void
cal_pop_energy(int POPSIZE,ga_struct *population,int ptnatom, int runatom, int cnatom, double *cell ,int argc, char **argv)
{
double efinal=0;
int i=0;
for(i=0;i<POPSIZE;i++)
{
// cal_energy(&efinal,population[i].gen,population[i].cgen,0,0,ptnatom, cnatom ,argc, argv);
efinal=cal_energy(population[i].gen,population[i].cgen,ptnatom,runatom,cnatom,cell);
population[i].ep=efinal;
}
}
void Recrystalization::recrystalization_algorithm() {
std::vector<cell> noRecrystalizationCells;
clock_t start,stop;
logg("start of recrystalization algorithm...");
start = clock();
randomRecGrains();
fill_no_recrystalization_list(&noRecrystalizationCells);
for (int i = 0; i < 1000; i++) {
srand(time(NULL));
while (noRecrystalizationCells.size() > 0) {
int number = rand() % noRecrystalizationCells.size();
cell grain = noRecrystalizationCells.at(number);
int era = number - 1;
if(era<0){
era = 0;
}
noRecrystalizationCells.erase(noRecrystalizationCells.begin() + era);
int tab[2];
int *p = tab;
cal_energy(grain.idx_i, grain.idx_j, p, cells);
if (p[0] < 0) {
int energy = 0;
energy = p[1] + H;
int energyRec = cells[grain.idx_i][grain.idx_j].energy + energy;
energy = cells[grain.idx_i][grain.idx_j].energy;
if (energyRec > energy) {
cells[grain.idx_i][grain.idx_j].energy = 0;
cells[grain.idx_i][grain.idx_j].id = p[0];
recrystalizationList.push_back(cells[grain.idx_i][grain.idx_j]);
}
}
}
fill_no_recrystalization_list(&noRecrystalizationCells);
if (noRecrystalizationCells.size() == 0) {
break;
}
}
stop = clock();
float t = (float)stop - (float)start;
loggTime("time of execution recrystalization: ",t);
//draw_data();
}
void
mate( int ptnatm, int runatm, int cnatm, double *cell, int esize,int POPSIZE,ga_struct *population,ga_struct *beta_population, int Temp, double e_mate, double ddptc,int min_step,int argc, char **argv)
{
int Nmetal=ptnatm+runatm;
int rand_index=0;
int randa=0;
int randb=0;
int min_index=0;
double rand_p=0.0;
int Na=0,Nb=0;
double plandelta=0;
double bulkd=1.0; //the distance between two bulk after join;
double parentrate=0.2;
double Ne_mate=e_mate*ptnatm;
double planex1,planex2;
double p2copy[Nmetal][3],p1copy[Nmetal][3];
double p2copy_2[Nmetal][3],p1copy_2[Nmetal][3];
planex1=0;
planex2=0;
int i,j,k,ii,jj;
int type1[Nmetal],type2[Nmetal];
int type1_s[Nmetal],type2_s[Nmetal];
int type_new[Nmetal];
int Npt,Ndiff,type_change;
int rank;
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
for (ii=0;ii<ptnatm ;ii++) type1[ii]=1;
for (ii=ptnatm;ii<Nmetal;ii++) type1[ii]=2;
FILE *fbad=fopen("bad.xyz","a+");
// FILE *fbad=fopen("bad.xyz","w");
// all graphene in this generation will be reset to c.coord.
