#include <species.h>

Inheritance diagram for Species_Base:

Collaboration diagram for Species_Base:

Public Member Functions
virtual	~Species_Base ()=0

int	xsize ()

int	size ()

void	set_inputBirthFlux (double b)

void	set_bfin_is_u0in (bool flag)

virtual void	resize (int _J)=0

virtual double	get_maxSize ()=0

virtual void	print ()=0

virtual void	set_xb (double _xb)=0

virtual void	set_ub (double _ub)=0

virtual void	set_birthTime (int i, double t0)=0

virtual void	setX (int i, double _x)=0

virtual void	setU (int i, double _u)=0

virtual double	getX (int i)=0

virtual double	getU (int i)=0

virtual double	init_density (int i, double x, void *env)=0

virtual void	initAndCopyExtraState (double t, void *env, std::vector< double >::iterator &it)=0

virtual void	initBoundaryCohort (double t, void *env)=0

virtual void	copyExtraStateToCohorts (std::vector< double >::iterator &it)=0

virtual void	copyCohortsExtraToState (std::vector< double >::iterator &it)=0

virtual double	establishmentProbability (double t, void *env)=0

virtual double	calc_boundary_u (double gb, double pe)=0

virtual double	get_boundary_u ()=0

virtual void	triggerPreCompute ()=0

virtual double	growthRate (int i, double x, double t, void *env)=0

virtual double	growthRateOffset (int i, double x, double t, void *env)=0

virtual std::vector< double >	growthRateGradient (int i, double x, double t, void *env, double grad_dx)=0

virtual std::vector< double >	growthRateGradientCentered (int i, double xplus, double xminus, double t, void *env)=0

virtual double	mortalityRate (int i, double x, double t, void *env)=0

virtual std::vector< double >	mortalityRateGradient (int i, double x, double t, void *env, double grad_dx)=0

virtual double	birthRate (int i, double x, double t, void *env)=0

virtual void	getExtraRates (std::vector< double >::iterator &it)=0

virtual void	addCohort ()=0

template<class T >
void	addCohort (T bc)

virtual void	removeDensestCohort ()=0

virtual void	removeDenseCohorts (double dxcut)=0

virtual void	removeDeadCohorts (double ucut)=0

Public Attributes
double	birth_flux_in

bool	bfin_is_u0in = false

double	xb

bool	is_resident

Protected Attributes
int	J

int	n_extra_statevars = 0

std::list< double >	birth_flux_out_history

std::vector< double >	X

std::vector< double >	x

std::vector< double >	h

std::vector< double >	schedule

Friends
class	Solver

Detailed Description

Definition at line 15 of file species.h.

Constructor & Destructor Documentation

◆ ~Species_Base()

Species_Base::~Species_Base ( )

pure virtual

Definition at line 4 of file species.cpp.

4 {

5 }

Member Function Documentation

◆ addCohort() [1/2]

virtual void Species_Base::addCohort ( )

pure virtual

Implemented in Species< Model >.

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◆ addCohort() [2/2]

template<class T >

void Species_Base::addCohort ( T bc )

Definition at line 8 of file species.tpp.

                                 {
     (dynamic_cast<Species<T>>(*this)).addCohort(bc);
 }

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◆ birthRate()

virtual double Species_Base::birthRate	(	int	i,
		double	x,
		double	t,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

◆ calc_boundary_u()

virtual double Species_Base::calc_boundary_u	(	double	gb,
		double	pe
	)

pure virtual

Implemented in Species< Model >.

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◆ copyCohortsExtraToState()

virtual void Species_Base::copyCohortsExtraToState ( std::vector< double >::iterator & it )

pure virtual

Implemented in Species< Model >.

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◆ copyExtraStateToCohorts()

virtual void Species_Base::copyExtraStateToCohorts ( std::vector< double >::iterator & it )

pure virtual

Implemented in Species< Model >.

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◆ establishmentProbability()

virtual double Species_Base::establishmentProbability	(	double	t,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

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◆ get_boundary_u()

virtual double Species_Base::get_boundary_u ( )

pure virtual

Implemented in Species< Model >.

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◆ get_maxSize()

virtual double Species_Base::get_maxSize ( )

pure virtual

Implemented in Species< Model >.

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◆ getExtraRates()

virtual void Species_Base::getExtraRates ( std::vector< double >::iterator & it )

pure virtual

Implemented in Species< Model >.

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◆ getU()

virtual double Species_Base::getU ( int i )

pure virtual

Implemented in Species< Model >.

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◆ getX()

virtual double Species_Base::getX ( int i )

pure virtual

Implemented in Species< Model >.

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◆ growthRate()

virtual double Species_Base::growthRate	(	int	i,
		double	x,
		double	t,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

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◆ growthRateGradient()

virtual std::vector<double> Species_Base::growthRateGradient	(	int	i,
		double	x,
		double	t,
		void *	env,
		double	grad_dx
	)

pure virtual

Implemented in Species< Model >.

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◆ growthRateGradientCentered()

virtual std::vector<double> Species_Base::growthRateGradientCentered	(	int	i,
		double	xplus,
		double	xminus,
		double	t,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

◆ growthRateOffset()

virtual double Species_Base::growthRateOffset	(	int	i,
		double	x,
		double	t,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

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◆ init_density()

virtual double Species_Base::init_density	(	int	i,
		double	x,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

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◆ initAndCopyExtraState()

virtual void Species_Base::initAndCopyExtraState	(	double	t,
		void *	env,
		std::vector< double >::iterator &	it
	)

pure virtual

Implemented in Species< Model >.

