-
Notifications
You must be signed in to change notification settings - Fork 0
/
SeedBankClass.cpp
219 lines (175 loc) · 12.4 KB
/
SeedBankClass.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
#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;
}