gmpChemicalReaction.h

/************************************************************************
**
** Copyright (C) 2014 by Carlos Augusto Teixera Mendes
** All rights reserved.
**
** This file is part of the "GeMA" software. It's use should respect
** the terms in the license agreement that can be found together
** with this source code.
** It is provided AS IS, with NO WARRANTY OF ANY KIND,
** INCLUDING THE WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR
** A PARTICULAR PURPOSE.
**
************************************************************************/
 
#ifndef _GEMA_PLUGIN_CHEMICAL_REACTION_H_
#define _GEMA_PLUGIN_CHEMICAL_REACTION_H_
 
#include "gmpChemicalFemPhysics.h"
#include <gmSimulationData.h>
 
#pragma warning( push ) // Phreeqc messes with warning 4251 and ends-up re-enabling it
#include <IPhreeqc.hpp>
#pragma warning( pop )
 
 
class GMP_CHEMICAL_FEM_PHYSICS_API_EXPORT GmpChemicalReaction : public GmpChemicalFemPhysics
{
public:
        GmpChemicalReaction(GmSimulationData* simulation, QString id, QString description, const GmLogCategory& logger);
        virtual ~GmpChemicalReaction();
 
        // Comments on the base class
        virtual const char* pluginType() const { return "chemicalReaction"; }
 
        // Comments on the base class
        virtual const QVariantMap* physicsMetaDataMap();
 
        // Comments on the base class
        virtual bool checkLoadedData();
 
        // Comments on the base class
        virtual bool beforeElementStiffnessLoop(const GmpFemMatrixSet& elemMatrices, const GmpFemVectorSet& elemVectors);
        
        // INITIAL CONDITIONS SIMULATION
 
        // Function to fill in IPhreeqc input data for initial condition
         virtual void createIPhreeqcIC(IPhreeqc& R,  int node);
 
        // Function to Run IPhreeqc for calculate initial condition
        virtual bool runIPhreeqcIC(IPhreeqc& R);
 
        // save IPhreeqc Results value to node mesh attributes for Initial Conditions
        virtual bool saveIPhreeqcValuestoMeshIC(IPhreeqc& R, int node);
        
        //BOUNDARY CONDITIONS VALUE  SIMULATION
 
        // Function to fill IPhreeqc input data for Boundary Conditions
         virtual bool createIPhreeqcBC(IPhreeqc& R);
 
        //Function to run Iphreeqc Boundary Conditions
        virtual bool runIPhreeqcBC(IPhreeqc& R);
 
        // Save IPhreeqc Results value to Boundary Conditions
        virtual bool saveIPhreeqcValuestoBCNode(IPhreeqc& R);
        
        // RUN IPREEQC FOR NODE VALUE CALCULATIOS 
        // Function to fill in IPhreeqc input data
        virtual bool createIPhreeqcInput(IPhreeqc& R, int node);
 
        // Function to Run IPhreeqc
        virtual bool runIPhreeqc(IPhreeqc& R);
 
        // save IPhreeqc value to node mesh attributes
        virtual bool saveIPhreeqcValuestoNode(IPhreeqc& R, int node);
 
        // concatenate input data
        char *concatenateChar(std::string name, long double val);
        char *concatenateChar(std::string name, GmVector val);
        char *concatenateChar(std::string name, long double val1, std::string name2, long double val2);
        char *concatenateChar(std::string name, long double val1, std::string name2);
        char *concatenateChar(std::string name, std::string name2, int val1, std::string name3);
        // Fill parameters to solution and equilibrium reaction
        virtual GmVector fillSolutionParameters(GmCellAccessor* ac, const GmElement* e, const GmVector* coord, int ip) const;
        virtual GmMatrix fillEquilibriumParameters(GmCellAccessor* ac, const GmElement* e, const GmVector* coord, int ip) const;
 
        // Get results after convergence 
        virtual bool calcDerivedResults(bool nonLinearSolver);
 
        // method to run Iphreeqc at every node fo the mesh
        virtual bool runIphreeqcNodes();
 
        // funtion  to run Iphreeqc to calculate initial condition to mesh
        virtual bool runInitIphreeqcNodes();
 
        // function  to run Iphreeqc for boundary conditions value 
        virtual bool runBCIPhreeqc();
 
        // read node reaction values
        virtual void getReactionValues(const GmElement* e, const GmVector& Rg, GmVector& Re, int pos) const;
 
        // Fill vector for element data
        virtual void FillElementalReaction(const GmElement* e, GmVector& elemFe, const GmVector& Fr, int pos) const;
        char buffer[200];
 
protected:
 
        virtual bool reactionRate(const GmElement* e, const GmVector* ip, int ipIndex, const GmVector& N,
                const GmVector& C, double wtJ, GmVector& elemFe, GmMatrix& elemK,
                bool needsFe, bool needsK);
 
        enum iPhreeqcReactionPhysicsAttributeIds
        {
                IPHREEQC_DATABASE_ID = GmpChemicalFemPhysics::NUM_ATTRIBUTE_IDS,  
                REACTION_TYPE_ID,     
                TEMP_A_ID,
                PE_A_ID,
                DW_A_ID,
                MW_A_ID,
                ALK_A_ID,
                PH_A_ID,
                Ca_A_ID,
                Cl_A_ID,
                Mg_A_ID,
                C_A_ID,
                Fe_A_ID,
                Na_A_ID,
                NEc_A_ID,
                NEd_A_ID,
                SIc_A_ID,
                SId_A_ID,
                nKc_A_ID,
                nKd_A_ID,
                SRc_A_ID,
                SRd_A_ID,
                POROS_A_ID, 
                // Boundary conditions fluid compositions
                TEMP_Abc_ID,
                PE_Abc_ID,
                DW_Abc_ID,
                MW_Abc_ID,
                ALK_Abc_ID,
                PH_Abc_ID,
                Ca_Abc_ID,
                Cl_Abc_ID,
                Mg_Abc_ID,
                C_Abc_ID,
                Fe_Abc_ID,
                Na_Abc_ID,
                
 
                // --- NO ADDING BELOW THIS LINE
                NUM_ATTRIBUTE_IDS,  
        };
 
        enum NodeAttributeIds
        {
                IonSol_NA_ID = GmpChemicalFemPhysics::NUM_NA_IDS, 
                IonSolOld_NA_ID,     
                SIndex_NA_ID,        
                SIndexOld_NA_ID,
                PH_NA_ID,            
                PHOld_NA_ID,
                EqRxn_NA_ID,         
                EqRxnOld_NA_ID,
                Mineral_NA_ID,       
                MineralOld_NA_ID,
                poroM_NA_ID,         
                poroMOld_NA_ID,
                KinCtr_NA_ID,        
                KinCtrOld_NA_ID,
 
                // ------    NO ADDING BELOW THIS LINE
                NUM_NA_IDS,  
        };
 
        enum iPHreeqcReactionElemPropertyIds
        {
                TemSol_ID = GmpChemicalFemPhysics::NUM_PROPERTY_IDS,  
                BonCon_D,
                Fip_D,
 
 
                // --- NO ADDING BELOW THIS LINE
                NUM_PROPERTY_IDS,  
        };
 
private:
        IPhreeqc _IPhreeqcReaction;   // IPhreeqc reaction
 
};
 
#endif