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genetic.cpp2
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genetic.cpp2
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#include <iostream>
#include <fstream>
#include <stdio.h>
#include <stdlib.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>
#include <math.h>
using namespace std;
#include "pTable.h"
#include "genetic.h"
#include "mopac.h"
#include "gcode.h"
#include "fragment.h"
//#include "icoord.h"
//#include "xyzlist.h"
//#include "CatsGen.h"
//#include "DFT.h"
#include "utils.h"
#define NUM_ALL_PERM 9450
void Genetic::fragment_prop()
{
string path = "./Scratch/features/mopac";
mkdir(path.c_str(),S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
// string dir = pInp->inp_sgen.lib;
string dir = "./Scratch/features/";
int nreg = pInp->inp_sgen.n_regs;
int ncap = pInp->inp_sgen.n_caps;
for (int i=0; i < nreg + ncap; i++)
{
Fragment* p_frag = new Fragment(pInp);
p_frag->init(dir,i);
p_frag->get_all_props(dir);
pFrags.push_back(p_frag);
}
ofstream csv_reg;
string csv_reg_fname = "fragment_reg_prop.csv";
csv_reg.open(csv_reg_fname.c_str());
csv_reg << setprecision(6);
ofstream csv_cap;
string csv_cap_fname = "fragment_cap_prop.csv";
csv_cap.open(csv_cap_fname.c_str());
csv_cap << setprecision(6);
csv_cap << "frag_index,";
csv_reg << "frag_index,";
vector<string>::iterator it_flist;
for (it_flist = pInp->feature_list.begin(); it_flist < pInp->feature_list.end(); it_flist++)
{
csv_cap << *it_flist << ",";
csv_reg << *it_flist << ",";
}
csv_cap << endl;
csv_reg << endl;
cout << "Calculated Properties of Fragments:" << endl;
vector<Fragment*>::iterator it;
int i = 0;
for (it = pFrags.begin(); it != pFrags.end(); it++)
{
i++;
if (i == 1)
cout << "regular fragments:" << endl;
if (i == nreg+1)
cout << "cap fragments:" << endl;
(*it)->print_fragment_prop();
if (i <= nreg)
{
csv_reg << i << ",";
(*it)->print_props_csv(csv_reg);
csv_reg << endl;
}
else
{
csv_cap << i << ",";
(*it)->print_props_csv(csv_cap);
csv_cap << endl;
}
}
cout << endl << endl;
csv_reg.close();
csv_cap.close();
#if 0
vector<int>::iterator it_i;
for (it_i = pInp->feature_list.begin(); it_i < pInp->feature_list.end(); i++)
{
vector<Fragment*> tmp(pFrags);
auto comp = [](const Fragment* x, const Fragment* y)
{return x->f_props[*it_i].val < y->f_props[*it_i].val ; };
sort(tmp.begin(), tmp.end(), comp);
for (it = tmp.begin(); it != tmp.end(); it++)
{
(*it)->print_frag_prop(*it_i); // sort by "pol" and print (which feature index is 1 )
}
}
#endif
return;
}
//cluster all candidates in the given feature space the for first sampling
void Genetic::init_feature_space()
{
int nfrags = pInp->inp_sgen.n_regs;
int ncaps = pInp->inp_sgen.n_caps;
string code;
Fragment* pfrag;
// int count = 0;
ofstream summary;
summary.open("entire_space.csv");
summary << setprecision(6);
for (int i=0; i < nfrags; i++)
// for (int i=0; i < 1; i++)
{
string istr = StringTools::int2str(i+1,1,"0");
// for (int j=0; j < 2; j++)
for (int k=0; k < nfrags; k++)
{
string kstr = StringTools::int2str(k+1,1,"0");
for (int j=0; j < ncaps; j++)
{
string jstr = StringTools::int2str(j+1+nfrags, 1, "0");
code = "0(" + istr + "-1(" + kstr + "-1(" + jstr + "-1)))";
// cout << "********genecode: " << code << " *********"<< endl;
summary << i+1 << "-" << k+1 << "-" << j+nfrags+1 << ",";
pfrag = pFrags[i];
