text: /* ----------------------------------------------------------------------
     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 "npair_half_multi_newton.h"
  #include "neigh_list.h"
  #include "atom.h"
  #include "atom_vec.h"
  #include "molecule.h"
  #include "domain.h"
  #include "my_page.h"
  #include "error.h"
  
  using namespace LAMMPS_NS;
  
  /* ---------------------------------------------------------------------- */
  
  NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
  
  /* ----------------------------------------------------------------------
     binned neighbor list construction with full Newton's 3rd law
     each owned atom i checks its own bin and other bins in Newton stencil
     multi-type stencil is itype dependent and is distance checked
     every pair stored exactly once by some processor
  ------------------------------------------------------------------------- */
  
  void NPairHalfMultiNewton::build(NeighList *list)
  {
    int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
    tagint tagprev;
    double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
    int *neighptr,*s;
    double *cutsq,*distsq;
  
    double **x = atom->x;
    int *type = atom->type;
    int *mask = atom->mask;
    tagint *tag = atom->tag;
    tagint *molecule = atom->molecule;
    tagint **special = atom->special;
    int **nspecial = atom->nspecial;
    int nlocal = atom->nlocal;
    if (includegroup) nlocal = atom->nfirst;
  
    int *molindex = atom->molindex;
    int *molatom = atom->molatom;
    Molecule **onemols = atom->avec->onemols;
    if (molecular == Atom::TEMPLATE) moltemplate = 1;
    else moltemplate = 0;
  
    int *ilist = list->ilist;
    int *numneigh = list->numneigh;
    int **firstneigh = list->firstneigh;
    MyPage<int> *ipage = list->ipage;
  
    int inum = 0;
    ipage->reset();
  
    for (i = 0; i < nlocal; i++) {
      n = 0;
      neighptr = ipage->vget();
  
      itype = type[i];
      xtmp = x[i][0];
      ytmp = x[i][1];
      ztmp = x[i][2];
      if (moltemplate) {
        imol = molindex[i];
        iatom = molatom[i];
        tagprev = tag[i] - iatom - 1;
      }
  
      // 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 != Atom::ATOMIC) {
            if (!moltemplate)
              which = find_special(special[i],nspecial[i],tag[j]);
            else if (imol >= 0)
              which = find_special(onemols[imol]->special[iatom],
                                   onemols[imol]->nspecial[iatom],
                                   tag[j]-tagprev);
            else which = 0;
            if (which == 0) neighptr[n++] = j;
            else if (domain->minimum_image_check(delx,dely,delz))
              neighptr[n++] = j;
            else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
          } else neighptr[n++] = j;
        }
      }
  
      // loop over all atoms in other bins in stencil, store every pair
      // skip if i,j neighbor cutoff is less than bin distance
  
      ibin = atom2bin[i];
      s = stencil_multi[itype];
      distsq = distsq_multi[itype];
      cutsq = cutneighsq[itype];
      ns = nstencil_multi[itype];
      for (k = 0; k < ns; k++) {
        for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
          jtype = type[j];
          if (cutsq[jtype] < distsq[k]) continue;
  
          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 != Atom::ATOMIC) {
              if (!moltemplate)
                which = find_special(special[i],nspecial[i],tag[j]);
              else if (imol >= 0)
                which = find_special(onemols[imol]->special[iatom],
                                     onemols[imol]->nspecial[iatom],
                                     tag[j]-tagprev);
              else which = 0;
              if (which == 0) neighptr[n++] = j;
              else if (domain->minimum_image_check(delx,dely,delz))
                neighptr[n++] = j;
              else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
            } else neighptr[n++] = j;
          }
        }
      }
  
      ilist[inum++] = i;
      firstneigh[i] = neighptr;
      numneigh[i] = n;
      ipage->vgot(n);
      if (ipage->status())
        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
    }
  
    list->inum = inum;
  }
  