EndoMesh.h

Go to the documentation of this file.

/**********************************************************************
** 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 _ENDO_MESH_H
#define _ENDO_MESH_H

class EndoMesh: public MeshCompt
{
    public:
        EndoMesh();
        ~EndoMesh();
        // Field assignment stuff
        void setRpower( const Eref& e, double v );
        double getRpower( const Eref& e ) const;
        void setRscale( const Eref& e, double v );
        double getRscale( const Eref& e ) const;
        void setApower( const Eref& e, double v );
        double getApower( const Eref& e ) const;
        void setAscale( const Eref& e, double v );
        double getAscale( const Eref& e ) const;
        void setVpower( const Eref& e, double v );
        double getVpower( const Eref& e ) const;
        void setVscale( const Eref& e, double v );
        double getVscale( const Eref& e ) const;
        void setSurround( const Eref& e, ObjId v );
        ObjId getSurround( const Eref& e ) const;
        void setDoAxialDiffusion( const Eref& e, bool v );
        bool getDoAxialDiffusion( const Eref& e ) const;

        // FieldElement assignment stuff for MeshEntries

        unsigned int getMeshType( unsigned int fid ) const;
        unsigned int getMeshDimensions( unsigned int fid ) const;
        unsigned int innerGetDimensions() const;
        double getMeshEntryVolume( unsigned int fid ) const;
        vector< double > getCoordinates( unsigned int fid ) const;
        vector< double > getDiffusionArea( unsigned int fid ) const;
        vector< double > getDiffusionScaling( unsigned int fid ) const;
        double extendedMeshEntryVolume( unsigned int fid ) const;


        unsigned int innerGetNumEntries() const;
        void innerSetNumEntries( unsigned int n );

        vector< unsigned int > getParentVoxel() const;
        const vector< double >& vGetVoxelVolume() const;
        const vector< double >& vGetVoxelMidpoint() const;
        const vector< double >& getVoxelArea() const;
        const vector< double >& getVoxelLength() const;

        double vGetEntireVolume() const;

        bool vSetVolumeNotRates( double volume );
        // Dest funcs

        void innerBuildDefaultMesh( const Eref& e,
            double volume, unsigned int numEntries );

        void innerHandleRequestMeshStats(
            const Eref& e,
            const SrcFinfo2< unsigned int, vector< double > >*
                meshStatsFinfo
        );

        void innerHandleNodeInfo(
            const Eref& e,
            unsigned int numNodes, unsigned int numThreads );

        // inherited virtual funcs for Boundary

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

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

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


        static const Cinfo* initCinfo();

    private:
        ObjId surround_;    
        const MeshCompt* parent_;

        Id insideMeshes_;   

        double rPower_;     
        double rScale_;     
        double aPower_;     
        double aScale_;     
        double vPower_;     
        double vScale_;     

        bool doAxialDiffusion_; 
};

#endif  // _ENDO_MESH_H