[ck2cti] Improve handling of duplicate species

Warn when a species is given multiple times in the input list. Do not add the
duplicate species to speciesList.

Resolves Issue 199.

interfaces/cython/cantera/ck2cti.py

@@ -1395,10 +1395,11 @@ class Parser(object):
                             break
                         if token in self.speciesDict:
                             species = self.speciesDict[token]
+                            self.warn('Found additional declaration of species {0}'.format(species))
                         else:
                             species = Species(label=token)
                             self.speciesDict[token] = species
-                        self.speciesList.append(species)
+                            self.speciesList.append(species)
 
                 elif tokens[0].upper().startswith('THER') and contains(line, 'NASA9'):
                     entryPosition = 0

interfaces/cython/cantera/test/test_convert.py

@@ -113,6 +113,19 @@ class chemkinConverterTest(utilities.CanteraTest):
         self.assertTrue(gas.n_species, 3)
         self.assertTrue(gas.n_reactions, 2)
 
+    def test_duplicate_species(self):
+        self.assertRaises(ck2cti.InputParseError,
+                          lambda: convertMech('../data/duplicate-species.inp',
+                                              outName='duplicate-species.cti',
+                                              quiet=True))
+
+        convertMech('../data/duplicate-species.inp',
+                    outName='duplicate-species.cti',
+                    quiet=True, permissive=True)
+
+        gas = ct.Solution('duplicate-species.cti')
+        self.assertEqual(gas.species_names, ['foo','bar','baz'])
+
     def test_pathologicalSpeciesNames(self):
         convertMech('../data/species-names.inp',
                     outName='species-names.cti', quiet=True)

test/data/duplicate-species.inp

@@ -0,0 +1,28 @@
+Elements
+H  C
+END
+SPECIES
+foo bar baz bar
+bar bar
+bar
+END
+thermo
+    300.000  1000.000  5000.000
+foo                     C   1H   4          G   200.000  3500.000  1000.000    1
+ 7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13    2
+-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05    3
+-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00                   4
+bar                     C   1H   4          G   200.000  3500.000  1000.000    1
+ 7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13    2
+-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05    3
+-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00                   4
+baz                     C   1H   4          G   200.000  3500.000  1000.000    1
+ 7.48514950E-02 1.33909467E-02-5.73285809E-06 1.22292535E-09-1.01815230E-13    2
+-9.46834459E+03 1.84373180E+01 5.14987613E+00-1.36709788E-02 4.91800599E-05    3
+-4.84743026E-08 1.66693956E-11-1.02466476E+04-4.64130376E+00                   4
+end
+
+reactions
+foo + bar = 2 baz      1.2345e12  1.0  200.0
+2foo + baz = 3bar      5.4321e10  1.0  500.0
+end