[Input] Move all duplicate reaction checking out of ck2yaml

Use the more comprehensive duplicate reaction check in
Kinetics::checkDuplicates when validating the mechanism.

Parse the error message generated by Kinetics::checkDuplicates to determine
the line number in the original input file, which is more useful to users
than the line number in the newly-generated YAML file.

interfaces/cython/cantera/ck2yaml.py

@@ -1783,51 +1783,12 @@ def readline():
         for h in header:
             self.header_lines.append(h[indent:])
 
-        self.check_duplicate_reactions()
-
         for index, reaction in enumerate(self.reactions):
             reaction.index = index + 1
 
         if transportLines:
             self.parse_transport_data(transportLines, path, transport_start_line)
 
-    def check_duplicate_reactions(self):
-        """
-        Check for marked (and unmarked!) duplicate reactions. Raise exception
-        for unmarked duplicate reactions.
-
-        Pressure-independent and pressure-dependent reactions are treated as
-        different, so they don't need to be marked as duplicate.
-        """
-        possible_duplicates = defaultdict(list)
-        for r in self.reactions:
-            k = (tuple(r.reactants), tuple(r.products), r.kinetics.pressure_dependent)
-            possible_duplicates[k].append(r)
-
-        for reactions in possible_duplicates.values():
-            for r1,r2 in itertools.combinations(reactions, 2):
-                if r1.duplicate and r2.duplicate:
-                    pass  # marked duplicate reaction
-                elif (type(r1.kinetics) == ThreeBody and
-                      type(r2.kinetics) != ThreeBody):
-                    pass
-                elif (type(r1.kinetics) != ThreeBody and
-                      type(r2.kinetics) == ThreeBody):
-                    pass
-                elif (r1.third_body.upper() == 'M' and
-                      r1.kinetics.efficiencies.get(r2.third_body) == 0):
-                    pass  # explicit zero efficiency
-                elif (r2.third_body.upper() == 'M' and
-                      r2.kinetics.efficiencies.get(r1.third_body) == 0):
-                    pass  # explicit zero efficiency
-                elif r1.third_body != r2.third_body:
-                    pass  # distinct third bodies
-                else:
-                    raise InputError(
-                        'Encountered unmarked duplicate reaction {} '
-                        '(See lines {} and {} of the input file.).',
-                        r1, r1.line_number, r2.line_number)
-
     def parse_transport_data(self, lines, filename, line_offset):
         """
         Parse the Chemkin-format transport data in ``lines`` (a list of strings)
@@ -2095,14 +2056,33 @@ def convert_mech(input_file, thermo_file=None, transport_file=None,
             nReactions = len(parser.reactions) + sum(len(surf.reactions) for surf in parser.surfaces)
             print('Wrote YAML mechanism file to {0!r}.'.format(out_name))
             print('Mechanism contains {0} species and {1} reactions.'.format(len(parser.species_list), nReactions))
-        return surface_names
+        return parser, surface_names
+
+    def show_duplicate_reactions(self, error_message):
+        reactions = []
+        for line in error_message.split('\n'):
+            match = re.match('>.*# Reaction ([0-9]+)', line)
+            if match:
+                reactions.append(int(match.group(1))-1)
+
+        if len(reactions) != 2:
+            print(error_message)
+            return
+
+        equation = str(self.reactions[0])
+        lines = [self.reactions[i].line_number for i in reactions]
+        print('Undeclared duplicate reaction {}\nfound on lines {} and {} of '
+              ' the kinetics input file.'.format(equation, lines[0], lines[1]))
 
 
 def convert_mech(input_file, thermo_file=None, transport_file=None,
                  surface_file=None, phase_name='gas', extra_file=None,
                  out_name=None, quiet=False, permissive=None):
-    return Parser.convert_mech(input_file, thermo_file, transport_file, surface_file,
-                               phase_name, extra_file, out_name, quiet, permissive)
+    parser, surface_names = Parser.convert_mech(
+        input_file, thermo_file, transport_file, surface_file, phase_name,
+        extra_file, out_name, quiet, permissive)
+    return surface_names
+
 
 def main(argv):
 
@@ -2160,9 +2140,9 @@ def main(argv):
     else:
         out_name = os.path.splitext(thermo_file)[0] + '.yaml'
 
-    surfaces = Parser.convert_mech(input_file, thermo_file, transport_file,
-                                   surface_file, phase_name, extra_file,
-                                   out_name, quiet, permissive)
+    parser, surfaces = Parser.convert_mech(input_file, thermo_file,
+            transport_file, surface_file, phase_name, extra_file, out_name,
+            quiet, permissive)
 
     # Do full validation by importing the resulting mechanism
     if not input_file:
@@ -2187,7 +2167,11 @@ def main(argv):
         print('PASSED.')
     except RuntimeError as e:
         print('FAILED.')
-        print(e)
+        msg = str(e)
+        if ('Undeclared duplicate reactions' in msg):
+            parser.show_duplicate_reactions(msg)
+        else:
+            print(e)
         sys.exit(1)