Population_Manager Class Reference

Base class for all population managers for agent based models. More...

#include <PopulationManager.h>

Inheritance diagram for Population_Manager:

Public Member Functions
	Population_Manager (Landscape *a_l_ptr, int a_numberLifeStages=12)
virtual	~Population_Manager (void)
void	SetNoProbesAndSpeciesSpecificFunctions (int a_pn) override
	Sets up probe and species specifics. More...
void	OpenTheAOROutputProbe (const string &a_AORFilename) override
	Opens the AOR output file. More...
unsigned	GetLiveArraySize (int a_listindex) override
	Gets the number of 'live' objects for a list index in the TheArray. More...
unsigned	GetPopulationSize (int a_listindex) override
	Gets the number of species objects by default it is the same as LiveArray, however it could be different. This function should be used/overriden when we are interested in the number of the objects for presentation and not in inner maintenance of the PopulationManager and or TheArray. More...
void	IncLiveArraySize (int a_listindex)
	Increments the number of 'live' objects for a list index in the TheArray. More...
unsigned int	FarmAnimalCensus (unsigned int a_farm, unsigned int a_typeofanimal)
char *	SpeciesSpecificReporting (int a_species, int a_time) override
char *	ProbeReport (int a_time)
char *	ProbeReportTimed (int a_time)
void	ImpactProbeReport (int a_Time)
bool	BeginningOfMonth ()
void	LOG (const char *fname)
int	SupplyStepSize () const
void	Run (int NoTSteps) override
virtual unsigned	Probe (int ListIndex, Probe_Data *p_TheProbe)
virtual void	ImpactedProbe ()
virtual TAnimal *	SupplyAnimalPtr (unsigned int a_index, unsigned int a_animal)
	Returns the pointer indexed by a_index and a_animal. Note NO RANGE CHECK. More...
virtual unsigned	SupplyListIndexSize ()
unsigned	SupplyListSize (unsigned listindex) const
void	PushIndividual (const unsigned a_listindex, TAnimal *a_individual_ptr)
const char *	SupplyStateNames (int i) const
unsigned	SupplyStateNamesLength () const
virtual void	DisplayLocations ()
TAnimal *	FindIndividual (unsigned Type, TAnimal *a_me)
virtual TAnimal *	FindClosest (int x, int y, unsigned Type, TAnimal *a_me)
omp_nest_lock_t *	GetGuardMapElement (unsigned a_x_index, unsigned a_y_index)
	Return the guard map cell. More...
void	SetGuardMapElement (unsigned a_x_index, unsigned a_y_index)
	Set the given guard map cell. More...
void	UnsetGuardMapElement (unsigned a_x_index, unsigned a_y_index)
	Unset the given guard map cell. More...
void	UpdateGuardMap (int a_x, int a_y, int &a_index_x, int &a_index_y)
	Get the index of the guard map for the given location. More...
bool	OpenTheRipleysOutputProbe ()
bool	OpenTheMonthlyRipleysOutputProbe ()
bool	OpenTheReallyBigProbe ()
virtual void	TheAOROutputProbe ()
virtual void	TheRipleysOutputProbe (ofstream *a_prb)
	Special output functionality. More...
virtual void	TheReallyBigOutputProbe ()
void	CloseTheMonthlyRipleysOutputProbe () const
virtual void	CloseTheRipleysOutputProbe ()
virtual void	CloseTheReallyBigOutputProbe ()
TTypesOfPopulation	GetPopulationType ()
int	GetSeasonNumber ()
	Get the season number. More...
void	LamdaDeath (int x, int y)
void	LamdaBirth (int x, int y)
void	LamdaBirth (int x, int y, int z)
void	LamdaClear ()
void	LamdaDumpOutput ()
virtual int	SupplyPegPosx (int)
virtual int	SupplyPegPosy (int)
virtual int	SupplyCovPosx (int)
virtual int	SupplyCovPosy (int)
virtual bool	OpenTheFledgelingProbe ()
virtual bool	OpenTheBreedingPairsProbe ()
virtual bool	OpenTheBreedingSuccessProbe ()
virtual void	BreedingPairsOutput (int)
virtual int	TheBreedingFemalesProbe (int)
virtual int	TheFledgelingProbe ()
virtual void	BreedingSuccessProbeOutput (double, int, int, int, int, int, int, int)
virtual int	TheBreedingSuccessProbe (int &, int &, int &, int &, int &, int &)
virtual void	FledgelingProbeOutput (int, int)
virtual void	TheGeneticProbe (unsigned, int, unsigned &)
virtual void	GeneticsResultsOutput (FILE *, unsigned)
void	Debug_Shuffle (unsigned int Type)
virtual void	RunStepMethods ()
Public Member Functions inherited from Population_Manager_Base
	Population_Manager_Base (Landscape *L)
	The Population_Manager_Base constructor. More...
virtual void	Catastrophe (int)
	Must be re-implemented in descendent classes. More...
int	SupplySimW () const
	Returns landscape width in m. More...
int	SupplySimH () const
	Returns landscape height in m. More...
int	SupplySimWH () const
	Returns half the landscape width in m. More...
int	SupplySimHH () const
	Returns half the landscape height in m. More...
virtual int	ProbeFileInput (char *p_Filename, int p_ProbeNo)
	A stub to build specfic probes and functions. More...
int	SupplyListNameLength () const
const char *	SupplyListName (int a_i) const
	Get a list name from the list. More...
virtual void	SupplyLocXY (unsigned, unsigned, int &, int &)
	A stub for identifying an individual at a location. More...
virtual TAnimal *	FindClosest (int, int, unsigned)
	A stub for identifying an individual at a location. More...
std::string	SupplySimulationName ()
void	SetStepCounterInADay (int a_counter)
	Set step counter in a day. More...
int	GetStepCounterInADay (void)
	Return the sep counter in a day. More...
virtual double	GetAphidDensity (int, int)
	Return the aphid density, it is only used when aphid simulations are running. More...

Public Attributes
bool	ProbesSet {}
Public Attributes inherited from Population_Manager_Base
Probe_Data *	TheProbe [100] = {nullptr}
	Holds a list of pointers to standard output probes. More...

Protected Member Functions
virtual bool	StepFinished ()
	Methods to run the simulations. More...
virtual void	DoFirst ()
virtual void	DoBefore ()
virtual void	DoAfter ()
virtual void	DoLast ()
virtual void	DoSpecialBetweenLifeStages (int a_life_stage)
virtual void	SortX (unsigned Type)
void	SortXIndex (unsigned Type)
virtual void	SortY (unsigned Type)
void	SortState (unsigned Type)
void	SortStateR (unsigned Type)
virtual unsigned	PartitionLiveDead (unsigned Type)
virtual void	Shuffle_or_Sort (unsigned Type)
virtual void	Shuffle (unsigned Type)
virtual void	Catastrophe ()
Protected Member Functions inherited from Population_Manager_Base
	~Population_Manager_Base ()=default

Protected Attributes
vector< unsigned >	m_LiveArraySize
int	m_NoProbes = 0
std::vector< std::vector< omp_nest_lock_t * > >	m_MapGuard
	This is used to make sure animals will not behaviour at the same area - multi threads. More...
int	m_guard_cell_height_num
int	m_guard_cell_width_num
int	m_guard_cell_size
bool	m_is_paralleled
	This is used to indicate whether the species is paralleled. More...
const char *	StateNames [100] {}
int	m_StepSize {}
vector< vector< forward_list< TAnimal * > * > >	TheSubArrays
	Hold all the animal pointers. More...
vector< vector< int > >	TheSubArraysSizes
	Hold all the animal sizes in each thread. More...
vector< int >	m_LifeStageOrderVec
	The vector to store the life stage order for looping specie life stages. More...
vector< forward_list< TAnimal * >::iterator >	TheSubArraysIterators
	the iterator from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class. More...
vector< int >	TheSubArrayPreviousIndex
	the animal index number from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class. More...
vector< int >	TheSubArrayThreadIndex
	the thread index number from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class. More...
unsigned	StateNamesLength
FILE *	TestFile {}
FILE *	TestFile2 {}
vector< unsigned >	BeforeStepActions
	Holds the season list of possible before step actions. More...
int	m_SeasonNumber
	Holds the season number. Used when running goose and hunter sims. More...
TTypesOfPopulation	m_population_type {TOP_NoSpecies}
ofstream *	AOROutputPrb {}
ofstream *	RipleysOutputPrb {}
ofstream *	RipleysOutputPrb1 {}
ofstream *	RipleysOutputPrb2 {}
ofstream *	RipleysOutputPrb3 {}
ofstream *	RipleysOutputPrb4 {}
ofstream *	RipleysOutputPrb5 {}
ofstream *	RipleysOutputPrb6 {}
ofstream *	RipleysOutputPrb7 {}
ofstream *	RipleysOutputPrb8 {}
ofstream *	RipleysOutputPrb9 {}
ofstream *	RipleysOutputPrb10 {}
ofstream *	RipleysOutputPrb11 {}
ofstream *	RipleysOutputPrb12 {}
ofstream *	ReallyBigOutputPrb {}
AOR_Probe *	m_AOR_Probe {}
	A pointer to the AOR probe. More...
long int	lamdagrid [2][257][257] {}
Protected Attributes inherited from Population_Manager_Base
int	SimH
	stores the simulation height More...
int	SimW
	stores the simulation width More...
int	SimHH
	stores the simulation height halved More...
int	SimWH
	stores the simulation width halved More...
string	m_SimulationName
	stores the simulation name More...
Landscape *	m_TheLandscape
	holds an internal pointer to the landscape More...
int	m_ListNameLength {}
	the number of life-stages simulated in the population manager More...
const char *	m_ListNames [32] {}
	A list of life-stage names. More...
std::string	m_AORProbeFileName {"AOR_Probe.txt"}
	name of the AOR Probe file More...
std::string	m_ProbeFileName {"Probe.res"}
	name of the Probe file More...
int	m_step_counter_in_a_day
	Step counter in a day, this is used for the animals with finer step size other than one day. More...

Detailed Description

Base class for all population managers for agent based models.

The core of the handling of animal populations. All time-step code and most input/output is handled by this class and its descendents. This class effectively implements a state machine to facilitate simulation of animal behaviours and handle potential issues with concurrency. The PopulationManager class is never instantiated but must be used by deriving a descendent class.