for(i=0;i<1;i++)
{
// select two parents
for (j=0;j<2;j++)
{
do
{
rand_index=rand()%POPSIZE;
rand_p=rand()/(RAND_MAX*1.0);
} while(population[rand_index].fitness<rand_p);
if(j==0){randa=rand_index;}
if(j==1){randb=rand_index;}
// if(randa==randb){j=j-1;}
}
memcpy( p1copy,population[randa].gen,sizeof(p1copy));
memcpy( p2copy,population[randb].gen,sizeof(p2copy));
memcpy( type2,type1,sizeof(type1));
center(Nmetal,p1copy);
center(Nmetal,p2copy);
memcpy( p1copy_2,p1copy,sizeof(p1copy));
memcpy( p2copy_2,p2copy,sizeof(p2copy));
/// write_coord(fbad,ptnatm,runatm,cnatm,p1copy,beta_population[0].cgen,0);
// write_coord(fbad,ptnatm,runatm,cnatm,p1copy,beta_population[0].cgen,0);
// write_coord(fbad,ptnatm,runatm,cnatm,p2copy,beta_population[0].cgen,0);
qsort(p1copy,Nmetal,sizeof(p1copy[0]),cmp);
qsort(p2copy,Nmetal,sizeof(p2copy[0]),cmp);
/// write_coord(fbad,ptnatm,runatm,cnatm,p1copy,beta_population[0].cgen,0);
/// write_coord(fbad,ptnatm,runatm,cnatm,p2copy,beta_population[0].cgen,0);
for (ii=0;ii<=Nmetal;ii++){
for (j=0;j<=Nmetal;j++){
if (p1copy[ii][0]==p1copy_2[j][0]) type1_s[ii]=type1[j];
if (p2copy[ii][0]==p2copy_2[j][0]) type2_s[ii]=type2[j];
}
}
// for (ii=0;ii<13;ii++) printf("type1 atom[%d]= %d %lf\n",ii,type1_s[ii],p1copy[ii][0]);
Na=count_x(Nmetal,p1copy,0);
Nb=Nmetal-Na;
planex1=p1copy[Na-1][0];
planex2=p2copy[Na][0];
plandelta=planex1-planex2;
Npt=0;
Ndiff=0;
for (j=0;j<Nmetal;j++)
{
if(j<Na)
{
beta_population[i].gen[j][0]=p1copy[j][0];
beta_population[i].gen[j][1]=p1copy[j][1];
beta_population[i].gen[j][2]=p1copy[j][2];
type_new[j]=type1_s[j];
if(type_new[j]==1) Npt=Npt+1;
}
else
{
beta_population[i].gen[j][0]=p2copy[j][0]+plandelta-bulkd*plandelta/fabs(plandelta);
beta_population[i].gen[j][1]=p2copy[j][1];
beta_population[i].gen[j][2]=p2copy[j][2];
type_new[j]=type2_s[j];
if(type_new[j]==1) Npt=Npt+1;
}
}
Ndiff=ptnatm-Npt;
if(Ndiff>0) type_change=2;
if(Ndiff<0) {type_change=1; Ndiff=-Ndiff;}
for (j=Na;j<Nmetal;j++){
if (Ndiff==0) break;
if (type_new[j]==type_change){
type_new[j]=type_change%2+1;
Ndiff--;
}
}
k=0;
ii=0;
jj=ptnatm;
for (j=0;j<Nmetal;j++){
// printf("j=%d %d\n",j,type_new[j]);
if(type_new[j]==1) {k=ii; ii++;}
if(type_new[j]==2) {k=jj; jj++;}
p1copy[k][0]=beta_population[i].gen[j][0];
p1copy[k][1]=beta_population[i].gen[j][1];
p1copy[k][2]=beta_population[i].gen[j][2];
//// printf("k=%d %lf\n",k,p1copy[j][0]);
}
// for (ii=0;ii<13;ii++) printf("type atom[%d]= %d %lf\n",ii,type_new[ii],p1copy[ii][0]);
init_carbon_i(cnatm,POPSIZE, beta_population,i);
shift(ptnatm,beta_population[i].gen,ddptc);
memcpy( beta_population[i].gen,p1copy,sizeof(p1copy));
beta_population[i].ep=cal_energy(beta_population[i].gen,beta_population[i].cgen,ptnatm,runatm,cnatm,cell);
write_coord(fbad,ptnatm,runatm,cnatm,beta_population[i].gen,beta_population[0].cgen,0);
fflush(fbad);
if(population[randa].ep<population[randb].ep)
{min_index=randa;}
else
{min_index=randb;}
if(beta_population[i].ep-Ne_mate<population[min_index].ep)
{
printf("%dth core Eold= %12.4lf Enew= %12.4lf %d %d SUCCESSFULLY MATED !!! \n", rank,population[min_index].ep,beta_population[i].ep,randa,randb);
}
else
{
printf("%dth core Eold= %12.4lf Enew =%12.4f %d %d NOT MATED !!!\n" ,rank,population[min_index].ep,beta_population[i].ep,randa,randb);
i=i-1;
}
}
/// fclose(fbad);
}