Snag Decay Class Dynamics Version 2.0. More...

#include <SnagDecomp.h>

Inheritance diagram for clSnagDecomp:

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

	~clSnagDecomp ()
	Destructor. More...

void	Action ()
	Runs snags through the fall models and decay class transition matrix. More...

void	CalcGridValues ()
	Calculates live and cut basal area on a grid. More...

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

void	RegisterTreeDataMembers ()
	Registers the "SnagDecayClass" int data member. 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 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 Attributes
double	mp_fSnagTransProb [6][6]
	Species-specific matrices of transition probabilities. More...

double	m_fTreefallAlpha
	Parameters used in treefall and snag fall models. More...

double *	mp_fTreefallBeta

double	m_fTreefallDelta

double	m_fTreefallTheta

double	m_fTreefallIota

double	m_fTreefallLamda

double	m_fSnagfallAlpha

double *	mp_fSnagfallBeta

double *	mp_fSnagfallGamma

double	m_fSnagfallZeta

double	m_fSnagfallEta

double	m_fSnagfallKappa

double	m_fMinBreakHeight
	The minimum snag break height. More...

double	m_fMaxBreakHeight
	The maximum snag break height. More...

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

clGrid *	mp_oBasalAreaGrid
	Grid to hold live and cut basal area in local cells. More...

short int	m_iLiveBACode

short int	m_iCutBACode

float	m_fGridCellLength

short int **	mp_iSnagDCCode
	Holds relevant data member codes. More...

short int **	mp_iNewBreakCode

short int **	mp_iDeadCodes

short int *	mp_iAdultFallCode

short int *	mp_iOldBreakCode

short int *	mp_iIndexes

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

Detailed Description

Snag Decay Class Dynamics Version 2.0.

This class simulates the dynamics of standing dead trees as they pass through a series of decay classes and eventually fall.

Trees that die from natural causes in the timestep are run through a tree fall model to determine whether they become a snag, or fall and are removed from tree population. Snags created in previous timesteps are run through a separate fall model to determine whether they remain standing or are removed. Snags remaining standing are run through a decay class transition matrix (decay class is a parameter of the snag fall model).

This behavior adds one integer data member called "SnagDecayClass" representing snag decay class. There are five decay classes, numbered 1-5. Parameter values can be set to utilize fewer classes if desired.

This behavior adds two float data members called "NewBreakHeight" and "SnagOldBreakHeight", both of which represent the height at which a snag has broken. This is held by NewBreakHeight if the breakage occurred this timestep, or SnagOldBreakHeight otherwise. If the snag is unbroken or did not break at the appropriate time, the value of these members is -1.0.

This behavior adds one bool data member called "Fall". This represents whether or not a tree that has died this timestep has fallen (true), or remains standing as a snag (false).

Parameters correspond to the tree fall and snag fall models in Vanderwel et al. 2006 (Can. J. For. Res. 36: 2769-2779), and to a transition matrix representing the probability of undergoing a transition from a given decay class to another (or the same one) during the timestep. All transition matrix values must be non-negative and the sum of each column should add up to 1.

All parameters are based on a five-year timestep; the behavior will adjust fall probabilities for other timestep lengths if necessary.

This class's namestring and parameter call string are both "SnagDecayClassDynamics".

This behavior can be applied to adults and snags. It should run after mortality and before substrate and dead tree remover behaviors are applied in each timestep.

Author: Mark Vanderwel

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

Constructor & Destructor Documentation

◆ clSnagDecomp()

clSnagDecomp::clSnagDecomp ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager clSimManager object.

◆ ~clSnagDecomp()

clSnagDecomp::~clSnagDecomp ( )

Destructor.

Deletes arrays.

Member Function Documentation

◆ Action()

void clSnagDecomp::Action ( )

virtual

Runs snags through the fall models and decay class transition matrix.

A query is sent to the tree population to get all snags to which this behavior is applied. For each that is still standing, the new decay class is calculated and the value is placed in the "SnagDecayClass" int tree data member. Snags that fall are removed by calling clTreePopulation::KillTree()

Reimplemented from clBehaviorBase.

◆ CalcGridValues()

void clSnagDecomp::CalcGridValues ( )

Calculates live and cut basal area on a grid.

Grid cell size is a multiple of the tree population grid that approximates 20 x 20 m. Cut basal area is calculated if there was harvesting in the current timestep (behavior Disturbance). These values are later used in the tree and snag fall models.

◆ GetData()

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

virtual

Does setup for this behavior.

Steps:

Reads values from the parameter file and validates them.
Formats the query string, which is used to do tree searches

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr

if:

Any value in the transition matrix is less than 0.
The sum of values for each transition matrix column do not add up to 1.

Implements clWorkerBase.

