/**
* mate randomly the rest of population after elitism
*/
void
mate (ga_struct * population, ga_struct * beta_population)
{
int esize = POPSIZE * ELITRATE;
// elitism of top elements in array
elitism (population, beta_population, esize);
// mate the rest of shitty population xD
int m = esize, i1 = -1, i2 = -1, pos = -1, tsize = ELEMENTS * 4 + 1;
for (; m < POPSIZE; m++)
{
pos = rand () % tsize;
i1 = rand () % POPSIZE;
i2 = rand () % POPSIZE;
int i = 0;
for (; i < pos; i++)
{
beta_population[m].gen[i] = population[i1].gen[i];
}
for (i = pos; i < tsize; i++)
{
beta_population[m].gen[i] = population[i2].gen[i];
}
if (rand () < MUTATION)
{
mutate (&beta_population[m]);
}
}
}
void EvolutionaryAlgorithm::selectSurvivors(void)
{
elitism();
tournament.clear();
int needeSurviorsLeft = populationSize - survivors.size();
for (int tour = 0; tour < needeSurviorsLeft; tour++)
{
for(int participant = 0; participant < tournamentSize; participant++)
{
//add an individual that is not already surviving and is not too old to live on to the tournament;
int selectedIndividual = rand() % currentPopulation.size();
while (currentPopulation[selectedIndividual].getAlreadySurvived() || currentPopulation[selectedIndividual].getGoingToDie())
{
selectedIndividual = rand() % currentPopulation.size();
}
tournament.push_back(¤tPopulation[selectedIndividual]);
}
sort(tournament.begin(), tournament.end(), Individual::individualPointerLessThan);
survivors.push_back(tournament[0]->incrementAge());
tournament[0]->setAsSurvivor();
tournament.clear();
}
}
// Main algorithm.
void MOGA::compute()
{
if ( num_bits_ == 0 ) return;
double p;
// Build initial population.
initialization();
// Do generations.
for ( int i = 0; i < num_generations_; ++i )
{
while ( (int)population_.size() < 2 * num_individuals_ )
{
// Select a pair of individuals.
std::pair<int, int> s( selection() );
p = (double)std::rand() / (double)RAND_MAX;
if ( p <= Pc_ )
{
// Cross them.
std::pair<individual, individual> children(
crossover( population_[s.first], population_[s.second] ) );
p = (double)std::rand() / (double)RAND_MAX;
if ( p <= Pm_ )
{
// Mutate children.
mutation( children.first );
mutation( children.second );
}
// Repair children.
repair( children.first );
repair( children.second );
population_.push_back( children.first );
population_.push_back( children.second );
}
else
{
population_.push_back( population_[s.first] );
population_.push_back( population_[s.second] );
}
}
// Keep the best individuals.
elitism();
print();
}
// LOCAL SEARCH
solutions_.clear();
if ( Argument::local_search )
{
LocalSearch local( data_, cust_, fac_ );
local.pipe_fp_ = pipe_fp_;
for ( unsigned int i = 0; i < population_.size(); ++i )
{
local.search( population_[i] );
solutions_.merge( local.solutions_ );
}
}
// FINISHED - KEEP BEST VALUES
// Keep only "first rank" solutions.
