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SeedBankClass.cpp
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#include <fstream>
//#include <stdlib.h>
#include <cmath>
#include "MyMath.h"
#include "SeedBankClass.h"
#include "SeedClass.h"
#include "PlantClassConstants.h"
using namespace::std;
//---------------------------------------------------------------------------------------
clSeedBank::clSeedBank()
{
sb_ = new clSeed[MAX_SEED_BANK_SIZE];
seed_number_ = 0; // empty seedbank
seed_weight_ = 0.;
for ( int i=0; i<SPECIES_NUM; i++ ) species_seed_num_[i] = 0;
}
//---------------------------------------------------------------------------------------
clSeedBank::~clSeedBank()
{
delete[] sb_;
}
//---------------------------------------------------------------------------------------
void clSeedBank::initialize( clGridCell * gridcell_)
{
seed_number_ = 0; // empty seedbank
seed_weight_ = 0.;
for ( int i=0; i<MAX_SEED_BANK_SIZE; i++ ) sb_[i].initialize(gridcell_); //FLAGFLAG
}
//---------------------------------------------------------------------------------------
void clSeedBank::addSeed( clSeed sd )
{
if ( seed_number_<MAX_SEED_BANK_SIZE )
{
sb_[seed_number_] = sd;
seed_number_++;
seed_weight_ += sd.getSeedWeight();
species_seed_num_[sd.getSpeciesIndex()]++;
}
return;
}
//---------------------------------------------------------------------------------------
void clSeedBank::emptySeedBank()
{
for ( int i=0; i<SPECIES_NUM; i++ ) species_seed_num_[i] = 0;
seed_number_ = 0;
seed_weight_ = 0.;
return;
}
//---------------------------------------------------------------------------------------
clSeed clSeedBank::getRandomSeed()
{
return sb_[(int) RUnif(0, seed_number_)];
}
//---------------------------------------------------------------------------------------
void clSeedBank::runMutation()
{
for ( int i=0; i<seed_number_; i++ )
{
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckEvergreen( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getRainLight() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckSla( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getSla() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckAllocRoot( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getAllocRoot() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckAllocLeaf( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getAllocLeaf() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckRainThrOn( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getRainThrOn() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckRainThrOff( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getRainThrOff() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckLightThrOn( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getLightThrOn() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckLightThrOff( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getLightThrOff() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckRainLight( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getRainLight() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckBiomasPar1( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getBiomasPar1() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckBiomasPar2( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getBiomasPar2() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckRotfrmPar1( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getRotfrmPar1() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckRotfrmPar2( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getRotfrmPar2() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckRotfrmMaxD( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getRotfrmMaxD() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckWoodDensity( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getWoodDensity() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckLightExt( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getLightExt() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckAllocWood( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getAllocWood() );
#ifdef W_BRANCHES
if ( RUnif()<MUT_PROBABILITY ) {
sb_[i].setCheckAllocBranch( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getAllocBranch()/sb_[i].getAllocWood(), sb_[i].getAllocWood()); // MP; modification of the "raw" branch allocation trait
