CylMesh.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 _CYL_MESH_H
#define _CYL_MESH_H

class CylMesh: public MeshCompt
{
    public:
        CylMesh();
        ~CylMesh();
        //  Utility func

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

        // Field assignment stuff

        void setX0( const Eref& e, double v );
        double getX0( const Eref& e ) const;
        void setY0( const Eref& e, double v );
        double getY0( const Eref& e ) const;
        void setZ0( const Eref& e, double v );
        double getZ0( const Eref& e ) const;
        void setR0( const Eref& e, double v );
        double getR0( const Eref& e ) const;

        void setX1( const Eref& e, double v );
        double getX1( const Eref& e ) const;
        void setY1( const Eref& e, double v );
        double getY1( const Eref& e ) const;
        void setZ1( const Eref& e, double v );
        double getZ1( const Eref& e ) const;
        void setR1( const Eref& e, double v );
        double getR1( const Eref& e ) const;

        void innerSetCoords( const Eref& e, const vector< double >& v);
        void setCoords( const Eref& e, vector< double > v );
        vector< double > getCoords( const Eref& e ) const;

        void setDiffLength( const Eref& e, double v );
        double getDiffLength( const Eref& e ) const;

        double getTotLength() const;

        unsigned int innerGetDimensions() const;

        // FieldElement assignment stuff for MeshEntries

        unsigned int getMeshType( unsigned int fid ) const;
        unsigned int getMeshDimensions( unsigned int fid ) 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 );

        void transmitChange( const Eref& e );

        void buildStencil();

        // 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;

        double nearest( double x, double y, double z,
                        double& linePos, double& r ) const;

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

        // Inner specific functions needed by matchMeshEntries.
        void matchCylMeshEntries( const CylMesh* other,
            vector< VoxelJunction >& ret ) const;
        void matchCubeMeshEntries( const CubeMesh* other,
            vector< VoxelJunction >& ret ) const;
        void matchNeuroMeshEntries( const NeuroMesh* other,
            vector< VoxelJunction >& ret ) const;

        // Selects a grid volume for generating intersection with CubeMesh.
        double selectGridVolume( double h ) const;


        static const Cinfo* initCinfo();

    private:
        unsigned int numEntries_; // Number of subdivisions to use
        bool useCaps_; // Flag: Should the ends have hemispherical caps?
        bool isToroid_; // Flag: Should the ends loop around mathemagically?

        double x0_; 
        double y0_; 
        double z0_; 

        double x1_; 
        double y1_; 
        double z1_; 

        double r0_; 
        double r1_; 

        double diffLength_; 

        double surfaceGranularity_;

        double totLen_; 
        double rSlope_; 
        double lenSlope_; 
};

#endif  // _CYL_MESH_H