C++ MyPage::vget方法代码示例

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

    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;
    if (includegroup) nlocal = atom->nfirst;
    int molecular = atom->molecular;

    int *ilist = list->ilist;
    int *numneigh = list->numneigh;
    int **firstneigh = list->firstneigh;
    int nstencil = list->nstencil;
    int *stencil = list->stencil;
    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];

        // 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]);
                    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);
                    // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
                } else neighptr[n++] = 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]);
                        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);
                        // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
                    } else neighptr[n++] = j;
                }
            }
//.........这里部分代码省略.........

void Neighbor::skip_from(NeighList *list)
{
  int i,j,ii,jj,n,itype,jnum,joriginal;
  int *neighptr,*jlist;

  int *type = atom->type;
  int nlocal = atom->nlocal;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  MyPage<int> *ipage = list->ipage;

  int *ilist_skip = list->listskip->ilist;
  int *numneigh_skip = list->listskip->numneigh;
  int **firstneigh_skip = list->listskip->firstneigh;
  int num_skip = list->listskip->inum;
  if (list->ghostflag) num_skip += list->listskip->gnum;

  int *iskip = list->iskip;
  int **ijskip = list->ijskip;

  int inum = 0;
  ipage->reset();

  // 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 < num_skip; ii++) {
    i = ilist_skip[ii];
    itype = type[i];
    if (iskip[itype]) continue;

    n = 0;
    neighptr = ipage->vget();

    // loop over parent non-skip 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;
    }

    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;
  if (list->ghostflag) {
    int num = 0;
    for (i = 0; i < inum; i++)
      if (ilist[i] < nlocal) num++;
      else break;
    list->inum = num;
    list->gnum = inum - num;
  }
}

void Neighbor::half_bin_no_newton_ghost(NeighList *list)
{
    int i,j,k,n,itype,jtype,ibin,which;
    double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
    int xbin,ybin,zbin,xbin2,ybin2,zbin2;
    int *neighptr;

    // 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;

    int *ilist = list->ilist;
    int *numneigh = list->numneigh;
    int **firstneigh = list->firstneigh;
    int nstencil = list->nstencil;
    int *stencil = list->stencil;
    int **stencilxyz = list->stencilxyz;
    MyPage<int> *ipage = list->ipage;

    int inum = 0;
    ipage->reset();

    for (i = 0; i < nall; i++) {
        n = 0;
        neighptr = ipage->vget();

        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
        // when i is a ghost atom, must check if stencil bin is out of bounds
        // only store pair if i < j
        // stores own/own pairs only once
        // stores own/ghost pairs with owned atom only, on both procs
        // stores ghost/ghost pairs only once
        // no molecular test when i = ghost atom

        if (i < nlocal) {
            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(special[i],nspecial[i],tag[j]);
                            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;
                    }
                }
            }

        } else {
            ibin = coord2bin(x[i],xbin,ybin,zbin);
            for (k = 0; k < nstencil; k++) {
                xbin2 = xbin + stencilxyz[k][0];
                ybin2 = ybin + stencilxyz[k][1];
                zbin2 = zbin + stencilxyz[k][2];
                if (xbin2 < 0 || xbin2 >= mbinx ||
                        ybin2 < 0 || ybin2 >= mbiny ||
                        zbin2 < 0 || zbin2 >= mbinz) continue;
                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;

//.........这里部分代码省略.........

void Neighbor::granular_bin_newton(NeighList *list)
{
  int i,j,k,n,ibin;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  double radi,radsum,cutsq;
  int *neighptr;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  double **x = atom->x;
  double *radius = atom->radius;
  int *type = atom->type;
  int *mask = atom->mask;
  int *molecule = atom->molecule;
  int nlocal = atom->nlocal;
  if (includegroup) nlocal = atom->nfirst;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  int nstencil = list->nstencil;
  int *stencil = list->stencil;
  MyPage<int> *ipage = list->ipage;

  int inum = 0;
  ipage->reset();

  for (i = 0; i < nlocal; i++) {

    n = 0;
    neighptr = ipage->vget();

    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    radi = radius[i];

    // 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;
        }
      }

      if (exclude && exclusion(i,j,type[i],type[j],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;
      radsum = radi + radius[j];
      cutsq = (radsum+skin) * (radsum+skin);

      if (rsq <= cutsq) neighptr[n++] = 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]) {
        if (exclude && exclusion(i,j,type[i],type[j],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;
        radsum = radi + radius[j];
        cutsq = (radsum+skin) * (radsum+skin);

        if (rsq <= cutsq) 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;
}

void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
{
  int i,j,n,itype,jtype,which,bitmask;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr;