for ( unsigned int i = 0; i < population_.size(); ++i )
{
#if STRICT_CHECK
if ( population_[i].rank == 1 && is_feasible( population_[i] ) && population_[i].is_feasible() )
#else
if ( population_[i].rank == 1 && population_[i].is_feasible() )
#endif
{
#if STRICT_CHECK
// Check objective
is_valid( population_[i] );
#endif
Solution sol( getNbObjective() );
for ( int k = 0; k < getNbObjective(); ++k )
{
sol.setObj( k, population_[i].obj[k] );
}
solutions_.push_back( sol );
}
}
}
int main(int argc, char **argv){
int rc,num_processors,rank;
rc=MPI_Init(&argc,&argv);
if (rc != MPI_SUCCESS) {
printf("Error starting MPI program. Terminating\n");
MPI_Abort(MPI_COMM_WORLD, rc);
}
MPI_Comm_size(MPI_COMM_WORLD,&num_processors);
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
//**************************************************************************************//
// reading input information by all cores //
//**************************************************************************************//
FILE *fpenergy=fopen("./energy","w"); // Print the energy evolution
FILE *fprestart=fopen("./restart","w"); //print the generation and popsize coordinates
FILE *fpoptim=fopen("./optim.xyz","wb");
FILE *fp=fopen("data.txt","r");
time_t current_time;
double seconds,start,end,seconds_new,seconds_old,seconds_total;
struct timespec now,tmstart;
char* c_time_string,c_time_final;
int flag_converge=0;
int i=0;
srand(time(NULL)+rank);
clock_gettime(CLOCK_REALTIME, &tmstart);
printf("hello from processor %ld\n",rank);
start = (double)clock() /(double) CLOCKS_PER_SEC;
seconds_old= (double)(tmstart.tv_sec+tmstart.tv_nsec*1e-9);
current_time = time(NULL);
c_time_string = ctime(¤t_time);
printf("Current time is %s\n", c_time_string);
printf("hello from processor %ld\n",rank);
char skip[10];
FILE *fp_input2 = fopen("ga_dftb_input1.1","r");
int NSTEP=0;
int step=0;
double ee_mate=0 ; // the energy cretiria for accepting children cluster. the larger, the less restrict. can be 0.1 0 or -0.1
double ELITRATE=0.2;
int POPSIZE=0;
int min_step=0;
int NEWPOPSIZE=POPSIZE;
double delte=0.00001 ; //0.00001;
int ptnatm,runatm,cnatm;
double boxl=0;
double Mu=0.2;
double dptc;
int glob=0,globconvg=20;
double globe[30];
int Temp;
int flag_res=0;
double cell[9];
int esize=0;
int num_cores_child;
fscanf(fp_input2,"%d %d %d %s\n", &ptnatm, &runatm,&cnatm,&skip);
fscanf(fp_input2,"%d %s\n ", &POPSIZE,skip);
fscanf(fp_input2,"%d %s\n", &NSTEP,skip);
fscanf(fp_input2,"%d %s\n", &globconvg,skip);
fscanf(fp_input2,"%lf %s\n",&ELITRATE,skip);
fscanf(fp_input2,"%lf %s\n",&delte,skip);
fscanf(fp_input2,"%d %s\n",&Temp,skip);
fscanf(fp_input2,"%d %s\n",&min_step,skip);
fscanf(fp_input2,"%lf %s\n",&ee_mate,skip);
fscanf(fp_input2,"%lf %s\n",&dptc,skip);
fscanf(fp_input2,"%lf %s\n",&boxl,skip);
fscanf(fp_input2,"%d %s\n",&flag_res,skip);
fscanf(fp_input2,"%d %s\n",&num_cores_child,skip);
int ii=0;
for (ii=0;ii<3;ii++){
fscanf(fp_input2,"%lf %lf %lf\n", cell+ii*3+0,cell+ii*3+1,cell+ii*3+2);
//**************************************************************************************//
// Above are the information that all processors need to know //
//**************************************************************************************//
if(rank==0){
}
printf("********************JOB started*****************************\n");
printf("********************JOB started*****************************\n");
printf("********************JOB started*****************************\n\n\n");
printf("Attention!! The dftb excutable file must be in ~/bin and must be named 'dftb+' !!\n");
printf("Attention!! The dftb excutable file must be in ~/bin and must be named 'dftb+' !!\n");
printf("Attention!! The dftb excutable file must be in ~/bin and must be named 'dftb+' !!\n");
printf("Attention!! The dftb excutable file must be in ~/bin and must be named 'dftb+' !!\n");
printf("Attention!! The dftb excutable file must be in ~/bin and must be named 'dftb+' !!\n");
printf("Number of atoms %d %d %d\n", ptnatm,runatm,cnatm);
if(ptnatm+runatm>=Max_Atom || cnatm>=CMax_Atom) exitp("Number of atoms exceed allowed Max!");
