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clNCIBAGrowth Class Reference

NCI Basal Area growth - Version 1.0. More...

#include <NCIBAGrowth.h>

Inheritance diagram for clNCIBAGrowth:
clGrowthBase clBehaviorBase clWorkerBase

Public Member Functions

 clNCIBAGrowth (clSimManager *p_oSimManager)
 Constructor.
 
 ~clNCIBAGrowth ()
 Destructor.
 
float CalcDiameterGrowthValue (clTree *p_oTree, clTreePopulation *p_oPop, float fHeightGrowth)
 Returns the value in the tree's float data member that holds the value that was calculated by PreGrowthCalcs().
 
void PreGrowthCalcs (clTreePopulation *p_oPop)
 Calculates growth for all NCI trees.
 
void DoShellSetup (xercesc::DOMDocument *p_oDoc)
 Does setup.
 
void SetNameData (char *cNameString)
 Captures the namestring passed to this behavior.
 
- Public Member Functions inherited from clGrowthBase
 clGrowthBase (clSimManager *p_oSimManager)
 Constructor.
 
virtual ~clGrowthBase ()
 Destructor.
 
void Action ()
 Performs all growth calculations if "hooked".
 
virtual float CalcHeightGrowthValue (clTree *p_oTree, clTreePopulation *p_oPop, float fDiameterGrowth)
 Calculates the amount of height growth increase for a particular tree, if applicable.
 
virtual float GetGrowthMemberValue (clTree *p_oTree, float fDiameterGrowth)
 Calculates the value to go into a tree's "Growth" data member as the amount of growth.
 
growthType GetGrowthMethod ()
 Gets the method by which this behavior increments growth.
 
clGrowthOrgGetGrowthOrg ()
 Get the growth org object.
 
void RegisterTreeDataMembers ()
 Performs data member registrations for "Growth".
 
- Public Member Functions inherited from clBehaviorBase
virtual float GetBehaviorVersion ()
 Gets the behavior version number.
 
 clBehaviorBase (clSimManager *p_oSimManager)
 Constructor.
 
virtual ~clBehaviorBase ()
 Destructor.
 
virtual short int ValidateVersionNumber (float fTestVersion)
 Makes sure that the version number of a file passed is between the minimum and current version numbers.
 
virtual void SetSpeciesTypeCombos (short int iNumCombos, stcSpeciesTypeCombo *p_whatCombos)
 Sets the species/type combos for a behavior.
 
virtual short int GetNewTreeInts ()
 Gets the number of new tree integer data members this behavior wants to register.
 
virtual short int GetNewTreeFloats ()
 Gets the number of new tree float data members this behavior wants to register.
 
virtual short int GetNewTreeChars ()
 Gets the number of new tree character data members this behavior wants to register.
 
virtual short int GetNewTreeBools ()
 Gets the number of new tree bool data members this behavior wants to register.
 
virtual short int GetNumSpeciesTypeCombos ()
 Gets the number of species/type combos to which this behavior applies.
 
virtual short int GetNumBehaviorSpecies ()
 Gets the number of unique tree species to which this behavior applies.
 
struct stcSpeciesTypeCombo GetSpeciesTypeCombo (short int iIndex)
 Gets one of this behavior's type/species combos.
 
virtual short int GetBehaviorSpecies (short int iIndex)
 Gets one of the behavior's species.
 
short int GetBehaviorListNumber ()
 Gets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list.
 
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.
 
virtual DOMElement * GetParentParametersElement (xercesc::DOMDocument *p_oDoc)
 Formats the string for species/types query.
 
- Public Member Functions inherited from clWorkerBase
 clWorkerBase (clSimManager *p_oSimManager)
 Constructor.
 
virtual ~clWorkerBase ()
 Destructor.
 
char * GetName ()
 Gets the object's namestring.
 
void DoObjectSetup (xercesc::DOMDocument *p_oDoc, fileType iFileType)
 Triggers the setup process.
 
virtual void TimestepCleanup ()
 Performs any necessary cleanup operations at the end of a timestep.
 
virtual void EndOfRunCleanup ()
 Performs any necessary cleanup operations at the end of a run.
 
virtual void DoCommand (char *cCommand, char *cArguments)
 If a behavior has registered a command line command with the sim manager, this allows it to be called.
 

