[ck2cti] Allow elements/isotopes with custom atomic weights

Resolves #344

interfaces/cython/cantera/ck2cti.py

@@ -888,6 +888,7 @@ def __init__(self):
         self.warning_as_error = True
 
         self.elements = []
+        self.element_weights = {} # for custom elements only
         self.speciesList = []
         self.speciesDict = {}
         self.reactions = []
@@ -939,6 +940,16 @@ def getRateConstantUnits(self, length_dims, length_units, quantity_dims,
             units = '1' + units
         return units
 
+    def addElement(self, element_string):
+        if '/' in element_string:
+            name, weight, _ = element_string.split('/')
+            weight = fortFloat(weight)
+            name = name.capitalize()
+            self.elements.append(name)
+            self.element_weights[name] = weight
+        else:
+            self.elements.append(element_string.capitalize())
+
     def readThermoEntry(self, lines, TintDefault):
         """
         Read a thermodynamics entry for one species in a Chemkin-format file
@@ -1469,12 +1480,14 @@ def readline():
                             break
 
                         line, comment = readline()
+                        # Normalize custom atomic weights
+                        line = re.sub(r'\s*/\s*([0-9\.EeDd+-]+)\s*/', r'/\1/ ', line)
                         tokens.extend(line.split())
 
                     for token in tokens:
                         if token.upper() == 'END':
                             break
-                        self.elements.append(token.capitalize())
+                        self.addElement(token)
 
                 elif tokens[0].upper().startswith('SPEC'):
                     # List of species identifiers
@@ -1875,6 +1888,15 @@ def writeCTI(self, header=None, name='gas', transportModel='Mix',
             lines.append('          initial_state=state(temperature=300.0, pressure=OneAtm))')
             lines.append('')
 
+        # Write data on custom elements
+        if self.element_weights:
+            lines.append(delimiterLine)
+            lines.append('# Element data')
+            lines.append(delimiterLine)
+            lines.append('')
+            for name,weight in self.element_weights.items():
+                lines.append('element(symbol={0!r}, atomic_mass={1})'.format(name, weight))
+
         # Write the individual species data
         lines.append(delimiterLine)
         lines.append('# Species data')

interfaces/cython/cantera/test/test_convert.py

@@ -357,6 +357,15 @@ def test_reaction_comments2(self):
         self.assertIn('An end of line comment', text)
         self.assertIn('A comment after the last reaction', text)
 
+    def test_custom_element(self):
+        convertMech('../data/custom-elements.inp',
+                    outName='custom-elements.cti', quiet=True)
+        gas = ct.Solution('custom-elements.cti')
+        self.assertEqual(gas.n_elements, 4)
+        self.assertNear(gas.atomic_weight(2), 13.003)
+        self.assertEqual(gas.n_atoms('ethane', 'C'), 2)
+        self.assertEqual(gas.n_atoms('CC', 'C'), 1)
+        self.assertEqual(gas.n_atoms('CC', 'Ci'), 1)
 
 class CtmlConverterTest(utilities.CanteraTest):
     def test_sofc(self):

test/data/custom-elements.inp

@@ -0,0 +1,19 @@
+ELEMENTS
+    H     C     CI / 13.003  /AR
+END
+
+SPECIES
+    ethane   CC
+END
+
+THERM ALL
+    300.000  1000.000  5000.000
+ethane                  H 6  C 2            G100.000   5000.000  954.51        1
+ 4.58979653E+00 1.41508345E-02-4.75965676E-06 8.60302658E-10-6.21723639E-14    2
+-1.27217512E+04-3.61719603E+00 3.78034545E+00-3.24275729E-03 5.52385248E-05    3
+-6.38587529E-08 2.28639901E-11-1.16203413E+04 5.21029844E+00                   4
+CC                      H 6  C 1  CI1       G100.000   5000.000  954.51        1
+ 4.58979542E+00 1.41508364E-02-4.75965787E-06 8.60302924E-10-6.21723861E-14    2
+-1.27217507E+04-2.92404261E+00 3.78034578E+00-3.24276131E-03 5.52385395E-05    3
+-6.38587729E-08 2.28639990E-11-1.16203414E+04 5.90344446E+00                   4
+END