Tree fern establishment - Version 1.0. More...

#include <EpiphyticEstablishment.h>

Inheritance diagram for clEpiphyticEstablishment:

Public Member Functions
	clEpiphyticEstablishment (clSimManager *p_oSimManager)
	Constructor. More...

	~clEpiphyticEstablishment ()
	Destructor. More...

void	GetData (xercesc::DOMDocument *p_oDoc)
	Performs setup. More...

void	Action ()
	Performs establishment. More...

void	RegisterTreeDataMembers ()
	Overridden from clLightBase to do nothing. More...

float	CalcLightValue (clTree p_oTree, clTreePopulation p_oPop)
	Overridden from clLightBase to do nothing. More...

Public Member Functions inherited from clGLIBase
	clGLIBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clGLIBase ()
	Destructor. More...

float	GetSinMinSunAng ()
	Gets the sine of the minimum sun angle. More...

float	GetAziChunkConverter ()
	Gets the reciprocal of the size of a single azimuth sky grid division, in degrees. More...

float	GetRcpTanMinAng ()
	Gets the reciprocal of the tangent of the minimum sun angle. More...

Public Member Functions inherited from clLightBase
	clLightBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clLightBase ()
	Destructor. More...

void	Action ()
	Performs all light calculations. More...

void	RegisterTreeDataMembers ()
	Performs data member registrations for "Light". More...

clLightOrg *	GetLightOrg ()
	Gets the light org object. More...

float	GetMinSunAngle ()
	Gets the altitude angle below which the sky is assumed to be dark. More...

float	GetNumAziAng ()
	Gets the number of azimuth angles into which the sky hemisphere is divided. More...

float	GetNumAltAng ()
	Gets the number of altitude angles into which the sky hemisphere is divided. More...

float	GetMinAngRow ()
	Gets the row in the brightness array corresponding to the minimum solar angle. More...

float	GetBrightness (int alt, int azi)

Public Member Functions inherited from clBehaviorBase
virtual float	GetBehaviorVersion ()
	Gets the behavior version number. More...

	clBehaviorBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clBehaviorBase ()
	Destructor. More...

virtual short int	ValidateVersionNumber (float fTestVersion)
	Makes sure that the version number of a file passed is between the minimum and current version numbers. More...

virtual void	SetSpeciesTypeCombos (short int iNumCombos, stcSpeciesTypeCombo *p_whatCombos)
	Sets the species/type combos for a behavior. More...

virtual void	SetNameData (std::string sNameString)
	Sets the string for the parameter file behavior. More...

virtual short int	GetNewTreeInts ()
	Gets the number of new tree integer data members this behavior wants to register. More...

virtual short int	GetNewTreeFloats ()
	Gets the number of new tree float data members this behavior wants to register. More...

virtual short int	GetNewTreeChars ()
	Gets the number of new tree character data members this behavior wants to register. More...

virtual short int	GetNewTreeBools ()
	Gets the number of new tree bool data members this behavior wants to register. More...

virtual short int	GetNumSpeciesTypeCombos ()
	Gets the number of species/type combos to which this behavior applies. More...

virtual short int	GetNumBehaviorSpecies ()
	Gets the number of unique tree species to which this behavior applies. More...

struct stcSpeciesTypeCombo	GetSpeciesTypeCombo (short int iIndex)
	Gets one of this behavior's type/species combos. More...

virtual short int	GetBehaviorSpecies (short int iIndex)
	Gets one of the behavior's species. More...

short int	GetBehaviorListNumber ()
	Gets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list. More...

void	SetBehaviorListNumber (short int iNumber)
	Sets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list. More...

std::string	FormatSpeciesTypeQueryString ()
	Formats the string for species/types query. More...

virtual DOMElement *	GetParentParametersElement (xercesc::DOMDocument *p_oDoc)
	This will get the correct set of parameters for this behavior based on the behavior list position number. More...

Public Member Functions inherited from clWorkerBase
	clWorkerBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clWorkerBase ()
	Destructor. More...

std::string	GetName ()
	Gets the object's namestring. More...

clSimManager *	GetSimManager ()

void	DoObjectSetup (xercesc::DOMDocument *p_oDoc, fileType iFileType)
	Triggers the setup process. More...

virtual void	TimestepCleanup ()
	Performs any necessary cleanup operations at the end of a timestep. More...

virtual void	EndOfRunCleanup ()
	Performs any necessary cleanup operations at the end of a run. More...

