ChemCompt.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2010 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 _CHEM_COMPT_H
#define _CHEM_COMPT_H

#include "VoxelJunction.h"

class ChemCompt
{
    public:
        ChemCompt();
        virtual ~ChemCompt();
        // Field assignment stuff

        double getEntireVolume( const Eref& e ) const;

        // Virtual function to get vol of entire compartment.
        virtual double vGetEntireVolume() const = 0;

        void setEntireVolume( const Eref& e, double volume);

        double getOneVoxelVolume( const Eref& e, unsigned int voxel ) const;
        void setOneVoxelVolume( const Eref& e, unsigned int voxel,
                        double volume );

        unsigned int getDimensions() const;
        virtual unsigned int innerGetDimensions() const = 0;

        void setMethod( string method );
        string getMethod() const;

        bool getIsMembraneBound() const;
        void setIsMembraneBound( bool v );

        vector< double > getStencilRate( unsigned int row ) const;

        virtual vector< double > innerGetStencilRate( unsigned int row ) const = 0;

        vector< unsigned int > getStencilIndex( unsigned int row ) const;

        vector< double > getVoxelVolume() const;
        virtual const vector< double >& vGetVoxelVolume() const = 0;

        vector< double > getVoxelMidpoint() const;
        virtual const vector< double >& vGetVoxelMidpoint() const = 0;

        // Dest Finfo

        void setVolumeNotRates( double volume);

        virtual bool vSetVolumeNotRates( double volume) = 0;

        void buildDefaultMesh( const Eref& e,
            double volume, unsigned int numEntries );
        virtual void innerBuildDefaultMesh(
            const Eref& e,
            double volume, unsigned int numEntries ) = 0;

        /*
        void handleRequestMeshStats( const Eref& e );
        virtual void innerHandleRequestMeshStats(
            const Eref& e,
            const SrcFinfo2< unsigned int, vector< double > >*
                meshStatsFinfo
        ) = 0;
        */

        void handleNodeInfo( const Eref& e,
            unsigned int numNodes, unsigned int numThreads );
        virtual void innerHandleNodeInfo(
            const Eref& e,
            unsigned int numNodes, unsigned int numThreads ) = 0;

        void resetStencil();
        virtual void innerResetStencil() = 0;

        // FieldElementFinfo stuff for MeshEntry lookup

        unsigned int getNumEntries() const;
        virtual unsigned int innerGetNumEntries() const = 0;

        void setNumEntries( unsigned int num );
        virtual void innerSetNumEntries( unsigned int n ) = 0;

        MeshEntry* lookupEntry( unsigned int index );

        // Generic utility function
        static double distance( double x, double y, double z );

        // Utility function for volume rescaling

        void getChildConcs( const Eref& e, vector< double >& childConcs )
                const;

        unsigned int setChildConcs( const Eref& e,
            const vector< double >& childConcs, unsigned int start ) const;

        // Lookup funcs for Boundary
        /*
        Boundary* lookupBoundary( unsigned int index );
        void setNumBoundary( unsigned int num );
        unsigned int getNumBoundary( ) const;
        */

        void buildJunction( ChemCompt* other, vector< VoxelJunction >& ret );

        virtual void matchMeshEntries( const ChemCompt* other,
            vector< VoxelJunction > & ret ) const = 0;


        virtual double nearest( double x, double y, double z,
                        unsigned int& index ) const = 0;

        virtual void indexToSpace( unsigned int index,
                        double& x, double& y, double& z ) const = 0;

        void flipRet( vector< VoxelJunction >& ret ) const;

        // FieldElement assignment stuff for MeshEntries
        virtual unsigned int getMeshType( unsigned int fid )
            const = 0;
        virtual unsigned int getMeshDimensions( unsigned int fid )
            const = 0;
        virtual double getMeshEntryVolume( unsigned int fid )
            const = 0;
        //
        virtual void setMeshEntryVolume( unsigned int fid, double volume );

        virtual vector< double > getCoordinates( unsigned int fid )
            const = 0;
        virtual vector< unsigned int > getNeighbors( unsigned int fid )
            const = 0;
        virtual vector< double > getDiffusionArea( unsigned int fid )
            const = 0;
        virtual vector< double > getDiffusionScaling( unsigned int fid )
            const = 0;

        virtual double extendedMeshEntryVolume( unsigned int fid )
            const = 0;

        virtual void clearExtendedMeshEntryVolume() = 0;

        virtual unsigned int getStencilRow( unsigned int meshIndex,
                const double** entry, const unsigned int** colIndex )
                const = 0;


        virtual void extendStencil(
            const ChemCompt* other, const vector< VoxelJunction >& vj ) = 0;

        static SrcFinfo1< vector< double > >* voxelVolOut();

        static const Cinfo* initCinfo();

    private:
        MeshEntry entry_; 

        vector< Boundary > boundaries_;

        string method_;

        bool isMembraneBound_;
};

extern SrcFinfo5<
    double,
    vector< double >,
    vector< unsigned int>,
    vector< vector< unsigned int > >,
    vector< vector< unsigned int > >
    >* meshSplit();

#endif  // _CHEM_COMPT_H