void Neighbor::build(Atom &atom)
{
ncalls++;
const int nlocal = atom.nlocal;
const int nall = atom.nlocal + atom.nghost;
/* extend atom arrays if necessary */
#pragma omp master
if(nall > nmax) {
nmax = nall;
#ifdef ALIGNMALLOC
if(numneigh) _mm_free(numneigh);
numneigh = (int*) _mm_malloc(nmax * sizeof(int) + ALIGNMALLOC, ALIGNMALLOC);
if(neighbors) _mm_free(neighbors);
neighbors = (int*) _mm_malloc(nmax * maxneighs * sizeof(int) + ALIGNMALLOC, ALIGNMALLOC);
#else
if(numneigh) free(numneigh);
if(neighbors) free(neighbors);
numneigh = (int*) malloc(nmax * sizeof(int));
neighbors = (int*) malloc(nmax * maxneighs * sizeof(int));
#endif
}
#pragma omp barrier
/* bin local & ghost atoms */
binatoms(atom);
count = 0;
/* loop over each atom, storing neighbors */
const MMD_float* const x = atom.x;
const int* const type = atom.type;
int ntypes = atom.ntypes;
resize = 1;
#pragma omp barrier
while(resize) {
#pragma omp barrier
int new_maxneighs = maxneighs;
resize = 0;
#pragma omp barrier
OMPFORSCHEDULE
for(int i = 0; i < nlocal; i++) {
int* neighptr = &neighbors[i * maxneighs];
/* if necessary, goto next page and add pages */
int n = 0;
const MMD_float xtmp = x[i * PAD + 0];
const MMD_float ytmp = x[i * PAD + 1];
const MMD_float ztmp = x[i * PAD + 2];
const int type_i = type[i];
/* loop over atoms in i's bin,
*/
const int ibin = coord2bin(xtmp, ytmp, ztmp);
for(int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
int* loc_bin = &bins[jbin * atoms_per_bin];
if(ibin == jbin)
for(int m = 0; m < bincount[jbin]; m++) {
const int j = loc_bin[m];
//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists
if(((j == i) || (halfneigh && !ghost_newton && (j < i)) ||
(halfneigh && ghost_newton && ((j < i) || ((j >= nlocal) &&
((x[j * PAD + 2] < ztmp) || (x[j * PAD + 2] == ztmp && x[j * PAD + 1] < ytmp) ||
(x[j * PAD + 2] == ztmp && x[j * PAD + 1] == ytmp && x[j * PAD + 0] < xtmp))))))) continue;
const MMD_float delx = xtmp - x[j * PAD + 0];
const MMD_float dely = ytmp - x[j * PAD + 1];
const MMD_float delz = ztmp - x[j * PAD + 2];
const int type_j = type[j];
const MMD_float rsq = delx * delx + dely * dely + delz * delz;
if((rsq <= cutneighsq[type_i*ntypes+type_j])) neighptr[n++] = j;
}
else {
for(int m = 0; m < bincount[jbin]; m++) {
const int j = loc_bin[m];
if(halfneigh && !ghost_newton && (j < i)) continue;
const MMD_float delx = xtmp - x[j * PAD + 0];
const MMD_float dely = ytmp - x[j * PAD + 1];
const MMD_float delz = ztmp - x[j * PAD + 2];
const int type_j = type[j];
const MMD_float rsq = delx * delx + dely * dely + delz * delz;
if((rsq <= cutneighsq[type_i*ntypes+type_j])) neighptr[n++] = j;
}
}
}
numneigh[i] = n;
if(n >= maxneighs) {
resize = 1;
if(n >= new_maxneighs) new_maxneighs = n;
}
}
// #pragma omp barrier
if(resize) {
#pragma omp master
{
maxneighs = new_maxneighs * 1.2;
#ifdef ALIGNMALLOC
_mm_free(neighbors);
neighbors = (int*) _mm_malloc(nmax* maxneighs * sizeof(int) + ALIGNMALLOC, ALIGNMALLOC);
#else
free(neighbors);
neighbors = (int*) malloc(nmax* maxneighs * sizeof(int));
#endif
}
#pragma omp barrier
}
}
#pragma omp barrier
}
void Neighbor::build(Atom &atom)
{
ncalls++;
const int nlocal = atom.nlocal;
const int nall = atom.nlocal + atom.nghost;
/* extend atom arrays if necessary */
#pragma omp master
if(nall > nmax) {
nmax = nall;
if(numneigh) free(numneigh);
if(neighbors) free(neighbors);
numneigh = (int*) malloc(nmax * sizeof(int));
neighbors = (int*) malloc(nmax * maxneighs * sizeof(int*));
}
int omp_me = omp_get_thread_num();
int num_omp_threads = threads->omp_num_threads;
int master = -1;
#pragma omp master
master = omp_me;
#pragma omp barrier
/* bin local & ghost atoms */
binatoms(atom);
count = 0;
/* loop over each atom, storing neighbors */
const MMD_float* x = &atom.x[0][0];
resize = 1;
#pragma omp barrier
while(resize) {
#pragma omp barrier
int new_maxneighs = maxneighs;
resize = 0;
#pragma omp barrier
#pragma omp for schedule(static,CHUNKSIZE)
for(int i = 0; i < nlocal; i++) {
int* neighptr = &neighbors[i * maxneighs];
/* if necessary, goto next page and add pages */
int n = 0;
const MMD_float xtmp = x[3 * i + 0];
const MMD_float ytmp = x[3 * i + 1];
const MMD_float ztmp = x[3 * i + 2];
/* loop over atoms in i's bin,
*/
const int ibin = coord2bin(xtmp, ytmp, ztmp);
for(int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
int* loc_bin = &bins[jbin * atoms_per_bin];
if(ibin == jbin)
for(int m = 0; m < bincount[jbin]; m++) {
const int j = loc_bin[m];
//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists
if(((j == i) || (halfneigh && !ghost_newton && (j < i)) ||
(halfneigh && ghost_newton && ((j < i) || ((j >= nlocal) &&
((x[3 * j + 2] < ztmp) || (x[3 * j + 2] == ztmp && x[3 * j + 1] < ytmp) ||
(x[3 * j + 2] == ztmp && x[3 * j + 1] == ytmp && x[3 * j + 0] < xtmp))))))) continue;
const MMD_float delx = xtmp - x[3 * j + 0];
const MMD_float dely = ytmp - x[3 * j + 1];
const MMD_float delz = ztmp - x[3 * j + 2];
const MMD_float rsq = delx * delx + dely * dely + delz * delz;
if((rsq <= cutneighsq)) neighptr[n++] = j;
}
else {
for(int m = 0; m < bincount[jbin]; m++) {
const int j = loc_bin[m];
if(halfneigh && !ghost_newton && (j < i)) continue;
const MMD_float delx = xtmp - x[3 * j + 0];
const MMD_float dely = ytmp - x[3 * j + 1];
const MMD_float delz = ztmp - x[3 * j + 2];
const MMD_float rsq = delx * delx + dely * dely + delz * delz;
if((rsq <= cutneighsq)) neighptr[n++] = j;
}
}
}
numneigh[i] = n;
if(n >= maxneighs) {
resize = 1;
if(n >= new_maxneighs) new_maxneighs = n;
}
}
#pragma omp barrier
if(resize) {
#pragma omp master
{
free(neighbors);
maxneighs = new_maxneighs * 1.2;
neighbors = (int*) malloc(nmax* maxneighs * sizeof(int));
}
#pragma omp barrier
}
}
#pragma omp barrier
}