pfrag->print_props_csv(summary);
pfrag = pFrags[k];
pfrag->print_props_csv(summary);
pfrag = pFrags[j+nfrags];
pfrag->print_props_csv(summary);
summary << endl;
}
}
}
}
void Genetic::get_fit4test(Node<GANode>* pNode)
{
double MW=0;
double tmp;
int anumber;
for (size_t i=0; i< pNode->data.natoms; i++)
{
anumber = PTable::atom_number(pNode->data.anames[i]);
tmp = PTable::atom_mass(anumber);
MW = MW + tmp;
}
// pNode->score = exp((MW-1000)/100);
pNode->data.MW = MW;
// pNode->data.score = MW;
return;
}
void Genetic::hashinit()
{
int ngen = pInp->inp_ga.ga_stop + 1;
int popsize = pInp->inp_ga.pop_size;
int size = 2*(ngen*popsize) + 1;
cout << "size of hash_all:" << size << endl;
genehash_all.resize(size);
size = 2*popsize + 1;
cout << "size of hash_pop:" << size << endl;
genehash_pop.resize(size);
hash_record.resize(2*NUM_ALL_PERM+1);
}
long Genetic::BKDRHash(string str)
{
long seed = 131; // 31 131 1313 13131 131313 etc..
long hash = 0;
for(int i = 0; i < str.length(); i++)
{
hash = (hash * seed) + str.at(i);
}
// cout << "hash: " << hash << endl;
return (hash & 0x7FFFFFFF);
}
int Genetic::addtohash(vector<unique_ptr<LinkedList<Node<string> > > > & hashtable, string & str)
{
long size = hashtable.size();
long key = BKDRHash(str) % size;
// cout << key << endl;
if (hashtable[key].get() == NULL)
{
unique_ptr<LinkedList<Node<string> > > ptr(new LinkedList<Node<string> >());
hashtable[key] = move(ptr);
Node<string>* pNode = new Node<string>(str, NULL);
hashtable[key]->addnode(pNode);
}
else
{
Node<string>* pNode = new Node<string>(str,NULL);
hashtable[key]->addnode(pNode);
}
// cout << "Successfully add to hash table" << endl;
return 1;
}
int Genetic::addtohash_record(vector<unique_ptr<LinkedList<Node<record> > > > & hash_record, Node<record>* pNode)
{
long size = hash_record.size();
long key = BKDRHash(pNode->data.gene) % size;
if(hash_record[key].get() == NULL)
{
unique_ptr<LinkedList<Node<record> > > ptr(new LinkedList<Node<record> >());
hash_record[key] = move(ptr);
hash_record[key]->addnode(pNode);
// cout << "add new key" << endl;
}
else
{
hash_record[key]->addnode(pNode);
// cout << "exist key" << endl;
}
return 1;
}
int Genetic::searchhash(vector<unique_ptr<LinkedList<Node<string> > > > & hashtable, string & genecode)
{
long size = hashtable.size();
long key = BKDRHash(genecode) % size;
// cout << hashtable[key].get() << endl;
if (hashtable[key].get() == NULL) return 0; //new entry
else
{
if(hashtable[key]->findnode(genecode)) return 1; //not a new entry
else return 0; //new entry
}
}
void Genetic::searchhash_record(vector<unique_ptr<LinkedList<Node<record> > > > & hash_record, Node<GANode>* pNode)
{
cout << "run to here" << endl;
string genecode = pNode->data.gene;
cout << genecode << endl;
long size = hash_record.size();
cout << size << endl;
long key = BKDRHash(genecode) % size;
cout << key << endl;
Node<record>* ptr;
cout << hash_record[key].get() << endl;
ptr = hash_record[key]->getnode(genecode);
cout << ptr << endl;
pNode->data.HOMO = ptr->data.HOMO;
pNode->data.LUMO = ptr->data.LUMO;
pNode->data.MW = ptr->data.MW;
cout << ptr->data.HOMO << " " << ptr->data.LUMO << endl;
double score = oled_fit(ptr);
pNode->data.score = score;
cout << "score = " << score << endl;
return;
}
void Genetic::oled_score(Node<GANode>* pNode)
{
cout << "calculating score .... " << endl;
double score_homo;
