Fixed: Ck2yaml crashes if reaction equation has both ThreeBodyReactio…

…n and Falloff reaction types

Bug: check_duplicate_reactions breaks if sent a third body reaction and falloff reaction because r1.third_body (or r2) is None and has no attribute upper.

Fix: This changes the third body reaction type to have a .third_body of M and then in check_duplicate_reactions check that r1 and r2 are not a mixture of three body reaction type and something else.

Bug: if blank space in header, parser crashes due to regular expression search to determine indent size

Fix: check that the comment is not empty before trying to determine indent size

Improvement: inform user which reaction contains multiple reaction types

Added Tests for both issues fixed

interfaces/cython/cantera/ck2yaml.py

@@ -1051,29 +1051,30 @@ def read_kinetics_entry(self, entry, surface):
                             parser=self)
 
         def parse_expression(expression, dest):
-            falloff3b = None
+            third_body_name = None
             third_body = False  # simple third body reaction (non-falloff)
             photon = False
             for stoichiometry, species, kind in expression:
                 if kind == 'third-body':
                     third_body = True
+                    third_body_name = 'M'
                 elif kind == 'falloff3b':
-                    falloff3b = 'M'
+                    third_body_name = 'M'
                 elif kind.startswith('falloff3b:'):
-                    falloff3b = kind.split()[1]
+                    third_body_name = kind.split()[1]
                 elif kind == 'photon':
                     photon = True
                 else:
                     dest.append((stoichiometry, self.species_dict[species]))
 
-            return falloff3b, third_body, photon
+            return third_body_name, third_body, photon
 
-        falloff_3b_r, third_body, photon_r = parse_expression(reactants, reaction.reactants)
-        falloff_3b_p, third_body, photon_p = parse_expression(products, reaction.products)
+        third_body_name_r, third_body, photon_r = parse_expression(reactants, reaction.reactants)
+        third_body_name_p, third_body, photon_p = parse_expression(products, reaction.products)
 
-        if falloff_3b_r != falloff_3b_p:
+        if third_body_name_r != third_body_name_p:
             raise InputError('Third bodies do not match: "{}" and "{}" in'
-                ' reaction entry:\n\n{}', falloff_3b_r, falloff_3b_p, entry)
+                ' reaction entry:\n\n{}', third_body_name_r, third_body_name_p, entry)
 
         if photon_r:
             raise InputError('Reactant photon not supported. '
@@ -1085,7 +1086,7 @@ def parse_expression(expression, dest):
                 'removed.'.format(entry.strip()))
             reaction.reversible = False
 
-        reaction.third_body = falloff_3b_r
+        reaction.third_body = third_body_name_r
 
         # Determine the appropriate units for k(T) and k(T,P) based on the number of reactants
         # This assumes elementary kinetics for all reactions
@@ -1281,8 +1282,8 @@ def parse_expression(expression, dest):
         tests = [cheb_coeffs, pdep_arrhenius, low_rate, high_rate, third_body,
                  surface]
         if sum(bool(t) for t in tests) > 1:
-            raise InputError('Reaction entry contains parameters for more than '
-                'one reaction type.')
+            raise InputError('Reaction {} contains parameters for more than '
+                'one reaction type.', original_reaction)
 
         if cheb_coeffs:
             if Tmin is None or Tmax is None:
@@ -1396,7 +1397,8 @@ def readline():
                 tokens = line.split() or ['']
                 if inHeader and not line.strip():
                     header.append(comment.rstrip())
-                    indent = min(indent, re.search('[^ ]', comment).start())
+                    if comment.strip() != '': # skip indent calculation if empty
+                        indent = min(indent, re.search('[^ ]', comment).start())
 
                 if tokens[0].upper().startswith('ELEM'):
                     inHeader = False
@@ -1806,6 +1808,12 @@ def check_duplicate_reactions(self):
             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

interfaces/cython/cantera/test/test_convert.py

@@ -419,6 +419,16 @@ def test_surface_mech2(self):
         self.assertEqual(gas.n_reactions, 0)
         self.assertEqual(surf.n_reactions, 15)
 