Protected Member Functions
void	GetParameterFileData (xercesc::DOMDocument *p_oDoc)
	Declares arrays and fills them with parameter file data. More...

void	DoLightSetup ()
	Performs calculations required of light. More...

float	GetGLI (clTreePopulation *p_oPop, const float &fX, const float &fY, const float &fHeight)
	Gets the GLI for a given point. More...

void	GetTreeDataMemberCodes ()
	Gets the return codes for the "dead" tree data member. More...

void	FormatQueryString ()
	Formats the string in m_cQuery. More...

Protected Member Functions inherited from clGLIBase
void	AddTreeToGliFishEye (const float &fTargetX, const float &fTargetY, const float &fTargetHeight, clTree p_oNeighbor, clPlot p_oPlot, clTreePopulation p_oPop, clAllometry p_oAllom)
	Adds one shading neighbor to the fisheye photo array for a GLI calculation. More...

void	GLIFisheyeNoCanopyIntersect (const float &fTargetX, const float &fTargetY, const float &fNeighX, const float &fNeighY, const float &fNeighCanrad, const float &fNeighHeight, const short int &iNeighSpecies, const float &fTargetHeight, const float &fDistToNearEdge, clTree p_oNeighbor, clPlot p_oPlot, clAllometry *p_oAllom)
	Adds one shading neighbor to the fisheye photo array for a GLI calculation when the canopies of the two trees do not overlap. More...

void	GLIFisheyeCanopyIntersect (const float &fTargetX, const float &fTargetY, const float &fNeighX, const float &fNeighY, const float &fNeighCanrad, const float &fNeighHeight, const short int &iNeighSpecies, const float &fTargetHeight, clTree p_oNeighbor, clPlot p_oPlot, clAllometry *p_oAllom)
	Adds one shading neighbor to the fisheye photo array for a GLI calculation when the canopies of the two trees overlap. More...

Protected Member Functions inherited from clLightBase
void	GetData (xercesc::DOMDocument *p_oDoc)
	Triggers all light setup. More...

virtual void	DoShellSetup (xercesc::DOMDocument *p_oDoc)
	If a descendent class has specific setup needs, it can overload this function. More...

void	PopulateGLIBrightnessArray ()
	Populates the GLI brightness array. More...

void	PopulateSailLightBrightnessArray ()
	Populates the sail brightness array. More...

float	GetDayAngle (int iJulianDay)
	Computes day angle. More...

float	GetDeclination (float &fDayAngle)
	Computes solar declination. More...

float	GetEccentricity (float &fDayAngle)
	Computes solar eccentricity. More...

float	GetSunrise (float &fLatInRadians, float &fDeclination)
	Computes sunrise. More...

float	GetCosineOfZenithAngle (float &fDeclination, float &fLatInRadians, float &fTimeNow)
	Computes cosine of the zenith angle of the sun at a given time. More...

float	GetAltitudeAngle (float &fCosZenAng)
	Computes altitude angle of the sun at a given time in radians. More...

float	GetAzimuthAngle (float &fDeclination, float &fLatInRadians, float &fAltInRad, float &fTimeNow)
	Computes azimuth angle of the sun at a given time in radians in SORTIE azimuth coordinates. More...

float	GetAirmassEffect (float &fAltInDeg, float &fCosZenAng)
	Computes the airmass effect for a given altitude angle. More...

float	GetBeamRadiation (float &fClearSkyTransCoeff, float &fAirmass, float &fEccentricity, float &fCosZenAng)
	Computes beam radiation strength. More...

virtual float	GetLightExtinctionCoefficient (clTree *p_oTree)
	Gets the light extinction coefficent. More...

Protected Member Functions inherited from clWorkerBase
void	AssembleFileCode (int iFileType, int iFileVersion, char *cCode)
	Creates the proper identifying filecode for an XML file. More...

Protected Attributes
short int **	mp_iDeadCodes
	Codes for the "dead" tree data member. More...

char *	m_cQuery
	String to pass to clTreePopulation::Find() in order to get the trees for which to calculate volume. More...

double *	mp_fA
	a in the seedling probability equation. More...

double *	mp_fB
	b in the seedling probability equation. More...

double *	mp_fC
	c in the seedling probability equation. More...

double *	mp_fM
	m in the seedling height equation. More...

double *	mp_fN
	n in the seedling height equation. More...

double	m_fMaxSearchDistance
	Maximum search distance for shading neighbors. More...

int	m_iSeedlingSpecies
	Species of seedlings to disperse. More...

short int	m_iNumTotalSpecies
	Number of species. More...