score_homo = 1/(1+exp(-5.0* (-9.2 - pNode->data.HOMO)));
// if(pNode->data.HOMO < -9.5) score_homo = 1.0;
// else if (pNode->data.HOMO > -8.5) score_homo = 0.0;
// else score_homo = -8.5 - pNode->data.HOMO;
//or try sigmoid function for homo, score = homo*lumo
double score_lumo;
double diff = pNode->data.LUMO - (-1.0); /*hard-coded*/
score_lumo = 1000 * exp(-(diff*diff)/0.125); //2sigma = 0.5 (0.95 chance);
double score = score_lumo*score_homo;
cout << score << endl;
pNode->data.score = score;
return;
}
double Genetic::oled_fit(Node<record>* pNode)
{
cout << "calculating score .... " << endl;
double score_homo;
score_homo = 1/(1+exp(-5.0*(-9.2 - pNode->data.HOMO)));
// if(pNode->data.HOMO < -9.5) score_homo = 1.0;
// else if (pNode->data.HOMO > -8.5) score_homo = 0.0;
// else score_homo = -8.5 - pNode->data.HOMO;
//or try sigmoid function for homo, score = homo*lumo
double score_lumo;
double diff = pNode->data.LUMO - (-1.0);
score_lumo = 1000 * exp(-(diff*diff)/0.125); //2sigma = 0.5 (0.95 chance);
double score = score_lumo*score_homo;
return score;
}
void Genetic::crossover(string & genecode1, string & genecode2)
{
gTree gtree1(pInp);
gTree gtree2(pInp);
gtree1.readcode(genecode1);
gtree2.readcode(genecode2);
int count = 0;
int splice_layer = Utils::randomi2(gtree1.nlayers);
cout << "determine splice point: " << splice_layer << endl;
vector<int> splice_1;
vector<int> splice_2;
for (int i=0; i< gtree1.nnodes; i++)
{
if (gtree1.cArray[i].layer == splice_layer)
splice_1.push_back(i);
}
for (int i=0; i< gtree2.nnodes; i++)
{
if (gtree2.cArray[i].layer == splice_layer)
splice_2.push_back(i);
}
int splice1 = Utils::randomi(splice_1.size());
// cout << "splice 1: " << splice1 << endl;
int splice2 = Utils::randomi(splice_2.size());
// cout << "splice 2: " << splice2 << endl;
int node1_idx = gtree1.cArray[splice_1.at(splice1)].c_index;
// cout << "parent 1: " << parent1_idx << endl;
int node2_idx = gtree2.cArray[splice_2.at(splice2)].c_index;
TNode* parent1 = gtree1.getParentTree(node1_idx);
// cout << "parent 1: " << parent1 << " " << parent1->c_index << endl;
TNode* parent2 = gtree2.getParentTree(node2_idx);
if ((parent1->firstchild->c_index == splice_1.at(splice1)) && (parent2->firstchild->c_index == splice_2.at(splice2)))
{
swap_ptr(parent1->firstchild, parent2->firstchild);
swap_ptr(parent1->firstchild->nextsibling, parent2->firstchild->nextsibling);
}
else if ((parent1->firstchild->c_index == splice_1.at(splice1)) && (parent2->nextsibling->c_index == splice_2.at(splice2)))
{
swap_ptr(parent1->firstchild, parent2->nextsibling);
swap_ptr(parent1->firstchild->nextsibling, parent2->nextsibling->nextsibling);
}
else if ((parent1->nextsibling->c_index == splice_1.at(splice1)) && (parent2->firstchild->c_index == splice_2.at(splice2)))
{
swap_ptr(parent1->nextsibling, parent2->firstchild);
swap_ptr(parent1->nextsibling->nextsibling, parent2->firstchild->nextsibling);
}
else if ((parent1->nextsibling->c_index == splice_1.at(splice1)) && (parent2->nextsibling->c_index == splice_2.at(splice2)))
{
swap_ptr(parent1->nextsibling, parent2->nextsibling);
swap_ptr(parent1->nextsibling->nextsibling, parent2->nextsibling->nextsibling);
}
newcode1 = gtree1.tree_to_code();
newcode2 = gtree2.tree_to_code();
}
void Genetic::swap_ptr(TNode* & ptr1, TNode* & ptr2)
{
TNode* tmp;
tmp = ptr1;
ptr1 = ptr2;
ptr2 = tmp;
return;
}
