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enhanced_init_mut.cpp: cout << "cluster " << i << " : " << cluster_info[i]->size() << endl;
enhanced_init_mut.cpp: int pool = pInp->inp_ga.pop_size;
enhanced_init_mut.cpp: int num_pick_each_cluster = pool/cluster_info.size();
enhanced_init_mut.cpp: for (int i=0; i< cluster_info.size(); i++)
enhanced_init_mut.cpp: int random_idx = Utils::randomi(cluster_info[i]->size());
enhanced_init_mut.cpp: for (int i =0; i < cluster_info.size() && found != 1; i++)
enhanced_init_mut.cpp: int size_cluster = cluster_info[i]->size();
enhanced_init_mut.cpp: for (int j =0; j < size_cluster; j++)
enhanced_init_mut.cpp: int cluster_size = cluster_info[cluster]->size();
enhanced_init_mut.cpp: while (exist && count < cluster_size)
enhanced_init_mut.cpp: int random_idx = Utils::randomi(cluster_size);
gcode.cpp: int nbranches = tok_line.size();
gcode.cpp:// bblock.nbranches = int(bblock.xyzw.size());
gcode.cpp:// bblock.name.resize(bblock.natoms);
gcode.cpp:// bblock.coords.resize(3*bblock.natoms);
gcode.cpp: bblock.label_h.resize(bblock.natoms);
gcode.cpp:// bblock.name.resize(bblock.natoms);
gcode.cpp:// bblock.coords.resize(3*bblock.natoms);
gcode.cpp: bblock.label_h.resize(bblock.natoms);
gcode.cpp: for (int i=0; i< cArray.size(); i++)
gcode.cpp: cout << cArray[i].label << "\t" << cArray[i].tag << "\t" << cArray[i].plug << "\t" << cArray[i].acceptor << "\t" << cArray[i].layer << "\t" << cArray[i].xyzw.size()<< endl;
gcode.cpp: while (parent.xyzw.size()!= 0)
gcode.cpp: if ((i < nlayers) && (parent.xyzw.size() !=0))
gcode.cpp: int tag = cArray[parent.c_index].xyzw.size() - parent.xyzw.size() + 1;
gcode.cpp: bblock.c_index = int(cArray.size());
gcode.cpp: else if ((i == nlayers) && (parent.xyzw.size() != 0))
gcode.cpp: int tag = cArray[parent.c_index].xyzw.size() - parent.xyzw.size() + 1;
gcode.cpp: bblock.c_index = int(cArray.size());
gcode.cpp: cout << tmp.size() << endl;
gcode.cpp:// node.tag = tmp.back().nbranches - int(tmp.back().xyzw.size()) +1;
gcode.cpp: if (tmp.back().xyzw.size() != 1)
gcode.cpp:// node.tag = tmp.back().nbranches - int(tmp.back().xyzw.size()) +1;
gcode.cpp:// node.tag = tmp.back().nbranches - int(tmp.back().xyzw.size())+1;
gcode.cpp:// node.tag = tmp.back().nbranches - int(tmp.back().xyzw.size()) + 1;
gcode.cpp: if (tmp.back().xyzw.size() != 1)
gcode.cpp:// node.tag = tmp.back().nbranches - int(tmp.back().xyzw.size()) + 1;
gcode.cpp:// node.tag = tmp.back().nbranches - int(tmp.back().xyzw.size()) + 1;
gcode.cpp: node.c_index = int(cArray.size());
gcode.cpp: for (size_t i=0; i< cArray.size(); i++)
gcode.cpp: node.c_index = int(cArray.size())-1;
gcode.cpp: for (size_t i=0; i< cArray.size(); i++)
gcode.cpp: while (!q.empty() && result.size()!=total)
gcode.cpp: int index = int (cArray.size())-1;
gcode.cpp: vector<int> addorder(cArray.size());
gcode.cpp: addorder[(*it).c_index] = int(newpos.size())-1;
gcode.cpp: int n = int(l1nam.size());
gcode.cpp: addorder[(*it).c_index] = int(newpos.size())-1;
gcode.cpp: addorder[(*it).c_index] = int(newpos.size())-1;
