[ck2cti] Convert surface species with specific site occupancies

Entries in the species list like "C3H6(S)/2/" are now correctly identified as a
species named "C3H6(S)" which occupies 2 surface sites.

Fixes #444

interfaces/cython/cantera/ck2cti.py

@@ -103,11 +103,12 @@ class InputParseError(Exception):
 
 
 class Species(object):
-    def __init__(self, label):
+    def __init__(self, label, sites=None):
         self.label = label
         self.thermo = None
         self.transport = None
         self.note = None
+        self.sites = sites
         self.composition = None
 
     def __str__(self):
@@ -130,6 +131,8 @@ class Species(object):
                          'transport={0},'.format(self.transport.to_cti(14+indent)))
         if self.note:
             lines.append(prefix + 'note={0!r},'.format(self.note))
+        if self.sites is not None:
+            lines.append(prefix + 'size={0},'.format(self.sites))
 
         lines[-1] = lines[-1][:-1] + ')'
         lines.append('')
@@ -1626,11 +1629,17 @@ class Parser(object):
                     for token in tokens:
                         if token.upper() == 'END':
                             break
+                        if token.count('/') == 2:
+                            # species occupies a specific number of sites
+                            token, sites, _ = token.split('/')
+                            sites = float(sites)
+                        else:
+                            sites = None
                         if token in self.speciesDict:
                             species = self.speciesDict[token]
                             self.warn('Found additional declaration of species {0}'.format(species))
                         else:
-                            species = Species(label=token)
+                            species = Species(label=token, sites=sites)
                             self.speciesDict[token] = species
                             surf.speciesList.append(species)
 

interfaces/cython/cantera/test/test_convert.py

@@ -404,7 +404,8 @@ class chemkinConverterTest(utilities.CanteraTest):
         surf = ct.Interface('surface1.cti', 'PT_SURFACE', [gas])
 
         self.assertEqual(gas.n_reactions, 11)
-        self.assertEqual(surf.n_reactions, 14)
+        self.assertEqual(surf.n_reactions, 15)
+        self.assertEqual(surf.species('O2_Pt').size, 3)
 
         # Different units for rate constants in each input file
         # 62.1 kJ/gmol = 6.21e7 J/kmol

test/data/surface1.inp

@@ -1,5 +1,5 @@
 SITE/PT_SURFACE/    SDEN/2.72E-9/
-_Pt_ H_Pt H2O_Pt OH_Pt O_Pt
+_Pt_ H_Pt O2_Pt/3/ H2O_Pt OH_Pt O_Pt
 END
 THERMO ALL
   300.0   1000.0   3000.0
@@ -7,6 +7,10 @@ O_Pt               92491O   1PT  1          I    300.00   3000.00 1000.00      1
  0.19454180E+01 0.91761647E-03-0.11226719E-06-0.99099624E-10 0.24307699E-13    2
 -0.14005187E+05-0.11531663E+02-0.94986904E+00 0.74042305E-02-0.10451424E-05    3
 -0.61120420E-08 0.33787992E-11-0.13209912E+05 0.36137905E+01                   4
+O2_Pt              92491O   2PT  3          I    300.00   3000.00 1000.00      1
+ 0.19454180E+01 0.91761647E-03-0.11226719E-06-0.99099624E-10 0.24307699E-13    2
+-0.14005187E+05-0.11531663E+02-0.94986904E+00 0.74042305E-02-0.10451424E-05    3
+-0.61120420E-08 0.33787992E-11-0.13209912E+05 0.36137905E+01                   4
 H_Pt               92491H   1PT  1          I    300.00   3000.00 1000.00      1
  0.10696996E+01 0.15432230E-02-0.15500922E-06-0.16573165E-09 0.38359347E-13    2
 -0.50546128E+04-0.71555238E+01-0.13029877E+01 0.54173199E-02 0.31277972E-06    3
@@ -51,4 +55,5 @@ END
  H_Pt + O_Pt  =  OH_Pt + _Pt_                  3.70E+21  0.00    11500.0
  H_Pt + OH_Pt =  H2O_Pt + _Pt_                 3.70E+21  0.00    17400.0
  OH_Pt + OH_Pt = H2O_Pt + O_Pt                  3.70E+21  0.00    48200.0
+ O2_Pt = O2 + 3 _Pt_                           3.70E+21  0.00    11500.0
 END