sb_[i].setCheckAllocStem( sb_[i].getAllocWood(), sb_[i].getAllocBranch()); // MP; think I need to adjust branch and stem at the same time, make sure they add up to alloc_wood again in the end
}
#endif
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckAllocBark( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getAllocBark() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckAllocRepr( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getAllocRepr() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckAllocStor( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getAllocStor() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckSeedWeight( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getSeedWeight() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckCanfrmPar1( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getCanfrmPar1() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckCanfrmPar2( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getCanfrmPar2() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckCanfrmHBase( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getCanfrmHBase() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckP50( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getP50() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckStorToWood( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getStorToWood() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckStorToLeaf( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getStorToLeaf() );
if ( RUnif()<MUT_PROBABILITY )sb_[i].setCheckStemCount( RUnif( MUT_RATE_LO, MUT_RATE_UP ) *sb_[i].getStemCount() ); // NEW CAMILLE
sb_[i].setCheckAllocParameters();
}
return;
}
// -----------------------------------------------------------------------
// --- crossover ---------------------------------------------------------
// -----------------------------------------------------------------------
void clSeedBank::runCrossover()
{
int cum_seed_num[SPECIES_NUM+1];
for ( int i=0; i<SPECIES_NUM; i++ ) cum_seed_num[i] = -1;
cum_seed_num[0] = 0;
int ind = 0;
int xs1= 0;
int xs2= 0;
int xs3 = 0;
for ( int i=0; i<SPECIES_NUM; i++ )
{
if ( species_seed_num_[i]>0 )
{
cum_seed_num[ind+1] = cum_seed_num[ind]+species_seed_num_[i];
ind++;
}
}
int sp_ind_cur = sb_[0].getSpeciesIndex();
int sp_ind_old = sp_ind_cur;
int cnt_cum = 0;
for ( int i=0; i<seed_number_; i++ )
{
sp_ind_cur = sb_[i].getSpeciesIndex();
if ( sp_ind_cur != sp_ind_old ) cnt_cum++;
xs1 = RUnifInt(seed_number_);
//xs2 = (int)MyRound( RUnif( cum_seed_num[cnt_cum]-0.49, cum_seed_num[cnt_cum+1]-1.+0.49 ) ); // Useless now
//xs3 = (int)MyRound( RUnif( cum_seed_num[cnt_cum]-0.49, cum_seed_num[cnt_cum+1]-1.+0.49 ) ); // Useless now
//cout << setw(5) << i << setw(5) << xs1 << setw(5) << sb_[i].getSpeciesIndex() << setw(5) << sb_[xs1].getSpeciesIndex() << endl;
sp_ind_old = sp_ind_cur;
// species with a low number of seeds can crossover with any individual
if ( RUnif() < 1.-(species_seed_num_[sp_ind_cur]/(double)MAX_SEED_NUM*5.) )
{
// cout << species_seed_num_[sp_ind_cur] << " " << 1.-(species_seed_num_[sp_ind_cur]/(double)MAX_SEED_NUM*5.) << endl;
xs1 = (int)MyRound( RUnif( 0.49, seed_number_+0.49 ) );
//xs1 = RUnifInt(seed_number_); //FLAG MP proposed equivalent solution using integer random number generator directly
}
// cout << setw(10) << cum_seed_num[cnt_cum] << setw(10) << cum_seed_num[cnt_cum+1]-1 << setw(10) << xs1 << setw(10) << xs2 << setw(10) << xs3 << setw(10) << sb_[xs1].getSpeciesIndex() << setw(10) << sb_[xs2].getSpeciesIndex() << setw(10) << sb_[xs3].getSpeciesIndex() << setw(10) << sb_[i].getSpeciesIndex() << endl;
// cout << setw(5) << sb_[i].getSpeciesIndex() << setw(5) << sb_[i].getVegType() << setw(15) << sb_[i].getSla() << setw(15) << sb_[xs1].getSla() << setw(15) << sb_[xs2].getSla() << setw(15) << sb_[xs3].getSla() << setw(15) << tv << endl;
