MOOSE: mesh/CubeMesh.h Source File

00001 /**********************************************************************
00002 ** This program is part of 'MOOSE', the
00003 ** Messaging Object Oriented Simulation Environment.
00004 **           Copyright (C) 2011 Upinder S. Bhalla. and NCBS
00005 ** It is made available under the terms of the
00006 ** GNU Lesser General Public License version 2.1
00007 ** See the file COPYING.LIB for the full notice.
00008 **********************************************************************/
00009 
00010 #ifndef _CUBE_MESH_H
00011 #define _CUBE_MESH_H
00012 
00019 class CubeMesh: public MeshCompt
00020 {
00021     public: 
00022         CubeMesh();
00023         ~CubeMesh();
00024 
00026         // Field assignment stuff
00028 
00029         void setX0( double v );
00030         double getX0() const;
00031         void setY0( double v );
00032         double getY0() const;
00033         void setZ0( double v );
00034         double getZ0() const;
00035 
00036         void setX1( double v );
00037         double getX1() const;
00038         void setY1( double v );
00039         double getY1() const;
00040         void setZ1( double v );
00041         double getZ1() const;
00042 
00043         void setDx( double v );
00044         double getDx() const;
00045         void setDy( double v );
00046         double getDy() const;
00047         void setDz( double v );
00048         double getDz() const;
00049 
00050         void setNx( unsigned int v );
00051         unsigned int getNx() const;
00052         void setNy( unsigned int v );
00053         unsigned int getNy() const;
00054         void setNz( unsigned int v );
00055         unsigned int getNz() const;
00056 
00057         void innerSetCoords( const vector< double >& v );
00058         void setCoords( const Eref& e, vector< double > v );
00059         vector< double > getCoords( const Eref& e ) const;
00060 
00061         void setMeshToSpace( vector< unsigned int > v );
00062         vector< unsigned int > getMeshToSpace() const;
00063 
00064         void setSpaceToMesh( vector< unsigned int > v );
00065         vector< unsigned int > getSpaceToMesh() const;
00066 
00067         void setSurface( vector< unsigned int > v );
00068         vector< unsigned int > getSurface() const;
00069 
00070         unsigned int innerGetDimensions() const;
00071 
00072         void setIsToroid( bool v );
00073         bool getIsToroid() const;
00074 
00075         void setPreserveNumEntries( bool v );
00076         bool getPreserveNumEntries() const;
00077 
00078         void setAlwaysDiffuse( bool v );
00079         bool getAlwaysDiffuse() const;
00080 
00082         // FieldElement assignment stuff for MeshEntries
00084 
00086         unsigned int getMeshType( unsigned int fid ) const;
00088         unsigned int getMeshDimensions( unsigned int fid ) const;
00090         double getMeshEntryVolume( unsigned int fid ) const;
00092         vector< double > getCoordinates( unsigned int fid ) const;
00094         vector< double > getDiffusionArea( unsigned int fid ) const;
00096         vector< double > getDiffusionScaling( unsigned int fid ) const;
00097 
00099 
00104         double extendedMeshEntryVolume( unsigned int fid ) const;
00105 
00109         unsigned int innerGetNumEntries() const;
00111         void innerSetNumEntries( unsigned int n );
00112             
00113         void innerHandleRequestMeshStats(
00114             const Eref& e,
00115             const SrcFinfo2< unsigned int, vector< double > >*
00116                 meshStatsFinfo
00117         );
00118 
00119         void innerHandleNodeInfo(
00120             const Eref& e, 
00121             unsigned int numNodes, unsigned int numThreads );
00122 
00124         double vGetEntireVolume() const;
00125 
00127         // Dest funcs
00129 
00130         void buildMesh( Id geom, double x, double y, double z );
00131 
00132         void addStoich( Id stoich );
00133 
00135         void innerBuildDefaultMesh( const Eref& e,
00136             double volume, unsigned int numEntries );
00137 
00139         bool vSetVolumeNotRates( double volume );
00140 
00142         //  Utility func
00144 
00148         void updateCoords();
00149 
00150         unsigned int neighbor( unsigned int spaceIndex, 
00151             int dx, int dy, int dz ) const;
00152 
00153         void transmitChange( const Eref& e, double oldvol );
00154 
00155         bool isInsideCuboid( double x, double y, double z ) const;
00156         bool isInsideSpheroid( double x, double y, double z ) const;
00157 
00159         //  Stuff for junctions
00161 
00166         void matchMeshEntries( const ChemCompt* other,
00167             vector< VoxelJunction >& ret ) const;
00168 
00173         void matchCubeMeshEntries( const CubeMesh* other,
00174             vector< VoxelJunction >& ret ) const;
00175 
00176         // Some ugly stuff here for cyl meshes.
