ksolve/GssaVoxelPools.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 _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 updateDependentMathExpn( 
                const GssaSystem* g, unsigned int rindex );
        void updateDependentRates( 
            const vector< unsigned int >& deps, const Stoich* stoich );
        unsigned int pickReac() const;
        void setNumReac( unsigned int n );

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

        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 xferInOnlyProxies(
            const vector< unsigned int >& poolIndex,
            const vector< double >& values, 
            unsigned int numProxyPools,
            unsigned int voxelIndex );

        void setStoich( const Stoich* stoichPtr );

    private:
        double t_; 

        double atot_;

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

#endif  // _GSSA_VOXEL_POOLS_H

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