void Neighbor::skip_from_respa(NeighList *list)
{
int i,j,ii,jj,n,itype,jnum,joriginal,n_inner,n_middle;
int *neighptr,*jlist,*neighptr_inner,*neighptr_middle;
int *type = atom->type;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int inum_skip = list->listskip->inum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
NeighList *listinner = list->listinner;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int **pages_inner = listinner->pages;
int *numneigh_inner_skip = list->listskip->listinner->numneigh;
int **firstneigh_inner_skip = list->listskip->listinner->firstneigh;
NeighList *listmiddle;
int *numneigh_middle,**firstneigh_middle,**pages_middle;
int *numneigh_middle_skip,**firstneigh_middle_skip;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
pages_middle = listmiddle->pages;
numneigh_middle_skip = list->listskip->listmiddle->numneigh;
firstneigh_middle_skip = list->listskip->listmiddle->firstneigh;
}
int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
int npnt_inner = 0;
int npage_middle = 0;
int npnt_middle = 0;
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
if (npage_middle == listmiddle->maxpage)
pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
}
// loop over parent outer rRESPA list
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n++] = joriginal;
}
// loop over parent inner rRESPA list
jlist = firstneigh_inner_skip[i];
jnum = numneigh_inner_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_inner[n_inner++] = joriginal;
}
// loop over parent middle rRESPA list
if (respamiddle) {
jlist = firstneigh_middle_skip[i];
jnum = numneigh_middle_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr_middle[n_middle++] = joriginal;
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (n_inner > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (respamiddle) {
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (n_middle > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
list->inum = inum;
}
void Neighbor::skip_from_granular(NeighList *list)
{
int i,j,ii,jj,n,nn,itype,jnum,joriginal;
int *neighptr,*jlist,*touchptr,*touchptr_skip;
double *shearptr,*shearptr_skip;
int *type = atom->type;
int dnum = list->dnum;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int **firsttouch_skip = list->listskip->listgranhistory->firstneigh;
double **firstshear_skip = list->listskip->listgranhistory->firstdouble;
int inum_skip = list->listskip->inum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
NeighList *listgranhistory = list->listgranhistory;
int **firsttouch = listgranhistory->firstneigh;
double **firstshear = listgranhistory->firstdouble;
int **pages_touch = listgranhistory->pages;
double **pages_shear = listgranhistory->dpages;
int inum = 0;
int npage = 0;
int npnt = 0;
// loop over atoms in other list
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < inum_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) {
pages = list->add_pages();
pages_touch = listgranhistory->add_pages();
pages_shear = listgranhistory->dpages;
}
}
n = 0;
neighptr = &pages[npage][npnt];
nn = 0;
touchptr = &pages_touch[npage][npnt];
shearptr = &pages_shear[npage][dnum*npnt];
// loop over parent non-skip granular list and its history info
touchptr_skip = firsttouch_skip[i];
shearptr_skip = firstshear_skip[i];
jlist = firstneigh_skip[i];
jnum = numneigh_skip[i];
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (ijskip[itype][type[j]]) continue;
neighptr[n] = joriginal;
touchptr[n++] = touchptr_skip[jj];
for(int d = 0; d < dnum; d++)
shearptr[nn++] = shearptr_skip[dnum*jj+d];
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;
}
void Neighbor::respa_bin_newton(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int **pages_inner = listinner->pages;
NeighList *listmiddle;
int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
pages_middle = listmiddle->pages;
}
int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
int npnt_inner = 0;
int npage_middle = 0;
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
if (npage_middle == listmiddle->maxpage)
pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
}
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the right" of i
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
}
}
// loop over all atoms in other bins in stencil, store every pair
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
}
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom || npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
if (respamiddle) {
ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (npnt_middle >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
inum++;
}
list->inum = inum;
listinner->inum = inum;
if (respamiddle) listmiddle->inum = inum;
}
void Neighbor::respa_bin_newton_tri(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int **pages_inner = listinner->pages;
NeighList *listmiddle;
int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
pages_middle = listmiddle->pages;
}
int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
int npnt_inner = 0;
int npage_middle = 0;
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
if (npage_middle == listmiddle->maxpage)
pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
}
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
}
}
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
if (respamiddle &&
rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
}
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom || npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
if (respamiddle) {
ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (npnt_middle >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
inum++;
}
list->inum = inum;
listinner->inum = inum;
if (respamiddle) listmiddle->inum = inum;
}
void Neighbor::respa_nsq_no_newton(NeighList *list)
{
int i,j,n,itype,jtype,which,n_inner,n_middle,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) {
nlocal = atom->nfirst;
bitmask = group->bitmask[includegroup];
}
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
NeighList *listinner = list->listinner;
int *ilist_inner = listinner->ilist;
int *numneigh_inner = listinner->numneigh;
int **firstneigh_inner = listinner->firstneigh;
int **pages_inner = listinner->pages;
NeighList *listmiddle;
int *ilist_middle,*numneigh_middle,**firstneigh_middle,**pages_middle;
int respamiddle = list->respamiddle;
if (respamiddle) {
listmiddle = list->listmiddle;
ilist_middle = listmiddle->ilist;
numneigh_middle = listmiddle->numneigh;
firstneigh_middle = listmiddle->firstneigh;
pages_middle = listmiddle->pages;
}
int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
int npnt_inner = 0;
int npage_middle = 0;
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
if (npage_inner == listinner->maxpage)
pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
if (npage_middle == listmiddle->maxpage)
pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
}
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
if (rsq < cut_inner_sq) {
if (which == 0) neighptr_inner[n_inner++] = j;
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
}
}
ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom || npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner;
npnt_inner += n_inner;
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
if (respamiddle) {
ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
if (npnt_middle >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
inum++;
}
list->inum = inum;
listinner->inum = inum;
if (respamiddle) listmiddle->inum = inum;
}
