gmpIphreeqcReaction.h

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/************************************************************************
**
** 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_IPHREEQC_REACTION_H_
#define _GEMA_PLUGIN_IPHREEQC_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 GmpIphreeqcReaction : public GmpChemicalFemPhysics
{
public:
        GmpIphreeqcReaction(GmSimulationData* simulation, QString id, QString description, const GmLogCategory& logger);
        virtual ~GmpIphreeqcReaction();
 
        // Comments on the base class
        virtual const char* pluginType() const { return "iphreeqc"; }
 
        // Comments on the base class
        virtual const QVariantMap* physicsMetaDataMap();
 
        // Comments on the base class
        virtual bool checkLoadedData();
 
        // Checks required nodal accessors based on the phreeqc input file
        bool checksNodalAccessors();
 
        // Comments on the base class
        virtual bool beforeElementStiffnessLoop(const GmpFemMatrixSet& elemMatrices, const GmpFemVectorSet& elemVectors);
 
        bool createIPhreeqcInput(IPhreeqc& R, const char* dump, int node);
 
        // Function to Run IPhreeqc
        bool runIPhreeqc(IPhreeqc& R);
 
        // funtion  to run Iphreeqc to calculate initial condition to mesh
        bool evaluateInitialConditions(QString& input);
 
        // save IPhreeqc Results value to node mesh attributes for Initial Conditions
        virtual bool setsInitialConditions(IPhreeqc& R, int node);
 
        // Gets selected phreeqc output values
        bool getSelectedPhreeqcOutputs(IPhreeqc& phreeqc, GmVector& data, int node);
 
        // save IPhreeqc value to node mesh attributes
        bool saveIPhreeqcValuesToNode(IPhreeqc& R, int node);
 
        // Updates solution ions of each especies for the next Phreeqc simulation
        bool updatesSolution(IPhreeqc& R, GmValueAccessor* ionAcc, int node);
 
        // Updates kinetic reaction of each mineral for the next Phreeqc simulation 
        bool updatesKinetics(IPhreeqc& R, GmValueAccessor* ionAcc, int node);
 
        // UpdatesEquilibrium reaction of each mineral for the next Phreeqc simulation 
        bool updatesEquilibrium(IPhreeqc& R, GmValueAccessor* ionAcc, int node);
 
        // Loads chemical parameters from phreeqc input file 
        bool loadsChemicalParameters(QString& inputPhreeqc);
 
        // Loads selected output data from phreeqc input file
        bool loadsOutputData(const QString& line, QString& Keyword, QList<QPair<QString, int>>& data, int offset=1);
 
        // Extracts segment of string between two words
        QString extractSegment(const QString& input, const QString& startWord, const QString& endWord);
        
        // Get results after convergence 
        virtual bool calcDerivedResults(bool nonLinearSolver);
 
        // method to run Iphreeqc at every node fo the mesh
        bool runIphreeqcNodes();
 
        // read node reaction values
        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;
 
        // Read node mineral values 
        void getMineralValues(const GmElement* e, GmVector& Rg, GmVector & Re, int pos) const;
        
protected:
  // See comments on the base class
  virtual bool checkAndLoadPrivateData(LuaTable& table);
  // Fills reaction rate contribution
        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);
        // fill elemental mass
        bool fillElementalMass();
 
        enum iPhreeqcReactionPhysicsAttributeIds
        {
                IPHREEQC_DATABASE_ID = GmpChemicalFemPhysics::NUM_ATTRIBUTE_IDS,  
                INPUT_A_ID,           // Id for retrieving the phreeqc input file
                POROS_A_ID,
 
                // --- NO ADDING BELOW THIS LINE
                NUM_ATTRIBUTE_IDS,  
        };
 
  enum NodeAttributeIds
  {
    IonSol_NA_ID= GmpChemicalFemPhysics::NUM_NA_IDS, 
    IonSolOld_NA_ID,     
    SIndex_NA_ID,        
    EqM_NA_ID,           
    KiM_NA_ID,          
    poroM_NA_ID,        
    poroMOld_NA_ID,
 
    // ------    NO ADDING BELOW THIS LINE
    NUM_NA_IDS,  
  };
 
        enum GaussAttributeIds
        {
                MASS_GA_ID = GmpChemicalFemPhysics::NUM_GA_IDS,
 
 
                // --- NO ADDING BELOW THIS LINE
                NUM_GA_IDS,  
        };
 
private:
        bool                      _isKinetics; // Flags to identify kinetics reaction in phreeqc input file
        bool                   _isEquilibrium; // Flags to identify Equilibrium reaction in phreeqc input file
        bool                    _isSaturation; // Flags to identify saturation indices in the phreeqc input file
        int                             _nOut; // Size of phreeqc output data 
        IPhreeqc                    _iphreeqc; // IPhreeqc reaction
        QByteArray                  _dumpData; // variable to store compressing all dump data 
        QList<QPair<QString, int>>  _solution; // List containing the name and output position of solution ions
        QList<QPair<QString, int>> _kiMineral; // List containing the name and output position of kinetic minerals
        QList<QPair<QString, int>> _eqMineral; // List containing the name and output position of equilibium minerals
        QList<QPair<QString, int>> _siMineral; // List containing the name and output position of mineral saturation index 
        QString               _selectedOutput; // String containing the selected output of the phreeqc input file
 
};
 
#endif