printf("POPSIZE %d\n",POPSIZE);
printf("NSTEP %d\n",NSTEP);
printf("globconvg %d\n",globconvg);
printf("ELITRATE %lf\n",ELITRATE);
printf("delte %lf\n",delte);
printf("Temprature %d\n",Temp);
printf("minimiz step %d\n",min_step);
printf("ee_mate %lf\n",ee_mate);
printf("dptc %lf\n",dptc);
printf("intial boxl %lf\n",boxl);
printf("reading from pt_coord? %d\n",flag_res);
printf("Total number of processsors required %d\n",num_processors);
printf("Number of processors for each child %d\n",num_cores_child);
printf("\n\n\n******** end reading input information ***********************\n\n\n");
}
if(POPSIZE!=num_processors/num_cores_child){
printf("Error!,POPSZIE=%d num_processrs=%d num_cores_child=%d num_processrs/num_cores_child=%d",\
POPSIZE,num_processors,num_cores_child,num_processors/num_cores_child);
MPI_Abort(MPI_COMM_WORLD,0);
}
ga_struct *population = malloc(sizeof(ga_struct)*POPSIZE);
ga_struct *beta_population = malloc(sizeof(ga_struct)*POPSIZE);
//****************************************************************************************//
//define new mpi structure for data transfer between processors //
//****************************************************************************************//
int count=4;
int length[4]={1,3*Max_Atom,3*CMax_Atom,1};
MPI_Aint offset[4]={offsetof(ga_struct,fitness),offsetof(ga_struct,gen),offsetof(ga_struct,cgen),offsetof(ga_struct,ep)} ;
MPI_Datatype type[4]={MPI_DOUBLE,MPI_DOUBLE,MPI_DOUBLE,MPI_DOUBLE};
MPI_Datatype popDatatype;
MPI_Type_struct(count,length,offset,type,&popDatatype);
MPI_Type_commit(&popDatatype);
//****************************************************************************************//
//****************************************************************************************//
//Initialization the population for all processors //
//****************************************************************************************//
if(rank==0){
printf("Total number of processors is %d\n",num_processors);
printf("Total number of population is %d\n",POPSIZE);
printf ("For each candidate, there are %d processors to be used\n",num_processors/POPSIZE);
init_population(ptnatm+runatm,cnatm,POPSIZE,population,beta_population,boxl,flag_res);
printf("argc=%d\n",argc);
// int i=0,j=0;
// int esize=POPSIZE*ELITRATE;
cal_pop_energy(POPSIZE,population,ptnatm,runatm,cnatm,cell,argc, argv);
/// for (i=0;i<POPSIZE;i++){
//////// center(ptnatm+runatm,population[i].gen);
/// write_coord(fpoptim,ptnatm,runatm,cnatm,population[i].gen,population[i].cgen,population[i].ep);
// shift(ptnatm+runatm, population[i].gen,dptc);
/// }
// for (i=0;i<POPSIZE;i++)
// write_coord(fpoptim,ptnatm,runatm,cnatm,population[i].gen,population[i].cgen,population[i].ep);
fflush(fpoptim);
}
char command[30];
char filename[30];
sprintf(command,"mkdir core%d",rank);
system(command);
sprintf(command,"cp dftb_in.hsd *.coord *.skf core%d",rank);
system(command);
sprintf(filename,"core%d",rank);
chdir(filename);
system("pwd");
//****************************************************************************************//
// Loop started //
//****************************************************************************************//
for (step=0;step<NSTEP;step++){
//*********************************************************************************//
// master core preparation //
//*********************************************************************************//
if(rank==0){
cal_pop_energy(POPSIZE,population,ptnatm,runatm,cnatm,cell, argc, argv);
printf("\n\n\n\n***********************************************\n");
printf( "***********************************************\n");
printf( "***********************************************\n");
printf("Gen= %d starting optimization..................\n\n",step);
qsort (population, POPSIZE, sizeof(ga_struct),sort_func);
normal_fitness(POPSIZE,population);
for(i=0;i<POPSIZE;i++){
fprintf(fpenergy,"%d num %d %lf\n",step, i,population[i].ep);
fflush(fpenergy);
}
printf("fabs %lf\n",fabs(population[0].ep-population[POPSIZE-1].ep));
if(fabs(population[0].ep-population[POPSIZE-1].ep)<delte){