Constructor & Destructor Documentation

Population_Manager()

Population_Manager::Population_Manager	(	Landscape *	a_l_ptr,
		int	a_numberLifeStages = 12
	)

Constructor for the Population_Manager class

                                                                                 : Population_Manager_Base(a_l_ptr) {
    // create N empty arrays
    TheSubArraysIterators.resize(a_numberLifeStages);
    TheSubArrayPreviousIndex.resize(a_numberLifeStages);
    TheSubArrayThreadIndex.resize(a_numberLifeStages);
    TheSubArrays.resize(a_numberLifeStages);
    TheSubArraysSizes.resize(a_numberLifeStages);
    m_LifeStageOrderVec.resize(a_numberLifeStages);
    for (int i = 0; i < a_numberLifeStages; i++)
    {
        TheSubArrayPreviousIndex[i] = -1;
        TheSubArrayThreadIndex[i] = -1;
        TheSubArrays[i].resize(g_thread_count);
        TheSubArraysSizes[i].resize(g_thread_count);
        for (int j = 0; j < g_thread_count; j++){ 
            TheSubArrays[i][j] = new forward_list<TAnimal*>;
            TheSubArraysSizes[i][j] = 0;
        }
        m_LifeStageOrderVec[i] = i;
    }
 
    BeforeStepActions.resize(a_numberLifeStages);
    for (int i = 0; i < a_numberLifeStages; i++)
    {
        // Set default BeforeStepActions
        BeforeStepActions[i] = 0;
        m_ListNames[i] = "Unknown";
        m_LiveArraySize.push_back(0);
    }
    // modify this if they need to in descendent classes
    StateNamesLength = 0; // initialise this variable.
#ifdef __LAMBDA_RECORD
    ofstream fout("LambdaGridOuput.txt", ios_base::out);  // open for writing
    fout.close();
    LamdaClear();
#endif
    if (cfg_RipleysOutputMonthly_used.value()) { OpenTheMonthlyRipleysOutputProbe(); }
    // Ensure the GUI pointer is NULL in case we are not in GUI mode
    m_SeasonNumber = 0; // Ensure that we start in season number 0. Season number is incremented at day in year 183
 
    //initialise map guard thing
    m_guard_cell_size = cfg_MapGuardCellSize.value();
    m_guard_cell_height_num = SimH / m_guard_cell_size;
    m_guard_cell_width_num = SimW / m_guard_cell_size;
 
 
    m_MapGuard.resize(m_guard_cell_height_num);
    for(int j = 0; j < m_guard_cell_height_num; j++){
        m_MapGuard[j].resize(m_guard_cell_width_num);
        for(int k = 0; k < m_guard_cell_width_num; k++){
            m_MapGuard[j][k] = new omp_nest_lock_t;
            omp_init_nest_lock(m_MapGuard[j][k]);
        }
    }
 
    m_is_paralleled = false; //by default it is not paralleled
}

References BeforeStepActions, cfg_MapGuardCellSize, cfg_RipleysOutputMonthly_used, g_thread_count, LamdaClear(), m_guard_cell_height_num, m_guard_cell_size, m_guard_cell_width_num, m_is_paralleled, m_LifeStageOrderVec, Population_Manager_Base::m_ListNames, m_LiveArraySize, m_MapGuard, m_SeasonNumber, OpenTheMonthlyRipleysOutputProbe(), Population_Manager_Base::SimH, Population_Manager_Base::SimW, StateNamesLength, TheSubArrayPreviousIndex, TheSubArrays, TheSubArraysIterators, TheSubArraysSizes, TheSubArrayThreadIndex, CfgInt::value(), and CfgBool::value().

~Population_Manager()

Population_Manager::~Population_Manager ( void  )

virtual

Destructor for the Population_Manager class

                                            {
    // clean-up // no need to delete members of the array
    if (cfg_CfgRipleysOutputUsed.value()) { CloseTheRipleysOutputProbe(); }
    if (cfg_RipleysOutputMonthly_used.value()) { CloseTheMonthlyRipleysOutputProbe(); }
    if (cfg_ReallyBigOutputUsed.value()) { CloseTheReallyBigOutputProbe(); }
    if (cfg_AorOutput_used.value()) delete m_AOR_Probe;
    for (int i = 0; i < TheSubArrays.size(); i++)
    {
        for (int j = 0; j < TheSubArrays[i].size(); j++){
            for (auto it = TheSubArrays[i][j]->begin(); it != TheSubArrays[i][j]->end(); ++it){
                if(*it != nullptr)
                    delete *it;
            }
            if(TheSubArrays[i][j] != nullptr)
                delete TheSubArrays[i][j];
        }
    }
 
 
    for(int j = 0; j < m_guard_cell_height_num; j++){
        for(int k = 0; k < m_guard_cell_width_num; k++){
            omp_destroy_nest_lock(m_MapGuard[j][k]);
            delete m_MapGuard[j][k];
        }
    }
}

References cfg_AorOutput_used, cfg_CfgRipleysOutputUsed, cfg_ReallyBigOutputUsed, cfg_RipleysOutputMonthly_used, CloseTheMonthlyRipleysOutputProbe(), CloseTheReallyBigOutputProbe(), CloseTheRipleysOutputProbe(), m_AOR_Probe, m_guard_cell_height_num, m_guard_cell_width_num, m_MapGuard, TheSubArrays, and CfgBool::value().

Member Function Documentation

BeginningOfMonth()

bool Population_Manager::BeginningOfMonth

(

)

Is it the first day of the month?

                                          {
    if (m_TheLandscape->SupplyDayInMonth() == cfg_DayInMonth.value()) return true;
    return false;
}

References cfg_DayInMonth, Population_Manager_Base::m_TheLandscape, Landscape::SupplyDayInMonth(), and CfgInt::value().

Referenced by ImpactProbeReport(), and ProbeReport().

BreedingPairsOutput()

virtual void Population_Manager::BreedingPairsOutput ( int  )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

                                            {
    }

Referenced by SpeciesSpecificReporting().

BreedingSuccessProbeOutput()

virtual void Population_Manager::BreedingSuccessProbeOutput ( double  , int  , int  , int  , int  , int  , int  , int    )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

                                                                    {
    }

Referenced by SpeciesSpecificReporting().

Catastrophe()

void Population_Manager::Catastrophe ( void  )

protectedvirtual

This method MUST be overidden in descendent classes if this functionality is does not match with the animals requirements

Reimplemented in Beetle_Population_Manager, THare_Population_Manager, Skylark_Population_Manager, Vole_Population_Manager, Spider_Population_Manager, Oedothorax_Population_Manager, and Erigone_Population_Manager.

                                     {
}

CloseTheMonthlyRipleysOutputProbe()

void Population_Manager::CloseTheMonthlyRipleysOutputProbe

(

)

const

close the monthly probes

                                                                 {
    RipleysOutputPrb1->close();
    RipleysOutputPrb2->close();
    RipleysOutputPrb3->close();
    RipleysOutputPrb4->close();
    RipleysOutputPrb5->close();
    RipleysOutputPrb6->close();
    RipleysOutputPrb7->close();
    RipleysOutputPrb8->close();
    RipleysOutputPrb9->close();
    RipleysOutputPrb10->close();
    RipleysOutputPrb11->close();
    RipleysOutputPrb12->close();
}

References RipleysOutputPrb1, RipleysOutputPrb10, RipleysOutputPrb11, RipleysOutputPrb12, RipleysOutputPrb2, RipleysOutputPrb3, RipleysOutputPrb4, RipleysOutputPrb5, RipleysOutputPrb6, RipleysOutputPrb7, RipleysOutputPrb8, and RipleysOutputPrb9.

Referenced by ~Population_Manager().

CloseTheReallyBigOutputProbe()

void Population_Manager::CloseTheReallyBigOutputProbe ( )

virtual

close the probe

Reimplemented in TPredator_Population_Manager.

                                                      {
    if (ReallyBigOutputPrb != nullptr) ReallyBigOutputPrb->close();
    ReallyBigOutputPrb = nullptr;
}

References ReallyBigOutputPrb.

Referenced by ~Population_Manager().

CloseTheRipleysOutputProbe()

void Population_Manager::CloseTheRipleysOutputProbe ( )

virtual

close the probe

                                                    {
    if (cfg_RipleysOutputMonthly_used.value()) RipleysOutputPrb->close();
    RipleysOutputPrb = nullptr;
}

References cfg_RipleysOutputMonthly_used, RipleysOutputPrb, and CfgBool::value().

Referenced by ~Population_Manager().

Debug_Shuffle()

void Population_Manager::Debug_Shuffle

(

unsigned int

Type

)

DisplayLocations()

void Population_Manager::DisplayLocations ( )

virtual

Used to update the graphics when control is not returned to the ALMaSS_GUI between timesteps.

                                          {
}

DoAfter()

void Population_Manager::DoAfter ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Osmia_Population_Manager, and TPredator_Population_Manager.

                                 {
    //TODO: Add your source code here
}

Referenced by RunStepMethods().

DoBefore()

void Population_Manager::DoBefore ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Beetle_Population_Manager, Osmia_Population_Manager, and TPredator_Population_Manager.

                                  {
}

Referenced by RunStepMethods().

DoFirst()

void Population_Manager::DoFirst ( void  )

protectedvirtual

Can be used in descendent classes

Reimplemented in Spider_Population_Manager, Oedothorax_Population_Manager, Erigone_Population_Manager, Beetle_Population_Manager, THare_Population_Manager, Ladybird_Population_Manager, Skylark_Population_Manager, Bembidion_Population_Manager, Vole_Population_Manager, Osmia_Population_Manager, and TPredator_Population_Manager.

                                 {
}

Referenced by RunStepMethods().

DoLast()

void Population_Manager::DoLast ( )

protectedvirtual

Collects some data to describe the number of animals in each state at the end of the day

Reimplemented in Beetle_Population_Manager, THare_Population_Manager, PoecilusCupreus_Population_Manager, Osmia_Population_Manager, and TPredator_Population_Manager.

                                {
    //TODO: Add your source code here
}

Referenced by THare_Population_Manager::DoLast(), and RunStepMethods().

DoSpecialBetweenLifeStages()

virtual void Population_Manager::DoSpecialBetweenLifeStages ( int  a_life_stage )

inlineprotectedvirtual

Reimplemented in Ladybird_Population_Manager.

{;}

Referenced by RunStepMethods().

FarmAnimalCensus()

unsigned int Population_Manager::FarmAnimalCensus	(	unsigned int	a_farm,
		unsigned int	a_typeofanimal
	)

                                                                                                  {
    unsigned int No = 0;
    int temp_thread_num = omp_get_max_threads();
    for(int i=0; i<temp_thread_num; i++){
        for(auto it = TheSubArrays[a_typeofanimal][i]->begin(); it != TheSubArrays[a_typeofanimal][i]->end(); ++it){
            if((*it)->GetCurrentStateNo() < 0){
                continue;   
            }
            if (a_farm == (*it)->SupplyFarmOwnerRef()) No++;
        }
    }
    return No;
}

References TheSubArrays.

FindClosest()

TAnimal * Population_Manager::FindClosest ( int  x, int  y, unsigned  Type, TAnimal *  a_me  )

virtual

Finds the closest individual to an x,y point that is not a_me

                                                                                   {
 
    int distance = 100000000;
    TAnimal* TA = nullptr;
    int temp_thread_num = omp_get_max_threads();
    for(int j=0; j<temp_thread_num; j++){
        for(auto it = TheSubArrays[Type][j]->begin(); it != TheSubArrays[Type][j]->end(); ++it){
            int dx = (*it)->Supply_m_Location_x();
            int dy = (*it)->Supply_m_Location_y();
            dx = dx - x;
            dx *= dx;
            dy = dy - y;
            dy *= dy;
            int d = dx + dy;
            if (d < distance)
            {
                if ((*it) != a_me)
                {
                    if ((*it)->GetCurrentStateNo() != -1)
                    {
                        TA = (*it);
                        distance = d;
                    }
                }
            }
        }
    }
    return TA;
}

References TheSubArrays.

FindIndividual()

TAnimal * Population_Manager::FindIndividual	(	unsigned	Type,
		TAnimal *	a_me
	)

Gets a random live individual returned as TAnimal*

Gets a random individual that is not a_me

                                                                        {
    int i = static_cast<int>(GetLiveArraySize(Type) * g_rand_uni_fnc());
    int temp_thread_num = omp_get_max_threads();
 
    int temp_animal_num = 0;
    for(int j=0; j<temp_thread_num; j++){
        for(auto it = TheSubArrays[Type][j]->begin(); it != TheSubArrays[Type][j]->end(); ++it){
            if(temp_animal_num >= i){
                if((*it) != a_me){
                    return (*it);
                }
            }
            if(temp_animal_num == i){
                return nullptr;
            }
            temp_animal_num++;
        }
    }
    return nullptr;
}

References g_rand_uni_fnc(), GetLiveArraySize(), and TheSubArrays.

FledgelingProbeOutput()

virtual void Population_Manager::FledgelingProbeOutput ( int  , int    )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

                                                     {
    }

Referenced by SpeciesSpecificReporting().

GeneticsResultsOutput()

virtual void Population_Manager::GeneticsResultsOutput ( FILE *  , unsigned    )

inlinevirtual

Reimplemented in Vole_Population_Manager.