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckEvergreen( sb_[i].getEvergreen() + RUnif()*(sb_[xs1].getEvergreen() -sb_[i].getEvergreen()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckSla( sb_[i].getSla() + RUnif()*(sb_[xs1].getSla() -sb_[i].getSla()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckAllocRoot( sb_[i].getAllocRoot() + RUnif()*(sb_[xs1].getAllocRoot() -sb_[i].getAllocRoot()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckAllocLeaf( sb_[i].getAllocLeaf() + RUnif()*(sb_[xs1].getAllocLeaf() -sb_[i].getAllocLeaf()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckRainThrOn( sb_[i].getRainThrOn() + RUnif()*(sb_[xs1].getRainThrOn() -sb_[i].getRainThrOn()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckRainThrOff( sb_[i].getRainThrOff() + RUnif()*(sb_[xs1].getRainThrOff() -sb_[i].getRainThrOff()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckLightThrOn( sb_[i].getLightThrOn() + RUnif()*(sb_[xs1].getLightThrOn() -sb_[i].getLightThrOn()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckLightThrOff( sb_[i].getLightThrOff() + RUnif()*(sb_[xs1].getLightThrOff()-sb_[i].getLightThrOff()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckRainLight( sb_[i].getRainLight() + RUnif()*(sb_[xs1].getRainLight() -sb_[i].getRainLight()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckBiomasPar1( sb_[i].getBiomasPar1() + RUnif()*(sb_[xs1].getBiomasPar1() -sb_[i].getBiomasPar1()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckBiomasPar2( sb_[i].getBiomasPar2() + RUnif()*(sb_[xs1].getBiomasPar2() -sb_[i].getBiomasPar2()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckRotfrmPar1( sb_[i].getRotfrmPar1() + RUnif()*(sb_[xs1].getRotfrmPar1() -sb_[i].getRotfrmPar1()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckRotfrmPar2( sb_[i].getRotfrmPar2() + RUnif()*(sb_[xs1].getRotfrmPar2() -sb_[i].getRotfrmPar2()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckRotfrmMaxD( sb_[i].getRotfrmMaxD() + RUnif()*(sb_[xs1].getRotfrmMaxD() -sb_[i].getRotfrmMaxD()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckWoodDensity( sb_[i].getWoodDensity() + RUnif()*(sb_[xs1].getWoodDensity()-sb_[i].getWoodDensity()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckLightExt( sb_[i].getLightExt() + RUnif()*(sb_[xs1].getLightExt() -sb_[i].getLightExt()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckAllocWood( sb_[i].getAllocWood() + RUnif()*(sb_[xs1].getAllocWood() -sb_[i].getAllocWood()) );
#ifdef W_BRANCHES
if (RUnif()<CROSSOVER_CR) {
sb_[i].setCheckAllocBranch( sb_[i].getAllocBranch()/sb_[i].getAllocWood() + RUnif()*(sb_[xs1].getAllocBranch()/sb_[xs1].getAllocWood() -sb_[i].getAllocBranch()/sb_[i].getAllocWood()), sb_[i].getAllocWood() ); // MP; modification of the "raw" branch allocation trait
sb_[i].setCheckAllocStem( sb_[i].getAllocWood(), sb_[i].getAllocBranch()); // MP; think I need to adjust branch and stem at the same time, make sure they add up to alloc_wood again in the end
}
#endif
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckAllocBark( sb_[i].getAllocBark() + RUnif()*(sb_[xs1].getAllocBark() -sb_[i].getAllocBark()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckAllocRepr( sb_[i].getAllocRepr() + RUnif()*(sb_[xs1].getAllocRepr() -sb_[i].getAllocRepr()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckAllocStor( sb_[i].getAllocStor() + RUnif()*(sb_[xs1].getAllocStor() -sb_[i].getAllocStor()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckSeedWeight( sb_[i].getSeedWeight() + RUnif()*(sb_[xs1].getSeedWeight() -sb_[i].getSeedWeight()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckCanfrmPar1( sb_[i].getCanfrmPar1() + RUnif()*(sb_[xs1].getCanfrmPar1() -sb_[i].getCanfrmPar1()));
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckCanfrmPar2( sb_[i].getCanfrmPar2() + RUnif()*(sb_[xs1].getCanfrmPar2() -sb_[i].getCanfrmPar2()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckCanfrmHBase( sb_[i].getCanfrmHBase() + RUnif()*(sb_[xs1].getCanfrmHBase()-sb_[i].getCanfrmHBase()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckP50( sb_[i].getP50() + RUnif()*(sb_[xs1].getP50() -sb_[i].getP50()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckStorToWood( sb_[i].getStorToWood() + RUnif()*(sb_[xs1].getStorToWood() -sb_[i].getStorToWood()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckStorToLeaf( sb_[i].getStorToLeaf() + RUnif()*(sb_[xs1].getStorToLeaf() -sb_[i].getStorToLeaf()) );
if (RUnif()<CROSSOVER_CR) sb_[i].setCheckStemCount( sb_[i].getStemCount() + RUnif()*(sb_[xs1].getStemCount() -sb_[i].getStemCount()) ); // NEW CAMILLE
sb_[i].setCheckAllocParameters();
}
return;
}