Protected Attributes inherited from clGLIBase
float	m_fSinMinSunAng
	Sin of the min sun angle. More...

float	m_fAziChunkConverter
	Reciprocal of the size of a single azimuth sky grid division, in degrees. More...

float	m_fRcpTanMinAng
	1/tan (m_fMinSunAngle). More...

float *	mp_fAziSlope
	For each azimuth chunk of sky, this holds the slope of the line to the middle of the chunk. More...

Protected Attributes inherited from clLightBase
bool	m_bHooked
	Whether or not this shell object is hooked to clLightOrg. More...

bool	m_bNeedsCommonParameters
	Whether or not this shell object requires the common light parameters held in clLightOrg such as clLightOrg::m_iLastJulDay. More...

float **	mp_fBrightness
	Sky brightness array. More...

float **	mp_fPhoto
	Simulated fisheye photo array. More...

double	m_fMinSunAngle
	The altitude angle below which the sky is assumed to be dark. More...

double	m_fAzimuthOfNorth
	The azimuth angle of north. More...

int	m_iNumAziAng
	Number of azimuth angles into which the sky hemisphere is divided. More...

int	m_iNumAltAng
	Number of altitude angles into which the sky hemisphere is divided. More...

int	m_iMinAngRow
	Row in the brightness array corresponding to the minimum solar angle. More...

Protected Attributes inherited from clBehaviorBase
short int	m_iNumSpeciesTypeCombos
	How many type/species combos a behavior will act on. More...

short int	m_iNumBehaviorSpecies
	How many distinct species are in the combo list - important for filling species-specific values from parameter file. More...

short int *	mp_iWhatSpecies
	List of distinct species - for filling species-specific values from parameter file. More...

stcSpeciesTypeCombo *	mp_whatSpeciesTypeCombos
	Array of species/type combos that the behavior will act on. More...

short int	m_iNewTreeInts
	The number of new tree integer data members this behavior wants to add. More...

short int	m_iNewTreeFloats
	The number of new tree float data members this behavior wants to add. More...

short int	m_iNewTreeChars
	The number of new tree character data members this behavior wants to add. More...

short int	m_iNewTreeBools
	The number of new tree boolean data members this behavior wants to add. More...

short int	m_iBehaviorListNumber
	The number of this behavior in the behavior list, to differentiate between possible multiple copies of this behavior. More...

float	m_fVersionNumber
	Version number - this will be rounded to 2 digits after the decimal place. More...

std::string	m_sXMLRoot
	XML root that encloses the parameters for this behavior. More...

float	m_fMinimumVersionNumber
	Minimum version number - this behavior will run parameter data for a file marked between this number and the current version number, inclusive. More...

Protected Attributes inherited from clWorkerBase
std::string	m_sNameString
	If a behavior has registered a command line command with the sim manager, this allows it to be called. More...

clSimManager *	mp_oSimManager
	Pointer to the simulation manager object. More...

int *	mp_iAllowedFileTypes
	List of the input file types this object can handle. More...

int	m_iNumAllowedTypes
	Number of input file types this object can handle. More...

Additional Inherited Members
Static Protected Attributes inherited from clLightBase
static clLightOrg *	mp_oLightOrg
	clLightOrg object - this pointer is held in common by all shells More...

Detailed Description

Tree fern establishment - Version 1.0.

Treefern establishment simulates epiphytic seedlings that root when their substrate tree dies. Unusually for behaviors, this is applied to the species that serve as substrate rather than the species to which the seedlings will belong. This is because all of the function parameters depend on the species of the substrate trees.

When trees of one of the substrate species dies, it may allow exactly one of its epiphytic seedlings to root. The probability that a dead tree will produce a seedling is:

P = 1 - (1/ ( 1 + exp( a + b * H + c * GLI )))

where H is the height of the substrate tree, and GLI is the light level at the tree's location. The light level is calculated halfway between the ground and the base of the crown.

If a seedling is produced, its height is:

HS = m + n*H

where HS is the height of the seedling in cm, and H is the height of the substrate tree in m.

The parameters designate which species the seedlings are of, and all seedlings produced are only of that species. The seedling roots in the exact spot where the substrate tree was.

Dead substrate trees are identified as such by checking the value in their "dead" code. Thus it is important that this behavior run after mortality but before tree removal.