Protected Member Functions

void ValidateData ()
 Makes sure all input data is valid.
 
void GetGrowthCodes ()
 Gets the return codes for the "Growth" float tree data member for each tree kind to which this behavior applies.
 
float GetBasalAreasLargerNeighbors (clTree *p_oTarget, clTreePopulation *p_oPop)
 Calculates the sum of the basal areas for neighbors larger than the target tree's DBH.
 
float GetBasalAreasAllNeighbors (clTree *p_oTarget, clTreePopulation *p_oPop)
 Calculates the sum of the basal areas for all neighbors larger than the NCI min DBH.
 
void ReadParameterFile (xercesc::DOMDocument *p_oDoc)
 Reads data from the parameter file.
 
void AssembleUniqueTypes ()
 Assembles a unique list of types applied to this behavior and places it in mp_iWhatBehaviorTypes.
 
- Protected Member Functions inherited from clGrowthBase
void GetData (xercesc::DOMDocument *p_oDoc)
 Triggers all growth setup if an object is hooked.
 

Protected Attributes

short int ** mp_iGrowthCodes
 Holds return data codes for the "Growth" tree data member.
 
float * mp_fCrowdingSlope
 Crowding effect slope.
 
float * mp_fCrowdingSteepness
 Crowding effect steepness.
 
float * mp_fMaxCrowdingRadius
 Maximum search radius, in meters, in which to look for crowding neighbors.
 
float * mp_fMinimumNeighborDBH
 The minimum DBH, in cm, of neighbors to be included in NCI calculations.
 
float * mp_fXb
 Size effect variance parameter.
 
float * mp_fMaxPotentialValue
 Maximum potential growth value, in cm.
 
float * mp_fX0
 Size effect mode parameter.
 
float * mp_fGamma
 Size sensitivity to NCI parameter.
 
short int * mp_iIndexes
 Speeds access to the arrays.
 
short int * mp_iWhatBehaviorTypes
 List of types managed by this behavior.
 
float m_fMinSaplingHeight
 Minimum sapling height.
 
float m_fBADivisor
 Divisor for neighbor BA.
 
short int m_iNumBehaviorTypes
 Number of types managed by this behavior.
 
short int m_iNumTotalSpecies
 Keep our own copy for the destructor.
 
bool m_bUseOnlyLargerNeighbors
 Whether to use all trees larger than the minimum (false) or only neighbors larger than the target (true)
 
- Protected Attributes inherited from clGrowthBase
growthType m_iGrowthMethod
 The method by which this object plans to update tree dimensions.
 
float m_fConvertCmPerTSToMmPerYr
 Conversion factor from cm diameter growth per timestep to mm radial growth per year.
 
float m_fConvertMmPerYearToCmPerTS
 Conversion factor to take amounts from mm of radial growth per year to cm of diameter growth per timestep.
 
bool m_bHooked
 Wwhether or not this shell object is hooked to clGrowthOrg.
 
bool m_bGoLast
 Whether or not this behavior's growth should go last when used with a complementary growth behavior.
 
- Protected Attributes inherited from clBehaviorBase
short int m_iNumSpeciesTypeCombos
 How many type/species combos a behavior will act on.
 
short int m_iNumBehaviorSpecies
 How many distinct species are in the combo list - important for filling species-specific values from parameter file.
 
short int * mp_iWhatSpecies
 List of distinct species - for filling species-specific values from parameter file.
 
stcSpeciesTypeCombomp_whatSpeciesTypeCombos
 Array of species/type combos that the behavior will act on.
 
short int m_iNewTreeInts
 The number of new tree integer data members this behavior wants to add.
 
short int m_iNewTreeFloats
 The number of new tree float data members this behavior wants to add.
 
short int m_iNewTreeChars
 The number of new tree character data members this behavior wants to add.
 
short int m_iNewTreeBools
 The number of new tree boolean data members this behavior wants to add.
 
short int m_iBehaviorListNumber
 The number of this behavior in the behavior list, to differentiate between possible multiple copies of this behavior.
 
float m_fVersionNumber
 Version number - this will be rounded to 2 digits after the decimal place.
 
std::string m_sXMLRoot
 XML root that encloses the parameters for this behavior.
 
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.
 
- Protected Attributes inherited from clWorkerBase
char m_cNameString [MAX_NAMESTRING_SIZE]
 Object's identifying namestring.
 
int * mp_iAllowedFileTypes
 List of the input file types this object can handle.
 
int m_iNumAllowedTypes
 Number of input file types this object can handle.
 

