moved mechanism data into single dedicated storage struct

DetlevCM · Oct 30, 2017 · 02d86fe · 02d86fe
1 parent 5f7cefc
commit 02d86fe
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Showing 15 changed files with 275 additions and 250 deletions.
diff --git a/headers/Get_Input.h b/headers/Get_Input.h
@@ -17,9 +17,10 @@
 bool Handle_Mechanism_Input(
 		string ,
 		string ,
-		vector< string >& ,
-		vector< ThermodynamicData >& ,
-		vector< SingleReactionData >& ,
+		MechanismData& ,
+		//vector< string >& ,
+		//vector< ThermodynamicData >& ,
+		//vector< SingleReactionData >& ,
 		InitParam& ,
 		vector< double >&,
 		PressureVesselCalc &

diff --git a/headers/MyHeaders.h b/headers/MyHeaders.h
@@ -52,6 +52,7 @@ using std::istringstream;
 
 // structs definitions
 #include "structs/Structs.h"
+#include "structs/mechanism_storage.h"
 #include "structs/initial_conditions_parameters.h"
 
 // namespaces with global variables for performance reasons

diff --git a/headers/run_integrator/Run_Integrator.h b/headers/run_integrator/Run_Integrator.h
@@ -12,9 +12,8 @@
 void Choose_Integrator(
 		Filenames,
 		vector< double >,
-		vector< string > ,
-		vector< ThermodynamicData > ,
-		vector< SingleReactionData > &,
+		MechanismData ,
+		//vector< string > ,vector< ThermodynamicData > ,	vector< SingleReactionData > &,
 		InitParam,
 		vector< double >&,
 		PressureVesselCalc,
@@ -25,9 +24,8 @@ void Choose_Integrator(
 void Integrate_Liquid_Phase_Intel(
 		Filenames,
 		vector< double >,
-		vector< string > ,
-		vector< ThermodynamicData > ,
-		vector< SingleReactionData > &,
+		MechanismData ,
+		//vector< string > , vector< ThermodynamicData > , vector< SingleReactionData > &,
 		InitParam,
 		vector< double >&,
 		vector< vector < str_RatesAnalysis > > &
@@ -37,9 +35,8 @@ void Integrate_Liquid_Phase_Intel(
 void Integrate_Pressure_Vessel_Liquid_Phase_Intel(
 		Filenames,
 		vector< double >,
-		vector< string > ,
-		vector< ThermodynamicData > ,
-		vector< SingleReactionData > &,
+		MechanismData ,
+		//vector< string > , vector< ThermodynamicData > , vector< SingleReactionData > &,
 		InitParam,
 		vector< double >&,
 		PressureVesselCalc,
@@ -50,9 +47,8 @@ void Integrate_Pressure_Vessel_Liquid_Phase_Intel(
 void Integrate_Liquid_Phase_Odepack_LSODA(
 		Filenames,
 		vector< double >,
-		vector< string > ,
-		vector< ThermodynamicData > ,
-		vector< SingleReactionData > &,
+		MechanismData ,
+		//vector< string > ,vector< ThermodynamicData > ,vector< SingleReactionData > &,
 		InitParam,
 		vector< double >&,
 		vector< vector < str_RatesAnalysis > > &
@@ -61,9 +57,8 @@ void Integrate_Liquid_Phase_Odepack_LSODA(
 void Integrate_Gas_Phase_Odepack_LSODA(
 		Filenames,
 		vector< double >,
-		vector< string > ,
-		vector< ThermodynamicData > ,
-		vector< SingleReactionData > &,
+		MechanismData ,
+		//vector< string > ,vector< ThermodynamicData > ,vector< SingleReactionData > &,
 		InitParam,
 		vector< double >&,
 		vector< vector < str_RatesAnalysis > > &
@@ -73,9 +68,8 @@ void Integrate_Gas_Phase_Odepack_LSODA(
 void Integrate_Pressure_Vessel_Liquid_Phase_Odepack_LSODA(
 		Filenames,
 		vector< double >,
-		vector< string > ,
-		vector< ThermodynamicData > ,
-		vector< SingleReactionData > &,
+		MechanismData ,
+		//vector< string > ,vector< ThermodynamicData > ,vector< SingleReactionData > &,
 		InitParam,
 		vector< double >&,
 		PressureVesselCalc,

diff --git a/headers/structs/Structs.h b/headers/structs/Structs.h
@@ -33,15 +33,7 @@ struct JacobianData {
 
 
 
-struct SingleReactionData {
-	bool Reversible;
-	bool IsDuplicate;
-	double paramA;
-	double paramN;
-	double paramEa;
-	vector<double> Reactants;
-	vector<double> Products;
-};
+
 
 
 struct ReactionParameter {
@@ -122,25 +114,7 @@ struct MechanismAnalysisConfig {
 };
 
