gmpNeuralNetworkReaction.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_CHEMICAL_NEURALNETWORK_REACTION_H_
#define _GEMA_PLUGIN_CHEMICAL_NEURALNETWORK_REACTION_H_
 
#include "gmpChemicalFemPhysics.h"
#include <gmSimulationData.h>
#include <gmpFemNeuralNetwork.h>
#include <IPhreeqc.hpp>
 
 
class GMP_CHEMICAL_FEM_PHYSICS_API_EXPORT GmpNeuralNetworkReaction : public GmpChemicalFemPhysics
{
public:
        GmpNeuralNetworkReaction(GmSimulationData* simulation, QString id, QString description, const GmLogCategory& logger);
        virtual ~GmpNeuralNetworkReaction();
 
        // Comments on the base class
        virtual const char* pluginType() const { return "neuralNetwork"; }
 
        // 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);
 
        // save IPhreeqc Results value to node mesh attributes for Initial Conditions
        virtual bool saveIPhreeqcValuesToMeshIC(IPhreeqc& R, int node);
 
        virtual void runfile(IPhreeqc& R);
        virtual void SetOutputFile(IPhreeqc& R);
        // 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 runNeuralNetwork();
        // funtion  to run Iphreeqc to calculate initial condition to mesh
        virtual bool runInitIphreeqcNodes();
 
 
        // 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;
 
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);
 
        enum ANNPhysicsAttributeIds
        {
                IPHREEQC_DATABASE_ID = GmpChemicalFemPhysics::NUM_ATTRIBUTE_IDS,  
                REACTION_TYPE_ID,     
                RUNFILENAMW_ID,
                SRc_A_ID,
                SRd_A_ID,
                POROS_A_ID,
 
                // --- NO ADDING BELOW THIS LINE
                NUM_ATTRIBUTE_IDS,  
        };
 
        enum ANNNodeAttributeIds
        {
                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,
                Ctrate_NA_ID,        
                CtrateOld_NA_ID,
 
                // ------    NO ADDING BELOW THIS LINE
                NUM_NA_IDS,  
        };
 
        enum ANNGaussAttributeIds
        {
                MASS_GA_ID = GmpChemicalFemPhysics::NUM_GA_IDS,
 
 
                // --- NO ADDING BELOW THIS LINE
                NUM_GA_IDS,  
        };
 
private:
        IPhreeqc _IPhreeqcReaction;   // IPhreeqc reaction
        GmpFemNeuralNetwork* _net; 
};
 
#endif