◆ RegisterTreeDataMembers()

void clSnagDecomp::RegisterTreeDataMembers ( )

virtual

Registers the "SnagDecayClass" int data member.

The return codes are captured in the mp_iSnagDCCodes array.

Exceptions

modelErr if this behavior is being applied to any tree type except snags.

Reimplemented from clBehaviorBase.

Member Data Documentation

◆ m_cQuery

char* clSnagDecomp::m_cQuery

protected

String to pass to clTreePopulation::Find() in order to get the trees for which to run snag dynamics.

This will instigate a species search for all the species to which this behavior applies.

◆ m_fGridCellLength

float clSnagDecomp::m_fGridCellLength

protected

◆ m_fMaxBreakHeight

double clSnagDecomp::m_fMaxBreakHeight

protected

The maximum snag break height.

◆ m_fMinBreakHeight

double clSnagDecomp::m_fMinBreakHeight

protected

The minimum snag break height.

Actually break height is a height between min and max drawn from a uniform distribution.

◆ m_fSnagfallAlpha

double clSnagDecomp::m_fSnagfallAlpha

protected

◆ m_fSnagfallEta

double clSnagDecomp::m_fSnagfallEta

protected

◆ m_fSnagfallKappa

double clSnagDecomp::m_fSnagfallKappa

protected

◆ m_fSnagfallZeta

double clSnagDecomp::m_fSnagfallZeta

protected

◆ m_fTreefallAlpha

double clSnagDecomp::m_fTreefallAlpha

protected

Parameters used in treefall and snag fall models.

◆ m_fTreefallDelta

double clSnagDecomp::m_fTreefallDelta

protected

◆ m_fTreefallIota

double clSnagDecomp::m_fTreefallIota

protected

◆ m_fTreefallLamda

double clSnagDecomp::m_fTreefallLamda

protected

◆ m_fTreefallTheta

double clSnagDecomp::m_fTreefallTheta

protected

◆ m_iCutBACode

short int clSnagDecomp::m_iCutBACode

protected

◆ m_iLiveBACode

short int clSnagDecomp::m_iLiveBACode

protected

◆ m_iNumSpecies

int clSnagDecomp::m_iNumSpecies

protected

Keep a copy of this for the destructor.

◆ mp_fSnagfallBeta

double* clSnagDecomp::mp_fSnagfallBeta

protected

◆ mp_fSnagfallGamma

double* clSnagDecomp::mp_fSnagfallGamma

protected

◆ mp_fSnagTransProb

double clSnagDecomp::mp_fSnagTransProb[6][6]

protected

Species-specific matrices of transition probabilities.

Array size is 6 x 6.

◆ mp_fTreefallBeta

double* clSnagDecomp::mp_fTreefallBeta

protected

◆ mp_iAdultFallCode

short int* clSnagDecomp::mp_iAdultFallCode

protected

◆ mp_iDeadCodes

short int** clSnagDecomp::mp_iDeadCodes

protected

◆ mp_iIndexes

short int* clSnagDecomp::mp_iIndexes

protected

◆ mp_iNewBreakCode

short int** clSnagDecomp::mp_iNewBreakCode

protected

◆ mp_iOldBreakCode

short int* clSnagDecomp::mp_iOldBreakCode

protected

◆ mp_iSnagDCCode

short int** clSnagDecomp::mp_iSnagDCCode

protected

Holds relevant data member codes.

First array index is # species and second, if present, is type (adult or snag).

◆ mp_oBasalAreaGrid

clGrid* clSnagDecomp::mp_oBasalAreaGrid

protected

Grid to hold live and cut basal area in local cells.

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

SnagDecomp.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clSnagDecomp()

◆ ~clSnagDecomp()

Member Function Documentation

◆ Action()

◆ CalcGridValues()

◆ GetData()

◆ RegisterTreeDataMembers()

Member Data Documentation

◆ m_cQuery

◆ m_fGridCellLength

◆ m_fMaxBreakHeight

◆ m_fMinBreakHeight

◆ m_fSnagfallAlpha

◆ m_fSnagfallEta

◆ m_fSnagfallKappa

◆ m_fSnagfallZeta

◆ m_fTreefallAlpha

◆ m_fTreefallDelta

◆ m_fTreefallIota

◆ m_fTreefallLamda

◆ m_fTreefallTheta

◆ m_iCutBACode

◆ m_iLiveBACode

◆ m_iNumSpecies

◆ mp_fSnagfallBeta

◆ mp_fSnagfallGamma

◆ mp_fSnagTransProb

◆ mp_fTreefallBeta

◆ mp_iAdultFallCode

◆ mp_iDeadCodes

◆ mp_iIndexes

◆ mp_iNewBreakCode

◆ mp_iOldBreakCode

◆ mp_iSnagDCCode

◆ mp_oBasalAreaGrid