CubeMesh.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 _CUBE_MESH_H
#define _CUBE_MESH_H

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

        // Field assignment stuff

        void setX0( double v );
        double getX0() const;
        void setY0( double v );
        double getY0() const;
        void setZ0( double v );
        double getZ0() const;

        void setX1( double v );
        double getX1() const;
        void setY1( double v );
        double getY1() const;
        void setZ1( double v );
        double getZ1() const;

        void setDx( double v );
        double getDx() const;
        void setDy( double v );
        double getDy() const;
        void setDz( double v );
        double getDz() const;

        void setNx( unsigned int v );
        unsigned int getNx() const;
        void setNy( unsigned int v );
        unsigned int getNy() const;
        void setNz( unsigned int v );
        unsigned int getNz() const;

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

        void setMeshToSpace( vector< unsigned int > v );
        vector< unsigned int > getMeshToSpace() const;

        void setSpaceToMesh( vector< unsigned int > v );
        vector< unsigned int > getSpaceToMesh() const;

        void setSurface( vector< unsigned int > v );
        vector< unsigned int > getSurface() const;

        unsigned int innerGetDimensions() const;

        void setIsToroid( bool v );
        bool getIsToroid() const;

        void setPreserveNumEntries( bool v );
        bool getPreserveNumEntries() const;

        void setAlwaysDiffuse( bool v );
        bool getAlwaysDiffuse() 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 );

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

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

        double vGetEntireVolume() const;

        // Dest funcs

        void buildMesh( Id geom, double x, double y, double z );

        void addStoich( Id stoich );

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

        bool vSetVolumeNotRates( double volume );

        //  Utility func

        void updateCoords();

        unsigned int neighbor( unsigned int spaceIndex,
            int dx, int dy, int dz ) const;

        void transmitChange( const Eref& e, double oldvol );

        bool isInsideCuboid( double x, double y, double z ) const;
        bool isInsideSpheroid( double x, double y, double z ) const;

        //  Stuff for junctions

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

        void matchCubeMeshEntries( const CubeMesh* other,
            vector< VoxelJunction >& ret ) const;

        // Some ugly stuff here for cyl meshes.
        void matchCylMeshEntries( const ChemCompt* other,
            vector< VoxelJunction >& ret ) const;

        void matchAllEntries( const CubeMesh* other,
            vector< VoxelJunction >& ret ) const;


        /*
        void matchSameSpacing( const CubeMesh* other,
            vector< pair< unsigned int, unsigned int > >& ret ) const;
            */

        unsigned int numDims() const;

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

        unsigned int spaceToIndex( double x, double y, double z ) const;

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

        int compareMeshSpacing( const CubeMesh* other ) const;

        void defineIntersection( const CubeMesh* other,
            double& xmin, double &xmax,
            double& ymin, double &ymax,
            double& zmin, double &zmax ) const;

        void fillTwoDimSurface();

        void fillThreeDimSurface();

        const vector< unsigned int >& surface() const;
        //  Stuff for diffusion

        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;

        void buildStencil();
        void fillSpaceToMeshLookup();

        void deriveM2sFromS2m();

        void deriveS2mFromM2s();

        void assignVoxels(
                vector< pair< unsigned int, unsigned int > >& intersect,
                double xmin, double xmax,
                double ymin, double ymax,
                double zmin, double zmax
               ) const;

        void setDiffScale( const CubeMesh* other,
            vector< VoxelJunction >& ret ) const;
        void setJunctionVol( const CubeMesh* other,
            vector< VoxelJunction >& ret ) const;

        void updateM2s();
        void updateS2m();
        static const unsigned int EMPTY;
        static const unsigned int SURFACE;
        static const unsigned int ABUTX;
        static const unsigned int ABUTY;
        static const unsigned int ABUTZ;
        static const unsigned int MULTI;

        static const Cinfo* initCinfo();

    private:
        bool isToroid_; 
        bool preserveNumEntries_; 
        bool alwaysDiffuse_; 

        double x0_; 
        double y0_; 
        double z0_; 

        double x1_; 
        double y1_; 
        double z1_; 

        double dx_; 
        double dy_; 
        double dz_; 

        unsigned int nx_; 
        unsigned int ny_; 
        unsigned int nz_; 

        vector< unsigned int > m2s_;

        vector< unsigned int > s2m_;

        vector< unsigned int > surface_;
};

#endif  // _CUBE_MESH_H