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 clGrowthOrgmp_oGrowthOrg
 clGrowthOrg object - this pointer is held in common by all shells
 

Detailed Description

NCI Basal Area growth - Version 1.0.

This is a growth shell object which applies the NCI (neighborhood competition index) function. The competition index uses neighbor basal area.

The growth equation for one year's growth is:

Growth = Max Growth * Size Effect * Crowding Effect


where Max Growth is annual amount of diameter growth, and the Effects are values between 0 and 1 which serve to reduce the maximum.

The equation for Size Effect is:

SE = exp(-0.5(ln(DBH/X0)/Xb)2)

where:

Crowding Effect is calculated as:

CE = exp(-C * ( DBHγ * Σ BA / 1000)D)

where:

Neighbors can be all trees larger than the minimum NCI DBH, or only those trees with DBHs larger than the target, in square cm.

Snags and already-dead trees are never counted in the basal area sum.

The amount of growth is in cm/year. For multi-year timesteps, the behavior will calculate total growth with a loop. Each loop iteration will increment DBH for one year. For each year, the Size Effect (SE) value and the DBHγ portion of the Crowding Effect is recalculated with the previous year's new DBH value. All values for each year of growth are summed to get the growth for the timestep.

This cannot be applied to seedlings. An error will be thrown if seedlings are passed.

The parameter file call string for this to be diameter-incrementing with auto-height updating is "NCIBAGrowth"; for diameter-only incrementing, use "NCIBAGrowth diam only". The namestring for this behavior is "ncibagrowthshell".

Copyright 2011 Charles D. Canham.

Author
Lora E. Murphy


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

Constructor & Destructor Documentation

clNCIBAGrowth::clNCIBAGrowth ( clSimManager p_oSimManager)

Constructor.

Parameters
p_oSimManagerSim Manager object.
clNCIBAGrowth::~clNCIBAGrowth ( )

Destructor.

Member Function Documentation

void clNCIBAGrowth::AssembleUniqueTypes ( )
protected

Assembles a unique list of types applied to this behavior and places it in mp_iWhatBehaviorTypes.

float clNCIBAGrowth::CalcDiameterGrowthValue ( clTree p_oTree,
clTreePopulation p_oPop,
float  fHeightGrowth 
)
virtual

Returns the value in the tree's float data member that holds the value that was calculated by PreGrowthCalcs().

Parameters
p_oTreeTree to which to apply growth.
p_oPopTree population object.
fHeightGrowthAmount of height growth, in m (ignored).
Returns
Amount of diameter growth, in cm.

Reimplemented from clGrowthBase.

void clNCIBAGrowth::DoShellSetup ( xercesc::DOMDocument *  p_oDoc)
virtual

Does setup.

  1. AssembleUniqueTypes() is called to create a list of unique behavior types.
  2. ReadParameterFile() is called to read the parameter file's data.
  3. ValidateData() is called to validate the data.
  4. GetGrowthCodes() is called to get tree data return codes.
Parameters
p_oDocDOM tree of parsed input tree.

Reimplemented from clGrowthBase.

float clNCIBAGrowth::GetBasalAreasAllNeighbors ( clTree p_oTarget,
clTreePopulation p_oPop 
)
protected

Calculates the sum of the basal areas for all neighbors larger than the NCI min DBH.

Parameters
p_oTargetTarget tree for which to calculate the sum of neighbor basal areas.
p_oPopTree population, for getting neighbors.
Returns
Sum of neighbor basal areas, in square cm.
float clNCIBAGrowth::GetBasalAreasLargerNeighbors ( clTree p_oTarget,
clTreePopulation p_oPop 
)
protected

Calculates the sum of the basal areas for neighbors larger than the target tree's DBH.

Parameters
p_oTargetTarget tree for which to calculate the sum of neighbor basal areas.
p_oPopTree population, for getting neighbors.
Returns
Sum of neighbor basal areas, in square cm.
void clNCIBAGrowth::GetGrowthCodes ( )
protected

Gets the return codes for the "Growth" float tree data member for each tree kind to which this behavior applies.

Exceptions
modelErrif a code comes back -1 for any species/type combo to which this behavior is applied.
void clNCIBAGrowth::PreGrowthCalcs ( clTreePopulation p_oPop)
virtual

Calculates growth for all NCI trees.

The values are stashed in the "Growth" tree float data member for later application.

