/// \details
/// This is the first step in returning data structures to a consistent
/// state after the atoms move each time step. First we discard all
/// atoms in the halo link cells. These are all atoms that are
/// currently stored on other ranks and so any information we have about
/// them is stale. Next, we move any atoms that have crossed link cell
/// boundaries into their new link cells. It is likely that some atoms
/// will be moved into halo link cells. Since we have deleted halo
/// atoms from other tasks, it is clear that any atoms that are in halo
/// cells at the end of this routine have just transitioned from local
/// to halo atoms. Such atom must be sent to other tasks by a halo
/// exchange to avoid being lost.
/// \see redistributeAtoms
void updateLinkCells(LinkCell* boxes, Atoms* atoms)
{
emptyHaloCells(boxes);
for (int iBox=0; iBox<boxes->nLocalBoxes; ++iBox)
{
int iOff = iBox*MAXATOMS;
int ii=0;
while (ii < boxes->nAtoms[iBox])
{
int jBox = getBoxFromCoord(boxes, atoms->r[iOff+ii]);
if (jBox != iBox)
moveAtom(boxes, atoms, ii, iBox, jBox);
else
++ii;
}
}
}
void reBoxAll(simflat_t *s) {
int ibox;
for(ibox=0; ibox<s->nboxes; ibox++) {
int i;
int ixold[3];
int ioff;
getIxyz3(s, ibox, ixold);
i=0;
ioff = ibox*MAXATOMS;
while(i<s->natoms[ibox]) {
int ixnew[3];
int jbox;
int k;
real3 rnew;
memcpy(rnew,s->r[ioff],sizeof(rnew));
for(k=0; k<3; k++) {
if(s->r[ioff][k] < 0.0) {
ixnew[k] = ixold[k]-1;
rnew[k] += s->boxsize[k];
}
else if(s->r[ioff][k] >= s->boxsize[k]) {
ixnew[k] = ixold[k]+1;
rnew[k] -= s->boxsize[k];
}
else {
ixnew[k] = ixold[k];
}
}
jbox = getIBoxFromIxyz3NP(s,ixnew);
if((jbox<0)||(jbox==ibox)) {
/* do nothing if same box or non-periodic boundary */
i++;
ioff++;
}
else {
/* move atom to new box */
memcpy(s->r[ioff],rnew,sizeof(rnew));
moveAtom(s,i,ibox,jbox);
}
}
}
return;
}
static void reBox(simulation_t *s) {
extern int getBoxID(simulation_t *s, real_t x, real_t y, real_t z);
extern void moveAtom(simulation_t *s, int iId, int iBox, int jBox);
int iBox;
for(iBox=s->boxes.nboxes-1; iBox>=0; iBox--) {
int id;
int n;
int jBox;
domain_t *idm;
real_t *x, *y, *z;
idm = s->boxes.domains[iBox];
n = idm->nAtoms[0];
x = idm->x; y = idm->y; z = idm->z;
id = 0;
while ( id < idm->nAtoms[0]) {
jBox = getBoxID(s,x[id],y[id],z[id]);
if(jBox == iBox) id++;
else moveAtom(s,id,iBox,jBox);
}
}
return;
}