ksolve/VoxelPools.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 _VOXEL_POOLS_H
#define _VOXEL_POOLS_H

class Stoich;
class VoxelPools: public VoxelPoolsBase
{
    public: 
        VoxelPools();
        virtual ~VoxelPools();

        void reinit( double dt );
        // Solver interface functions

        void setStoich( Stoich* stoich, const OdeSystem* ode );

        void advance( const ProcInfo* p );

        void setInitDt( double dt );

        static int gslFunc( double t, const double* y, double *dydt, 
                        void* params );

        // Rate manipulation and calculation functions
        void setVolumeAndDependencies( double vol );

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

        void updateRates( const double* s, double* yprime ) const;

        void updateReacVelocities( 
                        const double* s, vector< double >& v ) const;


        void print() const;
    private:
#ifdef USE_GSL
        gsl_odeiv2_driver* driver_;
        gsl_odeiv2_system sys_;
#endif
};

#endif  // _VOXEL_POOLS_H

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