MOOSE: mesh/CylBase.h Source File

00001 /**********************************************************************
00002 ** This program is part of 'MOOSE', the
00003 ** Messaging Object Oriented Simulation Environment.
00004 **           Copyright (C) 2012 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 _CYL_BASE_H
00011 #define _CYL_BASE_H
00012 
00017 class CylBase
00018 {
00019     public:
00020         CylBase( double x, double y, double z, 
00021                         double dia, double length, unsigned int numDivs );
00022         CylBase();
00023 
00024         void setX( double v );
00025         double getX() const;
00026         void setY( double v );
00027         double getY() const;
00028         void setZ( double v );
00029         double getZ() const;
00030         void setDia( double v );
00031         double getDia() const;
00032         void setLength( double v );
00033         double getLength() const;
00034         void setNumDivs( unsigned int v );
00035         unsigned int getNumDivs() const;
00036         void setIsCylinder( bool v );
00037         bool getIsCylinder() const;
00038 
00040         double volume( const CylBase& parent ) const;
00041 
00045         double voxelVolume( const CylBase& parent, unsigned int fid ) const;
00046 
00057         vector< double > getCoordinates( const CylBase& parent,
00058                         unsigned int entry ) const;
00059 
00069         double getDiffusionArea( 
00070             const CylBase& parent, unsigned int index ) const;
00071 
00073         double getMiddleArea( 
00074             const CylBase& parent, unsigned int index ) const;
00075 
00077         double getVoxelLength() const;
00078 
00082         // Selects a grid size for generating intersection with CubeMesh.
00083         double selectGridSize( double h, double dia1, double granularity )
00084                 const;
00085 
00086         void matchCubeMeshEntries( const ChemCompt* other,
00087             const CylBase& parent,
00088             unsigned int startIndex,
00089             double granularity,
00090             vector< VoxelJunction >& ret,
00091            bool useCylinderCurve, bool useCylinderCap ) const;
00092 
00093         double nearest( double x, double y, double z,
00094                 const CylBase& parent,
00095                 double& linePos, double& r ) const;
00096 
00097         double nearest( double x, double y, double z,
00098                 const CylBase& parent,
00099                 unsigned int& index ) const;
00100 
00101     private:
00103         double x_; 
00104         double y_;
00105         double z_;
00106 
00107         double dia_; 
00108         double length_; 
00109         unsigned int numDivs_;  
00110         bool isCylinder_;   
00111 };
00112 
00113 #endif  // _CYL_BASE_H