string Genetic::mutation(string genecode)
{
string newcode = genecode;
int exist = 1;
while(exist)
{
gTree gtree(pInp);
gtree.readcode(newcode);
int splice = Utils::randomi(gtree.nnodes); //splice = [0, nnodes-1];
TNode* ptr = gtree.getNodeTree(splice);
gtree.destory(ptr->firstchild);
ptr->firstchild = NULL;
int layer = gtree.cArray[splice].layer;
cout << "mutation layer: " << layer << endl;
if (layer == 0)
ptr->label = Utils::randomi2(pInp->inp_sgen.n_seeds);
else if (layer < gtree.nlayers)
ptr->label = Utils::randomir(pInp->inp_sgen.n_seeds+1, pInp->inp_sgen.n_seeds +pInp->inp_sgen.n_regs);
else if (layer == gtree.nlayers)
ptr->label = Utils::randomir(pInp->inp_sgen.n_seeds+pInp->inp_sgen.n_regs+1, pInp->inp_sgen.n_seeds + pInp->inp_sgen.n_regs + pInp->inp_sgen.n_caps);
int nbranches = gtree.readlib_lite(ptr->label);
gtree.add_branch(ptr->firstchild, 1, nbranches, layer+1);
newcode = gtree.tree_to_code();
cout << "mutated gene:" << newcode << endl;
exist = searchhash(genehash_all, newcode);
if (exist) cout << "in the list already, mutate again" << endl;
}
cout << endl;
return newcode;
}
void Genetic::gen_node_random(Node<GANode>* pNode)
{
int exist = 1;
ncat++;
string genecode;
while(exist == 1)
{
gTree gtree(pInp);
if(gtree.newStruct())
genecode = gtree.printCode();
exist = searchhash(genehash_all, genecode);
// cout << exist << endl;
}
cout << "******unique entry ******" << endl;
addtohash(genehash_all,genecode);
addtohash(genehash_pop,genecode);
pNode->data.gene = genecode;
pNode->data.comment = StringTools::int2str(ncat, 4, "0");
cout << "come here check:" << pNode->data.comment<< endl;
cout << "1randomly create a molecule: " << genecode << endl;
#if 0
string cname = mmopt_folder + "ff.xyz" + pNode->data.comment;
ofstream xyzfile(cname.c_str());
gTree gtree2(pInp);
gtree2.gene2struc(pNode->data.gene, xyzfile);
xyzfile.close();
ifstream infile(cname.c_str());
pNode->data.get_xyz(infile);
infile.close();
#endif
pNode->data.flag = 0;
pNode->next = NULL;
pNext->addnode(pNode);
optr_list.push_back(ncat);
// get_fit4test(pNode); //get MW info
// Mopac::gen_inp(mopac_folder, pInp, pNode);
searchhash_record(hash_record, pNode);
return;
}
//if pNode->data.gene is unique
void Genetic::gen_node(Node<GANode>* pNode, int off_set)
{
ncat++;
int old_label;
addtohash(genehash_all,pNode->data.gene);
addtohash(genehash_pop, pNode->data.gene);
pNode->data.comment = StringTools::int2str(ncat, 4, "0");
/*hard-coded*/
#if 0
old_label = ncat + off_set;
string tmp = StringTools::int2str(old_label,4,"0");
#endif
#if 1
string cname = mmopt_folder + "ff.xyz" + pNode->data.comment;
// string cname = mmopt_folder + "ff.xyz" + tmp;
#if 0
ofstream xyzfile(cname.c_str());
gTree gtree(pInp);
gtree.gene2struc(pNode->data.gene, xyzfile);
xyzfile.close();
#endif
ifstream infile(cname.c_str());
pNode->data.get_xyz(infile);
// cout << ncat << " " << old_label << " " << pNode->data.natoms << endl;
infile.close();
#endif
pNode->data.flag = 0;
pNode->next = NULL;
pNext->addnode(pNode);
optr_list.push_back(ncat);
// Mopac::gen_inp(mopac_folder, pInp, pNode);
// get_fit4test(pNode); //get MW info
// oled_score(pNode);
// searchhash_record(hash_record, pNode);
cout << "Done gen_node()" << endl << endl;
return;
}
void Genetic::read_record()
{
string cwd = StringTools::getcwd_str();
string fname = cwd + "/record0";
ifstream record0(fname.c_str(),ios::in);