                                                            {
    }

GetGuardMapElement()

omp_nest_lock_t* Population_Manager::GetGuardMapElement ( unsigned  a_x_index, unsigned  a_y_index  )

inline

Return the guard map cell.

    {
        return m_MapGuard[a_y_index][a_x_index];
    }

References m_MapGuard.

GetLiveArraySize()

unsigned Population_Manager::GetLiveArraySize ( int  a_listindex )

inlineoverridevirtual

Gets the number of 'live' objects for a list index in the TheArray.

Reimplemented from Population_Manager_Base.

{ return m_LiveArraySize[a_listindex]; }

References m_LiveArraySize.

Referenced by Skylark_Population_Manager::BreedingPairsOutput(), Erigone_Population_Manager::Catastrophe(), Oedothorax_Population_Manager::Catastrophe(), Vole_Population_Manager::Catastrophe(), Skylark_Population_Manager::Catastrophe(), THare_Population_Manager::Catastrophe(), Beetle_Population_Manager::Catastrophe(), Beetle_Population_Manager::Catastrophe2(), Osmia_Population_Manager::DoBefore(), Erigone_Population_Manager::DoFirst(), Oedothorax_Population_Manager::DoFirst(), Vole_Population_Manager::DoFirst(), THare_Population_Manager::DoFirst(), AOR_Probe_Goose::DoProbe(), AOR_Probe::DoProbeInHaitatType(), THare_Population_Manager::ExtraPopMort(), FindIndividual(), Vole_Population_Manager::FindOutsideRadiusMale(), Vole_Population_Manager::FindRandomMale(), Vole_Population_Manager::GeneticsOutputFile(), Vole_Population_Manager::GeneticsResultsOutput(), GetPopulationSize(), Beetle_Population_Manager::GetPopulationSize(), THare_Population_Manager::Hunting(), THare_Population_Manager::HuntingDifferentiatedBeetleBankArea(), THare_Population_Manager::HuntingGrid(), Vole_Population_Manager::ImpactedProbe(), Vole_Population_Manager::LandscapeQuadrantOutputProbe(), THare_Population_Manager::MRROutputs(), THare_Population_Manager::POMOutputs(), Probe(), Beetle_Population_Manager::Probe(), Skylark_Population_Manager::ProbePOM(), Skylark_Population_Manager::ReHouse(), Vole_Population_Manager::ResistanceOutput(), Vole_Population_Manager::SendMessage(), Vole_Population_Manager::TheAgeSexLocationProbe(), Skylark_Population_Manager::TheBreedingFemalesProbe(), Skylark_Population_Manager::TheBreedingSuccessProbe(), Skylark_Population_Manager::TheFledgelingProbe(), Vole_Population_Manager::TheReallyBigOutputProbe(), Beetle_Population_Manager::TheReallyBigOutputProbe(), Erigone_Population_Manager::TheRipleysOutputProbe(), Oedothorax_Population_Manager::TheRipleysOutputProbe(), Vole_Population_Manager::TheRipleysOutputProbe(), Skylark_Population_Manager::TheRipleysOutputProbe(), THare_Population_Manager::TheRipleysOutputProbe(), Beetle_Population_Manager::TheRipleysOutputProbe(), and Vole_Population_Manager::TheSexRatiosProbe().

GetPopulationSize()

unsigned Population_Manager::GetPopulationSize ( int  a_listindex )

inlineoverridevirtual

Gets the number of species objects by default it is the same as LiveArray, however it could be different. This function should be used/overriden when we are interested in the number of the objects for presentation and not in inner maintenance of the PopulationManager and or TheArray.

Reimplemented from Population_Manager_Base.

Reimplemented in Beetle_Population_Manager.

{ return GetLiveArraySize(a_listindex); }

References GetLiveArraySize().

GetPopulationType()

TTypesOfPopulation Population_Manager::GetPopulationType ( )

inline

{ return m_population_type; }

References m_population_type.

GetSeasonNumber()

int Population_Manager::GetSeasonNumber ( )

inline

Get the season number.

{ return m_SeasonNumber; }

References m_SeasonNumber.

ImpactedProbe()

void Population_Manager::ImpactedProbe ( )

virtual

Special pesticide related probe. Overidden in descendent classes

Reimplemented in Vole_Population_Manager.

                                       {
}

Referenced by ImpactProbeReport().

ImpactProbeReport()

void Population_Manager::ImpactProbeReport

(

int

a_Time

)

Special probe

                                                     {
    for (int ProbeNo = 0; ProbeNo < 1; ProbeNo++)
    {
        // See if we need to record/update this one
        // if time/months/years ==0 or every time
        if (TheProbe[ProbeNo]->m_ReportInterval == 3 || (TheProbe[ProbeNo]->m_ReportInterval == 2 && BeginningOfMonth())
            || (TheProbe[ProbeNo]->m_ReportInterval == 1 && a_Time % 365 == 0)) { ImpactedProbe(); }
    }
}

References BeginningOfMonth(), ImpactedProbe(), and Population_Manager_Base::TheProbe.

Referenced by SpeciesSpecificReporting().

IncLiveArraySize()

void Population_Manager::IncLiveArraySize ( int  a_listindex )

inline

Increments the number of 'live' objects for a list index in the TheArray.

{ m_LiveArraySize[a_listindex]++; }

References m_LiveArraySize.

Referenced by Erigone_Population_Manager::CreateObjects(), Oedothorax_Population_Manager::CreateObjects(), Bembidion_Population_Manager::CreateObjects(), Vole_Population_Manager::CreateObjects(), PoecilusCupreus_Population_Manager::CreateObjects(), Osmia_Population_Manager::CreateObjects(), Skylark_Population_Manager::CreateObjects(), Ladybird_Population_Manager::CreateObjects(), THare_Population_Manager::CreateObjects(), and Vole_Population_Manager::CreateObjectsInit().

LamdaBirth() [1/2]

void Population_Manager::LamdaBirth ( int  x, int  y  )

inline

{ lamdagrid[0][x / __lgridsize][y / __lgridsize]++; }

References lamdagrid.

Referenced by Beetle_Egg_List::St_Hatch().

LamdaBirth() [2/2]

void Population_Manager::LamdaBirth ( int  x, int  y, int  z  )

inline

{ lamdagrid[0][x / __lgridsize][y / __lgridsize] += z; }

References lamdagrid.

LamdaClear()

void Population_Manager::LamdaClear ( )

inline

                      {
        for (int i = 0; i < 257; i++)
        {
            for (int j = 0; j < 257; j++)
            {
                lamdagrid[0][i][j] = 0;
                lamdagrid[1][i][j] = 0;
            }
        }
    }

References lamdagrid.

Referenced by Beetle_Population_Manager::DoFirst(), and Population_Manager().

LamdaDeath()

void Population_Manager::LamdaDeath ( int  x, int  y  )

inline

                                  {
        // inlined for speed
        lamdagrid[1][x / __lgridsize][y / __lgridsize]++;
    }

References lamdagrid.

Referenced by Beetle_Base::StDie().

LamdaDumpOutput()

void Population_Manager::LamdaDumpOutput

(

)

Special probe

                                         {
    ofstream fout("LambdaGridOuput.txt", ios_base::app); // open for writing
    for (int i = 0; i < 257; i++)
    {
        for (int j = 0; j < 257; j++) { fout << lamdagrid[0][i][j] << "\t" << lamdagrid[1][i][j] << endl; }
    }
    //fout << "NEXT" << endl;
    fout.close();
}

References lamdagrid.

Referenced by Beetle_Population_Manager::DoFirst().

LOG()

void Population_Manager::LOG

(

const char *

fname

)

Debug function used to log whatever is needed - this is just a place to write whatever is needed at the time - so contents vary

                                              {
    FILE* PFile = fopen(fname, "w");
    if (PFile)
    {
        m_TheLandscape->Warn("PopulationManager::LOG - Could not open file ", fname);
        exit(0);
    }
    AnimalPosition AP;
    for (unsigned listindex = 0; listindex < TheSubArrays.size(); listindex++)
    {
#ifndef __BCB__
        fprintf(PFile, "%s :\n", m_ListNames[listindex]);
#else
    fprintf( PFile, "%s :\n", m_ListNames[ listindex ].c_str() );
#endif
        for (unsigned j = 0; j < m_LiveArraySize[listindex]; j++)
        {
            AP = SupplyAnimalPtr(listindex, j)->SupplyPosition();
            fprintf(PFile, "%i %i %i\n", j, AP.m_x, AP.m_y);
        }
    }
    fclose(PFile);
}

References Population_Manager_Base::m_ListNames, m_LiveArraySize, Population_Manager_Base::m_TheLandscape, AnimalPosition::m_x, AnimalPosition::m_y, SupplyAnimalPtr(), TAnimal::SupplyPosition(), TheSubArrays, and Landscape::Warn().

OpenTheAOROutputProbe()

void Population_Manager::OpenTheAOROutputProbe ( const string &  a_AORFilename )

overridevirtual

Opens the AOR output file.

Reimplemented from Population_Manager_Base.

Reimplemented in Beetle_Population_Manager.

                                                                          {
    m_AORProbeFileName = a_AORFilename;
    m_AOR_Probe = new AOR_Probe(this, m_TheLandscape, a_AORFilename);
}

References m_AOR_Probe, Population_Manager_Base::m_AORProbeFileName, and Population_Manager_Base::m_TheLandscape.

OpenTheBreedingPairsProbe()

virtual bool Population_Manager::OpenTheBreedingPairsProbe ( )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

{ return false; }

OpenTheBreedingSuccessProbe()

virtual bool Population_Manager::OpenTheBreedingSuccessProbe ( )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

{ return false; }

OpenTheFledgelingProbe()

virtual bool Population_Manager::OpenTheFledgelingProbe ( )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

{ return false; }

OpenTheMonthlyRipleysOutputProbe()

bool Population_Manager::OpenTheMonthlyRipleysOutputProbe

(

)

open 12 ripley output probes, one for each month

                                                          {
    RipleysOutputPrb1 = new ofstream("RipleyOutput_Jan.txt");
    if (!RipleysOutputPrb1)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb2 = new ofstream("RipleyOutput_Feb.txt");
    if (!RipleysOutputPrb2)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb3 = new ofstream("RipleyOutput_Mar.txt");
    if (!RipleysOutputPrb3)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb4 = new ofstream("RipleyOutput_Apr.txt");
    if (!RipleysOutputPrb4)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb5 = new ofstream("RipleyOutput_May.txt");
    if (!RipleysOutputPrb5)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb6 = new ofstream("RipleyOutput_Jun.txt");
    if (!RipleysOutputPrb6)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb7 = new ofstream("RipleyOutput_Jul.txt");
    if (!RipleysOutputPrb7)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb8 = new ofstream("RipleyOutput_Aug.txt");
    if (!RipleysOutputPrb8)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb9 = new ofstream("RipleyOutput_Sep.txt");
    if (!RipleysOutputPrb9)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb10 = new ofstream("RipleyOutput_Oct.txt");
    if (!RipleysOutputPrb10)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb11 = new ofstream("RipleyOutput_Nov.txt");
    if (!RipleysOutputPrb11)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    RipleysOutputPrb12 = new ofstream("RipleyOutput_Dec.txt");
    if (!RipleysOutputPrb12)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    return true;
}

References cfg_RipleysOutput_filename, g_msg, RipleysOutputPrb1, RipleysOutputPrb10, RipleysOutputPrb11, RipleysOutputPrb12, RipleysOutputPrb2, RipleysOutputPrb3, RipleysOutputPrb4, RipleysOutputPrb5, RipleysOutputPrb6, RipleysOutputPrb7, RipleysOutputPrb8, RipleysOutputPrb9, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

Referenced by Population_Manager().

