Light Dependent Seed Survival - Version 1.1. More...

#include <LightDepSeedSurvival.h>

Inheritance diagram for clLightDepSeedSurvival:

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

	~clLightDepSeedSurvival ()
	Destructor. More...

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

void	Action ()
	Performs establishment. More...

void	SetNameData (std::string sNameString)
	Captures the namestring passed to this behavior. 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...

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 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	SetupGrid ()
	Populates required grid pointers. More...

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

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

void	GetTreeDataMemberCodes ()
	Gets the return codes for needed tree data members. More...

float	GetLightFavorability (const int &iSpecies, const float &fGLI)
	Calculates the light favorability for a given species and GLI. More...

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

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
clGrid *	mp_oSeedGrid
	Pointer to the "Dispersed Seeds" grid created by disperse behaviors. More...

clGrid *	mp_oStormLightGrid
	Pointer to the "Storm Light" grid created by clStormLight, if needed. More...

double **	mp_fLightExtCoeff
	Storm light extinction coefficients, if m_bUseStormLight is false. More...

double *	mp_fOptimumGLI
	Optimum light level at which there is no reduction in establishment - one per behavior species. More...

double *	mp_fLowGLISlope
	Slope of favorability dropoff below the optimum light level - one per behavior species. More...

double *	mp_fHighGLISlope
	Slope of favorability dropoff above the optimum light level - one per behavior species. More...

double	m_fLightHeight
	Height at which light is to be calculated, if m_bUseStormLight is false. More...

double	m_fMaxSearchDistance
	Maximum search distance for shading neighbors, if m_bUseStormLight is false. More...

short int *	mp_iSeedGridCode
	Data member codes for seed grid for number of seeds. More...

short int **	mp_iDamageCodes
	Holds return data codes for the "stm_dmg" tree data member, if m_bUseStormLight is false. More...

short int *	mp_iIndexes
	Speeds access to arrays. More...

short int	m_iNumTotalSpecies
	Number of species. More...

short int	m_iLightCode
	Index for the "Light" data member of the Storm Light grid, if m_bUseStormLight is true. More...

bool	m_bUseStormLight
	Whether or not to have this behavior calculate GLI (false) or get GLI from the Storm Light grid (true) 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

Light Dependent Seed Survival - Version 1.1.

This behavior assesses seed survival based on light levels. The starting number of seeds is created by any disperse behavior and placed in the grid "Dispersed Seeds". The number of seeds surviving out of this number is a function of GLI. Because of the need to calculate light levels, this class descends from clGLIBase.

The number of seeds of a given species that survive in a particular "Dispersed Seeds" grid cell is:

R_sp = S_sp * LE

where:

R_sp is the number of seeds surviving
S_sp is the starting number of seeds of the species, i.e. the number of seeds dispersed to that grid cell
LE is the light favorability, from 0 to 1

The number of seeds is given a random round.

LE is calculated from GLI as:

If GLI < GLI_opt, LE = 1 - (S_lo(GLI_opt - GLI))
If GLI = GLI_opt, LE = 1
If GLI > GLI_opt, LE = 1 - (S_hi(GLI - GLI_opt))

where

GLI is the global light index - GLI at the center of the "Dispersed Seeds" grid cell at a user-specified height
GLI_opt is the optimum GLI for the given species
S_lo is the slope of the dropoff in light favorability at GLIs below GLI_opt
S_hi is the slope of the dropoff in light favorability at GLIs above GLI_opt

GLI can come in two ways. The first method is that this behavior will calculate GLI like all other GLIs. There is one difference: neighbor trees that have hurricane damage have different light extinction coefficients from their undamaged neighbors. To achieve this, we override the function clLightBase::GetLightExtinctionCoefficient(). This effect is not required.

The second way is to get the GLI from the Storm Light grid.

A fatal error will be thrown if a disperse behavior is not used, or if Storm Light is the source of GLIs but it is not used.

The namestring and parameter file call string for this class is "LightDependentSeedSurvival" (for having this behavior calculate GLI) or "StormLightDependentSeedSurvival" (for having Storm Light be the GLI source). Apply this behavior to the desired species; use any type, since type will be ignored.