string line;
vector<string> tok_line;
getline(record0,line);
while(getline(record0,line))
{
Node<record>* pNode = new Node<record>();
tok_line = StringTools::tokenize(line," ");
pNode->data.gene = tok_line[0];
pNode->data.HOMO = atof(tok_line[1].c_str());
pNode->data.LUMO = atof(tok_line[2].c_str());
pNode->data.MW = atof(tok_line[3].c_str());
cout << pNode->data.gene << endl;
// pNode->data.score = atof(tok_line[3].c_str());
// cout << pNode->data.HOMO << " " << pNode->data.LUMO << endl;
addtohash_record(hash_record, pNode);
}
cout << "Finish reading record file" << endl;
record0.close();
return;
}
#if 0
double Genetic::getfit_Co(xyznode* pNode)
{
int index;
double alpha = 2.0;
index = 484*(pNode->ntemp - 1) + 22*(pNode->gene[0] - 1) + (pNode->gene[1] - 1);
pNode->binding = Eb[index];
pNode->h_affinity = Ha[index];
pNode->hydricity = Hyd[index];
double ref_Eb = 22.015367;
double ref_Ha = 338.684573;
double ref_Hyd = 181.023427;
double score;
//need to screen out some extremely weak binding first;
if (pNode->binding > 1000.0)
{
pNode->score = 0.0000;
}
else
{
pNode->score = exp((ref_Ha - pNode->h_affinity)/alpha);
// pNode->score = exp((ref_Ha - pNode->h_affinity)/alpha) + exp((ref_Hyd - pNode->hydricity)/50.0);
// double diff = pNode->binding - 20.;
// pNode->score = exp(-(diff*diff)/50.0); //standard dev = 5;
}
score = pNode->score;
return score;
}
#endif
void Genetic::spawn()
{
// int count = 0;
int pool = pInp->inp_ga.pop_size;
// vector<vector<int> > offsprings;
int npairs = pool/2;
int nextra = pool%2; // if odd pop_size
double random;
bool ptrs_identic;
vector<int> tmp;
vector<int>::iterator it;
if (ngen == 0)
{
#if 1
for (int i=0; i< pool; i++)
{
// ncat++;
Node<GANode>* pNode = new Node<GANode>();
gen_node_random(pNode);
}
#endif
/*enhanced-initiation*/
#if 0
enhanced_init_gen();
#endif
}
else
{
pNext->clear();
cout << "Current length of pNext List: " << pNext->listlength << endl;
// select_parents();
gen_pairs(pool);
for (int i=0; i < npairs; i++)
{
// offsprings.clear();
ptrs_identic = get_ptrs(i);
cout << "Applying genetic operator to " << i+1 << "-th pair " << endl;
cout << "parent1 : " << ptr1->data.gene << endl;
cout << "parent2 : " << ptr2->data.gene << endl;
cout << endl;
Node<GANode>* pNode1 = new Node<GANode>();
Node<GANode>* pNode2 = new Node<GANode>();
if(ptrs_identic)
{
cout << "***parent1 and parent2 are identical!***" << endl;
int exist = searchhash(genehash_pop, ptr1->data.gene);
if (!exist)
{
cout << "They are not in the current population" << endl;
pNode1 = cpy_node(ptr1);
pNext->addnode(pNode1); //clone one of them
pNode2->data.gene = mutation(ptr2->data.gene);
// pNode2->data.gene = enhanced_mutation(ptr2->data.gene);
gen_node(pNode2);
}
else
{
cout << "They are already in the Current population" << endl;
pNode1->data.gene = mutation(ptr1->data.gene);
// pNode1->data.gene = enhanced_mutation(ptr1->data.gene);
gen_node(pNode1);
pNode2->data.gene = mutation(ptr2->data.gene);
// pNode2->data.gene = enhanced_mutation(ptr2->data.gene);
gen_node(pNode2);
}
}
else
{
random = Utils::randomf(1.0);
cout << "Get random number: " << random << "; Compared with crossover rate " << pInp->inp_ga.cross_r << endl;
if (random < pInp->inp_ga.cross_r)
{
cout << "********Crossover and Mutation:********** " << endl;
bool done = false;
int count = 0;
while (count < 5) //hard-coded!!!!!!!!
