missed several syntax changes, updated

Author: ChrisBNEU

rmgpy/rmg/main.py

@@ -48,7 +48,7 @@
 import numpy as np
 import psutil
 import yaml
-from cantera import ck2cti
+from cantera import ck2yaml
 from scipy.optimize import brute
 
 import rmgpy.util as util
@@ -1088,14 +1088,14 @@ def execute(self, initialize=True, **kwargs):
 
         self.run_model_analysis()
 
-        # generate Cantera files chem.cti & chem_annotated.cti in a designated `cantera` output folder
+        # generate Cantera files chem.yaml & chem_annotated.yaml in a designated `cantera` output folder
         try:
             if any([s.contains_surface_site() for s in self.reaction_model.core.species]):
                 self.generate_cantera_files(os.path.join(self.output_directory, 'chemkin', 'chem-gas.inp'),
-                                            surfaceFile=(
+                                            surface_file=(
                                               os.path.join(self.output_directory, 'chemkin', 'chem-surface.inp')))
                 self.generate_cantera_files(os.path.join(self.output_directory, 'chemkin', 'chem_annotated-gas.inp'),
-                                            surfaceFile=(os.path.join(self.output_directory, 'chemkin',
+                                            surface_file=(os.path.join(self.output_directory, 'chemkin',
                                                                     'chem_annotated-surface.inp')))
             else:  # gas phase only
                 self.generate_cantera_files(os.path.join(self.output_directory, 'chemkin', 'chem.inp'))
@@ -1660,13 +1660,13 @@ def process_reactions_to_species(self, obj):
 
     def generate_cantera_files(self, chemkin_file, **kwargs):
         """
-        Convert a chemkin mechanism chem.inp file to a cantera mechanism file chem.cti
+        Convert a chemkin mechanism chem.inp file to a cantera mechanism file chem.yaml
         and save it in the cantera directory
         """
         transport_file = os.path.join(os.path.dirname(chemkin_file), 'tran.dat')
-        file_name = os.path.splitext(os.path.basename(chemkin_file))[0] + '.cti'
+        file_name = os.path.splitext(os.path.basename(chemkin_file))[0] + '.yaml'
         out_name = os.path.join(self.output_directory, 'cantera', file_name)
-        if 'surfaceFile' in kwargs:
+        if 'surface_file' in kwargs:
             out_name = out_name.replace('-gas.', '.')
         cantera_dir = os.path.dirname(out_name)
         try:
@@ -1676,14 +1676,14 @@ def generate_cantera_files(self, chemkin_file, **kwargs):
                 raise
         if os.path.exists(out_name):
             os.remove(out_name)
-        parser = ck2cti.Parser()
+        parser = ck2yaml.Parser()
         try:
-            parser.convertMech(chemkin_file, transportFile=transport_file, outName=out_name, quiet=True, permissive=True,
+            parser.convert_mech(chemkin_file, transport_file=transport_file, out_name=out_name, quiet=True, permissive=True,
                                **kwargs)
-        except ck2cti.InputParseError:
+        except ck2yaml.InputError:
             logging.exception("Error converting to Cantera format.")
             logging.info("Trying again without transport data file.")
-            parser.convertMech(chemkin_file, outName=out_name, quiet=True, permissive=True, **kwargs)
+            parser.convert_mech(chemkin_file, out_name=out_name, quiet=True, permissive=True, **kwargs)
 
     def initialize_reaction_threshold_and_react_flags(self):
         num_core_species = len(self.reaction_model.core.species)

rmgpy/rmg/mainTest.py

@@ -180,7 +180,7 @@ def test_make_cantera_input_file(self):
         outName = os.path.join(self.rmg.output_directory, 'cantera')
         files = os.listdir(outName)
         for f in files:
-            if '.cti' in f:
+            if '.yaml' in f:
                 try:
                     ct.Solution(os.path.join(outName, f))
                 except:
@@ -492,7 +492,7 @@ def test_chemkin_to_cantera_conversion(self):
         Tests that good and bad chemkin files raise proper exceptions
         """
 
-        from cantera.ck2cti import InputParseError
+        from cantera.ck2yaml import InputError
 
         for ck_input, works in self.chemkin_files.items():
             os.chdir(originalPath)
@@ -510,7 +510,7 @@ def test_chemkin_to_cantera_conversion(self):
             if works:
                 self.rmg.generate_cantera_files(os.path.join(os.getcwd(), 'chem001.inp'))
             else:
-                with self.assertRaises(InputParseError):
+                with self.assertRaises(InputError):
                     self.rmg.generate_cantera_files(os.path.join(os.getcwd(), 'chem001.inp'))
 
             # clean up

rmgpy/tools/canteramodel.py

@@ -203,7 +203,7 @@ def __init__(self, species_list=None, reaction_list=None, canteraFile='', output
         `species_list`: list of RMG species objects
         `reaction_list`: list of RMG reaction objects
         `reaction_map`: dict mapping the RMG reaction index within the `reaction_list` to cantera model reaction(s) indices
-        `canteraFile` path of the chem.cti file associated with this job
+        `canteraFile` path of the chem.yaml file associated with this job
         `conditions`: a list of `CanteraCondition` objects
         `sensitive_species`: a list of RMG species objects for conductng sensitivity analysis on
         `thermo_SA`: a boolean indicating whether or not to run thermo SA. By default, if sensitive_species is given,
@@ -289,19 +289,19 @@ def refresh_model(self):
 
     def load_chemkin_model(self, chemkin_file, transport_file=None, **kwargs):
         """
-        Convert a chemkin mechanism chem.inp file to a cantera mechanism file chem.cti 
+        Convert a chemkin mechanism chem.inp file to a cantera mechanism file chem.yaml 
         and save it in the output_directory
         Then load it into self.model
         """
-        from cantera import ck2cti
+        from cantera import ck2yaml
 
         base = os.path.basename(chemkin_file)
         base_name = os.path.splitext(base)[0]
-        out_name = os.path.join(self.output_directory, base_name + ".cti")
+        out_name = os.path.join(self.output_directory, base_name + ".yaml")
         if os.path.exists(out_name):
             os.remove(out_name)
-        parser = ck2cti.Parser()
-        parser.convertMech(chemkin_file, transportFile=transport_file, outName=out_name, **kwargs)
+        parser = ck2yaml.Parser()
+        parser.convert_mech(chemkin_file, transport_file=transport_file, out_name=out_name, **kwargs)
         self.model = ct.Solution(out_name)
 
     def modify_reaction_kinetics(self, rmg_reaction_index, rmg_reaction):