OpenTheReallyBigProbe()

bool Population_Manager::OpenTheReallyBigProbe

(

)

open the probe

                                               {
    ReallyBigOutputPrb = new ofstream(cfg_ReallyBigOutput_filename.value());
    if (!ReallyBigOutputPrb)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_ReallyBigOutput_filename.value());
        exit(1);
    }
    return true;
}

References cfg_ReallyBigOutput_filename, g_msg, ReallyBigOutputPrb, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

Referenced by Beetle_Population_Manager::Beetle_Population_Manager(), Erigone_Population_Manager::Init(), Oedothorax_Population_Manager::Init(), Vole_Population_Manager::Init(), Skylark_Population_Manager::Init(), and THare_Population_Manager::Init().

OpenTheRipleysOutputProbe()

bool Population_Manager::OpenTheRipleysOutputProbe

(

)

open the Ripley probe

                                                   {
    RipleysOutputPrb = new ofstream(cfg_RipleysOutput_filename.value());
    if (!RipleysOutputPrb)
    {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
                    cfg_RipleysOutput_filename.value());
        exit(1);
    }
    return true;
}

References cfg_RipleysOutput_filename, g_msg, RipleysOutputPrb, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

Referenced by Beetle_Population_Manager::Beetle_Population_Manager(), Erigone_Population_Manager::Init(), Oedothorax_Population_Manager::Init(), Vole_Population_Manager::Init(), Skylark_Population_Manager::Init(), and THare_Population_Manager::Init().

PartitionLiveDead()

unsigned Population_Manager::PartitionLiveDead ( unsigned  Type )

protectedvirtual

Delete the animals in the array

                                                            {
    m_LiveArraySize[Type] = 0;
    for (int j=0; j < TheSubArrays[Type].size(); j++){
        //new ones were created, add them to the array
        TheSubArraysSizes[Type][j] = 0;
        auto prev_it = TheSubArrays[Type][j]->before_begin();
        for (auto it = TheSubArrays[Type][j]->begin(); it != TheSubArrays[Type][j]->end();){
            //still alive
            if((*it)->GetCurrentStateNo()>=0){
                m_LiveArraySize[Type]++;
                TheSubArraysSizes[Type][j] += 1;
                prev_it = it;
                ++it; //only increment if not deleted
            }
            else{
                delete *it;
                it = TheSubArrays[Type][j]->erase_after(prev_it);
            }
        }
    }
 
    //let's check if there is thread without any live animals, then we move some to that thread from another thread
    for(int i=0; i<TheSubArrays[Type].size(); i++){
        if(TheSubArraysSizes[Type][i]==0){
            //find another thread with more than one animal
            for(int j=0; j<TheSubArrays[Type].size(); j++){
                if(TheSubArraysSizes[Type][j]>1){
                    int temp_moved_size = TheSubArraysSizes[Type][j]/2;
                    for(int k=0; k<=temp_moved_size; k++){
                        TheSubArrays[Type][i]->push_front(TheSubArrays[Type][j]->front());
                        TheSubArrays[Type][j]->pop_front();
                        TheSubArraysSizes[Type][i] += 1;
                        TheSubArraysSizes[Type][j] -= 1;
                    }
                    break;
                }
            }
        }
    }
    return m_LiveArraySize[Type];
}

References m_LiveArraySize, TheSubArrays, and TheSubArraysSizes.

Referenced by Ladybird_Population_Manager::DoFirst(), and Run().

Probe()

unsigned Population_Manager::Probe ( int  ListIndex, Probe_Data *  p_TheProbe  )

virtual

Default data probe. Rarely used in actuality but always available

Reimplemented in Beetle_Population_Manager.

                                                                        {
    // Counts through the list and goes through each area to see if the animal
    // is standing there and if the farm, veg or element conditions are met
    AnimalPosition Sp;
    long NumberSk = 0;
    // Four possibilities
    // either NoVegTypes or NoElementTypes or NoFarmTypes is >0 or all==0
    int temp_thread_num = omp_get_max_threads();
    if (p_TheProbe->m_NoFarms != 0)
    {
        for (int thread_id=0; thread_id<temp_thread_num; thread_id++){
            for(auto it = TheSubArrays[ListIndex][thread_id]->begin(); it != TheSubArrays[ListIndex][thread_id]->end(); ++it){
                if((*it)->GetCurrentStateNo() < 0){
                    continue;   
                }
                Sp = (*it)->SupplyPosition();
                unsigned Farm = (*it)->SupplyFarmOwnerRef();
                for (int i = 0; i < p_TheProbe->m_NoAreas; i++)
                {
                    if ((p_TheProbe->m_FullLandscapeProbe) || (Sp.m_x >= p_TheProbe->m_Rect[i].m_x1 && Sp.m_y >= p_TheProbe->m_Rect[i].m_y1 && Sp.
                        m_x <= p_TheProbe->m_Rect[i].m_x2 && Sp.m_y <= p_TheProbe->m_Rect[i].m_y2))
                        for (int k = 0; k < p_TheProbe->m_NoFarms; k++)
                        {
                            if (p_TheProbe->m_RefFarms[k] == Farm) NumberSk++; // it is in the square so increment number
                        }
                }
            }
        }
    }
    else if (p_TheProbe->m_NoEleTypes != 0)
    {
        for (int thread_id=0; thread_id<temp_thread_num; thread_id++){
            for(auto it = TheSubArrays[ListIndex][thread_id]->begin(); it != TheSubArrays[ListIndex][thread_id]->end(); ++it){
                if((*it)->GetCurrentStateNo() < 0){
                    continue;   
                }
                for (unsigned i = 0; i < p_TheProbe->m_NoAreas; i++)
                {
                if ((p_TheProbe->m_FullLandscapeProbe) || (Sp.m_x >= p_TheProbe->m_Rect[i].m_x1 && Sp.m_y >= p_TheProbe->m_Rect[i].m_y1 && Sp.
                    m_x <= p_TheProbe->m_Rect[i].m_x2 && Sp.m_y <= p_TheProbe->m_Rect[i].m_y2))
                    for (unsigned k = 0; k < p_TheProbe->m_NoEleTypes; k++)
                    {
                        if (p_TheProbe->m_RefEle[k] == Sp.m_EleType) NumberSk++;
                        // it is in the square so increment number
                    }
                }
            }
        }
    }
    else
    {
        if (p_TheProbe->m_NoVegTypes != 0)
        {
            for (int thread_id=0; thread_id<temp_thread_num; thread_id++){
                for(auto it = TheSubArrays[ListIndex][thread_id]->begin(); it != TheSubArrays[ListIndex][thread_id]->end(); ++it){
                    if((*it)->GetCurrentStateNo() < 0){
                        continue;   
                    }
                    Sp = (*it)->SupplyPosition();
                    for (unsigned i = 0; i < p_TheProbe->m_NoAreas; i++)
                    {
                        if ((p_TheProbe->m_FullLandscapeProbe) || (Sp.m_x >= p_TheProbe->m_Rect[i].m_x1 && Sp.m_y >= p_TheProbe->m_Rect[i].m_y1 && Sp.
                            m_x <= p_TheProbe->m_Rect[i].m_x2 && Sp.m_y <= p_TheProbe->m_Rect[i].m_y2))
                        {
                            for (unsigned k = 0; k < p_TheProbe->m_NoVegTypes; k++)
                            {
                                if (p_TheProbe->m_RefVeg[k] == Sp.m_VegType) NumberSk++;
                                // it is in the square so increment number
                            }
                        }
                    }
                }
            }
        }
        else // both must be zero
        {
            unsigned sz = static_cast<long>(GetLiveArraySize(ListIndex));
 
            // It is worth checking whether we have a total dump of all individuals
            // if so don't bother with asking each where it is
            if (p_TheProbe->m_FullLandscapeProbe)   return sz; 
            // Asking for a subset - need to test them all
            for (int thread_id=0; thread_id<temp_thread_num; thread_id++){
                for(auto it = TheSubArrays[ListIndex][thread_id]->begin(); it != TheSubArrays[ListIndex][thread_id]->end(); ++it){
                    if((*it)->GetCurrentStateNo() < 0){
                        continue;   
                    }
                    Sp = (*it)->SupplyPosition();
                    for (unsigned i = 0; i < p_TheProbe->m_NoAreas; i++)
                    {
                        if (Sp.m_x >= p_TheProbe->m_Rect[i].m_x1 && Sp.m_y >= p_TheProbe->m_Rect[i].m_y1 && Sp.m_x <=
                            p_TheProbe->m_Rect[i].m_x2 && Sp.m_y <= p_TheProbe->m_Rect[i].m_y2) NumberSk++;
                        // it is in the square so increment number
                    }
                }
            }
        }
    }
    return NumberSk;
}

References GetLiveArraySize(), AnimalPosition::m_EleType, Probe_Data::m_FullLandscapeProbe, Probe_Data::m_NoAreas, Probe_Data::m_NoEleTypes, Probe_Data::m_NoFarms, Probe_Data::m_NoVegTypes, Probe_Data::m_Rect, Probe_Data::m_RefEle, Probe_Data::m_RefFarms, Probe_Data::m_RefVeg, AnimalPosition::m_VegType, AnimalPosition::m_x, rectangle::m_x1, rectangle::m_x2, AnimalPosition::m_y, rectangle::m_y1, rectangle::m_y2, and TheSubArrays.

Referenced by ProbeReport(), and ProbeReportTimed().

ProbeReport()

char * Population_Manager::ProbeReport

(

int

a_time

)

                                              {
    char str[100]; // 100 out to be enough!!
    strcpy(g_Str, "");
    for (int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++)
    {
        int No = 0;
        // See if we need to record/update this one
        // if time/months/years ==0 or every time
        if (TheProbe[ProbeNo]->m_ReportInterval == 3 || (TheProbe[ProbeNo]->m_ReportInterval == 2 && BeginningOfMonth())
            || (TheProbe[ProbeNo]->m_ReportInterval == 1 && Time % 365 == 0))
        {
            // Goes through each area and sends a value to OutputForm
            unsigned Index = SupplyListIndexSize();
            for (unsigned listindex = 0; listindex < Index; listindex++)
            {
                if (TheProbe[ProbeNo]->m_TargetTypes[listindex]) No += static_cast<int>(Probe(
                    listindex, TheProbe[ProbeNo]));
            }
            TheProbe[ProbeNo]->FileOutput(No, Time, ProbeNo);
            sprintf(str, " %d ", No);
            strcat(g_Str, str);
        }
    }
    return g_Str;
}

References BeginningOfMonth(), Probe_Data::FileOutput(), g_Str, m_NoProbes, Probe(), SupplyListIndexSize(), and Population_Manager_Base::TheProbe.

Referenced by SpeciesSpecificReporting().

ProbeReportTimed()

char * Population_Manager::ProbeReportTimed

(

int

a_time

)

                                                   {
    char str[100]; // 100 ought to be enough!!
    strcpy(g_Str, "");
    for (int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++)
    {
        int No = 0;
        unsigned Index = SupplyListIndexSize();
        for (unsigned listindex = 0; listindex < Index; listindex++)
        {
            if (TheProbe[ProbeNo]->m_TargetTypes[listindex]) No += static_cast<int>(
                Probe(listindex, TheProbe[ProbeNo]));
        }
        TheProbe[ProbeNo]->FileOutput(No, Time, ProbeNo);
        sprintf(str, " %d ", No);
        strcat(g_Str, str);
    }
    return g_Str;
}

References Probe_Data::FileOutput(), g_Str, m_NoProbes, Probe(), SupplyListIndexSize(), and Population_Manager_Base::TheProbe.

PushIndividual()

void Population_Manager::PushIndividual	(	const unsigned	a_listindex,
		TAnimal *	a_individual_ptr
	)

                                                                                             {
    int temp_thread_num = omp_get_thread_num();
    //cout<<"Pushing individual to list index: "<<a_listindex<<" and thread number: "<<temp_thread_num<<endl;
    TheSubArrays[a_listindex][temp_thread_num]->push_front(a_individual_ptr);
}

References TheSubArrays.