gcode.cpp: anames.resize(natoms);
gcode.cpp: coords.resize(3*natoms);
gcode.cpp: xyzfile << anames.size() << endl;
gcode.cpp: for (size_t i=0; i < anames.size(); i++)
genetic.cpp: for (size_t i=0; i< pNode->data.natoms; i++)
genetic.cpp: int popsize = pInp->inp_ga.pop_size;
genetic.cpp: int size = 2*(ngen*popsize) + 1;
genetic.cpp: cout << "size of hash_all:" << size << endl;
genetic.cpp: genehash_all.resize(size);
genetic.cpp: size = 2*popsize + 1;
genetic.cpp: cout << "size of hash_pop:" << size << endl;
genetic.cpp: genehash_pop.resize(size);
genetic.cpp: hash_record.resize(2*NUM_ALL_PERM+1);
genetic.cpp: long size = hashtable.size();
genetic.cpp: long key = BKDRHash(str) % size;
genetic.cpp: long size = hash_record.size();
genetic.cpp: long key = BKDRHash(pNode->data.gene) % size;
genetic.cpp: long size = hashtable.size();
genetic.cpp: long key = BKDRHash(genecode) % size;
genetic.cpp: long size = hash_record.size();
genetic.cpp: cout << size << endl;
genetic.cpp: long key = BKDRHash(genecode) % size;
genetic.cpp: int splice1 = Utils::randomi(splice_1.size());
genetic.cpp: int splice2 = Utils::randomi(splice_2.size());
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp: int nextra = pool%2; // if odd pop_size
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp: int right = wheel.size()-1;
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp: double stepsize = wheel.back()/pool;
genetic.cpp: random += stepsize;
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp: double stepsize = wheel.back()/pool;
genetic.cpp: random += stepsize;
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp: double stepsize = wheel.back()/pool;
genetic.cpp: random += stepsize;
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp:// int pool = pInp->inpga.pop_size();
genetic.cpp: int bits = int(offspring.size());
genetic.cpp: int bits = int(string.size());
genetic.cpp: int gene_bits = int(gene.size());
genetic.cpp: parents.resize(2);
genetic.cpp: offsprings.resize(2);
genetic.cpp: ptr_array.resize(pInp->inp_ga.pop_size);
genetic.cpp: prob_array.resize(pInp->inp_ga.pop_size);
genetic.cpp: select_list.resize(pInp->inp_ga.pop_size);
genetic.cpp: permutation.resize(pInp->inp_ga.pop_size);
genetic.cpp: size_t ncats = target_list.size();
genetic.cpp: size_t gene_bits = offspring.size();
genetic.cpp: for (size_t i=0; i < ncats; i++)
genetic.cpp: for (size_t j=1; (j<gene_bits) && (status == 0); j++)
genetic.cpp: size_t ncats = target_list.size();
genetic.cpp: size_t nvars = rcodes.size();
genetic.cpp: for (size_t i=0; i < ncats; i++)
genetic.cpp: for (size_t j=0; (j < nvars) && (status == 0) ; j++)
genetic.cpp: for (size_t i=0; i < pNode->natoms; i++) frezlist[i]=0;
genetic.cpp: for (size_t i =0; i< joint.size(); i++)
genetic.cpp: for(size_t j=0; j< joint[i].size(); j++)
genetic.cpp: for (int i=0; i< pInp->inp_ga.pop_size; i++)
genetic.cpp: int pool = pInp->inp_ga.pop_size;
genetic.cpp: size_t s = score_list.size();
genetic.cpp: for(size_t j=0; j<s; j++)
genetic.cpp:// while (i != pInp->inp_ga.pop_size)
genetic.cpp: while (i != pInp->inp_ga.pop_size)