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clLightDepSeedSurvival()

clLightDepSeedSurvival::clLightDepSeedSurvival ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clLightDepSeedSurvival()

clLightDepSeedSurvival::~clLightDepSeedSurvival ( )

Destructor.

Member Function Documentation

◆ Action()

void clLightDepSeedSurvival::Action ( )

virtual

Performs establishment.

For each grid cell in "Dispersed Seeds", for each species, this takes the number of seeds and determines how many of them germinate. Steps for each grid cell:

Call GetGLI() to get the light level at the center of the grid cell.
For each species, call GetLightFavorability() to get the light favorability.
Calculate R_sp = S_sp*LE*exp(-c*S_sp^δ) for each species.
Create a seedling for each of R_sp for each species.

Reimplemented from clLightBase.

◆ CalcLightValue()

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

inlinevirtual

Overridden from clLightBase to do nothing.

Implements clLightBase.

◆ DoLightSetup()

void clLightDepSeedSurvival::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. This function does nothing if m_bUseStormLight is false.

◆ GetData()

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

virtual

Performs setup.

Calls:

Parameters

p_oDoc DOM tree of parsed input file.

Reimplemented from clLightBase.

◆ GetGLI()

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

protected

Gets the GLI for a given point.

If m_bUseStormLight is true, this gets the value of "Storm Light" for that grid. If false, this calculates GLI at the height in m_fLightHeight.

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.

Returns: GLI value.

◆ GetLightExtinctionCoefficient()

float clLightDepSeedSurvival::GetLightExtinctionCoefficient ( clTree * p_oTree )

protectedvirtual

Gets the light extinction coefficent.

If the tree has storm damage, the light extinction coefficient appropriate to the tree's damage category is returned. Otherwise the default light extinction coefficient behavior of clLightOrg is used.

Parameters

p_oTree Tree for which to obtain the light extinction coefficient.

Returns: The light extinction coefficient, as the proportion of light transmitted by the tree, as a value between 0 and 1.

Reimplemented from clLightBase.

◆ GetLightFavorability()

float clLightDepSeedSurvival::GetLightFavorability	(	const int &	iSpecies,
		const float &	fGLI
	)

protected

Calculates the light favorability for a given species and GLI.

This GLI is turned into a proportion germinating according to the following:

If GLI = optimum GLI for a species, then proportion germinating = 1.
If GLI < optimum GLI for a species, then proportion germinating = 1 -
(slope below optimum*(optimum GLI - actual GLI)).
If GLI > optimum GLI for a species, then proportion germinating = 1 - (slope above optimum*(actual GLI - optimum GLI)).

Parameters

iSpecies	Species for which to calculate light favorability.
fGLI	GLI value.

◆ GetParameterFileData()

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

protected

Declares arrays and fills them with parameter file data.

Parameters

p_oDoc Parsed parameter file.

Exceptions

modelErr

if:

m_bUseStormLight is false, and any of the light extinction coefficient values are not between 0 and 1.
m_bUseStormLight is false, and the value for m_fLightHeight is not zero or greater
The value for mp_fOptimumGLI is not between 0 and 100.
m_bUseStormLight is false, and the value for m_iNumAltDiv is not greater than 0.
m_bUseStormLight is false, and the value for m_iNumAziDiv is not greater than 0.

Parameters

p_oDoc DOM tree of parsed input file.

◆ GetTreeDataMemberCodes()

void clLightDepSeedSurvival::GetTreeDataMemberCodes ( )

protected

Gets the return codes for needed tree data members.

This declares and populates the mp_iDamageCodes array with the return codes for the "stm_dmg" tree int data member. It is not an error if they are not present. This function does nothing if m_bUseStormLight is false.

◆ RegisterTreeDataMembers()

void clLightDepSeedSurvival::RegisterTreeDataMembers ( )

inlinevirtual

Overridden from clLightBase to do nothing.

Reimplemented from clLightBase.

◆ SetNameData()

void clLightDepSeedSurvival::SetNameData ( std::string sNameString )

virtual

Captures the namestring passed to this behavior.

This is overridden from clBehaviorBase so we can capture the namestring passed. Since this class can create multiple kinds of behaviors that function differently, this will capture what kind of behavior this is supposed to be.

