GssaVoxelPools.h

Go to the documentation of this file.

/**********************************************************************
** 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 _GSSA_VOXEL_POOLS_BASE_H
#define _GSSA_VOXEL_POOLS_BASE_H

class Stoich;

class GssaVoxelPools: public VoxelPoolsBase
{
public:
    GssaVoxelPools();

    virtual ~GssaVoxelPools();


    // Solver interface functions
    void advance( const ProcInfo* p );
    void recalcTime( const GssaSystem* g, double currTime );
    void updateDependentMathExpn(
        const GssaSystem* g, unsigned int rindex, double time );
    void updateDependentRates(
        const vector< unsigned int >& deps, const Stoich* stoich );
    unsigned int pickReac();
    void setNumReac( unsigned int n );

    void advance( const ProcInfo* p, const GssaSystem* g );

    vector< unsigned int > numFire() const;

    bool refreshAtot( const GssaSystem* g );

    void reinit( const GssaSystem* g );

    void updateAllRateTerms( const vector< RateTerm* >& rates,
                             unsigned int numCoreRates  );
    void updateRateTerms( const vector< RateTerm* >& rates,
                          unsigned int numCoreRates, unsigned int index );

    double getReacVelocity( unsigned int r, const double* s ) const;
    void updateReacVelocities( const GssaSystem* g,
                               const double* s, vector< double >& v ) const;

    void setVolumeAndDependencies( double vol );

    void xferIn( XferInfo& xf,
                 unsigned int voxelIndex, const GssaSystem* g );

    void setStoich( const Stoich* stoichPtr );

private:
    double t_;

    double atot_;

    vector< double > v_;
    // Possibly we should put independent RNGS, so save one here.

    // Count how many times each reaction has fired.
    vector< unsigned int > numFire_;

    moose::RNG<double> rng_;

};

#endif  // _GSSA_VOXEL_POOLS_H