void LinkCells::retrieveNeighboringAtoms( const Vector& pos, unsigned& natomsper, std::vector<unsigned>& atoms ) const {
plumed_assert( natomsper==1 || natomsper==2 ); // This is really a bug. If you are trying to reuse this ask GAT for help
std::vector<unsigned> celn( findMyCell( pos ) );
for(int nx=LINKC_MIN(ncells[0]);nx<LINKC_MAX(ncells[0]);++nx){
int xval = celn[0] + nx;
xval=LINKC_PBC(xval,ncells[0])*nstride[0];
for(int ny=LINKC_MIN(ncells[1]);ny<LINKC_MAX(ncells[1]);++ny){
int yval = celn[1] + ny;
yval=LINKC_PBC(yval,ncells[1])*nstride[1];
for(int nz=LINKC_MIN(ncells[2]);nz<LINKC_MAX(ncells[2]);++nz){
int zval = celn[2] + nz;
zval=LINKC_PBC(zval,ncells[2])*nstride[2];
unsigned mybox=xval+yval+zval;
for(unsigned k=0;k<lcell_tots[mybox];++k){
unsigned myatom = lcell_lists[lcell_starts[mybox]+k];
if( myatom!=atoms[0] ){ // Ideally would provide an option to not do this
atoms[natomsper]=myatom;
natomsper++;
}
}
}
}
}
}
void LinkCells::addRequiredCells( const std::array<unsigned,3>& celn, unsigned& ncells_required,
std::vector<unsigned>& cells_required ) const {
unsigned nnew_cells=0;
for(int nx=LINKC_MIN(ncells[0]); nx<LINKC_MAX(ncells[0]); ++nx) {
int xval = celn[0] + nx;
xval=LINKC_PBC(xval,ncells[0])*nstride[0];
for(int ny=LINKC_MIN(ncells[1]); ny<LINKC_MAX(ncells[1]); ++ny) {
int yval = celn[1] + ny;
yval=LINKC_PBC(yval,ncells[1])*nstride[1];
for(int nz=LINKC_MIN(ncells[2]); nz<LINKC_MAX(ncells[2]); ++nz) {
int zval = celn[2] + nz;
zval=LINKC_PBC(zval,ncells[2])*nstride[2];
unsigned mybox=xval+yval+zval; bool added=false;
for(unsigned k=0; k<ncells_required; ++k) {
if( mybox==cells_required[k] ) { added=true; break; }
}
if( !added ) { cells_required[ncells_required+nnew_cells]=mybox; nnew_cells++; }
}
}
}
ncells_required += nnew_cells;
}
