VoxelPools.h

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/**********************************************************************
** This program is part of 'MOOSE', the
#include <boost/numeric/odeint.hpp>
** 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

#include "OdeSystem.h"
#include "VoxelPoolsBase.h"

#ifdef USE_BOOST_ODE
#include "BoostSys.h"
#endif


class Stoich;
class ProcInfo;

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

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

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

    const Stoich* getStoich( );

    void advance( const ProcInfo* p );

    void setInitDt( double dt );

#ifdef USE_GSL      /* -----  not USE_BOOST_ODE  ----- */
    static int gslFunc( double t, const double* y, double *dydt, void* params);
#elif  USE_BOOST_ODE
    static void evalRates( const vector_type_& y
                ,  vector_type_& dydt
                ,  const double t
                , VoxelPools* vp
                );
#endif     /* -----  not USE_BOOST_ODE  ----- */

    // 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_;
#elif USE_BOOST_ODE
    BoostSys sys_;
#endif

};

#endif  // _VOXEL_POOLS_H