void DeleteAtoms::delete_porosity(int narg, char **arg)
{
if (narg < 4) error->all(FLERR,"Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
double porosity_fraction = force->numeric(FLERR,arg[2]);
int seed = force->inumeric(FLERR,arg[3]);
options(narg-4,&arg[4]);
RanMars *random = new RanMars(lmp,seed + comm->me);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
}
int main() {
clock_t t1,t2;
t1=clock();
//code goes here
RanMars *random;
double seed = time(0)%1000;
cout << seed << endl;
random = new RanMars(seed);
cout << "----------------------" << endl;
cout << "T* \t rho* \t kinetic \t virial \t total pressure" << endl;
double low_temp = 1;
int boxes = 10;
Replica *r = new Replica[boxes];
for (int i=0; i<boxes; i++) {
r[i].set_temp(low_temp*pow(1.3,i));
}
int total_cycles=25000; //cycles - doesn't count the 500 initialization cycles
int swap_freq = 2; //how many cycles to wait between trying swaps
//this means on average a box gets swapped 2*3*10=60 steps
double current_temp = low_temp;
double *config = new double[total_cycles/swap_freq];
config[0]=current_temp;
double accept_count=0, total_count=0;
//loop through many moves
for (int ncycle=1; ncycle<=total_cycles; ncycle++) {
if (ncycle%500==0) {
t2=clock();
float diff ((float)t2-(float)t1);
float mins = diff / CLOCKS_PER_SEC /60;
cout<< ncycle << " cycles in: " << mins << " minutes" << endl;
}
for (int i=0; i<boxes; i++) {
r[i].cycle(ncycle, total_cycles);
}
if (ncycle<total_cycles) {
//idk how often to try these swap moves? I know we need to let the boxes equlibrate a little bit...
if (ncycle % swap_freq == 0) {
//choose box1
double rand = random->uniform();
int n = floor(rand*boxes);
//choose box2
rand = random->uniform();
int m = n-1;
if (rand>.5) {
m = n+1;
}
//check end points
//if temp m is out of bounds, wrap around
if (m==-1) {
m=boxes-1;
}
if (m==boxes) {
m=0;
}
// cout << "(" << r[n].temp << "," << r[m].temp << ")" << endl;
//swap box 1 and 2
bool accept = swap(r[n],r[m], random);
total_count++;
if (accept) {
accept_count++;
if (r[n].temp==current_temp)
current_temp = r[m].temp;
else if (r[m].temp==current_temp)
current_temp = r[n].temp;
}
config[ncycle/swap_freq]=current_temp;
//display current acceptance rate - should converge to around 20%
cout << accept_count/total_count << endl;
//print temps visited by config #1
ofstream temp_vists("files/tempsVisited.csv",ios::out);
for (int i=0; i<total_cycles/swap_freq; i++) {
temp_vists << i << "," << config[i] << endl;
}
}
}
}
return 0;
}