pnet.h

#ifndef  LM_PHYSIOLOGY_PNET_H_
#define  LM_PHYSIOLOGY_PNET_H_
 
 
#include  "mbe_legacymodel.h"
#include  "state/mbe_state.h"
#include  "ld_shared.h"
#include  "physiology/ld_plantfunctions.h"
#include  "physiology/ld_treedyn.h"
 
#include  <logging/cbm_logging.h>
 
namespace ldndc {
 
extern cbm::logger_t *  PhysiologyPNETLogger;

class  LDNDC_API  PhysiologyPNET  :  public  MBE_LegacyModel
{
    LMOD_EXPORT_MODULE_INFO(PhysiologyPNET,"physiology:pnet","Physiology PNET");
 
    /***  module specific constants  ***/

    static const double TMIN_NUP;

    static const double TMAX_NUP;

    static const double KM_NO3;

    static const double KM_NH4;

    static const double SRATEMAX;

    static const double C;

    static const double K;

    static const double P;

    static const double BETA;

    static const double TEQ;

    static const double TRANGE;

    static const double NUPTAIR;

    static const double GROWMAX;
 
 
    public:
        PhysiologyPNET(
                MoBiLE_State *,
                cbm::io_kcomm_t *,
                                timemode_e);
 
        ~PhysiologyPNET();
 
        lerr_t  register_ports( cbm::io_kcomm_t * );
        lerr_t  unregister_ports( cbm::io_kcomm_t * );
 
        lerr_t  configure( ldndc::config_file_t const *);
 
        lerr_t  initialize();
 
        lerr_t  solve();
 
        lerr_t  finalize() { return  LDNDC_ERR_OK; }

        lerr_t  sleep() { return  LDNDC_ERR_OK; }
        lerr_t  wake() { return  LDNDC_ERR_OK; }
 
        cbm::string_t branchfraction_opt;
        cbm::string_t crownlength_opt;
        bool competition_opt;
        bool rootgrowth_opt;
 
    private:
 
        cbm::io_kcomm_t *  io_kcomm;
 
        input_class_soillayers_t const &  sl_;
        input_class_setup_t const &  m_setup;
        input_class_siteparameters_t const *  m_sipar;
        input_class_species_t const *  m_species;
 
        substate_airchemistry_t const &  ac_;
        substate_microclimate_t const &  mc_;
        substate_physiology_t &  ph_;
        substate_soilchemistry_t &  sc_;
        substate_watercycle_t &  wc_;
 
        MoBiLE_PlantVegetation *  m_veg;
 
        LD_PlantFunctions  m_pf;
        TreeDynamics  m_treedyn;
 
        SubscribedEvent<LD_EventHandlerQueue>  m_HarvestEvents;
        SubscribedEvent<LD_EventHandlerQueue>  m_PlantEvents;
 
        lvector_t< double > no3_sl;
 
        double  latitude;
 
        double  FolNCon;
        double  accumulated_transpiration_old;
 
        unsigned int  year_start_, year_end_;
 
        lvector_t< double > LayerGrossPsn;  // for putting into layer specific assimilation variable
        template < typename  _E >
        struct  scalar_with_array_look_and_feel_t
        {
            _E  value;
            _E & operator=( _E const &  _value)
                { this->value = _value; return  this->value; }
            _E &  operator[]( size_t)
                { return  this->value; }
            _E &  operator[]( MoBiLE_Plant *)
                { return  this->value; }
        };
 
        /* NOTE  change this as soon as PNET becomes multi-species capable */
        scalar_with_array_look_and_feel_t< double >  mFolOld_vt;    // saved initial foliage biomass for new nitrogen concentration calculations
        scalar_with_array_look_and_feel_t< double >  mFrtOld_vt;    // saved initial fine root biomass for new nitrogen concentration calculations
        scalar_with_array_look_and_feel_t< double >  mBudOld_vt;    // saved initial bud (reserve) biomass for new nitrogen concentration calculations
        scalar_with_array_look_and_feel_t< double >  mSapOld_vt;    // saved initial sapwood biomass for new nitrogen concentration calculations
        scalar_with_array_look_and_feel_t< double >  mCorOld_vt;    // saved initial core wood biomass for new nitrogen concentration calculations
 
        lvector_t< double > mBudLoss_vt;
        lvector_t< double > mSapLoss_vt;
 
        double c_begin;                   // carbon balance variables
        double n_begin;                   // nitrogen balance variables
 
