Add uncertainty tests for correlated library match

Add some tests to make sure the correct index is referenced when assembling thermo sources that use libraries. For example, if CH3 is estimated from a CH4 library + a radical correction, we want to make sure the uncertainty source points to CH4 as the index for the library value used (as opposed to CH3)

Author: sevyharris

test/rmgpy/tools/uncertaintyTest.py

@@ -237,6 +237,54 @@ def test_uncertainty_assignment(self):
         assert np.isclose(thermo_covariance, expected_uncorrelated_thermo_uncertainties, rtol=1e-4).all()
         assert np.isclose(kinetic_covariance, expected_uncorrelated_kinetic_uncertainties, rtol=1e-4).all()
 
+    def test_source_correlations(self):
+        # Check some examples of different species containing the same sources
+
+        # ------------------------------------------------------------------------------
+        # Make sure CH3 (Library + Radical) has a library index/value in common with CH4
+        i_CH4 = rmgpy.tools.uncertainty.get_i_thing(rmgpy.species.Species(smiles='C'), self.uncertainty.species_list)
+        assert i_CH4 >= 0
+
+        i_CH3 = rmgpy.tools.uncertainty.get_i_thing(rmgpy.species.Species(smiles='[CH3]'), self.uncertainty.species_list)
+        assert i_CH3 >= 0
+
+        self.uncertainty.extract_sources_from_model()
+        self.uncertainty.assign_parameter_uncertainties(correlated=True)
+
+        src1 = self.uncertainty.species_sources_dict[self.uncertainty.species_list[i_CH4]]  # CH4
+        src2 = self.uncertainty.species_sources_dict[self.uncertainty.species_list[i_CH3]]  # CH3
+
+        assert 'Library' in src1
+        assert 'Library' in src2
+        assert 'GAV' in src2
+        assert src1['Library'] == src2['Library']  # make sure they refer to the same library source
+
+        # -----------------------------------------------------------------------------
+        # Make sure CH3X (Library + GAV + Adsorption Correction) has a library index/value in common with CH4 (Library)
+        i_CH3X = rmgpy.tools.uncertainty.get_i_thing(rmgpy.species.Species(smiles='C*'), self.uncertainty.species_list)
+        assert i_CH3X == -1
+        # This is not in the model, so add it to the species list
+        CH3X = rmgpy.species.Species(smiles='C*')
+        CH3X.thermo = self.uncertainty.database.thermo.get_thermo_data(CH3X)
+        self.uncertainty.species_list.append(CH3X)
+        try:
+            i_CH3X = rmgpy.tools.uncertainty.get_i_thing(CH3X, self.uncertainty.species_list)
+            assert i_CH3X >= 0
+
+            self.uncertainty.extract_sources_from_model()
+            self.uncertainty.assign_parameter_uncertainties(correlated=True)
+
+            src1 = self.uncertainty.species_sources_dict[self.uncertainty.species_list[i_CH4]]  # CH4
+            src2 = self.uncertainty.species_sources_dict[self.uncertainty.species_list[i_CH3X]]  # CH3X
+
+            assert 'Library' in src1
+            assert 'Library' in src2
+            assert 'ADS' in src2
+            assert 'GAV' in src2
+            assert src1['Library'] == src2['Library']  # make sure they refer to the same library source
+        finally:
+            self.uncertainty.species_list.pop()  # remove the extra species so it doesn't affect other tests
+
     def test_local_analysis(self):
         """
         Test to run uncorrelated and then correlated local_analysis and make sure the results are expected