Referenced by Erigone_Population_Manager::CreateObjects(), Oedothorax_Population_Manager::CreateObjects(), TPredator_Population_Manager::CreateObjects(), Bembidion_Population_Manager::CreateObjects(), Vole_Population_Manager::CreateObjects(), PoecilusCupreus_Population_Manager::CreateObjects(), Osmia_Population_Manager::CreateObjects(), Skylark_Population_Manager::CreateObjects(), Ladybird_Population_Manager::CreateObjects(), THare_Population_Manager::CreateObjects(), and Vole_Population_Manager::CreateObjectsInit().

Run()

void Population_Manager::Run ( int  NoTSteps )

overridevirtual

This is the main scheduling method for the population manager.
Note the structure of Shuffle_or_Sort(), DoFirst(), BeginStep, DoBefore(), Step looping until all are finished, DoAfter(), EndStep, DoLast().

Can do multiple time-steps here inside one landscape time-step (a day). This is used in the roe deer model to provide 10 minute behavioural time-steps.

It is necessary to remove any dead animals before the timestep starts. It is possible that animals are killed after their population manager Run method has been executed. This is the case with geese and hunters. Checking death first prevents this becomming a problem.

Reimplemented from Population_Manager_Base.

Reimplemented in TPredator_Population_Manager.

                                         {
    for (int t_steps = 0; t_steps < NoTSteps; t_steps++)
    {
        const unsigned size1 = SupplyListIndexSize();
        for (unsigned listindex = 0; listindex < size1; listindex++)
        {
            // Must check each object in the list for m_CurrentStateNo==-1
            m_LiveArraySize[listindex] = PartitionLiveDead(listindex);
        }
 
 
        // begin step actions ...
        // set all stepdone to false.... is this really necessary??
        for (int listindex = 0; listindex < size1; listindex++)
        {
            #pragma omp parallel
            {
            int thread_id = omp_get_thread_num();
            for(auto it = TheSubArrays[listindex][thread_id]->begin(); it != TheSubArrays[listindex][thread_id]->end(); ++it){
                (*it)->SetStepDone(false);
            }
            }
        }
        //Only do this when single thread is used
        if(omp_get_max_threads()<=1){
            for (unsigned listindex = 0; listindex < size1; listindex++)
            {
                // Call the Shuffle/Sort procedures
                if(m_LiveArraySize[listindex] > 1)
                    Shuffle_or_Sort(listindex);
            }
        }
 
                //Rest the fast read support variables for supply animal ptr
        for (unsigned listindex = 0; listindex < size1; listindex++)
        {
            TheSubArrayPreviousIndex[listindex] = 0;
            TheSubArrayThreadIndex[listindex] = 0;
            TheSubArraysIterators[listindex] = TheSubArrays[listindex][0]->begin();
 
            //let's find the first non-empty subarray
            for (int j = 0; j < TheSubArraysSizes[listindex].size(); j++){
                if(TheSubArraysSizes[listindex][j] > 0){
                    TheSubArrayThreadIndex[listindex] = j;
                    TheSubArraysIterators[listindex] = TheSubArrays[listindex][j]->begin();
                    break;
                }
            }
        }
 
        const int day = m_TheLandscape->SupplyDayInYear();
        const int year = m_TheLandscape->SupplyYearNumber();
        // Need to check if Ripleys Statistic needs to be saved
        if (cfg_CfgRipleysOutputUsed.value())
        {
            const int Year = m_TheLandscape->SupplyYearNumber();
            if (Year >= cfg_RipleysOutputFirstYear.value())
            {
                if (Year % cfg_RipleysOutput_interval.value() == 0)
                {
                    if (cfg_RipleysOutput_day.value() == day)
                    {
                        TheRipleysOutputProbe(RipleysOutputPrb); // Do the Ripley Probe
                    }
                }
            }
        }
        // Need to check if AOR output needs to be saved
        if (cfg_AorOutput_used.value())
        {
            if (year >= cfg_AorOutputFirstYear.value())
            {
                if (year % cfg_AorOutput_interval.value() == 0)
                {
                    if (cfg_AorOutput_day.value() == day)
                    {
                        // Do the AOR Probe
                        TheAOROutputProbe();
                    }
                }
            }
        }
        // Need to check if Monthly Ripleys Statistic needs to be saved
        if (cfg_RipleysOutputMonthly_used.value())
        {
            if (m_TheLandscape->SupplyDayInMonth() == 1)
            {
                if (year >= cfg_RipleysOutputFirstYear.value())
                {
                    if (year % cfg_RipleysOutput_interval.value() == 0)
                    {
                        int month = m_TheLandscape->SupplyMonth();
                        // Do the Ripley Probe
                        switch (month)
                        {
                        case 1:
                            TheRipleysOutputProbe(RipleysOutputPrb1);
                            break;
                        case 2:
                            TheRipleysOutputProbe(RipleysOutputPrb2);
                            break;
                        case 3:
                            TheRipleysOutputProbe(RipleysOutputPrb3);
                            break;
                        case 4:
                            TheRipleysOutputProbe(RipleysOutputPrb4);
                            break;
                        case 5:
                            TheRipleysOutputProbe(RipleysOutputPrb5);
                            break;
                        case 6:
                            TheRipleysOutputProbe(RipleysOutputPrb6);
                            break;
                        case 7:
                            TheRipleysOutputProbe(RipleysOutputPrb7);
                            break;
                        case 8:
                            TheRipleysOutputProbe(RipleysOutputPrb8);
                            break;
                        case 9:
                            TheRipleysOutputProbe(RipleysOutputPrb9);
                            break;
                        case 10:
                            TheRipleysOutputProbe(RipleysOutputPrb10);
                            break;
                        case 11:
                            TheRipleysOutputProbe(RipleysOutputPrb11);
                            break;
                        case 12:
                            TheRipleysOutputProbe(RipleysOutputPrb12);
                            break;
                        default:
                            g_msg->Warn("Population_Manager::Run ", "Wrong month");
                            exit(-1);
                        }
                    }
                }
            }
        }
        // Need to check if Really Big Probe needs to be saved
        if (cfg_ReallyBigOutputUsed.value())
        {
            if (year >= cfg_ReallyBigOutputFirstYear.value())
            {
                if (year % cfg_ReallyBigOutput_interval.value() == 0)
                {
                    if (cfg_ReallyBigOutput_day1.value() == day || cfg_ReallyBigOutput_day2.value() == day ||
                        cfg_ReallyBigOutput_day3.value() == day || cfg_ReallyBigOutput_day4.value() == day ||
                        cfg_ReallyBigOutput_day1.value() == -1)
                    {
                        // Do the Ripley Probe
                        TheReallyBigOutputProbe();
                    }
                }
            }
        }
        // Set the static variables for TAnimal (speed optimisation)
        TAnimal::SetDayInYear(day);
        TAnimal::SetTempToday(m_TheLandscape->SupplyTemp());
        RunStepMethods();
    } // End of time step loop
}

References cfg_AorOutput_day, cfg_AorOutput_interval, cfg_AorOutput_used, cfg_AorOutputFirstYear, cfg_CfgRipleysOutputUsed, cfg_ReallyBigOutput_day1, cfg_ReallyBigOutput_day2, cfg_ReallyBigOutput_day3, cfg_ReallyBigOutput_day4, cfg_ReallyBigOutput_interval, cfg_ReallyBigOutputFirstYear, cfg_ReallyBigOutputUsed, cfg_RipleysOutput_day, cfg_RipleysOutput_interval, cfg_RipleysOutputFirstYear, cfg_RipleysOutputMonthly_used, g_msg, m_LiveArraySize, Population_Manager_Base::m_TheLandscape, PartitionLiveDead(), RipleysOutputPrb, RipleysOutputPrb1, RipleysOutputPrb10, RipleysOutputPrb11, RipleysOutputPrb12, RipleysOutputPrb2, RipleysOutputPrb3, RipleysOutputPrb4, RipleysOutputPrb5, RipleysOutputPrb6, RipleysOutputPrb7, RipleysOutputPrb8, RipleysOutputPrb9, RunStepMethods(), TAnimal::SetDayInYear(), TAnimal::SetTempToday(), Shuffle_or_Sort(), Landscape::SupplyDayInMonth(), Landscape::SupplyDayInYear(), SupplyListIndexSize(), Landscape::SupplyMonth(), Landscape::SupplyTemp(), Landscape::SupplyYearNumber(), TheAOROutputProbe(), TheReallyBigOutputProbe(), TheRipleysOutputProbe(), TheSubArrayPreviousIndex, TheSubArrays, TheSubArraysIterators, TheSubArraysSizes, TheSubArrayThreadIndex, CfgInt::value(), CfgBool::value(), and MapErrorMsg::Warn().

RunStepMethods()

void Population_Manager::RunStepMethods ( )

virtual

                                        {
    //int size2;
    //const int size1 = SupplyListIndexSize();
    DoFirst();
    // call the begin-step-method of all objects
    //for (int listindex = 0; listindex < size1; listindex++)
    for (auto& listindex : m_LifeStageOrderVec)
    {
        //size2 = GetLiveArraySize(listindex);
        #pragma omp parallel
        {
            int thread_id = omp_get_thread_num();
            for(auto it = TheSubArrays[listindex][thread_id]->begin(); it != TheSubArrays[listindex][thread_id]->end(); ++it){
                int loc_x_cell = 0;
                int loc_y_cell = 0;
                if(m_is_paralleled) //only set the guard map  if multiple threads are used
                {
                    int loc_x = (*it)->Supply_m_Location_x();
                    int loc_y = (*it)->Supply_m_Location_y();
                    int loc_x_cell = loc_x / m_guard_cell_size;
                    int loc_y_cell = loc_y / m_guard_cell_size;
                    (*it)->SetGuardMapIndex(loc_x_cell, loc_y_cell);
                    omp_set_nest_lock(m_MapGuard[loc_y_cell][loc_x_cell]);
                }   
                (*it)->BeginStep();
                if(m_is_paralleled){
                    loc_x_cell = (*it)->SupplyGuardCellX();
                    loc_y_cell = (*it)->SupplyGuardCellY();
                    omp_unset_nest_lock(m_MapGuard[loc_y_cell][loc_x_cell]);
                }
            }
        }
    }
    DoBefore();
 
    // call the step-method of all objects
    do
    {
        for (auto& listindex : m_LifeStageOrderVec)
        {
            //size2 = GetLiveArraySize(listindex);
            //cout<<"Parallel starts..."<<endl;
            #pragma omp parallel
            {
                int thread_id = omp_get_thread_num();
                //cout<<" thread_id: "<<thread_id<<endl;
                //cout<<"listindex: "<<listindex<<" thread_id: "<<thread_id<<" j: "<<j<<endl;
                for(auto it = TheSubArrays[listindex][thread_id]->begin(); it != TheSubArrays[listindex][thread_id]->end(); ++it){
                    int loc_x_cell = 0;
                    int loc_y_cell = 0;
                    if(m_is_paralleled){ //only set the guard map  if multiple threads are used
                    //let's check the guard map
                        int loc_x = (*it)->Supply_m_Location_x();
                        int loc_y = (*it)->Supply_m_Location_y();
                        loc_x_cell = loc_x / m_guard_cell_size;
                        loc_y_cell = loc_y / m_guard_cell_size;
                        (*it)->SetGuardMapIndex(loc_x_cell, loc_y_cell);
                        omp_set_nest_lock(m_MapGuard[loc_y_cell][loc_x_cell]);
                    }
                    (*it)->Step();
 
