Absolute growth with suppression. More...

#include <AbsoluteGrowth.h>

Inheritance diagram for clAbsoluteGrowth:

Classes
struct	stcCodes
	Holds the return codes for the new float tree data members for a particular tree type. More...

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

	~clAbsoluteGrowth ()
	Destructor. More...

float	CalcDiameterGrowthValue (clTree p_oTree, clTreePopulation p_oPop, float fHeightGrowth)
	This applies diameter growth as described in the equation above. More...

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

void	DoShellSetup (xercesc::DOMDocument *p_oDoc)
	Does the setup for this behavior. More...

void	RegisterTreeDataMembers ()
	Registers the two float data members and captures the return codes. More...

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

virtual	~clMichMenBase ()
	Destructor. More...

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

virtual	~clGrowthBase ()
	Destructor. More...

void	Action ()
	Performs all growth calculations if "hooked". More...

virtual float	CalcHeightGrowthValue (clTree p_oTree, clTreePopulation p_oPop, float fDiameterGrowth)
	Calculates the amount of height growth increase for a particular tree, if applicable. More...

virtual void	PreGrowthCalcs (clTreePopulation *p_oPop)
	Performs calculations before any DBHs have been changed. More...

growthType	GetGrowthMethod ()
	Gets the method by which this behavior increments growth. More...

clGrowthOrg *	GetGrowthOrg ()
	Get the growth org object. More...

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

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	CalculateSuppressionThresholds (xercesc::DOMDocument p_oDoc, clTreePopulation p_oPop)
	Calculates the suppression threshold for each species. More...

float	CalculateSuppressionFactor (clTree *p_oTree, const float &fGli)
	Calculates a tree's suppression factor. More...

Protected Member Functions inherited from clMichMenBase
void	GetParameterFileData (xercesc::DOMDocument *p_oDoc)
	Extracts growth parameters. More...

float	CalculateMichaelisMentonDiam (short int &iSpecies, float &fGli)
	Calculates the result of the Michaelis-Menton function using diameter growth parameters. More...

float	CalculateMichaelisMentonHeight (short int &iSpecies, float &fGli)
	Calculates the result of the Michaelis-Menton function using height growth parameters. More...

float	ApplyGrowthLimits (const short int &iSpecies, const float &fAmountDiamIncrease, const float &fDiam)
	Applies applicable growth limits according to the flags set. More...

float	GetGrowthMemberValue (clTree *p_oTree, float fDiameterGrowth)
	Gets the proper value for the "Growth" data member for mortality calculations based on growth. More...

Protected Member Functions inherited from clGrowthBase
void	GetData (xercesc::DOMDocument *p_oDoc)
	Triggers all growth setup if an object is hooked. 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
double *	mp_fLengthLastSuppFactor
	Length last suppression factor - array size is number of species. More...

double *	mp_fLengthCurrReleaseFactor
	Length current release factor - array size is number of species. More...

double *	mp_fGliThreshold
	GLI threshold below which a tree is suppressed - array size is number of species. More...

double	m_fMortRateAtSuppression
	Mortality rate of suppressed trees. More...

int	m_iNumberYearsPerTimestep
	Number of years per timestep - from sim manager. More...

int	m_iYrsExceedThresholdBeforeSup
	Years exceeding threshold before a tree becomes suppressed. More...

int	m_iMaxYears
	Maximum number of years we'll track a tree's suppression and release data. More...

struct clAbsoluteGrowth::stcCodes *	mp_ylrCodes
	Return codes for "ylr" tree data member. More...

struct clAbsoluteGrowth::stcCodes *	mp_ylsCodes
	Return codes for "yls" tree data member. More...

short int	m_iNumBehaviorTypes
	Number of types managed by this behavior. More...

