updates to structure & output

updates to structure & output

headers/Get_Input.h

@@ -13,7 +13,8 @@
 #define INPUT_FUNCTIONS_
 
 
-void Handle_Mechanism_Input(
+//void Handle_Mechanism_Input(
+bool Handle_Mechanism_Input(
 		string ,
 		vector< string >& ,
 		vector< ThermodynamicData >& ,

headers/Global_Variables.hpp

@@ -0,0 +1,18 @@
+/*
+ * Global_Variables.hpp
+ *
+ *  Created on: 02.07.2015
+ *      Author: DetlevCM
+ */
+
+#ifndef SOURCE_GLOBAL_VARIABLES_HPP_
+#define SOURCE_GLOBAL_VARIABLES_HPP_
+
+
+
+// Shoddy implementation of PetroOxy logic
+extern PetroOxyCalculation PetroOxyData;
+extern int OxyGasSpeciesID;
+// end PetroOxy Logic
+
+#endif /* SOURCE_GLOBAL_VARIABLES_HPP_ */

headers/MyFunctions.h

@@ -103,4 +103,16 @@ vector< SingleReactionData > Make_Irreversible(
 );
 
 
+void Integrate(
+		string,
+		string,
+		string,
+		string,
+		vector< double >,
+		vector< string > ,
+		vector< SingleReactionData > &,
+		InitParam,
+		vector< double >&
+		);
+
 #endif /* _MY_OTHER_FUNCTIONS_ */

headers/MyHeaders.h

@@ -40,6 +40,8 @@ using std::istringstream;
 
 
 #include <Structs.h>
+#include <Namespaces.hpp>
+#include <Global_Variables.hpp>
 
 // Definitions of my functions
 #include <Get_Input.h>

headers/Namespaces.hpp

@@ -0,0 +1,25 @@
+/*
+ * Namespaces.hpp
+ *
+ *  Created on: 02.07.2015
+ *      Author: DetlevCM
+ */
+
+#ifndef SOURCE_NAMESPACES_HPP_
+#define SOURCE_NAMESPACES_HPP_
+
+
+namespace GlobalArrays{
+// Key parameters that define the whole reaction scheme - used globally via namespaces
+// Not sure if this is a good place to put it...
+extern vector< vector < str_RatesAnalysis > > RatesAnalysisData;
+extern vector< TrackSpecies > ProductsForRatesAnalysis;
+
+}
+
+
+
+
+
+
+#endif /* SOURCE_NAMESPACES_HPP_ */

headers/Solver_Calculations.h

@@ -18,7 +18,8 @@ void Calculate_Rate_Constant(
 		vector< double >& ,
 		const double ,
 		const vector< ReactionParameter >& ,
-		const vector< vector< double > >& ,
+		//const vector< vector< double > >& ,
+		const vector< CalculatedThermodynamics >& ,
 		const vector< TrackSpecies >& ,
 		const vector< double >&
 );
@@ -37,7 +38,8 @@ void CalculateReactionRates(
 
 
 void Calculate_Thermodynamics(
-		vector< vector< double > >& ,
+		//vector< vector< double > >& ,
+		vector< CalculatedThermodynamics >& ,
 		const double& ,
 		const vector< ThermodynamicData >&
 );

headers/Structs.h

@@ -23,9 +23,9 @@ struct JacobianSpecies{
 };
 
 struct JacobianData {
-	int ColumnWiseArrayPosition;
 	bool IsForward;
 	bool IsProduction;
+	int ColumnWiseArrayPosition;
 	int ReactionID;
 	double coefficient;
 	vector< JacobianSpecies > Species;
@@ -34,22 +34,22 @@ struct JacobianData {
 
 
 struct SingleReactionData {
-	vector<double> Reactants;
-	vector<double> Products;
+	bool Reversible;
+	bool IsDuplicate;
 	double paramA;
 	double paramN;
 	double paramEa;
-	bool Reversible;
-	bool IsDuplicate;
+	vector<double> Reactants;
+	vector<double> Products;
 };
 //*/
 
 //*
 struct ReactionParameter {
+	bool Reversible;
 	double paramA;
 	double paramN;
 	double paramEa;
-	bool Reversible;
 };
 //*/
 
@@ -71,6 +71,20 @@ struct InitSpecies {
 };
 
 
+struct ConstantInitRHSODE {
+	bool EnforceStability;
+	bool PetroOxy;
+	double temperature;
+	double PetroOxyTemperatureRise;
+};
+
+struct CalculatedThermodynamics {
+	double Hf;
+	double Cp;
+	double Cv;
+	double S;
+};
+
 struct InitParam {
 	bool irrev; // shoud be bool
 	bool PrintReacRates;
@@ -118,13 +132,13 @@ struct InitParam {
 
 
 struct PetroOxyCalculation {
+	bool HenryLawDiffusionLimitSet;
 	double SampleSize ; // Old 0
 	double HeadSpaceGas ; // Old 4
 	double HeadSpaceGasMol; // Old 6
 	double HenryConstantk; // Old 10
 	double HeadSpaceGasPressure; // Old 7
 	double HeadSpaceSolventComponentPressure; // Old 8
-	bool HenryLawDiffusionLimitSet;
 	double HenryLawDiffusionLimit;
 };
 

headers/Write_Output.h

@@ -73,7 +73,7 @@ void WriteReactions(
 
 void Write_Stoichiometric_Matrix_For_Opt(
 		string ,
-		const vector< string >& ,
+//		const vector< string >& ,
 		const vector< SingleReactionData >&
 );