Merge pull request #1630 from ReactionMechanismGenerator/bugfix_nasa_…

…as_dict Bugfix nasa as dict
ReactionMechanismGenerator · Jun 25, 2019 · 4fab586 · 4fab586
2 parents 93fac25 + 18a916f
commit 4fab586
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diff --git a/arkane/inputTest.py b/arkane/inputTest.py
@@ -43,6 +43,8 @@
 from rmgpy.statmech.rotation import NonlinearRotor
 from rmgpy.kinetics.tunneling import Eckart
 from rmgpy.exceptions import InputError
+from rmgpy.thermo.nasa import NASAPolynomial, NASA
+from rmgpy.molecule import Molecule
 
 from arkane.input import species, transitionState, reaction, SMILES, loadInputFile, process_model_chemistry
 
@@ -81,6 +83,37 @@ def test_species(self):
         self.assertIsInstance(spc0.transportData, TransportData)
         self.assertIsInstance(spc0.energyTransferModel, SingleExponentialDown)
 
+    def test_species_atomic_NASA_polynomial(self):
+        """
+        Test loading a atom with NASA polynomials
+        """
+        label0 = "H(1)"
+        kwargs = {"structure": SMILES('[H]'),
+                  "thermo": NASA(polynomials=[NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683], Tmin=(200, 'K'), Tmax=(1000, 'K')),
+                                              NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683], Tmin=(1000, 'K'), Tmax=(6000, 'K'))],
+                                 Tmin=(200, 'K'), Tmax=(6000, 'K'), comment="""Thermo library: FFCM1(-)"""),
+                  "energyTransferModel": SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'), T0=(300, 'K'), n=0.85)}
+        spc0 = species(label0, **kwargs)
+        self.assertEqual(spc0.label, label0)
+        self.assertEqual(spc0.SMILES, '[H]')
+        self.assertTrue(spc0.hasStatMech())
+        self.assertEqual(spc0.thermo, kwargs['thermo'])
+
+    def test_species_polyatomic_NASA_polynomial(self):
+        """
+        Test loading a species with NASA polynomials
+        """
+        label0 = "benzyl"
+        kwargs = {"structure": SMILES('[c]1ccccc1'),
+                  "thermo": NASA(polynomials=[NASAPolynomial(coeffs=[2.78632, 0.00784632, 7.97887e-05, -1.11617e-07, 4.39429e-11, 39695, 11.5114], Tmin=(100, 'K'), Tmax=(943.73, 'K')),
+                                              NASAPolynomial(coeffs=[13.2455, 0.0115667, -2.49996e-06, 4.66496e-10, -4.12376e-14, 35581.1, -49.6793], Tmin=(943.73, 'K'), Tmax=(5000, 'K'))],
+                                 Tmin=(100, 'K'), Tmax=(5000, 'K'), comment="""Thermo library: Fulvene_H + radical(CbJ)"""),
+                  "energyTransferModel": SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'), T0=(300, 'K'), n=0.85)}
+        spc0 = species(label0, **kwargs)
+        self.assertEqual(spc0.label, label0)
+        self.assertTrue(spc0.hasStatMech())
+        self.assertEqual(spc0.thermo, kwargs['thermo'])
+
     def test_transitionState(self):
         """
         Test loading a transition state from input file-like kew word arguments

diff --git a/rmgpy/thermo/nasa.pyx b/rmgpy/thermo/nasa.pyx
@@ -256,11 +256,16 @@ cdef class NASA(HeatCapacityModel):
                     poly_dict[key]['coeffs'] = poly.coeffs.tolist()
             i = i + 1
         output_dict['polynomials'] = poly_dict
-        output_dict['Tmin'] = self.Tmin.as_dict()
-        output_dict['Tmax'] = self.Tmax.as_dict()
-        output_dict['E0'] = self.E0.as_dict()
-        output_dict['Cp0'] = self.Cp0.as_dict()
-        output_dict['CpInf'] = self.CpInf.as_dict()
+        if self.Tmin:
+            output_dict['Tmin'] = self.Tmin.as_dict()
+        if self.Tmax:
+            output_dict['Tmax'] = self.Tmax.as_dict()
+        if self.E0:
+            output_dict['E0'] = self.E0.as_dict()
+        if self.Cp0:
+            output_dict['Cp0'] = self.Cp0.as_dict()
+        if self.CpInf:
+            output_dict['CpInf'] = self.CpInf.as_dict()
         if self.label != '':
             output_dict['label'] = self.label
         if self.comment != '':

diff --git a/rmgpy/thermo/nasaTest.py b/rmgpy/thermo/nasaTest.py
@@ -285,3 +285,33 @@ def testToNASA(self):
         self.assertEqual(wilhoit.comment,nasa.comment)
 
         # nasa to wilhoi performed in wilhoitTest
+
+    def test_nasa_as_dict_full(self):
+        """
+        Test that NASA.as_dict functions properly with all attributes
+        """
+        nasa_dict = self.nasa.as_dict()
+        self.assertEqual(nasa_dict['E0']['value'], self.E0)
+        self.assertEqual(nasa_dict['Tmin']['value'], self.Tmin)
+        self.assertEqual(nasa_dict['Tmax']['value'], self.Tmax)
+        self.assertEqual(nasa_dict['comment'], self.comment)
+        self.assertTupleEqual(tuple(nasa_dict['polynomials']['polynomial1']['coeffs']), tuple(self.coeffs_low))
+        self.assertTupleEqual(tuple(nasa_dict['polynomials']['polynomial2']['coeffs']), tuple(self.coeffs_high))
+        self.assertEqual(nasa_dict['polynomials']['polynomial1']['Tmin']['value'], self.Tmin)
+        self.assertEqual(nasa_dict['polynomials']['polynomial1']['Tmax']['value'], self.Tint)
+        self.assertEqual(nasa_dict['polynomials']['polynomial2']['Tmin']['value'], self.Tint)
+        self.assertEqual(nasa_dict['polynomials']['polynomial2']['Tmax']['value'], self.Tmax)
+
+    def test_nasa_as_dict_minimal(self):
+        """
+        Test that NASA.as_dict does not contain empty, optional attributes
+        """
+        nasa_dict = NASA().as_dict()
+        keys = nasa_dict.keys()
+        self.assertNotIn('Tmin', keys)
+        self.assertNotIn('Tmax', keys)
+        self.assertNotIn('E0', keys)
+        self.assertNotIn('Cp0', keys)
+        self.assertNotIn('CpInf', keys)
+        self.assertNotIn('label', keys)
+        self.assertNotIn('comment', keys)