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◆ initBoundaryCohort()

virtual void Species_Base::initBoundaryCohort	(	double	t,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

◆ mortalityRate()

virtual double Species_Base::mortalityRate	(	int	i,
		double	x,
		double	t,
		void *	env
	)

pure virtual

Implemented in Species< Model >.

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◆ mortalityRateGradient()

virtual std::vector<double> Species_Base::mortalityRateGradient	(	int	i,
		double	x,
		double	t,
		void *	env,
		double	grad_dx
	)

pure virtual

Implemented in Species< Model >.

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◆ print()

virtual void Species_Base::print ( )

pure virtual

Implemented in Species< Model >.

◆ removeDeadCohorts()

virtual void Species_Base::removeDeadCohorts ( double ucut )

pure virtual

Implemented in Species< Model >.

◆ removeDenseCohorts()

virtual void Species_Base::removeDenseCohorts ( double dxcut )

pure virtual

Implemented in Species< Model >.

◆ removeDensestCohort()

virtual void Species_Base::removeDensestCohort ( )

pure virtual

Implemented in Species< Model >.

◆ resize()

virtual void Species_Base::resize ( int _J )

pure virtual

Implemented in Species< Model >.

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◆ set_bfin_is_u0in()

void Species_Base::set_bfin_is_u0in ( bool flag )

Definition at line 40 of file species.cpp.

                                             {
     bfin_is_u0in = flag;
 }

◆ set_birthTime()

virtual void Species_Base::set_birthTime	(	int	i,
		double	t0
	)

pure virtual

Implemented in Species< Model >.

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◆ set_inputBirthFlux()

void Species_Base::set_inputBirthFlux ( double b )

Definition at line 30 of file species.cpp.

                                              {
     birth_flux_in = b;
 }

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◆ set_ub()

virtual void Species_Base::set_ub ( double _ub )

pure virtual

Implemented in Species< Model >.

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◆ set_xb()

virtual void Species_Base::set_xb ( double _xb )

pure virtual

Implemented in Species< Model >.

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◆ setU()

virtual void Species_Base::setU	(	int	i,
		double	_u
	)

pure virtual

Implemented in Species< Model >.

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◆ setX()

virtual void Species_Base::setX	(	int	i,
		double	_x
	)

pure virtual

Implemented in Species< Model >.

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◆ size()

int Species_Base::size ( )

◆ triggerPreCompute()

virtual void Species_Base::triggerPreCompute ( )

pure virtual

Implemented in Species< Model >.

◆ xsize()

int Species_Base::xsize ( )

Definition at line 45 of file species.cpp.

                        {
     return J;
 }

Friends And Related Function Documentation

◆ Solver

friend class Solver

friend

Definition at line 17 of file species.h.

Member Data Documentation

◆ bfin_is_u0in

bool Species_Base::bfin_is_u0in = false

Definition at line 37 of file species.h.

◆ birth_flux_in

double Species_Base::birth_flux_in

Definition at line 34 of file species.h.

◆ birth_flux_out_history

std::list<double> Species_Base::birth_flux_out_history

protected

Definition at line 23 of file species.h.

◆ h

std::vector<double> Species_Base::h

protected

Definition at line 30 of file species.h.

◆ is_resident

bool Species_Base::is_resident

Definition at line 42 of file species.h.

◆ J

int Species_Base::J

protected

Definition at line 20 of file species.h.

◆ n_extra_statevars

int Species_Base::n_extra_statevars = 0

protected

Definition at line 21 of file species.h.

◆ schedule

std::vector<double> Species_Base::schedule

protected

Definition at line 31 of file species.h.

◆ X

std::vector<double> Species_Base::X

protected

Definition at line 28 of file species.h.

◆ x

std::vector<double> Species_Base::x

protected

Definition at line 29 of file species.h.

◆ xb

double Species_Base::xb

Definition at line 41 of file species.h.

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

Public Member Functions

Public Attributes

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ~Species_Base()

Member Function Documentation

◆ addCohort() [1/2]

◆ addCohort() [2/2]

◆ birthRate()

◆ calc_boundary_u()

◆ copyCohortsExtraToState()

◆ copyExtraStateToCohorts()

◆ establishmentProbability()

◆ get_boundary_u()

◆ get_maxSize()

◆ getExtraRates()

◆ getU()

◆ getX()

◆ growthRate()

◆ growthRateGradient()

◆ growthRateGradientCentered()

◆ growthRateOffset()

◆ init_density()

◆ initAndCopyExtraState()

◆ initBoundaryCohort()

◆ mortalityRate()

◆ mortalityRateGradient()

◆ print()

◆ removeDeadCohorts()

◆ removeDenseCohorts()

◆ removeDensestCohort()

◆ resize()

◆ set_bfin_is_u0in()

◆ set_birthTime()

◆ set_inputBirthFlux()

◆ set_ub()

◆ set_xb()

◆ setU()

◆ setX()

◆ size()

◆ triggerPreCompute()

◆ xsize()

Friends And Related Function Documentation

◆ Solver

Member Data Documentation

◆ bfin_is_u0in

◆ birth_flux_in

◆ birth_flux_out_history

◆ h

◆ is_resident

◆ J

◆ n_extra_statevars

◆ schedule

◆ X

◆ x

◆ xb