  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;
  MyPage<int> *ipage = list->ipage;

  int inum = 0;
  ipage->reset();

  // loop over owned & ghost atoms, storing neighbors

  for (i = 0; i < nall; i++) {
    n = 0;
    neighptr = ipage->vget();

    itype = type[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];

    // loop over remaining atoms, owned and ghost
    // only store pair if i < j
    // stores own/own pairs only once
    // stores own/ghost pairs with owned atom only, on both procs
    // stores ghost/ghost pairs only once
    // no molecular test when i = ghost atom

    if (i < nlocal) {
      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]);
            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;
        }
      }

    } else {
      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]) 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 = atom->nlocal;
  list->gnum = inum - atom->nlocal;
}

void NPairHalfSizeNsqNewton::build(NeighList *list)
{
  int i,j,m,n,nn,itag,jtag,bitmask,dnum,dnumbytes;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  double radi,radsum,cutsq;
  int *neighptr,*touchptr;
  double *shearptr;

  int *npartner;
  tagint **partner;
  double **shearpartner;
  int **firsttouch;
  double **firstshear;
  MyPage<int> *ipage_touch;
  MyPage<double> *dpage_shear;
  NeighList *listhistory;

  double **x = atom->x;
  double *radius = atom->radius;
  tagint *tag = atom->tag;
  int *type = atom->type;
  int *mask = atom->mask;
  tagint *molecule = atom->molecule;
  int nlocal = atom->nlocal;
  int nall = nlocal + atom->nghost;
  if (includegroup) {
    nlocal = atom->nfirst;
    bitmask = group->bitmask[includegroup];
  }

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  MyPage<int> *ipage = list->ipage;

  FixShearHistory *fix_history = (FixShearHistory *) list->fix_history;
  if (fix_history) {
    fix_history->nlocal_neigh = nlocal;
    fix_history->nall_neigh = nall;
    npartner = fix_history->npartner;
    partner = fix_history->partner;
    shearpartner = fix_history->shearpartner;
    listhistory = list->listhistory;
    firsttouch = listhistory->firstneigh;
    firstshear = listhistory->firstdouble;
    ipage_touch = listhistory->ipage;
    dpage_shear = listhistory->dpage;
    dnum = listhistory->dnum;
    dnumbytes = dnum * sizeof(double);
  }

  int inum = 0;
  ipage->reset();
  if (fix_history) {
    ipage_touch->reset();
    dpage_shear->reset();
  }

  for (i = 0; i < nlocal; i++) {
    n = 0;
    neighptr = ipage->vget();
    if (fix_history) {
      nn = 0;
      touchptr = ipage_touch->vget();
      shearptr = dpage_shear->vget();
    }

    itag = tag[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    radi = radius[i];

    // loop over remaining atoms, owned and ghost

    for (j = i+1; j < nall; j++) {
      if (includegroup && !(mask[j] & bitmask)) continue;

      if (j >= nlocal) {
        jtag = tag[j];
        if (itag > jtag) {
          if ((itag+jtag) % 2 == 0) continue;
        } else if (itag < jtag) {
          if ((itag+jtag) % 2 == 1) continue;
        } else {
          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;
          }
        }
      }

      if (exclude && exclusion(i,j,type[i],type[j],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;
      radsum = radi + radius[j];
//.........这里部分代码省略.........

void Neighbor::granular_bin_no_newton(NeighList *list)
{
  int i,j,k,m,n,nn,ibin,d;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  double radi,radsum,cutsq;
  int *neighptr,*touchptr;
  double *shearptr;

  NeighList *listgranhistory;
  int *npartner,**partner;
  double **contacthistory;
  int **firsttouch;
  double **firstshear;
  MyPage<int> *ipage_touch;
  MyPage<double> *dpage_shear;
  int dnum; 

  double contactHistoryDistanceFactorSqr = contactHistoryDistanceFactor*contactHistoryDistanceFactor;

  // bin local & ghost atoms

  bin_atoms();

  // loop over each atom, storing neighbors

  double **x = atom->x;
  double *radius = atom->radius;
  int *tag = atom->tag;
  int *type = atom->type;
  int *mask = atom->mask;
  int *molecule = atom->molecule;
  int nlocal = atom->nlocal;
  if (includegroup) nlocal = atom->nfirst;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  int nstencil = list->nstencil;
  int *stencil = list->stencil;
  MyPage<int> *ipage = list->ipage;