genetic.cpp: Mopac::mopac_genqsh(filedir, joblist); //hard-coded for 0-gen case (joblist.size() = pop_size)
genetic.cpp: for(size_t i = 0; i < pRef->natoms; i++)
genetic.cpp: for (size_t j=0; j < pNode->natoms; j++)
genetic.cpp: for (size_t i=0; i < pRef->natoms; i++)
genetic.cpp: for (size_t i=0; i < pNode->natoms; i++)
genetic.cpp: size_t size = tok_line.size();
genetic.cpp: for (size_t i=0; i < size; i++)
genetic.cpp: for (size_t i = 0; i < pRef->data.natoms; i++)
genetic.cpp: for (size_t i = 0; i < pRef->data.natoms; i++)
genetic.cpp: genehash_pop.resize(2*pInp->inp_ga.pop_size+1);
icoord.cpp:int ICoord::alloc(int size){
icoord.cpp: natoms = size;
main.cpp: for (size_t i = 0; i < pRef->natoms; i++)
main.cpp:// pNode->element.resize(pNode->natoms);
main.cpp:// pNode->coords.resize(3*pNode->natoms);
mol2xyz.cpp: cout << "stophere " << index.size() << endl;
mol2xyz.cpp: for(int i=0; i<index.size(); i++)
mol2xyz.cpp: for(int i=0; i<index.size();i++)
mol2xyz.cpp: for(int i=0; i<tmp_atom.size(); i++)
mol2xyz.cpp: int size = label.size();
mol2xyz.cpp: cout << "size of label:" << size << endl;
mol2xyz.cpp: for(int i =0; i < size; i++)
mol2xyz.cpp: if (xyzw.size() != 1)
mol2xyz.cpp: if (xyzw.size() != 2)
mol2xyz.cpp: if (xyzw.size() != 3)
mol2xyz.cpp: if (xyzw.size() != 4)
mopac.cpp: for (int i=0; i < anames.size(); i++)
mopac.cpp: for (size_t i=0; i< pNode->data.natoms; i++)
mopac.cpp: for (size_t i=0; i < pNode->natoms; i++) frezlist[i]=0;
mopac.cpp: for (size_t i =0; i< joint.size(); i++)
mopac.cpp: for(size_t j=0; j< joint[i].size(); j++)
mopac.cpp: for (size_t i=0; i< pNode->natoms; i++)
mopac.cpp: for(size_t i=0; i < anames.size(); i++)
mopac.cpp: for(size_t i=0; i < pNode->natoms; i++)
mopac.cpp: size_t size = list.size();
mopac.cpp: size_t done = 0;
mopac.cpp: vector<int> mopacdone(size);
mopac.cpp: for (int i=0; i<size; i++)
mopac.cpp: } while(done != size);
nbo.cpp: for (int i=0;i<mheadersize;i++)
nbo.cpp: mo_occ.resize(nao);
nbo.cpp: bmo_occ.resize(nao);
nbo.cpp: bmo_atoms.resize(2*nao);
nbo.cpp: bmo_polar.resize(nao);
nbo.cpp: bmo_num.resize(nao);
nbo.cpp: vmo_occ.resize(nao);
nbo.cpp: vmo_atoms.resize(2*nao);
nbo.cpp: vmo_num.resize(nao);
nbo.cpp: anumbers.resize(natoms);
nbo.cpp: anames.resize(natoms);
nbo.cpp: xyz.resize(3*natoms);
nbo.cpp: q.resize(natoms);
nbo.cpp: mheadersize = 4 + natoms;
nbo.cpp: mheadersize += 6;
nbo.cpp: mheadersize += 6;
nbo.cpp: mheadersize += 6; //CPMZ fix
nbo.cpp:// mheader = new string[mheadersize];
nbo.cpp: mheader.resize(mheadersize);
nbo.cpp: MO.resize(nao*nao);
nbo.cpp: int nnew = tok_line.size();
nbo.cpp: nnew = tok_line.size() - 3;
nbo.cpp: int lsize = tok_line.size();
nbo.cpp: if (lsize<1) break;
nbo.cpp: else if (lsize==4)
nbo.cpp: else if (lsize>4)
nbo.cpp: wAO.resize(MAX_BASIS);
nbo.cpp: tAO.resize(MAX_BASIS);
nbo.cpp: mheadersize = 0;
nbo.cpp: mheadersize++;
nbo.cpp: mheader.resize(mheadersize+2);
nbo.cpp:// mheader = new string[mheadersize+2];
nbo.cpp: if (mc>=mheadersize) break;
nbo.cpp: mheadersize += 2;
nbo.cpp: if (tok_line.size()>1)
nbo.cpp: if (tok_line.size()<1)