 
-struct ThermodynamicData {
-	double TLow;
-	double THigh;
-	double TChange;
-	double NasaLow1;
-	double NasaLow2;
-	double NasaLow3;
-	double NasaLow4;
-	double NasaLow5;
-	double NasaLow6;
-	double NasaLow7;
-	double NasaHigh1;
-	double NasaHigh2;
-	double NasaHigh3;
-	double NasaHigh4;
-	double NasaHigh5;
-	double NasaHigh6;
-	double NasaHigh7;
-};
+
 
 
 struct str_RatesAnalysis

diff --git a/headers/structs/initial_conditions_parameters.h b/headers/structs/initial_conditions_parameters.h
@@ -75,7 +75,7 @@ struct InitParam {
 	bool PrintReacRates;
 
 	bool EnforceStability;
-	int nrspec;
+	//int nrspec;
 	vector< double > TimeEnd;
 	vector< double > TimeStep;
 	double temperature;
@@ -86,6 +86,8 @@ struct InitParam {
 	vector< InitSpecies > InitialGasSpecies;
 
 	// a block for mechanism reduction
+	// weirdly enough, this must be located after the initial species, as the code fails otherwise...
+	// for reasons unknownm, some parameters in this struct are apparently position dependant...
 	mechanism_reduction MechanismReduction;
 
 

diff --git a/headers/structs/mechanism_storage.h b/headers/structs/mechanism_storage.h
@@ -0,0 +1,49 @@
+/*
+ * mechanism_storage.h
+ *
+ *  Created on: 30 Oct 2017
+ *      Author: detlevcm
+ */
+
+#ifndef HEADERS_STRUCTS_MECHANISM_STORAGE_H_
+#define HEADERS_STRUCTS_MECHANISM_STORAGE_H_
+
+struct SingleReactionData {
+	bool Reversible;
+	bool IsDuplicate;
+	double paramA;
+	double paramN;
+	double paramEa;
+	vector<double> Reactants;
+	vector<double> Products;
+};
+
+struct ThermodynamicData {
+	double TLow;
+	double THigh;
+	double TChange;
+	double NasaLow1;
+	double NasaLow2;
+	double NasaLow3;
+	double NasaLow4;
+	double NasaLow5;
+	double NasaLow6;
+	double NasaLow7;
+	double NasaHigh1;
+	double NasaHigh2;
+	double NasaHigh3;
+	double NasaHigh4;
+	double NasaHigh5;
+	double NasaHigh6;
+	double NasaHigh7;
+};
+
+struct MechanismData {
+
+	vector< string > Species;
+	vector< ThermodynamicData > Thermodynamics;
+	vector< SingleReactionData > Reactions;
+};
+
+
+#endif /* HEADERS_STRUCTS_MECHANISM_STORAGE_H_ */
diff --git a/source/Main.cpp b/source/Main.cpp
@@ -55,24 +55,24 @@ int main(int argc, char* argv[])
 	// The main variables that store the information from a reaction mechanism after
 	// it is read in, namely the species, thermodynamic data and reactions.
 
-	vector< string > Species; // Species list
-	vector< ThermodynamicData > Thermodynamics; // Thermodynamic Data
-	vector< SingleReactionData > Reactions; // Reactions
+	//vector< string > Species; // Species list
+	//vector< ThermodynamicData > Thermodynamics; // Thermodynamic Data
+	//vector< SingleReactionData > Reactions; // Reactions
 
 
 	InitParam InitialParameters; // Initial Conditions/Parameters
 	vector< double > InitialSpeciesConcentration;
 	PressureVesselCalc PetroOxyDataInitial; // PetroOxy Specific Initial Data
 
+	MechanismData Reaction_Mechanism;
 
 	// Handle All the Data Input - The Arrays Contain the required information
 	//			"chem.inp",
 	bool Mechanism_Read_In = Handle_Mechanism_Input(
 			mechanism_filename,
 			initial_data_filename,
-			Species,
-			Thermodynamics,
-			Reactions,
+			Reaction_Mechanism,
+			//Species,Thermodynamics,Reactions,
 			InitialParameters,
 			InitialSpeciesConcentration,
 			PetroOxyDataInitial
@@ -93,19 +93,19 @@ int main(int argc, char* argv[])
 			Write_Stoichiometric_Matrix_For_Opt
 			(
 					"stoichiometry_matrix.txt" ,
-					Reactions
+					Reaction_Mechanism.Reactions
 			);
 			Input_File_For_Ehsan_Opt
 			(
 					"mechanism.txt" ,
-					Reactions
+					Reaction_Mechanism.Reactions
 			);
 		}
 
 
 		int i; 	// useful counter
-		int Number_Species = (int) Species.size();
-		int Number_Reactions = (int) Reactions.size();
+		int Number_Species = (int) Reaction_Mechanism.Species.size();
+		int Number_Reactions = (int) Reaction_Mechanism.Reactions.size();
 		vector< double > KeyRates; // for mechanism reduction
 