Parameters

sNameString Behavior's namestring.

Reimplemented from clBehaviorBase.

◆ SetupGrid()

void clLightDepSeedSurvival::SetupGrid ( )

protected

Populates required grid pointers.

This gets a pointer to the "Dispersed Seeds" grid and all its data members, and does the same for the "Storm Light" grid if m_bUseStormLight is true.

Exceptions

modelErr if the "Dispersed Seeds" grid does not exist, or if the "Storm Light" grid does not exist and m_bUseStormLight is true.

Member Data Documentation

◆ m_bUseStormLight

bool clLightDepSeedSurvival::m_bUseStormLight

protected

Whether or not to have this behavior calculate GLI (false) or get GLI from the Storm Light grid (true)

◆ m_fLightHeight

double clLightDepSeedSurvival::m_fLightHeight

protected

Height at which light is to be calculated, if m_bUseStormLight is false.

◆ m_fMaxSearchDistance

double clLightDepSeedSurvival::m_fMaxSearchDistance

protected

Maximum search distance for shading neighbors, if m_bUseStormLight is false.

◆ m_iLightCode

short int clLightDepSeedSurvival::m_iLightCode

protected

Index for the "Light" data member of the Storm Light grid, if m_bUseStormLight is true.

◆ m_iNumTotalSpecies

short int clLightDepSeedSurvival::m_iNumTotalSpecies

protected

Number of species.

For the destructor.

◆ mp_fHighGLISlope

double* clLightDepSeedSurvival::mp_fHighGLISlope

protected

Slope of favorability dropoff above the optimum light level - one per behavior species.

◆ mp_fLightExtCoeff

double** clLightDepSeedSurvival::mp_fLightExtCoeff

protected

Storm light extinction coefficients, if m_bUseStormLight is false.

Array size is m_iNumTotalSpecies by 2 - number of damage categories.

◆ mp_fLowGLISlope

double* clLightDepSeedSurvival::mp_fLowGLISlope

protected

Slope of favorability dropoff below the optimum light level - one per behavior species.

◆ mp_fOptimumGLI

double* clLightDepSeedSurvival::mp_fOptimumGLI

protected

Optimum light level at which there is no reduction in establishment - one per behavior species.

◆ mp_iDamageCodes

short int** clLightDepSeedSurvival::mp_iDamageCodes

protected

Holds return data codes for the "stm_dmg" tree data member, if m_bUseStormLight is false.

Array size is number of total species by 2 (saplings and adults).

◆ mp_iIndexes

short int* clLightDepSeedSurvival::mp_iIndexes

protected

Speeds access to arrays.

◆ mp_iSeedGridCode

short int* clLightDepSeedSurvival::mp_iSeedGridCode

protected

Data member codes for seed grid for number of seeds.

Array size is # behavior species.

◆ mp_oSeedGrid

clGrid* clLightDepSeedSurvival::mp_oSeedGrid

protected

Pointer to the "Dispersed Seeds" grid created by disperse behaviors.

◆ mp_oStormLightGrid

clGrid* clLightDepSeedSurvival::mp_oStormLightGrid

protected

Pointer to the "Storm Light" grid created by clStormLight, if needed.

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

LightDepSeedSurvival.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clLightDepSeedSurvival()

◆ ~clLightDepSeedSurvival()

Member Function Documentation

◆ Action()

◆ CalcLightValue()

◆ DoLightSetup()

◆ GetData()

◆ GetGLI()

◆ GetLightExtinctionCoefficient()

◆ GetLightFavorability()

◆ GetParameterFileData()

◆ GetTreeDataMemberCodes()

◆ RegisterTreeDataMembers()

◆ SetNameData()

◆ SetupGrid()

Member Data Documentation

◆ m_bUseStormLight

◆ m_fLightHeight

◆ m_fMaxSearchDistance

◆ m_iLightCode

◆ m_iNumTotalSpecies

◆ mp_fHighGLISlope

◆ mp_fLightExtCoeff

◆ mp_fLowGLISlope

◆ mp_fOptimumGLI

◆ mp_iDamageCodes

◆ mp_iIndexes

◆ mp_iSeedGridCode

◆ mp_oSeedGrid

◆ mp_oStormLightGrid