fprintf(fpenergy,"%d %lf %lf global minimum \n",step,population[0].ep,population[0].fitness);
globe[glob]=population[POPSIZE-1].ep;
glob=glob+1;
}
if(glob>20){
if(fabs(globe[glob]-globe[glob-20])<delte){
fprintf(fpenergy,"%d %lf %lf final global minimum \n",step,population[0].ep,population[0].fitness);
flag_converge=1;
}
}
///// PPreserve the first esize parentes from the previous generation. copy from population to beta_population
esize=POPSIZE*ELITRATE;
if (esize<1){esize=1;}
elitism(esize,ptnatm+runatm, cnatm,population,beta_population);
for (i=1;i<num_processors;i++)
MPI_Send(population,POPSIZE,popDatatype,i,0,MPI_COMM_WORLD);
//send coordinates and energy information to other ith processors
}else MPI_Recv(population,POPSIZE,popDatatype,0,0,MPI_COMM_WORLD,MPI_STATUS_IGNORE);
//*********************************************************************************//
// master core preparation ended //
//*********************************************************************************//
//*********************************************************************************//
// other cores mating start //
//*********************************************************************************//
//receive coordinates and energy information from 0(master) core
MPI_Bcast(&flag_converge, 1, MPI_INT,0,MPI_COMM_WORLD);
// printf("rank=%d,xyz=%lf\n",rank,population[0].gen[0][0]);
if(flag_converge ==1) {MPI_Finalize(); exit(0);}
// for (i=0;i<POPSIZE;i++)
// write_coord(fpoptim,ptnatm,runatm,cnatm,population[i].gen,population[i].cgen,population[i].ep);
fflush(fpoptim);
// printf("rank=%d,xyz=%lf\n",rank,population[0].gen[0][0]);
// Generate the rest part of beta_generation by mating process
if(rank!=0&&rank<POPSIZE)
mate(ptnatm,runatm,cnatm,cell,esize,POPSIZE,population,beta_population,Temp,ee_mate,dptc,min_step,argc, argv);
MPI_Barrier(MPI_COMM_WORLD);
if(rank!=0&&rank<POPSIZE)
MPI_Send(&beta_population[0],1,popDatatype,0,1,MPI_COMM_WORLD); //send the information of first children(optimized) from other processors to master core
//*********************************************************************************//
// other cores mating ended //
//*********************************************************************************//
if(rank==0){
for (i=1;i<POPSIZE;i++)
MPI_Recv(&population[i],1,popDatatype,i,1,MPI_COMM_WORLD,MPI_STATUS_IGNORE); //recieve coordinates and energy information to other ith processors
if (ptnatm!=0&&runatm!=0)
mutate_perm (ptnatm,runatm, Mu, POPSIZE, beta_population);
fprestart=fopen("./restart","w");
for (i=0;i<POPSIZE;i++){
write_coord(fpoptim,ptnatm,runatm,cnatm,population[i].gen,population[i].cgen,population[i].ep);
write_coord(fprestart,ptnatm,runatm,cnatm,population[i].gen,population[i].cgen,population[i].ep);
fflush(fpoptim);
fflush(fprestart);
}
fclose(fprestart);
clock_gettime(CLOCK_REALTIME, &now);
seconds_new = (double)((now.tv_sec+now.tv_nsec*1e-9));
seconds=seconds_new-seconds_old;
seconds_total = (double)((now.tv_sec+now.tv_nsec*1e-9) - (double)(tmstart.tv_sec+tmstart.tv_nsec*1e-9));
printf("\nWall time for this generation is %lf s\n",seconds);
printf("\nWall time totally %lf s\n",seconds_total);
seconds_old=seconds_new;
}
}
//*********************************************************************************
//************************************loop ended***********************************
//*********************************************************************************
if(rank==0){
printf("\n********************JOB FINISHED*****************************\n");
fclose(fpenergy);
fclose(fpoptim);
///////// time information
current_time = time(NULL);
c_time_string = ctime(¤t_time);
printf("Current time is %s\n", c_time_string);
// measure elapsed wall time
clock_gettime(CLOCK_REALTIME, &now);
seconds = (double)((now.tv_sec+now.tv_nsec*1e-9) - (double)(tmstart.tv_sec+tmstart.tv_nsec*1e-9));
printf("wall time %fs\n", seconds);
// measure CPU time
end = (double)clock() / (double) CLOCKS_PER_SEC;
printf("cpu time %fs\n", end - start);
printf("\n********************JOB FINISHED*****************************\n");
free(population);
free(beta_population);
}
}