                    //only update the position if multiple threads are used
                    if(m_is_paralleled){
                        loc_x_cell = (*it)->SupplyGuardCellX();
                        loc_y_cell = (*it)->SupplyGuardCellY();
                        omp_unset_nest_lock(m_MapGuard[loc_y_cell][loc_x_cell]);
                    }
                }
            }
            DoSpecialBetweenLifeStages(listindex);
            //cout<<"Parallel ends!!!"<<endl;
        } // for listindex
    }
    while (!StepFinished());
    DoAfter();
    // call the end-step-method of all objects
    for (auto& listindex : m_LifeStageOrderVec)
    {
        //size2 = GetLiveArraySize(listindex);
        #pragma omp parallel
        {
            int thread_id = omp_get_thread_num();
            for(auto it = TheSubArrays[listindex][thread_id]->begin(); it != TheSubArrays[listindex][thread_id]->end(); ++it){
                int loc_x_cell = 0;
                int loc_y_cell = 0;
                if(m_is_paralleled){ //only set the guard map  if multiple threads are used
                    int loc_x = (*it)->Supply_m_Location_x();
                    int loc_y = (*it)->Supply_m_Location_y();
                    loc_x_cell = loc_x / m_guard_cell_size;
                    loc_y_cell = loc_y / m_guard_cell_size;
                    (*it)->SetGuardMapIndex(loc_x_cell, loc_y_cell);
                    omp_set_nest_lock(m_MapGuard[loc_y_cell][loc_x_cell]);
                }
                (*it)->EndStep();
                if(m_is_paralleled){
                    loc_x_cell = (*it)->SupplyGuardCellX();
                    loc_y_cell = (*it)->SupplyGuardCellY();
                    omp_unset_nest_lock(m_MapGuard[loc_y_cell][loc_x_cell]);
                }
            }
        }
    }
    // ----------------
    // end of this step actions
    // For each animal list
 
    DoLast();
}

References DoAfter(), DoBefore(), DoFirst(), DoLast(), DoSpecialBetweenLifeStages(), m_guard_cell_size, m_is_paralleled, m_LifeStageOrderVec, m_MapGuard, StepFinished(), and TheSubArrays.

Referenced by Run().

SetGuardMapElement()

void Population_Manager::SetGuardMapElement ( unsigned  a_x_index, unsigned  a_y_index  )

inline

Set the given guard map cell.

    {
        omp_set_nest_lock(m_MapGuard[a_y_index][a_x_index]);
    }

References m_MapGuard.

Referenced by Beetle_Egg_List::DailyMortality(), Beetle_Egg_List::ExtremeTempMortality(), and Beetle_Egg_List::St_Hatch().

SetNoProbesAndSpeciesSpecificFunctions()

void Population_Manager::SetNoProbesAndSpeciesSpecificFunctions ( int  a_pn )

overridevirtual

Sets up probe and species specifics.

Reimplemented from Population_Manager_Base.

                                                                        {
    // This function relies on the fact that g_Species has been set already
    m_NoProbes = a_pn;
    m_TheLandscape->SetSpeciesFunctions(g_Species);
}

References g_Species, m_NoProbes, Population_Manager_Base::m_TheLandscape, and Landscape::SetSpeciesFunctions().

Shuffle()

void Population_Manager::Shuffle ( unsigned  Type )

protectedvirtual

Run once through the list swapping randomly chosen elements

                                              {
    int temp_thread_num = omp_get_max_threads();
    for(int i=0; i<temp_thread_num; i++){
        auto it = TheSubArrays[Type][i]->begin();
        auto prev_it = TheSubArrays[Type][i]->begin();
        it++; //start from the second element
        TAnimal* temp;
        for(; it != TheSubArrays[Type][i]->end(); ++it){
            if(g_rand_uni_fnc() < 0.5){
                //swap the elements
                temp = *it;
                *it = *prev_it;
                *prev_it = temp;
            }
            prev_it = it;
        }
        //TheSubArrays[Type][i]->sort([](TAnimal* a, TAnimal*b) { return g_rand_uni_fnc()>=0.5; } );
    }
}

References g_rand_uni_fnc(), and TheSubArrays.

Referenced by Vole_Population_Manager::DoFirst(), and Shuffle_or_Sort().

Shuffle_or_Sort()

void Population_Manager::Shuffle_or_Sort ( unsigned  Type )

protectedvirtual

This method is used to determine whether the array of animals should be shuffled or sorted.
To do nothing ensure that the BeforeStepActions[] is set appropriately // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = sortXIndex, 4 = do nothing

                                                      {
    switch (BeforeStepActions[Type])
    {
    case 0:
        Shuffle(Type);
        break;
    case 1:
        SortX(Type);
        break;
    case 2:
        SortY(Type);
        break;
    case 3: // Do nothing
        break;
    case 4:
        if (g_rand_uni_fnc() < static_cast<double>(1. / 500)) Shuffle(Type);
        break;
    default:
        m_TheLandscape->Warn("Population_Manager::Shuffle_or_Sort", "- BeforeStepAction Unknown");
        exit(1);
    }
}

References BeforeStepActions, g_rand_uni_fnc(), Population_Manager_Base::m_TheLandscape, Shuffle(), SortX(), SortY(), and Landscape::Warn().

Referenced by Run().

SortState()

void Population_Manager::SortState ( unsigned  Type )

protected

Sort TheSubArrays w.r.t. the current state attribute

                                                {
    int temp_thread_num = omp_get_max_threads();
    for(int i=0; i<temp_thread_num; i++){
        TheSubArrays[Type][i]->sort([](TAnimal* A1, TAnimal*A2) { return A1->WhatState() < A2->WhatState(); } );
    }
}

References TheSubArrays, and TAnimal::WhatState().

SortStateR()

void Population_Manager::SortStateR ( unsigned  Type )

protected

Sort TheSubArrays w.r.t. the current state attribute in reverse order

                                                 {
    int temp_thread_num = omp_get_max_threads();
    for(int i=0; i<temp_thread_num; i++){
        TheSubArrays[Type][i]->sort([](TAnimal* A1, TAnimal*A2) { return A1->GetCurrentStateNo() > A2->GetCurrentStateNo(); } );
    }
}

References TALMaSSObject::GetCurrentStateNo(), and TheSubArrays.

SortX()

void Population_Manager::SortX ( unsigned  Type )

protectedvirtual

Sort TheSubArrays w.r.t. the m_Location_x attribute

                                            {
    int temp_thread_num = omp_get_max_threads();
    for(int i=0; i<temp_thread_num; i++){
        TheSubArrays[Type][i]->sort([](TAnimal* A1, TAnimal*A2) { return A1->Supply_m_Location_x() < A2->Supply_m_Location_x(); } );
    }
}

References TAnimal::Supply_m_Location_x(), and TheSubArrays.

Referenced by Shuffle_or_Sort().

SortXIndex()

void Population_Manager::SortXIndex ( unsigned  Type )

protected

SortY()

void Population_Manager::SortY ( unsigned  Type )

protectedvirtual

Sort TheSubArrays w.r.t. the m_Location_y attribute

                                            {
    int temp_thread_num = omp_get_max_threads();
    for(int i=0; i<temp_thread_num; i++){
        TheSubArrays[Type][i]->sort([](TAnimal* A1, TAnimal*A2) { return A1->Supply_m_Location_y() < A2->Supply_m_Location_y(); } );
    }
}

References TAnimal::Supply_m_Location_y(), and TheSubArrays.

Referenced by Shuffle_or_Sort().

SpeciesSpecificReporting()

char * Population_Manager::SpeciesSpecificReporting ( int  a_species, int  a_time  )

overridevirtual

This method handles species specific outputs. This is one place to do it. More commonly this is done in descendent classes

Reimplemented from Population_Manager_Base.

                                                                            {
    strcpy(g_Str, "");
    if (a_species == -1) { return g_Str; }
    // Vole Model
    if (a_species == 1)
    {
        /*
  // The next lines are obselete code from genetic simulations
  float MeanNoAlleles;
      float MeanHO;
      float MeanHE;
      unsigned size;
  
      if ( m_time % ( 365 * 24 * 60 ) == 0 ) // End of year
      {
  
        // empty the GenStruc data
        for ( int ProbeNo = 0; ProbeNo < ( int )m_NoProbes; ProbeNo++ ) {
          fprintf( m_GeneticsFile, "%d ", m_time );
          int TotalSize = 0;
          m_AManager->AlFreq->Flush();
          for ( unsigned listindex = 0; listindex <= 1; listindex++ ) {
            size = 0;
            m_AManager->TheGeneticProbe( listindex, ProbeNo, size );
            TotalSize += size;
          }
          if ( TotalSize > 0 ) {
            m_AManager->AlFreq->CalcAF();
            m_AManager->AlFreq->CalcNoAlleles();
            m_AManager->AlFreq->CalcHE();
            m_AManager->AlFreq->CalcHO( TotalSize );
          }
          // Get the means
          // For N alleles
          int NA = 0;
          float NHO = 0;
          float NHE = 0;
          for ( int l = 0; l < 16; l++ ) {
            NA += m_AManager->AlFreq->SupplyNoAlleles( l );
          }
          MeanNoAlleles = ( float )NA / 16.0;
          for ( int l = 0; l < 16; l++ ) {
            NHO += m_AManager->AlFreq->SupplyHO( l );
          }
          MeanHO = NHO / 16.0;
          for ( int l = 0; l < 16; l++ ) {
            NHE += m_AManager->AlFreq->SupplyHE( l );
          }
          MeanHE = NHE / 16.0;
  
          // Do some output
          // Output is to two files, the genetics file and the AllelerequencyFile
          fprintf( m_GeneticsFile, "%2.2f ", MeanNoAlleles );
          fprintf( m_GeneticsFile, "%1.3f ", MeanHO );
          fprintf( m_GeneticsFile, "%1.3f ", MeanHE );
          for ( int l = 0; l < 16; l++ ) {
            fprintf( m_GeneticsFile, "%04i ", m_AManager->AlFreq->SupplyNoAlleles( l ) );
          }
          for ( int l = 0; l < 16; l++ ) {
            fprintf( m_GeneticsFile, "%1.3f ", m_AManager->AlFreq->SupplyHO( l ) );
          }
          for ( int l = 0; l < 16; l++ ) {
            fprintf( m_GeneticsFile, "%1.3f ", m_AManager->AlFreq->SupplyHE( l ) );
          }
          fprintf( m_GeneticsFile, "\n" );
          fprintf( m_AlleleFreqsFile, "%d ", m_time );
          for ( int l = 0; l < 16; l++ ) {
            for ( int al = 0; al < 4; al++ ) {
              fprintf( m_AlleleFreqsFile, "%1.3f ", m_AManager->AlFreq->SupplyAF( l, al ) );
            }
          }
          fprintf( m_AlleleFreqsFile, "\n" );
        }
        // make sure progress reaches the disk
        fflush( m_GeneticsFile );
        fflush( m_AlleleFreqsFile );
      }
  
      if ( cfg_UseEasyPop.value()) {
        int targettime=a_time % ( 365 * 100 );
        if ( (  targettime == 59 ) ||(targettime == 181)||(targettime ==304)||(targettime ==59+365)||(targettime ==181+365)||(targettime ==304+365)) {
            for ( unsigned listindex = 0; listindex <= 1; listindex++ ) {
              GeneticsResultsOutput( m_EasyPopRes, listindex);
          }
          fflush( m_EasyPopRes );
        }
      }
  */
        /* Three times a year reporting
      if ( m_time % 365 == 60 ) ProbeReportNow( m_time );
      if ( m_time % 365 == 152 ) ProbeReportNow( m_time );
      if ( m_time % 365 == 273 ) ProbeReportNow( m_time ); */
        ProbeReport(a_time);
#ifdef __SpecificPesticideEffectsVinclozolinLike__
    ImpactProbeReport( a_time );
#endif
#ifdef __WithinOrchardPesticideSim__
    ImpactProbeReport( a_time );
#endif
    }
    // Skylark Model
    else if (a_species == 0)
    {
        int No;
        int a_day = a_time % 365;
        if (a_time % 365 == 364)
        {
            //Write the Breeding Attempts Probe
            int BreedingFemales, YoungOfTheYear, TotalPop, TotalFemales, TotalMales, BreedingAttempts;
            No = TheBreedingSuccessProbe(BreedingFemales, YoungOfTheYear, TotalPop, TotalFemales, TotalMales,
                                         BreedingAttempts);
            float bs = 0;
            if (BreedingFemales > 0)
            {
                bs = No / static_cast<float>(BreedingFemales);
                //bs = successful breeding attempt per attempting to breed female
            }
            BreedingSuccessProbeOutput(bs, BreedingFemales, YoungOfTheYear, TotalPop, TotalFemales, TotalMales, a_time,
                                       BreedingAttempts);
        }
        if (a_day == 152)
        {
            // Need to fill in the landscape from 1st June, it will change before
            // the count of fledgelings is needed
            m_TheLandscape->FillVegAreaData();
        }
        if (a_day == 197)
        {
            for (int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++)
            {
                No = TheFledgelingProbe();
                // Do some output
                FledgelingProbeOutput(No, a_time);
            }
        }
#ifdef __SKPOM
    // This is clunky but for purposes of validation we want probes throughout the year
    // First get the breeding pairs data.
    BreedingPairsOutput(a_day);
#else
        ProbeReport(a_time);
#endif
    }
    else return ProbeReport(a_time);
    return g_Str;
}

References BreedingPairsOutput(), BreedingSuccessProbeOutput(), Landscape::FillVegAreaData(), FledgelingProbeOutput(), g_Str, ImpactProbeReport(), m_NoProbes, Population_Manager_Base::m_TheLandscape, ProbeReport(), TheBreedingSuccessProbe(), and TheFledgelingProbe().