Protected Attributes inherited from clMichMenBase
double *	mp_fSlopeDiamGrowthResponse
	Slope of diameter growth response. More...

double *	mp_fSlopeHeightGrowthResponse
	Slope of height growth response. More...

double *	mp_fAdultConstBAInc
	Adult constant basal area increment in cm2/timestep (parameter file value is expected in cm2/yr). More...

double *	mp_fAdultConstRadInc
	Adult constant radial increment in cm/timestep (parameter file value is expected in mm/yr). More...

double *	mp_fAsympDiamGrowth
	Asymptotic diameter growth. More...

double *	mp_fAsympHeightGrowth
	Asymptotic height growth. More...

bool	m_bConstRadialLimited
	Whether or not growth is limited to constant radial increment. More...

bool	m_bConstBasalAreaLimited
	Whether or not growth is limited to constant basal area increment. More...

Protected Attributes inherited from clGrowthBase
growthType	m_iGrowthMethod
	The method by which this object plans to update tree dimensions. More...

float	m_fConvertCmPerTSToMmPerYr
	Conversion factor from cm diameter growth per timestep to mm radial growth per year. More...

float	m_fConvertMmPerYearToCmPerTS
	Conversion factor to take amounts from mm of radial growth per year to cm of diameter growth per timestep. More...

bool	m_bHooked
	Wwhether or not this shell object is hooked to clGrowthOrg. More...

bool	m_bGoLast
	Whether or not this behavior's growth should go last when used with a complementary growth behavior. 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
Public Types inherited from clGrowthBase
enum	growthType { diameter_auto, diameter_only, height_only }
	Values describing the method by which the object instance of this class plans to implement tree growth. More...

Static Protected Attributes inherited from clGrowthBase
static clGrowthOrg *	mp_oGrowthOrg
	clGrowthOrg object - this pointer is held in common by all shells More...

Detailed Description

Absolute growth with suppression.

This is a growth shell object which applies the Michaelis-Menton function to find absolute growth with suppression and release dynamics.

The growth equation is Y = SF * (A * gli) / ((A/S) + gli), where Y is the log10 of new radial growth in mm/yr, SF is the suppression factor, A is asymptotic diameter growth, GLI is global light index, and S is the slope of growth response. Growth can be limited to a radial increment or an area increment, or unlimited. An object of this class can support either diameter-only updating or diameter updating with automatic height adjustment.

Suppression is calculated as SF = e^{(g*YLR - d*YLS)}, where g is the value in mp_fLengthCurrReleaseFactor, d is the value in mp_fLengthLastSuppFactor, YLR is the years of the last (or current) release period, and YLS is the years of the last (or current) suppression period.

An object of this class can be created in several ways. Use the strings "AbsRadialGrowth", "AbsBAGrowth", and "AbsUnlimGrowth" to create behaviors that calculate a diameter increase with automatic height adjustment. These strings represent absolute growth limited by constant radial increment, absolute growth limited by constant basal area increment, and unlimited absolute growth, respectively. Add the string " diam only" (example - "AbsBAGrowth diam only") to tell this behavior that only the tree's diameter, and not its height, should be updated.

The namestring for this class is "absolutegrowthshell". It is probable that there will be more than one object of this class created.

This object will add two int data members to the applicable trees, "ycr" and "yls" (for years of current release and years of last suppression).

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clAbsoluteGrowth()

clAbsoluteGrowth::clAbsoluteGrowth ( clSimManager * p_oSimManager )

Constructor.

Sets the namestring.

Parameters

p_oSimManager Sim manager for the run.

◆ ~clAbsoluteGrowth()

clAbsoluteGrowth::~clAbsoluteGrowth ( )

Destructor.

Member Function Documentation

◆ CalcDiameterGrowthValue()

float clAbsoluteGrowth::CalcDiameterGrowthValue	(	clTree *	p_oTree,
		clTreePopulation *	p_oPop,
		float	fHeightGrowth
	)

virtual

This applies diameter growth as described in the equation above.

Parameters

p_oTree	Pointer to the tree to which to apply growth.
p_oPop	Pointer to the tree population object.
fHeightGrowth	Amount of height growth, in m (ignored).

Returns: The amount of diameter growth increase, in cm.

Reimplemented from clGrowthBase.

◆ CalculateSuppressionFactor()

float clAbsoluteGrowth::CalculateSuppressionFactor	(	clTree *	p_oTree,
		const float &	fGli
	)

protected

Calculates a tree's suppression factor.