  FixContactHistory *fix_history = list->fix_history; 
  if (fix_history) {
    npartner = fix_history->npartner_; 
    partner = fix_history->partner_; 
    contacthistory = fix_history->contacthistory_; 
    listgranhistory = list->listgranhistory;
    firsttouch = listgranhistory->firstneigh;
    firstshear = listgranhistory->firstdouble;
    ipage_touch = listgranhistory->ipage;
    dpage_shear = listgranhistory->dpage;
    dnum = listgranhistory->dnum; 
  }

  int inum = 0;
  ipage->reset();
        if (fix_history) {
    ipage_touch->reset();
    dpage_shear->reset();
    }

  for (i = 0; i < nlocal; i++) {
    n = 0;
    neighptr = ipage->vget();
    if (fix_history) {
      nn = 0;
      touchptr = ipage_touch->vget();
      shearptr = dpage_shear->vget();
    }

    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    radi = radius[i];
    ibin = coord2bin(x[i]);

    // loop over all atoms in surrounding bins in stencil including self
    // only store pair if i < j
    // stores own/own pairs only once
    // stores own/ghost pairs on both procs

    for (k = 0; k < nstencil; k++) {
      for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
        if (j <= i) continue;
        if (exclude && exclusion(i,j,type[i],type[j],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;
        radsum = radi + radius[j];
        cutsq = (radsum+skin) * (radsum+skin);
        
        if (rsq <= cutsq) {
          neighptr[n] = j;
          
          if (fix_history) {
            if (rsq < radsum*radsum*contactHistoryDistanceFactorSqr)
                {
              for (m = 0; m < npartner[i]; m++)
//.........这里部分代码省略.........

void Neighbor::respa_bin_no_newton(NeighList *list)
{
  int i,j,k,n,itype,jtype,ibin,n_inner,n_middle=0;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*neighptr_inner,*neighptr_middle = NULL;

  // 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 molecular = atom->molecular;
  if (includegroup) nlocal = atom->nfirst;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  int nstencil = list->nstencil;
  int *stencil = list->stencil;
  MyPage<int> *ipage = list->ipage;

  NeighList *listinner = list->listinner;
  int *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle = NULL;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
  }

  int inum = 0;
  int which = 0;
  int minchange = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  for (i = 0; i < nlocal; i++) {
    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

    itype = type[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    ibin = coord2bin(x[i]);

    // loop over all atoms in surrounding bins in stencil including self
    // only store pair if i < j
    // stores own/own pairs only once
    // stores own/ghost pairs on both procs

    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(special[i],nspecial[i],tag[j]);
            if (which == 0) neighptr[n++] = j;
            else if ((minchange = domain->minimum_image_check(delx,dely,delz))) 
              neighptr[n++] = j;
            else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
          } else neighptr[n++] = j;

          if (rsq < cut_inner_sq) {
            if (which == 0) neighptr_inner[n_inner++] = j;
            else if (minchange) neighptr_inner[n_inner++] = j;
//.........这里部分代码省略.........

void Neighbor::respa_nsq_no_newton(NeighList *list)
{
  int i,j,n,itype,jtype,n_inner,n_middle=0,bitmask=0;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*neighptr_inner,*neighptr_middle = NULL;

  // 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;
  MyPage<int> *ipage = list->ipage;

  NeighList *listinner = list->listinner;
  int *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle = NULL;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
  }

  int inum = 0;
  int which = 0;
  int minchange = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  for (i = 0; i < nlocal; i++) {
    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

    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]);
          if (which == 0) neighptr[n++] = j;
          else if ((minchange = domain->minimum_image_check(delx,dely,delz))) 
            neighptr[n++] = j;
          else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
        } else neighptr[n++] = j;

        if (rsq < cut_inner_sq) {
          if (which == 0) neighptr_inner[n_inner++] = j;
          else if (minchange) neighptr_inner[n_inner++] = j;
          else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
        }

        if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
          if (which == 0) neighptr_middle[n_middle++] = j;
          else if (minchange) neighptr_middle[n_middle++] = j;
          else if (which > 0)
            neighptr_middle[n_middle++] = j ^ (which << SBBITS);
//.........这里部分代码省略.........

void NPairHalffullNewton::build(NeighList *list)
{
  int i,j,ii,jj,n,jnum,joriginal;
  int *neighptr,*jlist;
  double xtmp,ytmp,ztmp;

  double **x = atom->x;
  int nlocal = atom->nlocal;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  MyPage<int> *ipage = list->ipage;

  int *ilist_full = list->listfull->ilist;
  int *numneigh_full = list->listfull->numneigh;
  int **firstneigh_full = list->listfull->firstneigh;
  int inum_full = list->listfull->inum;

  int inum = 0;
  ipage->reset();

  // loop over parent full list

  for (ii = 0; ii < inum_full; ii++) {
    n = 0;
    neighptr = ipage->vget();

    i = ilist_full[ii];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];

