ksolve/Ksolve.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/

#ifndef _KSOLVE_H
#define _KSOLVE_H

class Stoich;

class Ksolve: public ZombiePoolInterface
{
    public: 
        Ksolve();
        ~Ksolve();

        // Field assignment stuff
        string getMethod() const;
        void setMethod( string method );

        double getEpsAbs() const;
        void setEpsAbs( double val );
        
        double getEpsRel() const;
        void setEpsRel( double val );

        Id getStoich() const;
        void setStoich( Id stoich ); 

        Id getDsolve() const;
        void setDsolve( Id dsolve ); 

        unsigned int getNumLocalVoxels() const;
        unsigned int getNumAllVoxels() const;
        void setNumAllVoxels( unsigned int num );

        vector< double > getNvec( unsigned int voxel) const;
        void setNvec( unsigned int voxel, vector< double > vec );

        double getEstimatedDt() const;

        // Dest Finfos
        void process( const Eref& e, ProcPtr p );
        void reinit( const Eref& e, ProcPtr p );
        void initProc( const Eref& e, ProcPtr p );
        void initReinit( const Eref& e, ProcPtr p );
        void updateVoxelVol( vector< double > vols );
        // Utility for SrcFinfo

        // Solver interface functions
        unsigned int getPoolIndex( const Eref& e ) const;
        unsigned int getVoxelIndex( const Eref& e ) const;
        
        // ZombiePoolInterface inherited functions

        void setN( const Eref& e, double v );
        double getN( const Eref& e ) const;
        void setNinit( const Eref& e, double v );
        double getNinit( const Eref& e ) const;
        void setDiffConst( const Eref& e, double v );
        double getDiffConst( const Eref& e ) const;

        void setNumPools( unsigned int num );
        unsigned int getNumPools() const;
        VoxelPoolsBase* pools( unsigned int i );
        double volume( unsigned int i ) const;

        void getBlock( vector< double >& values ) const;
        void setBlock( const vector< double >& values );

        void matchJunctionVols( vector< double >& vols, Id otherCompt ) 
                const;
    
        void updateRateTerms( unsigned int index );

        // Functions for cross-compartment transfer
        void setupXfer( Id myKsolve, Id otherKsolve, 
                        unsigned int numProxyMols,
                        const vector< VoxelJunction >& vj );

        void assignXferIndex( unsigned int numProxyMols, 
                        unsigned int xferCompt,
                        const vector< vector< unsigned int > >& voxy );

        void assignXferVoxels( unsigned int xferCompt );

        unsigned int assignProxyPools( const map< Id, vector< Id > >& xr,
                    Id myKsolve, Id otherKsolve, Id otherComptId );

        void buildCrossReacVolScaling( Id otherKsolve,
                const vector< VoxelJunction >& vj );
        // for debugging
        void print() const;

        static SrcFinfo2< Id, vector< double > >* xComptOut();
        static const Cinfo* initCinfo();
    private:
        string method_;
        double epsAbs_;
        double epsRel_;
        vector< VoxelPools > pools_;

        unsigned int startVoxel_;

        Stoich* stoichPtr_;

        Id dsolve_;

        ZombiePoolInterface* dsolvePtr_;
};

#endif  // _KSOLVE_H

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