Trees to which this behavior is applied ( that is, substrate trees) must also have a mortality behavior applied. This can only be applied to saplings and adults.

This behavior's name string and parameter file call string are both "EpiphyticEstablishment".

Author: Lora E. Murphy

Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)

Constructor & Destructor Documentation

◆ clEpiphyticEstablishment()

clEpiphyticEstablishment::clEpiphyticEstablishment ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clEpiphyticEstablishment()

clEpiphyticEstablishment::~clEpiphyticEstablishment ( )

Destructor.

Member Function Documentation

◆ Action()

void clEpiphyticEstablishment::Action ( )

virtual

Performs establishment.

This finds dead individuals of the establishment substrate species; calculates the GLI halfway up the trunk; and uses that to determine the probability that a seedling will root. If a seedling roots, its height is calculated. Then its xy coordinates and height are saved until all dead substrate trees have been processed. Then all seedlings are created at once. The reason seedlings are created at the end is because the height calculation may in fact make them saplings. Then they would affect GLI calculations.

Reimplemented from clBehaviorBase.

◆ CalcLightValue()

float clEpiphyticEstablishment::CalcLightValue	(	clTree *	p_oTree,
		clTreePopulation *	p_oPop
	)

inlinevirtual

Overridden from clLightBase to do nothing.

Implements clLightBase.

◆ DoLightSetup()

void clEpiphyticEstablishment::DoLightSetup ( )

protected

Performs calculations required of light.

This calculates the brightness array for GLI and the values for m_fAziChunkConverter, m_fRcpTanMinAng, mp_fAziSlope, m_fSinMinSunAng, m_iMinAngRow, and m_fMaxSearchDistance.

◆ FormatQueryString()

void clEpiphyticEstablishment::FormatQueryString ( )

protected

Formats the string in m_cQuery.

This value will be used in Action() to pass to clTreePopulation::Find() in order to get the trees to act on.

◆ GetData()

void clEpiphyticEstablishment::GetData ( xercesc::DOMDocument * p_oDoc )

virtual

Performs setup.

Calls:

Parameters

p_oDoc DOM tree of parsed input file.

Implements clWorkerBase.

◆ GetGLI()

float clEpiphyticEstablishment::GetGLI	(	clTreePopulation *	p_oPop,
		const float &	fX,
		const float &	fY,
		const float &	fHeight
	)

protected

Gets the GLI for a given point.

Parameters

p_oPop	Tree population, for getting shading neighbors.
fX	X coordinate of point for which to get GLI.
fY	Y coordinate of point for which to get GLI.
fHeight	Height at which to get GLI.

Returns: GLI value.

◆ GetParameterFileData()

void clEpiphyticEstablishment::GetParameterFileData ( xercesc::DOMDocument * p_oDoc )

protected

Declares arrays and fills them with parameter file data.

Parameters

p_oDoc Parsed parameter file.

Exceptions

modelErr

if:

Any of the light extinction coefficient values are not between 0 and 1.
The value for m_iNumAltDiv is not greater than 0.
The value for m_iNumAziDiv is not greater than 0.

Parameters

p_oDoc DOM tree of parsed input file.

◆ GetTreeDataMemberCodes()

void clEpiphyticEstablishment::GetTreeDataMemberCodes ( )

protected

Gets the return codes for the "dead" tree data member.

This declares and populates the mp_iDeadCodes array with the return codes for the "dead" tree int data member.

Exceptions

modelErr if a tree to which this species is applied does not have a "dead" code, or if this is applied to anything but saplings or adults.

◆ RegisterTreeDataMembers()

void clEpiphyticEstablishment::RegisterTreeDataMembers ( )

inlinevirtual

Overridden from clLightBase to do nothing.

Reimplemented from clBehaviorBase.

Member Data Documentation

◆ m_cQuery

char* clEpiphyticEstablishment::m_cQuery

protected

String to pass to clTreePopulation::Find() in order to get the trees for which to calculate volume.

This will instigate a species/type search for all the species and types to which this behavior applies.

◆ m_fMaxSearchDistance

double clEpiphyticEstablishment::m_fMaxSearchDistance

protected

Maximum search distance for shading neighbors.

◆ m_iNumTotalSpecies

short int clEpiphyticEstablishment::m_iNumTotalSpecies

protected

Number of species.

For the destructor.

◆ m_iSeedlingSpecies

int clEpiphyticEstablishment::m_iSeedlingSpecies

protected

Species of seedlings to disperse.