{
crossover(ptr1->data.gene, ptr2->data.gene);
int exist1 = searchhash(genehash_all,newcode1);
int exist2 = searchhash(genehash_all,newcode2);
if ((!exist1) && (!exist2))
{
cout << "find unique offsprings" << endl;
done = true;
break;
}
count++;
}
// cout << "offspring 1: " << newcode1 << endl;
// cout << "offspring 2: " << newcode2 << endl;
if (!done)
{
newcode1 = ptr1->data.gene;
newcode2 = ptr2->data.gene;
}
cout << "offspring 1: " << newcode1 << endl;
cout << "offspring 2: " << newcode2 << endl;
double random;
random = Utils::randomf(1.0);
if (random < pInp->inp_ga.muta_r)
{
cout << "ptr1 is under mutation" << endl;
newcode1 = mutation(newcode1);
}
random = Utils::randomf(1.0);
if (random < pInp->inp_ga.muta_r)
{
cout << "ptr2 is under mutation" << endl;
newcode2 = mutation(newcode2);
}
int exist1 = searchhash(genehash_all, newcode1);
int exist2 = searchhash(genehash_all, newcode2);
if (exist1)
{
cout << "newcode 1 is already in the list" << endl;
newcode1 = mutation(newcode1);
// newcode1 = enhanced_mutation(newcode1);
}
if (exist2)
{
cout << "newcode 2 is already in the list" << endl;
newcode2 = mutation(newcode2);
// newcode2 = enhanced_mutation(newcode2);
//
}
pNode1->data.gene = newcode1;
pNode2->data.gene = newcode2;
cout << "save new molecules to the list" << endl;
gen_node(pNode1);
gen_node(pNode2);
} //end if
else
{
cout << "*********Clone********" << endl;
double random;
random = Utils::randomf(1.0);
if (random < pInp->inp_ga.muta_r)
{
cout << "prt1 is under mutation" << endl;
newcode1 = mutation(ptr1->data.gene);
pNode1->data.gene = newcode1;
gen_node(pNode1);
}
else
{
int exist = searchhash(genehash_pop, ptr1->data.gene);
if (!exist)
{
cout << "prt 1 not in the current population" << endl;
pNode1 = cpy_node(ptr1);
pNext->addnode(pNode1); //clone one of them
}
else
{
cout << "prt1 already in the Current population" << endl;
pNode1->data.gene = mutation(ptr1->data.gene);
// pNode1->data.gene = enhanced_mutation(ptr1->data.gene);
gen_node(pNode1);
}
}
random = Utils::randomf(1.0);
if (random < pInp->inp_ga.muta_r)
{
cout << "prt2 is under mutation" << endl;
newcode2 = mutation(ptr2->data.gene);
pNode2->data.gene = newcode2;
gen_node(pNode2);
}
else
{
int exist = searchhash(genehash_pop, ptr2->data.gene);
if (!exist)
{
cout << "prt2 is not in the current population" << endl;
pNode2 = cpy_node(ptr2);
pNext->addnode(pNode2); //clone one of them
}
else
{
cout << "prt2 is already in the Current population" << endl;
pNode2->data.gene = mutation(ptr2->data.gene);
// pNode2->data.gene = enhanced_mutation(ptr2->data.gene);
gen_node(pNode2);
}
}
} //else for ****Clone****
} // end of (prts_identic) else
} //end of loop
if (nextra)
{
Node<GANode>* pOdd = new Node<GANode>();
ncat++;
int flag = permutation[pool-1];
Node<GANode>* pointer = ptr_array[select_list[flag]];
