diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp new file mode 100644 index 0000000000000000000000000000000000000000..495cb7f43c2deb9113aa8144f0360632b4d80b56 --- /dev/null +++ b/src/neigh_half_bin.cpp @@ -0,0 +1,322 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void Neighbor::half_bin_no_newton(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr; + + // bin local & ghost atoms + + bin_atoms(); + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + int *molecule = atom->molecule; + int nlocal = atom->nlocal; + int nall = atom->nlocal + atom->nghost; + int molecular = atom->molecular; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + int **pages = list->pages; + int nstencil = list->nstencil; + int *stencil = list->stencil; + + int inum = 0; + int npage = 0; + int npnt = 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; + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = coord2bin(x[i]); + + for (k = 0; k < nstencil; k++) { + for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) { + if (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(i,j); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (which > 0) neighptr[n++] = which*nall + j; + } + } + } + + ilist[inum] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + inum++; + npnt += n; + if (npnt >= pgsize) + error->one("Neighbor list overflow, boost neigh_modify one or page"); + } + + list->inum = inum; +} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void Neighbor::half_bin_newton(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr; + + // bin local & ghost atoms + + bin_atoms(); + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + int *molecule = atom->molecule; + int nlocal = atom->nlocal; + int nall = atom->nlocal + atom->nghost; + int molecular = atom->molecular; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + int **pages = list->pages; + int skip = list->skip; + int nstencil = list->nstencil; + int *stencil = list->stencil; + + int inum = 0; + int npage = 0; + int npnt = 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; + + 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 && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && 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(i,j); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (which > 0) neighptr[n++] = 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(i,j); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (which > 0) neighptr[n++] = which*nall + j; + } + } + } + + ilist[inum] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + inum++; + npnt += n; + if (npnt >= pgsize) + error->one("Neighbor list overflow, boost neigh_modify one or page"); + } + + list->inum = inum; +} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void Neighbor::half_bin_newton_tri(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr; + + // bin local & ghost atoms + + bin_atoms(); + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + int *molecule = atom->molecule; + int nlocal = atom->nlocal; + int nall = atom->nlocal + atom->nghost; + int molecular = atom->molecular; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + int **pages = list->pages; + int nstencil = list->nstencil; + int *stencil = list->stencil; + + int inum = 0; + int npage = 0; + int npnt = 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; + + 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 <= x) + // this excludes self-self interaction + + 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 && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && 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(i,j); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (which > 0) neighptr[n++] = which*nall + j; + } + } + } + + ilist[inum] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + inum++; + npnt += n; + if (npnt >= pgsize) + error->one("Neighbor list overflow, boost neigh_modify one or page"); + } + + list->inum = inum; +}