void sumAtoms(SimFlat* s)
{
// sum atoms across all processers
s->atoms->nLocal = 0;
for (int i = 0; i < s->boxes->nLocalBoxes; i++)
{
s->atoms->nLocal += s->boxes->nAtoms[i];
}
startTimer(commReduceTimer);
addIntParallel(&s->atoms->nLocal, &s->atoms->nGlobal, 1);
stopTimer(commReduceTimer);
}
/// Creates atom positions on a face centered cubic (FCC) lattice with
/// nx * ny * nz unit cells and lattice constant lat.
/// Set momenta to zero.
void createFccLattice(int nx, int ny, int nz, real_t lat, SimFlat* s)
{
const real_t* localMin = s->domain->localMin; // alias
const real_t* localMax = s->domain->localMax; // alias
int nb = 4; // number of atoms in the basis
real3 basis[4] = { {0.25, 0.25, 0.25},
{0.25, 0.75, 0.75},
{0.75, 0.25, 0.75},
{0.75, 0.75, 0.25} };
// create and place atoms
int begin[3];
int end[3];
for (int ii=0; ii<3; ++ii)
{
begin[ii] = floor(localMin[ii]/lat);
end[ii] = ceil (localMax[ii]/lat);
}
real_t px,py,pz;
px=py=pz=0.0;
for (int ix=begin[0]; ix<end[0]; ++ix)
for (int iy=begin[1]; iy<end[1]; ++iy)
for (int iz=begin[2]; iz<end[2]; ++iz)
for (int ib=0; ib<nb; ++ib)
{
real_t rx = (ix+basis[ib][0]) * lat;
real_t ry = (iy+basis[ib][1]) * lat;
real_t rz = (iz+basis[ib][2]) * lat;
if (rx < localMin[0] || rx >= localMax[0]) continue;
if (ry < localMin[1] || ry >= localMax[1]) continue;
if (rz < localMin[2] || rz >= localMax[2]) continue;
int id = ib+nb*(iz+nz*(iy+ny*(ix)));
putAtomInBox(s->boxes, s->atoms, id, 0, rx, ry, rz, px, py, pz);
}
// set total atoms in simulation
startTimer(commReduceTimer);
addIntParallel(&s->atoms->nLocal, &s->atoms->nGlobal, 1);
stopTimer(commReduceTimer);
assert(s->atoms->nGlobal == nb*nx*ny*nz);
}
