/// 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);
}
/// The unloadBuffer function for a halo exchange of atom data.
/// Iterates the receive buffer and places each atom that was received
/// into the link cell that corresponds to the atom coordinate. Note
/// that this naturally accomplishes transfer of ownership of atoms that
/// have moved from one spatial domain to another. Atoms with
/// coordinates in local link cells automatically become local
/// particles. Atoms that are owned by other ranks are automatically
/// placed in halo kink cells.
/// \see HaloExchangeSt::unloadBuffer for an explanation of the
/// unloadBuffer parameters.
void unloadAtomsBuffer(void* vparms, void* data, int face, int bufSize, char* charBuf)
{
AtomExchangeParms* parms = (AtomExchangeParms*) vparms;
SimFlat* s = (SimFlat*) data;
AtomMsg* buf = (AtomMsg*) charBuf;
int nBuf = bufSize / sizeof(AtomMsg);
assert(bufSize % sizeof(AtomMsg) == 0);
for (int ii=0; ii<nBuf; ++ii)
{
int gid = buf[ii].gid;
int type = buf[ii].type;
real_t rx = buf[ii].rx;
real_t ry = buf[ii].ry;
real_t rz = buf[ii].rz;
real_t px = buf[ii].px;
real_t py = buf[ii].py;
real_t pz = buf[ii].pz;
putAtomInBox(s->boxes, s->atoms, gid, type, rx, ry, rz, px, py, pz);
}
}
/// The unloadBuffer function for a halo exchange of atom data.
/// Iterates the receive buffer and places each atom that was received
/// into the link cell that corresponds to the atom coordinate. Note
/// that this naturally accomplishes transfer of ownership of atoms that
/// have moved from one spatial domain to another. Atoms with
/// coordinates in local link cells automatically become local
/// particles. Atoms that are owned by other ranks are automatically
/// placed in halo kink cells.
/// \see HaloExchangeSt::unloadBuffer for an explanation of the
/// unloadBuffer parameters.
/// @param face Not used for this function. The only reason we keep it is to match the unloadForcesBuffer declaration
void unloadAtomsBuffer(void* vparms, void* data, int face, int bufSize, char* charBuf)
{
AtomExchangeParms* parms = (AtomExchangeParms*) vparms;
SimFlat* sim = (SimFlat*) data;
assert(bufSize % sizeof(AtomMsg) == 0);
int nBuf = bufSize / sizeof(AtomMsg);
if(sim->method == CPU_NL)
{
AtomMsg* buf = (AtomMsg*) charBuf;
// const int nlUpdateRequired = neighborListUpdateRequired(s->atoms->neighborList,s->boxes,s->atoms);
const int nlUpdateRequired = neighborListUpdateRequired(sim);
for (int ii=0; ii<nBuf; ++ii)
{
int gid = buf[ii].gid;
int type = buf[ii].type;
real_t rx = buf[ii].rx;
real_t ry = buf[ii].ry;
real_t rz = buf[ii].rz;
real_t px = buf[ii].px;
real_t py = buf[ii].py;
real_t pz = buf[ii].pz;
if(nlUpdateRequired){
int iOff = putAtomInBox(sim->boxes, sim->atoms, gid, type, rx, ry, rz, px, py, pz);
if(iOff >= (MAXATOMS*sim->boxes->nLocalBoxes))
hashTablePut(sim->atomExchange->hashTable, iOff); //remember iOff only for particles which are mapped to haloCells
else //putting particle to local
sim->atoms->neighborList->updateLinkCellsRequired = 1;
}else{
int iOff = hashTableGet(sim->atomExchange->hashTable);
updateAtomInBoxAt(sim->boxes, sim->atoms, gid, type, rx, ry, rz, px, py, pz,iOff);
}
}
}else{
unloadAtomsBufferToGpu(charBuf, nBuf, sim, sim->gpu_atoms_buf, sim->boundary_stream);
}
}
