MOOSE: ksolve/ZombiePoolInterface.h Source File

00001 /**********************************************************************
00002 ** This program is part of 'MOOSE', the
00003 ** Messaging Object Oriented Simulation Environment.
00004 **           Copyright (C) 2003-2014 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 _ZOMBIE_POOL_INTERFACE_H
00011 #define _ZOMBIE_POOL_INTERFACE_H
00012 
00019 class ZombiePoolInterface
00020 {
00021     public:
00022         ZombiePoolInterface();
00023 
00025         virtual void setNinit( const Eref& e, double val ) = 0;
00027         virtual double getNinit( const Eref& e ) const = 0;
00028 
00030         virtual void setN( const Eref& e, double val ) = 0;
00032         virtual double getN( const Eref& e ) const = 0;
00033 
00035         virtual void setDiffConst( const Eref& e, double val ) = 0;
00037         virtual double getDiffConst( const Eref& e ) const = 0;
00038 
00041         virtual void setMotorConst( const Eref& e, double val )
00042         {;}
00043 
00045         virtual void setNumPools( unsigned int num ) = 0;
00047         virtual unsigned int getNumPools() const = 0;
00048 
00050         virtual void setNumAllVoxels( unsigned int numVoxels ) = 0;
00052         virtual unsigned int getNumLocalVoxels() const = 0;
00054         virtual VoxelPoolsBase* pools( unsigned int i ) = 0;
00055 
00057         virtual double volume( unsigned int i ) const = 0;
00058 
00074         virtual void getBlock( vector< double >& values ) const = 0;
00075 
00082         virtual void setBlock( const vector< double >& values ) = 0;
00083 
00090         virtual void setStoich( Id stoich ) = 0;
00091 
00093         virtual void setDsolve( Id dsolve ) = 0;
00094 
00096         virtual void setCompartment( Id compartment );
00097         Id getCompartment() const;
00098 
00100         void setupCrossSolverReacs( 
00101             const map< Id, vector< Id > >& xr, 
00102             Id otherStoich );
00103         void setupCrossSolverReacVols( 
00104             const vector< vector< Id > >& subCompts, 
00105             const vector< vector< Id > >& prdCompts );
00106 
00107         void filterCrossRateTerms( const vector< Id >& xreacs,
00108                         const vector< pair< Id, Id > >& xrt );
00115         virtual void updateRateTerms( unsigned int index = ~0U ) = 0;
00116 
00118         virtual unsigned int getPoolIndex( const Eref& er ) const = 0;
00120         // Utility functions for Cross-compt reaction setup.
00122         void xComptIn( const Eref& e, Id srcZombiePoolInterface,
00123                           vector< double > values );
00124         // void xComptOut( const Eref& e );
00125         void assignXferVoxels( unsigned int xferCompt );
00126         void assignXferIndex( unsigned int numProxyMols,
00127             unsigned int xferCompt,
00128             const vector< vector< unsigned int > >& voxy );
00129         void setupXfer( Id myZombiePoolInterface, 
00130             Id otherZombiePoolInterface,
00131             unsigned int numProxyMols, const vector< VoxelJunction >& vj );
00132          unsigned int assignProxyPools( const map< Id, vector< Id > >& xr,
00133             Id myZombiePoolInterface, Id otherZombiePoolInterface, 
00134             Id otherComptId );
00135         void matchJunctionVols( vector< double >& vols, Id otherComptId )
00136                 const;
00137         
00139     protected:
00144         Id stoich_;
00145 
00147         Id compartment_;
00148 
00153         vector< XferInfo > xfer_;
00154 
00156         bool isBuilt_;
00157 };
00158 
00159 #endif  // _ZOMBIE_POOL_INTERFACE_H