pOdd->data.gene = mutation(pointer->data.gene);
}
} //end of else
}
//stochastic acceptance O(1) version
void Genetic::select_parents()
{
/*
int pool = pInp->inp_ga.pop_size;
int i = 0;
while(i < pool)
{
// int random = Utils::randomi(pool);
double random2 = Utils::randomf(1.0);
int index = int(random2 * pool);
if (random2 < prob_array[index]/max_prob)
{
select_list[i] = index; //accepted
i++;
}
}
*/
if (pInp->inp_ga.RWS == true)
{
cout << "run RWS" << endl;
select_RWS();
}
else if (pInp->inp_ga.SUS == true)
{
select_RWS_SUS();
}
else if (pInp->inp_ga.B_Tournament == true)
select_binary_tournament();
else if (pInp->inp_ga.L_Rank == true)
select_linear_rank_based(pInp->inp_ga.L_Rank_rate);
else if (pInp->inp_ga.E_Rank == true)
{
cout << "run E Rank" << endl;
select_exp_rank_based(pInp->inp_ga.E_Rank_base);
}
cout << "Done selection operation" << endl;
}
void Genetic::select_RWS() //roulette Wheel selection
{
int pool = pInp->inp_ga.pop_size;
vector<double> wheel(pool+1);
int i = 0;
wheel[0] = 0.0;
while(i < pool)
{
wheel[i+1] = prob_array[i] + wheel[i];
cout << "wheel " << i+1 << " " << wheel[i+1] << endl;
i++;
}
i = 0;
while(i<pool)
{
double random = Utils::randomf(wheel.back());
cout << random << endl;
select_list[i] = select_binary_search(wheel, random);
cout << "select " << select_list[i] << endl;
i++;
}
}
int Genetic::select_binary_search(vector<double> & wheel, double random)
{
int left = 0;
int right = wheel.size()-1;
int mid;
while (left <= right)
{
mid = left + (right-left)/2;
if (wheel[mid] == random) return mid;
else if (wheel[mid] < random)
left = mid+1;
else
right = mid-1;
}
return (left-1);
}
void Genetic::select_RWS_SUS() //roulette Wheel + stocastic universal sampling
{
int pool = pInp->inp_ga.pop_size;
vector<double> wheel(pool+1);
int i = 0;
wheel[0] = 0.0;
while(i < pool)
{
wheel[i+1] = prob_array[i] + wheel[i];
i++;
}
i = 0;
double random = Utils::randomf(wheel.back());
double stepsize = wheel.back()/pool;
while (i < pool)
{
select_list[i] = select_binary_search(wheel, random);
random += stepsize;
if (random > wheel.back())
random = fmod(random, wheel.back());
i++;
}
}
void Genetic::select_linear_rank_based(double rate) //the reproduction rate of worst individual
{
int pool = pInp->inp_ga.pop_size;
vector<double> wheel(pool+1);
int i = 0;
wheel[0] = 0.0;
while(i < pool)
{
wheel[i+1]= (rate + 2 * (1 - rate) * (pool-i-1)/(pool-1))/double(pool) + wheel[i];
cout << "wheel " << i+1 << " " << wheel[i+1] << endl;
i++;
}
i = 0;
double stepsize = wheel.back()/pool;
double random = Utils::randomf(wheel.back());
while(i< pool)
{
cout << random << endl;
select_list[i] = select_binary_search(wheel,random);
cout << "select " << select_list[i] << endl;
random += stepsize;
if (random > wheel.back())
random = fmod(random,wheel.back());