ksolve/VoxelPoolsBase.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 _VOXEL_POOLS_BASE_H
#define _VOXEL_POOLS_BASE_H

class RateTerm;
class Stoich;
class VoxelPoolsBase
{
    public: 
        VoxelPoolsBase();
        virtual ~VoxelPoolsBase();

        // Compute access operations.
        void resizeArrays( unsigned int totNumPools );

        unsigned int size() const;

        const double* S() const;

        vector< double >& Svec();

        double* varS();

        const double* Sinit() const;

        double* varSinit();

        void reinit();

        void setVolume( double vol );
        double getVolume() const;

        virtual void setVolumeAndDependencies( double vol );
        
        // Field assignment functions

        void setN( unsigned int i, double v );
        double getN( unsigned int ) const;
        void setNinit( unsigned int, double v );
        double getNinit( unsigned int ) const;
        void setDiffConst( unsigned int, double v );
        double getDiffConst( unsigned int ) const;
        // Functions to set up rates vector

        virtual void updateAllRateTerms( const vector< RateTerm* >& rates,
                unsigned int numCoreRates ) = 0;  

        virtual void updateRateTerms( const vector< RateTerm* >& rates,
                unsigned int numCoreRates, unsigned int index ) = 0;

        void filterCrossRateTerms( const vector< Id >& offSolverReacs, const vector< pair< Id, Id > >& offSolverReacCompts );

        // Functions to handle cross-compartment reactions.

        void xferIn( const vector< unsigned int >& poolIndex,
                const vector< double >& values, 
                const vector< double >& lastValues,
                unsigned int voxelIndex );

        void xferInOnlyProxies(
            const vector< unsigned int >& poolIndex,
            const vector< double >& values, 
            unsigned int numProxyPools,
            unsigned int voxelIndex );

        void xferOut( unsigned int voxelIndex,
                vector< double >& values,
                const vector< unsigned int >& poolIndex );
        void addProxyVoxy( unsigned int comptIndex, 
                        Id comptId, unsigned int voxel );
        void addProxyTransferIndex( unsigned int comptIndex, 
                        unsigned int transferIndex );


        bool hasXfer( unsigned int comptIndex ) const;

        bool isVoxelJunctionPresent( Id i1, Id i2 ) const;
        // Functions for cross-compartment rate scaling.

        void resetXreacScale( unsigned int size );

        void forwardReacVolumeFactor( unsigned int i, double volume );

        void backwardReacVolumeFactor( unsigned int i, double volume );

        double getXreacScaleSubstrates( unsigned int i ) const;

        double getXreacScaleProducts( unsigned int i ) const;

        void scaleVolsBufsRates( double ratio, const Stoich* stoichPtr );

        void print() const;

    protected:
        const Stoich* stoichPtr_;
        vector< RateTerm* > rates_;

    private:
        vector< double > S_;

        vector< double > Sinit_;

        vector< vector< unsigned int > > proxyPoolVoxels_;
        vector< vector< unsigned int > > proxyTransferIndex_;

        map< Id, unsigned int > proxyComptMap_;

        double volume_;

        vector< double > xReacScaleSubstrates_;

        vector< double > xReacScaleProducts_;
};

#endif  // _VOXEL_POOLS_BASE_H

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