Add ASCII, XML support to build_reaction_set

In reality, both formats are using XML to parse the kinetics, but
the ASCII format requires an additional flag for the filename for
the kinetics data whereas XML it will all be stashed in one place.

This commit is also leveraging a new Antioch API that was part of
libantioch/antioch#261. Thus, the minimum Antioch hash that will
be required after this commit is  libantioch/antioch@7cebf19.

We'll work on ChemKinParser support later.

src/properties/src/antioch_mixture_builder_base.C

@@ -78,11 +78,76 @@ namespace GRINS
     std::unique_ptr<Antioch::ReactionSet<libMesh::Real> >
       reaction_set( new Antioch::ReactionSet<libMesh::Real>(chem_mix) );
 
-    std::string kinetics_data_filename = MaterialsParsing::parse_chemical_kinetics_datafile_name( input, material );
-
     bool verbose_read = input("screen-options/verbose_kinetics_read", false );
 
-    Antioch::read_reaction_set_data_xml<libMesh::Real>( kinetics_data_filename, verbose_read, *reaction_set );
+    std::string prefix(this->antioch_prefix(material));
+    std::string gas_mixture_option(prefix+"/gas_mixture");
+
+    Antioch::ParsingType parsing_type = this->get_antioch_parsing_type(input,material);
+
+    switch(parsing_type)
+      {
+        // We're actually going to use Antioch's XML parser to parse the kinetics,
+        // but we distinguish ASCII because we need a separate GRINS input option
+        // to get the kinetics file. In the XML case, everything is in one XML file
+        // whereas with the ASCII, we have \infty files...
+      case(Antioch::ASCII):
+        {
+          std::string old_option("Materials/"+material+"/GasMixture/kinetics_data");
+          std::string new_option(prefix+"/kinetics_data");
+
+          std::string filename;
+          if( input.have_variable(old_option) )
+            {
+              // Deprecated message is in this function call
+              filename = MaterialsParsing::parse_chemical_kinetics_datafile_name( input, material );
+            }
+          else if( input.have_variable(new_option) )
+            filename = input(new_option,std::string("DIE!"));
+
+          else
+            libmesh_error_msg("ERROR: Could not valid input for "+new_option+"!\n");
+
+          if( input.have_variable(gas_mixture_option) )
+            {
+              std::string gas_mixture = input(gas_mixture_option,"DIE!");
+              Antioch::XMLParser<libMesh::Real> parser(filename, gas_mixture, verbose_read);
+              Antioch::read_reaction_set_data<libMesh::Real>( verbose_read, *reaction_set, &parser );
+            }
+          else
+            {
+              std::string msg = "WARNING: Option "+gas_mixture_option+" not found!\n";
+              msg += "         The first kinetics data set in the file "+filename+"\n";
+              msg += "         will be used. This is DEPRECATED behavior. In the future,\n";
+              msg += "         the option "+gas_mixture_option+" will be required.\n";
+              grins_warning(msg);
+
+              Antioch::read_reaction_set_data<libMesh::Real>( filename, verbose_read, *reaction_set, Antioch::XML );
+            }
+          break;
+        }
+      case(Antioch::XML):
+        {
+          std::string chem_data_option(prefix+"/"+MaterialsParsing::chemical_data_option());
+          std::string chem_data_filename = input(chem_data_option,std::string("DIE!"));
+
+          MaterialsParsing::check_for_input_option(input,gas_mixture_option);
+          std::string gas_mixture = input(gas_mixture_option,"DIE!");
+
+          Antioch::XMLParser<libMesh::Real> parser(chem_data_filename, gas_mixture, verbose_read);
+          Antioch::read_reaction_set_data<libMesh::Real>( verbose_read, *reaction_set, &parser );
+          break;
+        }
+      case(Antioch::CHEMKIN):
+        {
+          libmesh_not_implemented();
+          break;
+        }
+      default:
+        libmesh_error_msg("ERROR: Invalid Antioch parsing type!");
+      }
+
+
 
     return reaction_set;
   }