        C2H6.thermo = ThermoData(
+            Tdata = ([300,400,500,600,800,1000,1500],'K'),
+            Cpdata = ([12.565,15.512,18.421,21.059,25.487,28.964,34.591],'cal/(mol*K)','+|-',[0.8,1.1,1.3,1.4,1.5,1.5,1.2]),
+            H298 = (-20.028,'kcal/mol','+|-',0.1),
+            S298 = (54.726,'cal/(mol*K)','+|-',0.6),
+            comment="""Thermo library: DFT_QCI_thermo"""
+            )
+        CH3CF2CH3 = Species(smiles="CC(F)(F)C")
+        CH3CF2CH3.thermo = NASA(
+            polynomials = [
+                NASAPolynomial(coeffs=[3.89769,0.00706735,0.000140168,-3.37628e-07,2.51812e-10,-68682.1,8.74321], Tmin=(10,'K'), Tmax=(436.522,'K')),
+                NASAPolynomial(coeffs=[2.78849,0.0356982,-2.16715e-05,6.45057e-09,-7.47989e-13,-68761.2,11.1597], Tmin=(436.522,'K'), Tmax=(3000,'K')),
+            ],
+            Tmin = (10,'K'), Tmax = (3000,'K'), Cp0 = (33.2579,'J/(mol*K)'), CpInf = (249.434,'J/(mol*K)'),
+            comment="""Thermo library: CHOF_G4"""
+            )
+        kinetics = Arrhenius(A=(0.222791,'cm^3/(mol*s)'), n=3.59921, Ea=(320.496,'kJ/mol'), T0=(1,'K'), Tmin=(298,'K'), Tmax=(2500,'K'), comment="""Training Rxn 54 for 1,2_Insertion_carbene""")
+        self.reaction = Reaction(reactants=[CF2,C2H6],products=[CH3CF2CH3],kinetics=kinetics)
+        self.reaction_w0 = 519000 # J/mol
+
     def test_a_factor(self):
         """
         Test that the ArrheniusBM A property was properly set.
@@ -510,17 +546,26 @@ def test_fit_to_data(self):
         """
         Test the ArrheniusBM.fit_to_data() method.
         """
+        Tdata = np.array([300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500])
+
         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,
                             )
-
+        kdata = np.array([reaction.kinetics.get_rate_coefficient(T) for T in Tdata])
         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)
+        arrhenius = arrhenius_bm.to_arrhenius(reaction.get_enthalpy_of_reaction(298))
+        for T, k in zip(Tdata, kdata):
+            self.assertAlmostEqual(k, arrhenius.get_rate_coefficient(T), delta=1e-6 * k)
+
+        # A second check, with a different reaction
+        arrhenius_bm = ArrheniusBM().fit_to_reactions([self.reaction], w0=self.reaction_w0)
+        arrhenius = arrhenius_bm.to_arrhenius(self.reaction.get_enthalpy_of_reaction(298))
+        kdata = np.array([self.reaction.kinetics.get_rate_coefficient(T) for T in Tdata])
+        for T, k in zip(Tdata, kdata):
+            self.assertAlmostEqual(k, arrhenius.get_rate_coefficient(T), delta=1e-6 * k)
 
     def test_get_activation_energy(self):
         """
@@ -1201,3 +1246,8 @@ def test_generate_reverse_rate_coefficient(self):
                                                                                                         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()
+
+################################################################################
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))