nbo.cpp: MO.resize(dim*nao);
read_inp.cpp:// feature_list(hard_code, hard_code + sizeof(hard_code) / sizeof(int))
read_inp.cpp: for (size_t i=0; i < tok_line2.size(); i++)
read_inp.cpp: else if (line.find("population_size")!=string::npos)
read_inp.cpp: inp_ga.pop_size = atoi(tok_line[1].c_str());
read_inp.cpp: ref_xyz.anames.resize(ref_xyz.natoms);
read_inp.cpp: ref_xyz.coords.resize(3*ref_xyz.natoms);
read_inp.cpp: seed.name.resize(seed.natoms);
read_inp.cpp: seed.label.resize(seed.natoms);
read_inp.cpp: seed.coords.resize(3*seed.natoms);
read_inp.cpp: seed.nbranches = int(seed.xyzw.size());
read_inp.cpp: size_t natoms = unsigned(xyzf_ref.natoms);
read_inp.cpp: for (size_t i=0; i < tok_line2.size(); i++)
read_inp.cpp: xyzf_ref.label.push_back(tmp2); /*size == nlabels*/
read_inp.cpp: for(size_t i=0; i < inpfiles.size() ; i++)
read_inp.cpp: size_t natom = unsigned(natoms);
read_inp.cpp: for (size_t i=0; i < tok_line2.size(); i++)
read_inp.cpp:for (size_t j =0; j < r_sym.size(); j++)
simple_genetic.cpp: for (size_t i=0; i< pNode->data.natoms; i++)
simple_genetic.cpp: int popsize = pInp->inp_ga.pop_size;
simple_genetic.cpp: int size = 2*(ngen*popsize) + 1;
simple_genetic.cpp: cout << "size of hash_all:" << size << endl;
simple_genetic.cpp:// genehash_all.resize(size);
simple_genetic.cpp: size = 2*popsize + 1;
simple_genetic.cpp: cout << "size of hash_pop:" << size << endl;
simple_genetic.cpp:// genehash_pop.resize(size);
simple_genetic.cpp: hash_record.resize(2*NUM_ALL_PERM+1);
simple_genetic.cpp: long size = hashtable.size();
simple_genetic.cpp: long key = BKDRHash(str) % size;
simple_genetic.cpp: long size = hash_record.size();
simple_genetic.cpp: long key = BKDRHash(pNode->data.gene) % size;
simple_genetic.cpp: long size = hashtable.size();
simple_genetic.cpp: long key = BKDRHash(genecode) % size;
simple_genetic.cpp: long size = hash_record.size();
simple_genetic.cpp:// cout << size << endl;
simple_genetic.cpp: long key = BKDRHash(genecode) % size;
simple_genetic.cpp: int splice1 = Utils::randomi(splice_1.size());
simple_genetic.cpp: int splice2 = Utils::randomi(splice_2.size());
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp: int nextra = pool%2; // if odd pop_size
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp: int right = wheel.size()-1;
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp: double stepsize = wheel.back()/pool;
simple_genetic.cpp: random += stepsize;
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp: double stepsize = wheel.back()/pool;
simple_genetic.cpp: random += stepsize;
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp: double stepsize = wheel.back()/pool;
simple_genetic.cpp: random += stepsize;
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp:// int pool = pInp->inpga.pop_size();
simple_genetic.cpp: int bits = int(offspring.size());
simple_genetic.cpp: int bits = int(string.size());
simple_genetic.cpp: int gene_bits = int(gene.size());
simple_genetic.cpp: parents.resize(2);
simple_genetic.cpp: offsprings.resize(2);
simple_genetic.cpp: ptr_array.resize(pInp->inp_ga.pop_size);
