plamox.h

 
#ifndef  LM_PHYSIOLOGY_PLAMOX_H_
#define  LM_PHYSIOLOGY_PLAMOX_H_
 
#include  "mbe_legacymodel.h"
#include  "state/mbe_state.h"
#include  "ld_shared.h"
 
#include  <input/remotesensing/remotesensing.h>
 
#include  "physiology/ld_plantfunctions.h"
#include  "physiology/ld_rootsystem.h"
#include  "physiology/ld_nitrogenfixation.h"
#include  "physiology/ld_transpiration.h"
#include  "physiology/ld_vernalization.h"
#include  "watercycle/ld_droughtstress.h"
#include  "physiology/ld_stomatalconductance.h"
#include  "physiology/photofarquhar/berryball.h"
 
#include  "eventhandler/graze/graze.h"
#include  "eventhandler/cut/cut.h"
 
 
namespace ldndc {
 
#define  ON_ENTRY 1
#define  ON_EXIT 2
 
extern cbm::logger_t *  PhysiologyPlaMoxLogger;
 
struct BaseRootSystemDNDC;
class  NitrogenFixation;
 
class  LDNDC_API  PhysiologyPlaMox  :  public  MBE_LegacyModel
{
    LMOD_EXPORT_MODULE_INFO(PhysiologyPlaMox,"physiology:plamox","Physiology PlaMox");
 
    enum plant_life_cycle_e
    {
        ANNUAL = 0,
        BIENNIAL,
        PLURIENNIAL,
        PERENNIAL
    };
 
public:
 
    PhysiologyPlaMox(
                     MoBiLE_State *,
                     cbm::io_kcomm_t *,
                     timemode_e);
 
    ~PhysiologyPlaMox();
 
    lerr_t  configure( ldndc::config_file_t const *);
    lerr_t  register_ports( cbm::io_kcomm_t *);
    lerr_t  initialize();
 
    lerr_t  solve();
    lerr_t  unregister_ports( cbm::io_kcomm_t *);
    lerr_t  finalize() { return  LDNDC_ERR_OK; }
 
    lerr_t  sleep() { return  LDNDC_ERR_OK; }
    lerr_t  wake() { return  LDNDC_ERR_OK; }
 
private:
 
    MoBiLE_State *  m_state;
    cbm::io_kcomm_t *  io_kcomm;
 
    /* required input classes */
    input_class_climate_t const &  cl_;
    input_class_setup_t const *  m_setup;
    input_class_soillayers_t const &  sl_;
    input_class_species_t const *  m_species;
    input_class_speciesparameters_t const * m_speciesparameters;
    input_class_siteparameters_t const * m_siteparameters;
    remotesensing::input_class_remotesensing_t const *  rm_;
 
    MoBiLE_PlantVegetation *  m_veg;
 
    /* required state components */
    substate_airchemistry_t & ac_;
    substate_microclimate_t &  mc_;
    substate_physiology_t &  ph_;
    substate_soilchemistry_t &  sc_;
    substate_watercycle_t &  wc_;
 
    /* management handling */
    SubscribedEvent<LD_EventHandlerQueue>  m_HarvestEvents;
    SubscribedEvent<LD_EventHandlerQueue>  m_PlantEvents;
 
    PublishedField<double>  aboveground_biomass;
    PublishedField<double>  maturity_status;
    PublishedField<double>  growing_degree_days_maturity;
    PublishedField<double>  dEmerg;
 
    PublishedField<double>  carbon_plant_biomass_total_exported_from_field;
    PublishedField<double>  carbon_plant_biomass_fruit_exported_from_field;
    PublishedField<double>  nitrogen_plant_biomass_total_exported_from_field;
    PublishedField<double>  nitrogen_plant_biomass_fruit_exported_from_field;
 
    EventHandlerGraze  m_eventgraze;
    EventHandlerCut  m_eventcut;
 
    BerryBall plamox_berryball;
 
    NitrogenFixation *plamox_nitrogen_fixation;
 
    ldndc::growable_array < BaseRootSystemDNDC*, 1000, 1 >  plamox_root_system;
 
