MeshCompt.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2011 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 _MESH_COMPT_H
#define _MESH_COMPT_H

class MeshCompt: public ChemCompt
{
    public:
        MeshCompt();
        ~MeshCompt();


        double extendedMeshEntryVolume( unsigned int fid ) const;

        void clearExtendedMeshEntryVolume();

        void innerResetStencil();

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

        const SparseMatrix< double >& getStencil() const;

        vector< unsigned int > getNeighbors( unsigned int fid ) const;

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

        void addRow( unsigned int index, const vector< double >& entry,
            const vector< unsigned int >& colIndex );

        void setStencilSize( unsigned int numRows, unsigned int numCols );


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

        virtual vector< unsigned int > getParentVoxel() const = 0;
        virtual const vector< double >& getVoxelArea() const = 0;
        virtual const vector< double >& getVoxelLength() const = 0;

    private:

        SparseMatrix< double > coreStencil_;

        SparseMatrix< double > m_;

        vector< double > extendedMeshEntryVolume_;
};

// Helper class for setting up and sorting rows of matrix entries.
class Ecol {
    public:
        Ecol( double e, unsigned int col )
            : e_( e ), col_( col )
        {;}

        Ecol()
            : e_( 0 ), col_( 0 )
        {;}

        bool operator<( const Ecol& other ) const
        {
            return col_ < other.col_;
        }

        double e_;
        double col_;
};

#endif  // _MESH_COMPT_H