simple_genetic.cpp: prob_array.resize(pInp->inp_ga.pop_size);
simple_genetic.cpp: select_list.resize(pInp->inp_ga.pop_size);
simple_genetic.cpp: permutation.resize(pInp->inp_ga.pop_size);
simple_genetic.cpp: size_t ncats = target_list.size();
simple_genetic.cpp: size_t gene_bits = offspring.size();
simple_genetic.cpp: for (size_t i=0; i < ncats; i++)
simple_genetic.cpp: for (size_t j=1; (j<gene_bits) && (status == 0); j++)
simple_genetic.cpp: size_t ncats = target_list.size();
simple_genetic.cpp: size_t nvars = rcodes.size();
simple_genetic.cpp: for (size_t i=0; i < ncats; i++)
simple_genetic.cpp: for (size_t j=0; (j < nvars) && (status == 0) ; j++)
simple_genetic.cpp: for (size_t i=0; i < pNode->natoms; i++) frezlist[i]=0;
simple_genetic.cpp: for (size_t i =0; i< joint.size(); i++)
simple_genetic.cpp: for(size_t j=0; j< joint[i].size(); j++)
simple_genetic.cpp: for (int i=0; i< pInp->inp_ga.pop_size; i++)
simple_genetic.cpp: int pool = pInp->inp_ga.pop_size;
simple_genetic.cpp: size_t s = score_list.size();
simple_genetic.cpp: for(size_t j=0; j<s; j++)
simple_genetic.cpp:// while (i != pInp->inp_ga.pop_size)
simple_genetic.cpp: while (i != pInp->inp_ga.pop_size)
simple_genetic.cpp: Mopac::mopac_genqsh(filedir, joblist); //hard-coded for 0-gen case (joblist.size() = pop_size)
simple_genetic.cpp: for(size_t i = 0; i < pRef->natoms; i++)
simple_genetic.cpp: for (size_t j=0; j < pNode->natoms; j++)
simple_genetic.cpp: for (size_t i=0; i < pRef->natoms; i++)
simple_genetic.cpp: for (size_t i=0; i < pNode->natoms; i++)
simple_genetic.cpp: size_t size = tok_line.size();
simple_genetic.cpp: for (size_t i=0; i < size; i++)
simple_genetic.cpp: for (size_t i = 0; i < pRef->data.natoms; i++)
simple_genetic.cpp: for (size_t i = 0; i < pRef->data.natoms; i++)
simple_genetic.cpp:// genehash_pop.resize(2*pInp->inp_ga.pop_size+1);
stringtools.cpp: for(size_t i = 0; i < s.length(); i++){
stringtools.cpp: size=Mindestlaenge des ergebnisstrings,
stringtools.cpp:string StringTools::int2str(int integer, int size, const string spaceStr)
stringtools.cpp: for (int i=s.length(); i< size; i++)
stringtools.cpp: string::size_type where = value.find_last_not_of(" \t");
stringtools.cpp: string::size_type sbegin, send;
stringtools.cpp: // find size of string
stringtools.cpp: string::size_type sbegin, send;
stringtools.cpp: // find size of string
stringtools.cpp: string::size_type start_index, end_index;
utils.cpp:int Diagonalize(double* A, double* eigen, int size){
utils.cpp: // printf(" in diagonalize call, size: %i \n",size);
utils.cpp: int N = size;
utils.cpp: int LDA = size;
utils.cpp: for (int i=0;i<size;i++)
utils.cpp: for (int i=0;i<size;i++)
utils.cpp: for (int j=0;j<size;j++)
utils.cpp: A[i*size+j] = EVec[i*size+j];
utils.cpp:int Diagonalize(double* A, double* eigenvecs, double* eigen, int size){
utils.cpp: printf(" in diagonalize call, size: %i \n",size);
utils.cpp: int N = size;
utils.cpp: int LDA = size;
utils.cpp: for (int i=0;i<size;i++)
utils.cpp: for (int j=0;j<size;j++)
utils.cpp: eigenvecs[i*size+j] = EVec[i*size+j];