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; }