 		// We have now pre-processed all information, time to set up the ODEs and the solver
@@ -117,7 +117,7 @@ int main(int argc, char* argv[])
 		if(InitialParameters.MechanismAnalysis.MaximumRates)
 		{
 			// Initialise array
-			vector < str_RatesAnalysis > temp((int) Reactions.size());
+			vector < str_RatesAnalysis > temp((int) Reaction_Mechanism.Reactions.size());
 			for(i=0;i<Number_Species;i++)
 			{
 				RatesAnalysisData.push_back(temp);
@@ -128,7 +128,7 @@ int main(int argc, char* argv[])
 
 		if(InitialParameters.MechanismAnalysis.StreamRatesAnalysis)
 		{
-			PrepareStreamRatesAnalysis(Species,"");
+			PrepareStreamRatesAnalysis(Reaction_Mechanism.Species,"");
 		}
 
 
@@ -149,7 +149,7 @@ int main(int argc, char* argv[])
 					OutputFilenames.Species,
 					InitialParameters.Solver_Parameters.separator,
 					Number_Species,
-					Species,
+					Reaction_Mechanism.Species,
 					InitialParameters.GasPhase
 			);
 
@@ -174,7 +174,8 @@ int main(int argc, char* argv[])
 			Choose_Integrator(
 					OutputFilenames,
 					InitialSpeciesConcentration,
-					Species,Thermodynamics,Reactions,
+					Reaction_Mechanism,
+					//Species,Thermodynamics,Reactions,
 					InitialParameters,
 					KeyRates,
 					PetroOxyDataInitial,
@@ -185,8 +186,12 @@ int main(int argc, char* argv[])
 			if(InitialParameters.MechanismReduction.ReduceReactions != 0)
 			{
 				vector< SingleReactionData > ReducedReactions;
-				ReducedReactions = ReduceReactionsNew(Species, Reactions, KeyRates);
+				ReducedReactions = ReduceReactionsNew(Reaction_Mechanism.Species, Reaction_Mechanism.Reactions, KeyRates);
 
+				MechanismData Reduced_Reaction_Mechanism;
+				Reduced_Reaction_Mechanism.Species = Reaction_Mechanism.Species;
+				Reduced_Reaction_Mechanism.Thermodynamics = Reaction_Mechanism.Thermodynamics;
+				Reduced_Reaction_Mechanism.Reactions = ReducedReactions;
 
 				// start a second run only if reduced scheme is not empty and has size different
 				// to original scheme
@@ -200,7 +205,7 @@ int main(int argc, char* argv[])
 
 					Number_Reactions = (int) ReducedReactions.size();
 
-					WriteReactions("reduced_scheme.txt", Species, ReducedReactions);
+					WriteReactions("reduced_scheme.txt", Reduced_Reaction_Mechanism.Species, ReducedReactions);
 
 					InitialParameters.MechanismReduction.ReduceReactions = 0; // switch off reduction...
 
@@ -229,14 +234,14 @@ int main(int argc, char* argv[])
 
 					if(InitialParameters.MechanismAnalysis.StreamRatesAnalysis)
 					{
-						PrepareStreamRatesAnalysis(Species,OutputFilenames.Prefix);
+						PrepareStreamRatesAnalysis(Reduced_Reaction_Mechanism.Species,OutputFilenames.Prefix);
 					}
 
 					WriteNewLabelsSpecies(
 							OutputFilenames.Species,
 							InitialParameters.Solver_Parameters.separator,
 							Number_Species,
-							Species,
+							Reduced_Reaction_Mechanism.Species,
 							InitialParameters.GasPhase
 					);
 					WriteLabelsReactionRates(
@@ -250,7 +255,8 @@ int main(int argc, char* argv[])
 					Choose_Integrator(
 							OutputFilenames,
 							InitialSpeciesConcentration,
-							Species,Thermodynamics,ReducedReactions,
+							Reduced_Reaction_Mechanism,
+							//Species,Thermodynamics,ReducedReactions,
 							InitialParameters,
 							KeyRates,
 							PetroOxyDataInitial,
@@ -262,7 +268,7 @@ int main(int argc, char* argv[])
 					ReportAccuracy(
 							InitialParameters.Solver_Parameters.separator,
 							Number_Species,
-							Species,
+							Reduced_Reaction_Mechanism.Species,
 							"reduction_accuracy_report.txt",
 							"concentrations.txt",
 							"reduced_concentrations.txt"

diff --git a/source/get_input/Get_Initial_Conditions.cpp b/source/get_input/Get_Initial_Conditions.cpp
@@ -91,7 +91,7 @@ void Get_Initial_Conditions(
 
 
 	/* Other functions */
-	InitialParameters.nrspec = 0;
+	//InitialParameters.nrspec = 0;
 
 	/* Code extension for Gas Phase */
 	InitialParameters.GasPhase = false; // default not gas phase