00177         void matchCylMeshEntries( const ChemCompt* other,
00178             vector< VoxelJunction >& ret ) const;
00179 
00184         void matchAllEntries( const CubeMesh* other,
00185             vector< VoxelJunction >& ret ) const;
00186 
00187 
00188         /*
00190         void matchSameSpacing( const CubeMesh* other,
00191             vector< pair< unsigned int, unsigned int > >& ret ) const;
00192             */
00193 
00195         unsigned int numDims() const;
00196         
00198         void indexToSpace( unsigned int index, 
00199                         double& x, double& y, double& z ) const;
00200 
00202         unsigned int spaceToIndex( double x, double y, double z ) const;
00203 
00208         double nearest( double x, double y, double z, unsigned int& index )
00209                 const;
00210         
00212         int compareMeshSpacing( const CubeMesh* other ) const;
00213 
00215         void defineIntersection( const CubeMesh* other,
00216             double& xmin, double &xmax,
00217             double& ymin, double &ymax,
00218             double& zmin, double &zmax ) const;
00219         
00221         void fillTwoDimSurface();
00222 
00225         void fillThreeDimSurface();
00226 
00228         const vector< unsigned int >& surface() const;
00230         //  Stuff for diffusion
00232 
00234         vector< unsigned int > getParentVoxel() const;
00235         const vector< double >& vGetVoxelVolume() const;
00236         const vector< double >& vGetVoxelMidpoint() const;
00237         const vector< double >& getVoxelArea() const;
00238         const vector< double >& getVoxelLength() const;
00239 
00251         void buildStencil();
00252         void fillSpaceToMeshLookup();
00253 
00259         void deriveM2sFromS2m();
00260 
00266         void deriveS2mFromM2s();
00267 
00268         void assignVoxels( 
00269                 vector< pair< unsigned int, unsigned int > >& intersect,
00270                 double xmin, double xmax, 
00271                 double ymin, double ymax, 
00272                 double zmin, double zmax
00273                ) const;
00274         
00276         void setDiffScale( const CubeMesh* other,
00277             vector< VoxelJunction >& ret ) const;
00279         void setJunctionVol( const CubeMesh* other,
00280             vector< VoxelJunction >& ret ) const;
00281 
00282         void updateM2s();
00283         void updateS2m();
00285         static const unsigned int EMPTY;
00286         static const unsigned int SURFACE;
00287         static const unsigned int ABUTX;
00288         static const unsigned int ABUTY;
00289         static const unsigned int ABUTZ;
00290         static const unsigned int MULTI;
00291 
00292         static const Cinfo* initCinfo();
00293 
00294     private:
00295         bool isToroid_; 
00296         bool preserveNumEntries_; 
00297         bool alwaysDiffuse_; 
00298 
00299         double x0_; 
00300         double y0_; 
00301         double z0_; 
00302 
00303         double x1_; 
00304         double y1_; 
00305         double z1_; 
00306 
00307         double dx_; 
00308         double dy_; 
00309         double dz_; 
00310 
00311         unsigned int nx_; 
00312         unsigned int ny_; 
00313         unsigned int nz_; 
00314 
00330         vector< unsigned int > m2s_;
00331 
00339         vector< unsigned int > s2m_;
00340 
00345         vector< unsigned int > surface_;
00346 };
00347 
00348 #endif  // _CUBE_MESH_H