SteadyStateGsl.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment,
** also known as GENESIS 3 base code.
**           copyright (C) 2003-2009 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 _STEADYSTATE_H
#define _STEADYSTATE_H
class SteadyState
{
#ifdef DO_UNIT_TESTS
    friend void testSteadyState();
#endif
    public:
        SteadyState();
        ~SteadyState();

        // Field function definitions
        Id getStoich() const ;
        void setStoich( Id s );
        bool badStoichiometry() const;
        bool isInitialized() const;
        unsigned int getRank() const;
        unsigned int getNumVarPools() const;
        unsigned int getNiter() const;
        unsigned int getMaxIter() const;
        void setMaxIter( unsigned int value );
        string getStatus() const;
        double getConvergenceCriterion() const;
        void setConvergenceCriterion( double value );
        double getTotal( const unsigned int i ) const;
        void setTotal( const unsigned int i, double val );
        double getEigenvalue( const unsigned int i ) const;
        void setEigenvalue( double val, const unsigned int i );
        unsigned int getStateType() const;
        unsigned int getNnegEigenvalues() const;
        unsigned int getNposEigenvalues() const;
        unsigned int getSolutionStatus() const;

        // Msg Dest function definitions
        void setupMatrix();
        void settleFunc();
        void resettleFunc();
        void settle( bool forceSetup );
        void showMatricesFunc();
        void showMatrices();
        void randomizeInitialCondition( const Eref& e);
        static void assignY( double* S );
        // static void randomInitFunc();
        // void randomInit();
        // Utility functions for randomInit
        /*
        int isLastConsvMol( int i );
        void recalcRemainingTotal(
            vector< double >& y, vector< double >& tot );
        */
#ifdef USE_GSL
        void fitConservationRules(
            gsl_matrix* U,
            const vector< double >& eliminatedTotal,
            vector< double >&yi
        );
#endif

        // funcs to handle externally imposed changes in mol N
        static void setMolN( double y, unsigned int i );
        // static void assignStoichFunc( void* stoich );
        // void assignStoichFuncLocal( void* stoich );
        void classifyState( const double* T );
        static const double EPSILON;
        static const double DELTA;

        static const Cinfo* initCinfo();

    private:
        void setupSSmatrix();

        // Internal fields.
        unsigned int nIter_;
        unsigned int maxIter_;
        bool badStoichiometry_;
        string status_;
        bool isInitialized_;
        bool isSetup_;
        double convergenceCriterion_;

#ifdef USE_GSL
        gsl_matrix* LU_;
        gsl_matrix* Nr_;
        gsl_matrix* gamma_;
#endif
        Id stoich_;
        unsigned int numVarPools_;
        unsigned int nReacs_;
        unsigned int rank_;

        vector< double > total_;
        bool reassignTotal_;
        unsigned int nNegEigenvalues_;
        unsigned int nPosEigenvalues_;
        vector< double > eigenvalues_;
        unsigned int stateType_;
        unsigned int solutionStatus_;
        unsigned int numFailed_;
        VoxelPools pool_;
};

extern const Cinfo* initSteadyStateCinfo();
#endif // _STEADYSTATE_H