    LD_PlantFunctions  m_pf;
 
    lvector_t< double > no3_sl;
    lvector_t< double > nh4_sl;
    lvector_t< double > don_sl;
 
    bool have_drought_stress;
    bool have_heat_stress;
    cbm::string_t droughtstress_method;
 
    cbm::string_t::cbmstring_array_t plantfamilies;
 
    double const FTS_TOT_;
 
    /***********************************/
    /* Mobile state exchange variables */
    /***********************************/
 
    lvector_t< long long int > seconds_crop_planting;
 
    lvector_t< double > gdd_grain_filling;
 
    lvector_t< double > hypoxia;
 
    lvector_t< int > days_after_emergence;
 
    lvector_t< std::string > location;
    lvector_t< double > dw_retranslocation_stem;
    lvector_t< double > dw_retranslocation_foliage;
    lvector_t< double > dw_fol_old;
    lvector_t< double > lai_dynamic;
 
    /*************************/
    /* PlaMox only variables */
    /*************************/
 
    std::map< std::string, double > gdd_target;
 
    /*---------------*/
    /* model options */
 
    bool have_automatic_nitrogen;
 
    double automatic_nitrogen_uptake;
 
    /*-----------------------------*/
    /* carbon and nitrogen balance */
 
    double photoperiod_min;
    double photoperiod_max;
    double tot_c_;
    double tot_n_;
 
    double timestep_c_assi;
 
    double n_at_planting;
 
    /*-----------------*/
    /* state variables */
 
    lvector_t< double > transplanting_shock_vt;
 
    lvector_t< int > yearly_cuts;
 
    lvector_t< bool > reset_phenology;
    
    lvector_t< double > n_plant;
 
    lvector_t< double >  allocation_factor_leafs;
 
    lvector_t< double >  allocation_factor_stems;
 
    lvector_t< double >  allocation_factor_fruit;
 
    lvector_t< double >  allocation_factor_roots;
 
    lvector_t< double >  lai_min;
 
    lvector_t< double >  fractional_cover;
 
    lvector_t< double >  chill_factor;
 
    lvector_t< double >  chill_units;
 
    lvector_t< double >  m_fruit_maximum;
 
    lvector_t< double >  spikelets_sterility;
 
    lvector_t< double >  nc_fol_opt;
 
    lvector_t< unsigned int >  root_q_vt_;
 
    lvector_t< double > daytime_temperatures; 
 
    lvector_t< double > influence_heat_daily;
 
    double influence_heat_reduction_grainfilling;
 
    
    double day_of_flowering;
 
    //double timing_heatshock;
    //double duration_heatshock;
 
    double Tcrit;
    double Tzero;
 
    double c_total_exported;
    double c_fruit_exported;
    double n_total_exported;
    double n_fruit_exported;
 
 
    /********************/
    /* function members */
    /********************/
 
    lerr_t
    PlaMox_step_init();
 
    lerr_t
    PlaMox_step_resize();
    lerr_t
    PlaMox_step_out();
 
    lerr_t
    PlaMox_management();
 
    lerr_t
    PlaMox_planting();
 
    lerr_t
    PlaMox_event_plant( MoBiLE_Plant *, EventAttributes const &);
 
    lerr_t
    PlaMox_harvest();
 
    lerr_t
    PlaMox_event_harvest( MoBiLE_Plant *, EventAttributes const &);
 
    lerr_t
    PlaMox_reset_phenology( MoBiLE_Plant * /* plant species */);
 
    lerr_t
    PlaMox_photosynthesis( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_vernalization( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_growing_degree_days( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_heat_stress_limitation(MoBiLE_Plant* _vt /* plant species */);
 
    void
    PlaMox_plant_development_crop( MoBiLE_Plant * /* plant species */);
 
    lerr_t
    PlaMox_allocation_grass( MoBiLE_Plant * /* plant species */);
 
    lerr_t
    PlaMox_bud_burst( MoBiLE_Plant * /* plant species */);
 
    lerr_t
    PlaMox_redistribution( MoBiLE_Plant * /* plant species */);
    
    void
    PlaMox_respiration( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_exsudation( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_nitrogen_uptake( MoBiLE_Plant * /* plant species */);
 
    lerr_t
    PlaMox_nitrogen_fixation( MoBiLE_Plant * /* plant species */);
 
    lerr_t
    PlaMox_senescence( MoBiLE_Plant * /* plant species */);
 