The suppression factor is a number greater than 0 that is multiplied times growth to modify it. A factor of 1 returned indicates no suppression. This will also manage the yls and ycr variables to keep track of length of time of suppression and release.

If the years exceeding threshold before suppression variable is greater than the number of years per timestep then the suppression factor is always 1.

Parameters

p_oTree	The tree for which suppression is being calculated
fGli	The tree's gli value

Returns: Tree's suppression factor.

◆ CalculateSuppressionThresholds()

void clAbsoluteGrowth::CalculateSuppressionThresholds	(	xercesc::DOMDocument *	p_oDoc,
		clTreePopulation *	p_oPop
	)

protected

Calculates the suppression threshold for each species.

This will have to read mortality parameters to do this.

Parameters

p_oDoc	Parsed DOM tree of parameter file.
p_oPop	Tree population object.

◆ DoShellSetup()

void clAbsoluteGrowth::DoShellSetup ( xercesc::DOMDocument * p_oDoc )

virtual

Does the setup for this behavior.

It reads in suppression/release data and checks values, and validates that all species/type combos use light (each must have "Light" registered).

Parameters

p_oDoc Parsed parameter file object.

Exceptions

modelErr if any species/type combo to which this behavior is applied does not have a light behavior.

Reimplemented from clGrowthBase.

◆ RegisterTreeDataMembers()

void clAbsoluteGrowth::RegisterTreeDataMembers ( )

virtual

Registers the two float data members and captures the return codes.

Reimplemented from clBehaviorBase.

◆ SetNameData()

void clAbsoluteGrowth::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.

Member Data Documentation

◆ m_fMortRateAtSuppression

double clAbsoluteGrowth::m_fMortRateAtSuppression

protected

Mortality rate of suppressed trees.

◆ m_iMaxYears

int clAbsoluteGrowth::m_iMaxYears

protected

Maximum number of years we'll track a tree's suppression and release data.

◆ m_iNumBehaviorTypes

short int clAbsoluteGrowth::m_iNumBehaviorTypes

protected

Number of types managed by this behavior.

◆ m_iNumberYearsPerTimestep

int clAbsoluteGrowth::m_iNumberYearsPerTimestep

protected

Number of years per timestep - from sim manager.

◆ m_iYrsExceedThresholdBeforeSup

int clAbsoluteGrowth::m_iYrsExceedThresholdBeforeSup

protected

Years exceeding threshold before a tree becomes suppressed.

◆ mp_fGliThreshold

double* clAbsoluteGrowth::mp_fGliThreshold

protected

GLI threshold below which a tree is suppressed - array size is number of species.

◆ mp_fLengthCurrReleaseFactor

double* clAbsoluteGrowth::mp_fLengthCurrReleaseFactor

protected

Length current release factor - array size is number of species.

This is the old parameter G.

◆ mp_fLengthLastSuppFactor

double* clAbsoluteGrowth::mp_fLengthLastSuppFactor

protected

Length last suppression factor - array size is number of species.

This is the old parameter D.

◆ mp_ylrCodes

struct clAbsoluteGrowth::stcCodes * clAbsoluteGrowth::mp_ylrCodes

protected

Return codes for "ylr" tree data member.

Array size is number of types.

◆ mp_ylsCodes

struct clAbsoluteGrowth::stcCodes * clAbsoluteGrowth::mp_ylsCodes

protected

Return codes for "yls" tree data member.

Array size is number of types.

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

AbsoluteGrowth.h

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clAbsoluteGrowth()

◆ ~clAbsoluteGrowth()

Member Function Documentation

◆ CalcDiameterGrowthValue()

◆ CalculateSuppressionFactor()

◆ CalculateSuppressionThresholds()

◆ DoShellSetup()

◆ RegisterTreeDataMembers()

◆ SetNameData()

Member Data Documentation

◆ m_fMortRateAtSuppression

◆ m_iMaxYears

◆ m_iNumBehaviorTypes

◆ m_iNumberYearsPerTimestep

◆ m_iYrsExceedThresholdBeforeSup

◆ mp_fGliThreshold

◆ mp_fLengthCurrReleaseFactor

◆ mp_fLengthLastSuppFactor

◆ mp_ylrCodes

◆ mp_ylsCodes