        // - water balance variables
        double DWater;                    // average relative water availability (drought) during an integration step (mm)
        double FolLitSum;                 // litterfall (gDW m-2)
 
        double tra;                       // transpiration
        double uptNAir;
 
        // - physical environment variables (representing the average day of the integration timestep (day or month))
 
        double Dvpd;                      // Gradient on vapour pressure deficit (?)
        double DayResp;                   // Respiration during daytime (?)
        double NightResp;                 // Respiration during nighttime (?)
        double CanopyNetPsn;              // Canopy net photosynthesis (?)
        double CanopyGrossPsn;            // Canopy gross photosynthesis (?)
        double FolProdCMo;                // foliage carbon production over the integration timestep (day or month) (?)
        double FolGRespMo;                // foliage growth respiration over the integration timestep (day or month) (?)
        double NetPsnMo;                  // net photosynthesis over the integration timestep (day or month) (?)
        double CanopyGrossPsnMo;          // canopy gross photosynthesis over the integration timestep (day or month) (?)
        double RootCAddMo;                // fine root growth over the integration timestep (day or month)
 
        // - allocation and mass variables
        double qwodfolact;                // relation between wood and foliage biomass at the start of the year
        double transfDWbs;                // annual mass transfer from reserves (buds) to (sap)wood (gC m-2)
        double transfDWsb;                // annual mass transfer from (sap)wood to reserves (buds) (gC m-2)
        double WoodC;                     // living wood carbon (gC m-2)
        double BudC;                      // reserve carbon for future foliage (gC m-2)
        double RootC;                     // fine root carbon (gC m-2)
        double FolMass;                   // foliage biomass (gDW m-2)
        double FolMassMax;                // maximum summer foliar biomass (gDW m-2) (not really a parameter)
        double FolMassMin;                // minimum summer foliar biomass (gDW m-2) (not really a parameter)
        double FolReten;                  // foliage retention time (yr) (not really a parameter)
 
        double WoodMRespMo;               // daily maintanance respiration of the wood
        double WoodGRespMo;               // daily growth respiration of the wood
        double RootMRespMo;               // daily maintanance root respiration
        double RootGRespMo;               // daily root growth respiration
        double WoodProdCMo;               // daily wood production
        double RootProdCMo;               // daily carbon loss form the root system other than respiration;
 
        double PosCBalMass;               
        double PosCBalMassTot;            
        double PosCBalMassIx;             
 
        double LightEffMin;               
        double WoodCStart;                
        double BudCStart;                 
 
        // other variables
        double fFrost;
        bool mature;
 
        /***  methods  ***/
 
        lerr_t step_init();
 
        lerr_t step_out();
 
        void balance_check( MoBiLE_Plant *p, unsigned int _i);
 
// sk:unused        /*! CalcFrostDamage
// sk:unused         *
// sk:unused         */
// sk:unused        double CalcFrostDamage();

        void update_nitrogen_concentration( MoBiLE_Plant *);

        void YearlyReset( MoBiLE_Plant *);

        void Phenology(
                       MoBiLE_Plant *,
                       int /*GrowthPhase*/,
                       double /*DWater*/);

        void Photosyn( MoBiLE_Plant *);

        void AllocateMo( MoBiLE_Plant *);

        void AllocateYr( MoBiLE_Plant *);

        void N_uptake( MoBiLE_Plant *, double &);

        void Update( MoBiLE_Plant *, double  /*upt1_vt*/, double  /*upt2_vt*/);

        void TransformPhysiology( MoBiLE_Plant *);
 
        lerr_t CalcVegStructure();

        size_t get_na_max_pnet();
 
};
} /*namespace ldndc*/
 
#endif  /*  !LM_PHYSIOLOGY_PNET_H_  */