StepFinished()

bool Population_Manager::StepFinished ( void  )

protectedvirtual

Methods to run the simulations.

Returns true if and only if all objects have finished the current step

Reimplemented in TPredator_Population_Manager.

                                          {
    for (int listindex = 0; listindex < TheSubArrays.size(); listindex++)
    {
        for (int j=0; j < TheSubArrays[listindex].size(); j++){
            for (auto it = TheSubArrays[listindex][j]->begin(); it != TheSubArrays[listindex][j]->end(); ++it){
                if (!(*it)->GetStepDone()) return false;
            }
        }
    }
    return true;
}

References TheSubArrays.

Referenced by RunStepMethods().

SupplyAnimalPtr()

virtual TAnimal* Population_Manager::SupplyAnimalPtr ( unsigned int  a_index, unsigned int  a_animal  )

inlinevirtual

Returns the pointer indexed by a_index and a_animal. Note NO RANGE CHECK.

Reimplemented from Population_Manager_Base.

                                                                                  {
        //reset
        if(a_animal == 0 || a_animal < TheSubArrayPreviousIndex[a_index]){
            //let's find the first non-empty subarray
            TheSubArrayPreviousIndex[a_index] = 0;
            TheSubArrayThreadIndex[a_index] = 0;
            TheSubArraysIterators[a_index] = TheSubArrays[a_index][0]->begin();
            for (int j = 0; j < TheSubArraysSizes[a_index].size(); j++){
                if(TheSubArraysSizes[a_index][j] > 0){
                    TheSubArrayThreadIndex[a_index] = j;
                    TheSubArraysIterators[a_index] = TheSubArrays[a_index][j]->begin();
                    break;
                }
            }
            if(a_animal == 0)
                return *(TheSubArraysIterators[a_index]);
        }
 
        if(a_animal == TheSubArrayPreviousIndex[a_index]){
            return *(TheSubArraysIterators[a_index]);
        }
 
        //start the search from right after the previous position
        int temp_animal_num = TheSubArrayPreviousIndex[a_index];
        int temp_thread_num = TheSubArrayThreadIndex[a_index];
 
        TheSubArraysIterators[a_index]++;
        while(temp_animal_num < a_animal){
            for (auto it = TheSubArraysIterators[a_index]; it != TheSubArrays[a_index][temp_thread_num]->end(); ++it)
            {   
                temp_animal_num++;
                if(temp_animal_num == a_animal){
                    TheSubArrayPreviousIndex[a_index] = temp_animal_num;
                    TheSubArrayThreadIndex[a_index] = temp_thread_num;
                    TheSubArraysIterators[a_index] = it;
                    return *it;
                }
            }
            //we need to move to the next thread subarray and search from the beginning
            temp_thread_num++;
            TheSubArraysIterators[a_index] = TheSubArrays[a_index][temp_thread_num]->begin();
        }
 
        //if reach here means error happens,quite 
        exit(1);
    }

References TheSubArrayPreviousIndex, TheSubArrays, TheSubArraysIterators, TheSubArraysSizes, and TheSubArrayThreadIndex.

Referenced by Skylark_Population_Manager::BreedingPairsOutput(), Erigone_Population_Manager::Catastrophe(), Oedothorax_Population_Manager::Catastrophe(), Vole_Population_Manager::Catastrophe(), Skylark_Population_Manager::Catastrophe(), THare_Population_Manager::Catastrophe(), Beetle_Population_Manager::Catastrophe(), Beetle_Population_Manager::Catastrophe2(), Osmia_Population_Manager::DoBefore(), Erigone_Population_Manager::DoFirst(), Oedothorax_Population_Manager::DoFirst(), Vole_Population_Manager::DoFirst(), Bembidion_Population_Manager::DoFirst(), THare_Population_Manager::DoFirst(), AOR_Probe_Goose::DoProbe(), AOR_Probe::DoProbeInHaitatType(), THare_Population_Manager::ExtraPopMort(), Vole_Population_Manager::FindOutsideRadiusMale(), Vole_Population_Manager::FindRandomMale(), Vole_Population_Manager::GeneticsOutputFile(), Vole_Population_Manager::GeneticsResultsOutput(), Vole_Population_Manager::GetVoleAllele(), THare_Population_Manager::Hunting(), THare_Population_Manager::HuntingDifferentiatedBeetleBankArea(), THare_Population_Manager::HuntingGrid(), Vole_Population_Manager::ImpactedProbe(), TPredator_Population_Manager::InOtherTerritory(), LOG(), THare_Population_Manager::MRROutputs(), Osmia_Population_Manager::Osmia_Population_Manager(), THare_Population_Manager::POMOutputs(), TPredator_Population_Manager::PredSampleFile(), Beetle_Population_Manager::Probe(), Skylark_Population_Manager::ProbePOM(), Skylark_Population_Manager::ReHouse(), Vole_Population_Manager::ResistanceOutput(), TPredator_Population_Manager::Run(), Vole_Population_Manager::SendMessage(), TPredator_Population_Manager::StepFinished(), Skylark_Population_Manager::TheBreedingFemalesProbe(), Skylark_Population_Manager::TheBreedingSuccessProbe(), Skylark_Population_Manager::TheFledgelingProbe(), Vole_Population_Manager::TheReallyBigOutputProbe(), Beetle_Population_Manager::TheReallyBigOutputProbe(), Erigone_Population_Manager::TheRipleysOutputProbe(), Oedothorax_Population_Manager::TheRipleysOutputProbe(), Skylark_Population_Manager::TheRipleysOutputProbe(), THare_Population_Manager::TheRipleysOutputProbe(), Beetle_Population_Manager::TheRipleysOutputProbe(), and Vole_Population_Manager::TheSexRatiosProbe().

SupplyCovPosx()

virtual int Population_Manager::SupplyCovPosx ( int  )

inlinevirtual

{ return 0; }

SupplyCovPosy()

virtual int Population_Manager::SupplyCovPosy ( int  )

inlinevirtual

{ return 0; }

SupplyListIndexSize()

virtual unsigned Population_Manager::SupplyListIndexSize ( )

inlinevirtual

{ return static_cast<unsigned>(TheSubArrays.size()); }

References TheSubArrays.

Referenced by THare_Population_Manager::DoFirst(), ProbeReport(), Skylark_Population_Manager::ProbeReportPOM(), ProbeReportTimed(), TPredator_Population_Manager::Run(), Run(), and TPredator_Population_Manager::StepFinished().

SupplyListSize()

unsigned Population_Manager::SupplyListSize ( unsigned  listindex ) const

inline

                                                      {
        int return_value = 0;
        for (unsigned i = 0; i < TheSubArraysSizes[listindex].size(); i++)
        {
            return_value += TheSubArraysSizes[listindex][i];
        }
        return return_value; 
    }

References TheSubArraysSizes.

Referenced by TPredator_Population_Manager::InOtherTerritory(), Osmia_Population_Manager::Osmia_Population_Manager(), TPredator_Population_Manager::PredAutumnSample(), TPredator_Population_Manager::PredSampleFile(), TPredator_Population_Manager::PredSpringAutumnSample(), TPredator_Population_Manager::PredSpringSample(), TPredator_Population_Manager::Run(), and TPredator_Population_Manager::StepFinished().

SupplyPegPosx()

virtual int Population_Manager::SupplyPegPosx ( int  )

inlinevirtual

{ return 0; }

SupplyPegPosy()

virtual int Population_Manager::SupplyPegPosy ( int  )

inlinevirtual

{ return 0; }

SupplyStateNames()

const char* Population_Manager::SupplyStateNames ( int  i ) const

inline

{ return StateNames[i]; }

References StateNames.

Referenced by Skylark_Female::Step(), and Skylark_Male::Step().

SupplyStateNamesLength()

unsigned Population_Manager::SupplyStateNamesLength ( ) const

inline

{ return StateNamesLength; }

References StateNamesLength.

SupplyStepSize()

int Population_Manager::SupplyStepSize ( ) const

inline

{ return m_StepSize; }

References m_StepSize.

TheAOROutputProbe()

void Population_Manager::TheAOROutputProbe ( )

virtual

This method must be overridden in descendent classes

Reimplemented in Beetle_Population_Manager, THare_Population_Manager, Skylark_Population_Manager, Ladybird_Population_Manager, Osmia_Population_Manager, Vole_Population_Manager, Spider_Population_Manager, Oedothorax_Population_Manager, and Erigone_Population_Manager.

                                           {
}

Referenced by Run().

TheBreedingFemalesProbe()

virtual int Population_Manager::TheBreedingFemalesProbe ( int  )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

{ return 0; }

TheBreedingSuccessProbe()

virtual int Population_Manager::TheBreedingSuccessProbe ( int &  , int &  , int &  , int &  , int &  , int &    )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

                                                   { return 0; }

Referenced by SpeciesSpecificReporting().

TheFledgelingProbe()

virtual int Population_Manager::TheFledgelingProbe ( )

inlinevirtual

Reimplemented in Skylark_Population_Manager.

{ return 0; }

Referenced by SpeciesSpecificReporting().

TheGeneticProbe()

virtual void Population_Manager::TheGeneticProbe ( unsigned  , int  , unsigned &    )

inlinevirtual

                                                                 {
    }

TheReallyBigOutputProbe()

void Population_Manager::TheReallyBigOutputProbe ( )

virtual

This method must be overridden in descendent classes

Reimplemented in Beetle_Population_Manager, and Vole_Population_Manager.

                                                 {
}

Referenced by Run().

TheRipleysOutputProbe()

void Population_Manager::TheRipleysOutputProbe ( ofstream *  a_prb )

virtual

Special output functionality.

This method must be overridden in descendent classes

Reimplemented in Beetle_Population_Manager, and Vole_Population_Manager.

                                                          {
}

Referenced by Run().

UnsetGuardMapElement()

void Population_Manager::UnsetGuardMapElement ( unsigned  a_x_index, unsigned  a_y_index  )

inline

Unset the given guard map cell.

    {
        omp_unset_nest_lock(m_MapGuard[a_y_index][a_x_index]);
    }

References m_MapGuard.

Referenced by Beetle_Egg_List::DailyMortality(), Beetle_Egg_List::ExtremeTempMortality(), and Beetle_Egg_List::St_Hatch().