Steps:

  1. Get all trees for this behavior.
  2. For each tree, calculate the sum of basal areas by calling the function GetBasalAreas(). Stash the value in "Growth" for each tree.
  3. Go through all the NCI trees again. Calculate the amount of growth for each using the equations above. Use the function pointers to make sure that the proper function forms are used. Stash the end result in "Growth".

This must be called first of any growth stuff, since it uses other trees' DBHs to calculate NCI, and these must be before growth has been applied.

Growth per timestep is calculated by looping over the number of years per timestep and incrementing the DBH.

Parameters
p_oPopTree population object.

Reimplemented from clGrowthBase.

void clNCIBAGrowth::ReadParameterFile ( xercesc::DOMDocument *  p_oDoc)
protected

Reads data from the parameter file.

Parameters
p_oDocDOM tree of parsed input tree.
Exceptions
modelErrif this behavior has been applied to any types except sapling and adult.
void clNCIBAGrowth::SetNameData ( char *  cNameString)
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
cNameStringBehavior's namestring.

Reimplemented from clBehaviorBase.

void clNCIBAGrowth::ValidateData ( )
protected

Makes sure all input data is valid.

The following must all be true:

  • Max radius of neighbor effects must be > 0
  • Max growth for each species must be > 0
  • X0 (size effect mode) for each species must be > 0
  • Xb (size effect variance) for each species must not = 0
Exceptions
modelErrif any of the above conditions are not met.

Member Data Documentation

bool clNCIBAGrowth::m_bUseOnlyLargerNeighbors
protected

Whether to use all trees larger than the minimum (false) or only neighbors larger than the target (true)

float clNCIBAGrowth::m_fBADivisor
protected

Divisor for neighbor BA.

float clNCIBAGrowth::m_fMinSaplingHeight
protected

Minimum sapling height.

For doing neighbor searches.

short int clNCIBAGrowth::m_iNumBehaviorTypes
protected

Number of types managed by this behavior.

short int clNCIBAGrowth::m_iNumTotalSpecies
protected

Keep our own copy for the destructor.

This is the total number of tree species.

float* clNCIBAGrowth::mp_fCrowdingSlope
protected

Crowding effect slope.

C in Crowding Effect equation above. Array is sized number of species to which this behavior applies. This array is accessed by using the index returned for mp_iIndexes[species number].

float* clNCIBAGrowth::mp_fCrowdingSteepness
protected

Crowding effect steepness.

D in Crowding Effect equation above. Array is sized number of species to which this behavior applies. This array is accessed by using the index returned for mp_iIndexes[species number].

float* clNCIBAGrowth::mp_fGamma
protected

Size sensitivity to NCI parameter.

γ in Crowding Effect equation above. Array assumed to be sized number of species to which this behavior applies. This array is accessed by using the index returned for mp_iIndexes[species number].

float* clNCIBAGrowth::mp_fMaxCrowdingRadius
protected

Maximum search radius, in meters, in which to look for crowding neighbors.

For calculating the Crowding Effect. Array is sized number of species to which this behavior applies. This array is accessed by using the index returned for mp_iIndexes[species number].

float* clNCIBAGrowth::mp_fMaxPotentialValue
protected

Maximum potential growth value, in cm.

Array is sized number of species to which this behavior applies. This array is accessed by using the index returned for mp_iIndexes[species number].

float* clNCIBAGrowth::mp_fMinimumNeighborDBH
protected

The minimum DBH, in cm, of neighbors to be included in NCI calculations.

Array is sized number of species.

float* clNCIBAGrowth::mp_fX0
protected

Size effect mode parameter.

X0 in Size Effect equation above. Array is sized number of species to which this behavior applies. This array is accessed by using the index returned for mp_iIndexes[species number].

float* clNCIBAGrowth::mp_fXb
protected

Size effect variance parameter.

Xb in Size Effect equation above. Array is sized number of species to which this behavior applies. This array is accessed by using the index returned for mp_iIndexes[species number].

short int** clNCIBAGrowth::mp_iGrowthCodes
protected

Holds return data codes for the "Growth" tree data member.

Array size is number of species to which this behavior applies by 2 (saplings and adults).

short int* clNCIBAGrowth::mp_iIndexes
protected

Speeds access to the arrays.

Array size is number of species.

short int* clNCIBAGrowth::mp_iWhatBehaviorTypes
protected

List of types managed by this behavior.


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