Gsolve.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2014 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 _GSOLVE_H
#define _GSOLVE_H

class Stoich;
class Gsolve: public ZombiePoolInterface
{
public:
    Gsolve();
    ~Gsolve();

    // Assignment operator required for c++11
    Gsolve& operator=(const Gsolve& );

    // Field assignment stuff
    Id getStoich() const;
    void setStoich( Id stoich ); 
    Id getCompartment() const;
    void setCompartment( Id compt );

    unsigned int getNumLocalVoxels() const;
    unsigned int getNumAllVoxels() const;
    void setNumAllVoxels( unsigned int num );

    void setNumPools( unsigned int num ); 
    unsigned int getNumPools() const; 
    VoxelPoolsBase* pools( unsigned int i ); 
    double volume( unsigned int i ) const;

    vector< double > getNvec( unsigned int voxel) const;
    void setNvec( unsigned int voxel, vector< double > vec );
    // Dest Finfos
    void process( const Eref& e, ProcPtr p );
    void reinit( const Eref& e, ProcPtr p );
    void initProc( const Eref& e, ProcPtr p );
    void initReinit( const Eref& e, ProcPtr p );

    void updateVoxelVol( vector< double > vols );

    // Solver setup functions
    void rebuildGssaSystem();
    void fillMmEnzDep();
    void fillPoolFuncDep();
    void fillIncrementFuncDep();
    void insertMathDepReacs( unsigned int mathDepIndex,
                             unsigned int firedReac );
    void makeReacDepsUnique();

    // Solver interface functions
    unsigned int getPoolIndex( const Eref& e ) const;
    unsigned int getVoxelIndex( const Eref& e ) const;
    vector< unsigned int > getNumFire( unsigned int voxel) const;

    void setDsolve( Id dsolve );

    // ZombiePoolInterface inherited functions

    void setN( const Eref& e, double v );
    double getN( const Eref& e ) const;
    void setNinit( const Eref& e, double v );
    double getNinit( const Eref& e ) const;
    void setDiffConst( const Eref& e, double v );
    double getDiffConst( const Eref& e ) const;

    void getBlock( vector< double >& values ) const;
    void setBlock( const vector< double >& values );

    void updateRateTerms( unsigned int index );


    // A wrapper to call advance function of GssaVoxelPool
    // concurrently.
    void parallel_advance(int begin, int end, size_t nWorkers
                          , ProcPtr p , const GssaSystem* sys
                         );

    bool getRandInit() const;
    void setRandInit( bool val );

    bool getClockedUpdate() const;
    void setClockedUpdate( bool val );

#if PARALLELIZE_GSOLVE_WITH_CPP11_ASYNC
    unsigned int getNumThreads( ) const;
    void setNumThreads( unsigned int x );
#endif

    static const Cinfo* initCinfo();
private:

#if PARALLELIZE_GSOLVE_WITH_CPP11_ASYNC

    unsigned int numThreads_;
#endif

    GssaSystem sys_;
    vector< GssaVoxelPools > pools_;

    unsigned int startVoxel_;

    Stoich* stoichPtr_;

    Id dsolve_;

    ZombiePoolInterface* dsolvePtr_;

    bool useClockedUpdate_;
};

#endif  // _GSOLVE_H