+    def test_third_body_plus_falloff_reactions(self):
+        self.convert('third_body_plus_falloff_reaction.inp')
+        gas = ct.Solution('third_body_plus_falloff_reaction' + self.ext)
+        self.assertEqual(gas.n_reactions, 2)
+
+    def test_blank_line_in_header(self):
+        self.convert('blank_line_in_header.inp')
+        gas = ct.Solution('blank_line_in_header' + self.ext)
+        self.assertEqual(gas.n_reactions, 1)
+
 
 class ck2ctiTest(converterTestCommon, utilities.CanteraTest):
     ext = '.cti'

test/data/blank_line_in_header.inp

@@ -0,0 +1,29 @@
+!Title Test
+
+ELEMENTS
+H  C
+END
+
+SPECIES
+CH3             CH2             H
+END
+
+THERMO ALL
+   300.000  1000.000  6000.000
+H                       H  1 C  0 O  0      G     200.0    6000.0    1000.0    1
+ 2.49985211E+00 2.34582548E-07-1.16171641E-10 2.25708298E-14-1.52992005E-18    2
+ 2.54738024E+04-4.45864645E-01 2.49975925E+00 6.73824499E-07 1.11807261E-09    3
+-3.70192126E-12 2.14233822E-15 2.54737665E+04-4.45574009E-01 2.62191345E+04    4
+CH2                     H  2 C  1 N  0      G     200.0    6000.0    1000.0    1
+ 2.81412990E+00 3.79513443E-03-7.38424949E-07 7.19948955E-11-2.63188525E-15    2
+ 4.61859709E+04 6.52945537E+00 3.74842895E+00 1.07655977E-03 3.62462012E-06    3
+-4.46165519E-09 1.95224874E-12 4.58990472E+04 1.63509483E+00 4.70886746E+04    4
+CH3                     H  3 C  1 O  0      G   200.0   6000.0   1000.0        1
+ 2.92198336E+00 5.37478625E-03-1.99748367E-06 2.97584806E-10-1.71860088E-14    2
+ 1.65446753E+04 5.25396822E+00 3.61264389E+00 3.09209041E-03 9.25474611E-07    3
+-1.65776770E-09 6.07243533E-13 1.63849955E+04 1.79994780E+00 1.76047468E+04    4
+END
+
+REACTIONS
+CH3=CH2+H             6.E14         0.0        0.0
+END

test/data/third_body_plus_falloff_reaction.inp

@@ -0,0 +1,30 @@
+ELEMENTS
+H  C
+END
+
+SPECIES
+CH3             CH2             H
+END
+
+THERMO
+   300.000  1000.000  6000.000
+H                       H  1 C  0 O  0      G     200.0    6000.0    1000.0    1
+ 2.49985211E+00 2.34582548E-07-1.16171641E-10 2.25708298E-14-1.52992005E-18    2
+ 2.54738024E+04-4.45864645E-01 2.49975925E+00 6.73824499E-07 1.11807261E-09    3
+-3.70192126E-12 2.14233822E-15 2.54737665E+04-4.45574009E-01 2.62191345E+04    4
+CH2                     H  2 C  1 N  0      G     200.0    6000.0    1000.0    1
+ 2.81412990E+00 3.79513443E-03-7.38424949E-07 7.19948955E-11-2.63188525E-15    2
+ 4.61859709E+04 6.52945537E+00 3.74842895E+00 1.07655977E-03 3.62462012E-06    3
+-4.46165519E-09 1.95224874E-12 4.58990472E+04 1.63509483E+00 4.70886746E+04    4
+CH3                     H  3 C  1 O  0      G   200.0   6000.0   1000.0        1
+ 2.92198336E+00 5.37478625E-03-1.99748367E-06 2.97584806E-10-1.71860088E-14    2
+ 1.65446753E+04 5.25396822E+00 3.61264389E+00 3.09209041E-03 9.25474611E-07    3
+-1.65776770E-09 6.07243533E-13 1.63849955E+04 1.79994780E+00 1.76047468E+04    4
+END
+
+REACTIONS  CAL/MOLE  MOLES
+H+CH2+M=CH3+M             6.E14         0.0        0.0
+H+CH2(+M)<=>CH3(+M)                      6.0E+14     .000        .00
+     LOW  /  1.040E+26   -2.760   1600.00/
+     TROE/   .5620  91.00  5836.00  8552.00/
+END