    /* senescence */
    lerr_t
    PlaMox_abscission( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_drought( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_transpiration( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_update_root_structure( MoBiLE_Plant *,
                                  double);
 
    void
    PlaMox_update_height( MoBiLE_Plant *);
 
    void
    PlaMox_update_ground_cover( MoBiLE_Plant *);
 
    void
    PlaMox_update_foliage_structure( MoBiLE_Plant *);
 
    void
    PlaMox_update_specific_leaf_area( MoBiLE_Plant *);
 
    void
    PlaMox_update_nitrogen_concentrations( MoBiLE_Plant *);
 
    double
    PlaMox_get_nitrogen_deficiency( MoBiLE_Plant * /* plant species */);
 
    double
    PlaMox_get_biomass_induced_downregulation( MoBiLE_Plant *);
 
    double
    PlaMox_get_age_factor( MoBiLE_Plant * /* plant species */);
 
    double
    PlaMox_get_frost_factor( MoBiLE_Plant *,
                             double);
 
    double
    PlaMox_get_hypoxia_factor( MoBiLE_Plant * /* plant species */);
 
    double
    PlaMox_get_heat_factor( MoBiLE_Plant * /* plant species */);
 
    double
    PlaMox_get_foliage_nitrogen_concentration( MoBiLE_Plant * /* plant species */);
 
    double
    PlaMox_n_opt( MoBiLE_Plant * /* plant species */);
 
    void
    PlaMox_balance_check( int /*stage*/);
 
    lerr_t  PLAMOX_CHECK_FOR_NEGATIVE_VALUE( char const *  /*name*/);
 
 
    /*****************/
    /* class members */
    /*****************/
 
    class PlaMoxIterator
    {
        public:
 
            PlaMoxIterator(MoBiLE_PlantVegetation *_vg,
                           cbm::string_t::cbmstring_array_t &_f,
                           PlantIterator const &_it) :
                            vegetation( _vg),
                            plantfamilies( _f),
                            iterator( _it)
            {
                if ( this->vegetation && this->not_my_family())
                {
                    this->find_next();
                }
            }
            ~PlaMoxIterator(){}
 
        private:
 
            bool not_my_family()
            {
                if ( this->iterator != this->vegetation->end())
                {
                    for (size_t i = 0; i < this->plantfamilies.size(); ++i)
                    {
                        cbm::string_t family = ":";
                        family << this->plantfamilies[i] <<":";
                        if ( this->vegetation->is_family( this->iterator, family.c_str()))
                        {
                            return false;
                        }
                    }
                }
                return true;
            }
 
            void find_next()
            {
                while ( ++this->iterator != this->vegetation->end() && not_my_family())
                {}
            }
 
        public:
 
            PlaMoxIterator operator++()
            {
                this->find_next();
                return *this;
            }
 
            MoBiLE_Plant * operator*()
            {
                return this->iterator.operator*();
            }
 
            bool operator==(const PlaMoxIterator &_it) const
            {
                return this->iterator.operator==( _it.iterator);
            }
 
            bool operator!=(const PlaMoxIterator &_it) const
            {
                return this->iterator.operator!=( _it.iterator);
            }
 
        private:
            MoBiLE_PlantVegetation *vegetation;
            cbm::string_t::cbmstring_array_t plantfamilies;
            PlantIterator iterator;
    };
 
    PlaMoxIterator begin();
 
    PlaMoxIterator end();
    
    plant_life_cycle_e
    PlaMox_get_life_cycle( MoBiLE_Plant *);
};
} /*namespace ldndc*/
 
#endif  /*  !LM_PHYSIOLOGY_PLAMOX_H_  */