Allow colons in species names in CTI phase definitions

Cantera · Nov 25, 2016 · 3300611 · 3300611
1 parent 05ad05c
commit 3300611
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Showing 3 changed files with 44 additions and 34 deletions.
diff --git a/interfaces/cython/cantera/ctml_writer.py b/interfaces/cython/cantera/ctml_writer.py
@@ -1767,29 +1767,8 @@ def __init__(self,
         # dictionary of species names
         self._spmap = {}
 
-        # for each species string, check whether or not the species
-        # are imported or defined locally. If imported, the string
-        # contains a colon (:)
-        for sp in self._species:
-            icolon = sp.find(':')
-            if icolon > 0:
-                #datasrc, spnames = sp.split(':')
-                datasrc = sp[:icolon].strip()
-                spnames = sp[icolon+1:]
-                self._sp.append((datasrc+'.xml', spnames))
-            else:
-                spnames = sp
-                self._sp.append(('', spnames))
-
-            for s in spnames.split():
-                self._spmap[s] = self._dim
-
         self._rxns = reactions
 
-        # check that species have been declared
-        if len(self._spmap) == 0:
-            raise CTI_Error('No species declared for phase '+self._name)
-
         # and that only one species is declared if it is a pure phase
         if self.is_pure() and len(self._spmap) > 1:
             raise CTI_Error('Stoichiometric phases must  declare exactly one species, \n'+
@@ -1819,7 +1798,6 @@ def conc_dim(self):
         rate coefficients."""
         return (1, -self._dim)
 
-
     def buildrxns(self, p):
 
         if isinstance(self._rxns, str):
@@ -1865,6 +1843,34 @@ def buildrxns(self, p):
 
 
     def build(self, p):
+        # for each species string, check whether or not the species
+        # are imported or defined locally. If imported, the string
+        # contains a colon (:)
+        for sp in self._species:
+            foundColon = False
+            allLocal = True
+            for token in sp.split():
+                if ':' in sp:
+                    foundColon = True
+                if token not in _speciesnames:
+                    allLocal = False
+
+            if foundColon and not allLocal:
+                icolon = sp.find(':')
+                datasrc = sp[:icolon].strip()
+                spnames = sp[icolon+1:]
+                self._sp.append((datasrc+'.xml', spnames))
+            else:
+                spnames = sp
+                self._sp.append(('', spnames))
+
+            for s in spnames.split():
+                self._spmap[s] = self._dim
+
+        # check that species have been declared
+        if len(self._spmap) == 0:
+            raise CTI_Error('No species declared for phase '+self._name)
+
         p.addComment('    phase '+self._name+'     ')
         ph = p.addChild('phase')
         ph['id'] = self._name

diff --git a/interfaces/cython/cantera/test/test_convert.py b/interfaces/cython/cantera/test/test_convert.py
@@ -142,22 +142,22 @@ def test_pathologicalSpeciesNames(self):
                     outName=pjoin(self.test_work_dir, 'species-names.cti'), quiet=True)
         gas = ct.Solution('species-names.cti')
 
-        self.assertEqual(gas.n_species, 6)
+        self.assertEqual(gas.n_species, 7)
         self.assertEqual(gas.species_name(0), '(Parens)')
         self.assertEqual(gas.species_name(1), '@#$%^-2')
-        self.assertEqual(gas.species_name(2), '[xy2]*{.}')
-        self.assertEqual(gas.species_name(3), 'plus+')
-        self.assertEqual(gas.species_name(4), 'eq=uals')
-        self.assertEqual(gas.species_name(5), 'plus')
+        self.assertEqual(gas.species_name(3), '[xy2]*{.}')
+        self.assertEqual(gas.species_name(4), 'plus+')
+        self.assertEqual(gas.species_name(5), 'eq=uals')
+        self.assertEqual(gas.species_name(6), 'plus')
 
         self.assertEqual(gas.n_reactions, 6)
         nu = gas.product_stoich_coeffs() - gas.reactant_stoich_coeffs()
-        self.assertEqual(list(nu[:,0]), [-1, -1, 2, 0, 0, 0])
-        self.assertEqual(list(nu[:,1]), [-2, 3, -1, 0, 0, 0])
-        self.assertEqual(list(nu[:,2]), [-1, 0, 0, 1, 0, 0])
-        self.assertEqual(list(nu[:,3]), [3, 0, 0, -2, -1, 0])
-        self.assertEqual(list(nu[:,4]), [2, 0, 0, -1, 0, -1])
-        self.assertEqual(list(nu[:,5]), [1, 0, 0, 1, -1, -1])
+        self.assertEqual(list(nu[:,0]), [-1, -1, 0, 2, 0, 0, 0])
+        self.assertEqual(list(nu[:,1]), [-2, 3, 0, -1, 0, 0, 0])
+        self.assertEqual(list(nu[:,2]), [-1, 0, 0, 0, 1, 0, 0])
+        self.assertEqual(list(nu[:,3]), [3, 0, 0, 0, -2, -1, 0])
+        self.assertEqual(list(nu[:,4]), [2, 0, 0, 0, -1, 0, -1])
+        self.assertEqual(list(nu[:,5]), [1, 0, 0, 0, 1, -1, -1])
 
     def test_unterminatedSections(self):
         with self.assertRaises(ck2cti.InputParseError):

diff --git a/test/data/species-names.inp b/test/data/species-names.inp
@@ -2,7 +2,7 @@ Elements
 H  C
 End
 SPEC
-(Parens)  @#$%^-2  [xy2]*{.}  plus+ eq=uals plus
+(Parens)  @#$%^-2  co:lons [xy2]*{.}  plus+ eq=uals plus
 end
 
 thermo
@@ -15,6 +15,10 @@ thermo
  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
+co:lons                 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
 [xy2]*{.}               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