UpdateGuardMap()

void Population_Manager::UpdateGuardMap ( int  a_x, int  a_y, int &  a_index_x, int &  a_index_y  )

inline

Get the index of the guard map for the given location.

    {
        int temp_index_x = a_x / m_guard_cell_size;
        int temp_index_y = a_y / m_guard_cell_size;
        
        //a new cell, we need to reset the guard
        if(a_index_x != temp_index_x || a_index_y != temp_index_y){
            omp_unset_nest_lock(m_MapGuard[a_index_y][a_index_x]);
            omp_set_nest_lock(m_MapGuard[temp_index_y][temp_index_x]);
            a_index_x = temp_index_x;
            a_index_y = temp_index_y;
        }
        
    }

References m_guard_cell_size, and m_MapGuard.

Referenced by Spider_Juvenile::BalloonTo(), Beetle_Base::Beetle_1M_Move(), Vole_JuvenileMale::Dispersal(), Vole_Male::Dispersal(), Vole_JuvenileFemale::Dispersal(), Vole_Base::Escape(), Osmia_Female::FindNestLocation(), Ladybird_Adult::FindTarget(), Ladybird_Adult::LongRangeFind(), Vole_Base::MoveTo(), Beetle_Adult::MoveToNoList(), Beetle_Adult::MoveToWithPlacesList(), THare::Run(), THare::Running(), TPredator::st_Dispersal(), Osmia_Female::st_Dispersal(), Hare_Juvenile::st_Dispersal(), Vole_Male::st_Eval_n_Explore(), TPredator::st_Movement(), Vole_Female::st_Special_Explore(), Beetle_Adult::TryToReproduce(), and Spider_Juvenile::WalkTo().

Member Data Documentation

AOROutputPrb

ofstream* Population_Manager::AOROutputPrb {}

protected

BeforeStepActions

vector<unsigned> Population_Manager::BeforeStepActions

protected

Holds the season list of possible before step actions.

Referenced by Beetle_Population_Manager::Beetle_Population_Manager(), Erigone_Population_Manager::Init(), Oedothorax_Population_Manager::Init(), Vole_Population_Manager::Init(), Skylark_Population_Manager::Init(), THare_Population_Manager::Init(), Population_Manager(), Shuffle_or_Sort(), and Spider_Population_Manager::Spider_Population_Manager().

lamdagrid

long int Population_Manager::lamdagrid[2][257][257] {}

protected

Referenced by LamdaBirth(), LamdaClear(), LamdaDeath(), and LamdaDumpOutput().

m_AOR_Probe

AOR_Probe* Population_Manager::m_AOR_Probe {}

protected

A pointer to the AOR probe.

Referenced by OpenTheAOROutputProbe(), Beetle_Population_Manager::OpenTheAOROutputProbe(), Erigone_Population_Manager::TheAOROutputProbe(), Oedothorax_Population_Manager::TheAOROutputProbe(), Vole_Population_Manager::TheAOROutputProbe(), Osmia_Population_Manager::TheAOROutputProbe(), Ladybird_Population_Manager::TheAOROutputProbe(), Skylark_Population_Manager::TheAOROutputProbe(), THare_Population_Manager::TheAOROutputProbe(), Beetle_Population_Manager::TheAOROutputProbe(), and ~Population_Manager().

m_guard_cell_height_num

int Population_Manager::m_guard_cell_height_num

protected

Referenced by Population_Manager(), and ~Population_Manager().

m_guard_cell_size

int Population_Manager::m_guard_cell_size

protected

Referenced by Ladybird_Population_Manager::DoFirst(), Erigone_Population_Manager::Init(), Oedothorax_Population_Manager::Init(), Population_Manager(), RunStepMethods(), and UpdateGuardMap().

m_guard_cell_width_num

int Population_Manager::m_guard_cell_width_num

protected

Referenced by Population_Manager(), and ~Population_Manager().

m_is_paralleled

bool Population_Manager::m_is_paralleled

protected

This is used to indicate whether the species is paralleled.

Referenced by Beetle_Population_Manager::Beetle_Population_Manager(), Ladybird_Population_Manager::DoFirst(), Vole_Population_Manager::Init(), THare_Population_Manager::Init(), Osmia_Population_Manager::Osmia_Population_Manager(), Population_Manager(), RunStepMethods(), and Spider_Population_Manager::Spider_Population_Manager().

m_LifeStageOrderVec

vector<int> Population_Manager::m_LifeStageOrderVec

protected

The vector to store the life stage order for looping specie life stages.

Referenced by Ladybird_Population_Manager::Ladybird_Population_Manager(), Population_Manager(), and RunStepMethods().

m_LiveArraySize

vector<unsigned> Population_Manager::m_LiveArraySize

protected

Referenced by Beetle_Population_Manager::DoBeetleActiveProbe(), Ladybird_Population_Manager::DoFirst(), Ladybird_Population_Manager::DoSpecialBetweenLifeStages(), GetLiveArraySize(), IncLiveArraySize(), LOG(), PartitionLiveDead(), Population_Manager(), and Run().

m_MapGuard

std::vector<std::vector<omp_nest_lock_t*> > Population_Manager::m_MapGuard

protected

This is used to make sure animals will not behaviour at the same area - multi threads.

Referenced by Ladybird_Population_Manager::DoFirst(), GetGuardMapElement(), Erigone_Population_Manager::Init(), Oedothorax_Population_Manager::Init(), Population_Manager(), RunStepMethods(), SetGuardMapElement(), UnsetGuardMapElement(), UpdateGuardMap(), and ~Population_Manager().

m_NoProbes

int Population_Manager::m_NoProbes = 0

protected

Referenced by ProbeReport(), Skylark_Population_Manager::ProbeReportPOM(), ProbeReportTimed(), SetNoProbesAndSpeciesSpecificFunctions(), and SpeciesSpecificReporting().

m_population_type

TTypesOfPopulation Population_Manager::m_population_type {TOP_NoSpecies}

protected

Referenced by Beetle_Population_Manager::Beetle_Population_Manager(), Bembidion_Population_Manager::Bembidion_Population_Manager(), Beetle_Population_Manager::DayDegreeCalculations(), GetPopulationType(), Erigone_Population_Manager::Init(), Oedothorax_Population_Manager::Init(), Vole_Population_Manager::Init(), Skylark_Population_Manager::Init(), THare_Population_Manager::Init(), Ladybird_Population_Manager::Ladybird_Population_Manager(), PoecilusCupreus_Population_Manager::PoecilusCupreus_Population_Manager(), and TPredator_Population_Manager::TPredator_Population_Manager().

m_SeasonNumber

int Population_Manager::m_SeasonNumber

protected

Holds the season number. Used when running goose and hunter sims.

Referenced by GetSeasonNumber(), and Population_Manager().

m_StepSize

int Population_Manager::m_StepSize {}

protected

Referenced by Vole_Population_Manager::Init(), and SupplyStepSize().

ProbesSet

bool Population_Manager::ProbesSet {}

ReallyBigOutputPrb

ofstream* Population_Manager::ReallyBigOutputPrb {}

protected

Referenced by Beetle_Population_Manager::Beetle_Population_Manager(), CloseTheReallyBigOutputProbe(), Erigone_Population_Manager::Init(), Oedothorax_Population_Manager::Init(), Vole_Population_Manager::Init(), Skylark_Population_Manager::Init(), THare_Population_Manager::Init(), OpenTheReallyBigProbe(), Vole_Population_Manager::TheReallyBigOutputProbe(), Beetle_Population_Manager::TheReallyBigOutputProbe(), and TPredator_Population_Manager::TPredator_Population_Manager().

RipleysOutputPrb

ofstream* Population_Manager::RipleysOutputPrb {}

protected

Referenced by CloseTheRipleysOutputProbe(), OpenTheRipleysOutputProbe(), Run(), and TPredator_Population_Manager::TPredator_Population_Manager().

RipleysOutputPrb1

ofstream* Population_Manager::RipleysOutputPrb1 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb10

ofstream* Population_Manager::RipleysOutputPrb10 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb11

ofstream* Population_Manager::RipleysOutputPrb11 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb12

ofstream* Population_Manager::RipleysOutputPrb12 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb2

ofstream* Population_Manager::RipleysOutputPrb2 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb3

ofstream* Population_Manager::RipleysOutputPrb3 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb4

ofstream* Population_Manager::RipleysOutputPrb4 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb5

ofstream* Population_Manager::RipleysOutputPrb5 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb6

ofstream* Population_Manager::RipleysOutputPrb6 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb7

ofstream* Population_Manager::RipleysOutputPrb7 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb8

ofstream* Population_Manager::RipleysOutputPrb8 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

RipleysOutputPrb9

ofstream* Population_Manager::RipleysOutputPrb9 {}

protected

Referenced by CloseTheMonthlyRipleysOutputProbe(), OpenTheMonthlyRipleysOutputProbe(), and Run().

StateNames

const char* Population_Manager::StateNames[100] {}

protected

Referenced by Beetle_Population_Manager::Beetle_Population_Manager(), Vole_Population_Manager::Init(), Skylark_Population_Manager::Init(), THare_Population_Manager::Init(), Spider_Population_Manager::Spider_Population_Manager(), and SupplyStateNames().

StateNamesLength

unsigned Population_Manager::StateNamesLength

protected

Referenced by Population_Manager(), and SupplyStateNamesLength().

TestFile

FILE* Population_Manager::TestFile {}

protected

Referenced by Vole_Population_Manager::Init().

TestFile2

FILE* Population_Manager::TestFile2 {}

protected

Referenced by Vole_Population_Manager::Init().

TheSubArrayPreviousIndex

vector<int> Population_Manager::TheSubArrayPreviousIndex

protected

the animal index number from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class.

Referenced by Population_Manager(), Run(), and SupplyAnimalPtr().

TheSubArrays

vector<vector<forward_list<TAnimal*>*> > Population_Manager::TheSubArrays

protected

Hold all the animal pointers.

Referenced by Bembidion_Population_Manager::Bembidion_Population_Manager(), Beetle_Population_Manager::DoBeetleActiveProbe(), Ladybird_Population_Manager::DoExtremeTempActions(), Ladybird_Population_Manager::DoFirst(), Ladybird_Population_Manager::DoSpecialBetweenLifeStages(), FarmAnimalCensus(), FindClosest(), FindIndividual(), Ladybird_Population_Manager::Ladybird_Population_Manager(), LOG(), PartitionLiveDead(), PoecilusCupreus_Population_Manager::PoecilusCupreus_Population_Manager(), Population_Manager(), Probe(), PushIndividual(), Run(), RunStepMethods(), Shuffle(), SortState(), SortStateR(), SortX(), SortY(), StepFinished(), SupplyAnimalPtr(), SupplyListIndexSize(), and ~Population_Manager().

TheSubArraysIterators

vector<forward_list<TAnimal*>::iterator> Population_Manager::TheSubArraysIterators

protected

the iterator from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class.

Referenced by Population_Manager(), Run(), and SupplyAnimalPtr().

TheSubArraysSizes

vector<vector<int> > Population_Manager::TheSubArraysSizes

protected

Hold all the animal sizes in each thread.

Referenced by Ladybird_Population_Manager::DoSpecialBetweenLifeStages(), PartitionLiveDead(), Population_Manager(), Run(), SupplyAnimalPtr(), and SupplyListSize().

TheSubArrayThreadIndex

vector<int> Population_Manager::TheSubArrayThreadIndex

protected

the thread index number from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class.

Referenced by Population_Manager(), Run(), and SupplyAnimalPtr().

---

The documentation for this class was generated from the following files:

• /builds/ALMaSS/ALMaSS_MIDox/BatchALMaSS/PopulationManager.h
• /builds/ALMaSS/ALMaSS_MIDox/BatchALMaSS/PopulationManager.cpp