    // loop over full neighbor list

    jlist = firstneigh_full[i];
    jnum = numneigh_full[i];

    for (jj = 0; jj < jnum; jj++) {
      joriginal = jlist[jj];
      j = joriginal & NEIGHMASK;
      if (j < nlocal) {
        if (i > j) continue;
      } else {
        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;
        }
      }
      neighptr[n++] = joriginal;
    }

    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;
}

void NPairHalfBinNewtonSSA::build(NeighList *list)
{
  int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
  tagint tagprev;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr;

  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;
  int nall = nlocal + atom->nghost;
  if (includegroup) nlocal = atom->nfirst;
  int *ssaAIR = atom->ssaAIR;

  int *molindex = atom->molindex;
  int *molatom = atom->molatom;
  Molecule **onemols = atom->avec->onemols;
  int molecular = atom->molecular;
  if (molecular == 2) moltemplate = 1;
  else moltemplate = 0;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  MyPage<int> *ipage = list->ipage;

  NStencilSSA *ns_ssa = dynamic_cast<NStencilSSA*>(ns);
  if (!ns_ssa) error->one(FLERR, "NStencil wasn't a NStencilSSA object");
  int nstencil_half = ns_ssa->nstencil_half;
  int nstencil_full = ns_ssa->nstencil;

  NBinSSA *nb_ssa = dynamic_cast<NBinSSA*>(nb);
  if (!nb_ssa) error->one(FLERR, "NBin wasn't a NBinSSA object");
  int *bins_ssa = nb_ssa->bins_ssa;
  int *binhead_ssa = nb_ssa->binhead_ssa;
  int *gbinhead_ssa = nb_ssa->gbinhead_ssa;

  int inum = 0;

  ipage->reset();

  // loop over owned atoms, storing half of the neighbors

  for (i = 0; i < nlocal; i++) {
    int AIRct[8] = { 0 };
    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 local atoms in i's bin
    // just store them, since j is beyond i in linked list

    for (j = bins_ssa[i]; j >= 0; j = bins_ssa[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) {
          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;
      }
    }

    ibin = coord2bin(x[i]);

    // loop over all local atoms in other bins in "half" stencil

    for (k = 0; k < nstencil_half; k++) {
      for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; 
           j = bins_ssa[j]) {
//.........这里部分代码省略.........

void Neighbor::skip_from_granular_off2on(NeighList *list)
{
  int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
  tagint itag,jtag;
  int *neighptr,*jlist,*touchptr,*touchptr_skip;
  double *shearptr,*shearptr_skip;

  NeighList *listgranhistory;
  int *npartner;
  tagint **partner;
  double **shearpartner;
  int **firsttouch;
  double **firstshear;
  MyPage<int> *ipage_touch;
  MyPage<double> *dpage_shear;

  tagint *tag = atom->tag;
  int *type = atom->type;
  int nlocal = atom->nlocal;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  MyPage<int> *ipage = list->ipage;

  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;

  FixShearHistory *fix_history = list->fix_history;
  if (fix_history) {
    fix_history->nlocal_neigh = nlocal;
    fix_history->nall_neigh = nlocal + atom->nghost;
    npartner = fix_history->npartner;
    partner = fix_history->partner;
    shearpartner = fix_history->shearpartner;
    listgranhistory = list->listgranhistory;
    firsttouch = listgranhistory->firstneigh;
    firstshear = listgranhistory->firstdouble;
    ipage_touch = listgranhistory->ipage;
    dpage_shear = listgranhistory->dpage;
    dnum = listgranhistory->dnum;
    dnumbytes = dnum * sizeof(double);
  }

  int inum = 0;
  ipage->reset();
  if (fix_history) {
    ipage_touch->reset();
    dpage_shear->reset();
  }

  // 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;
    itag = tag[i];

    n = 0;
    neighptr = ipage->vget();
    if (fix_history) {
      nn = 0;
      touchptr = ipage_touch->vget();
      shearptr = dpage_shear->vget();
    }

    // loop over parent non-skip granular list and optionally its history info

    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;

      // only keep I,J when J = ghost if Itag < Jtag

      jtag = tag[j];
      if (j >= nlocal && jtag < itag) continue;

      neighptr[n] = joriginal;

      // no numeric test for current touch
      // just use FSH partner list to infer it
      // would require distance calculation for spheres
      // more complex calculation for surfs

      if (fix_history) {
        for (m = 0; m < npartner[i]; m++)
          if (partner[i][m] == jtag) break;
        if (m < npartner[i]) {
//.........这里部分代码省略.........

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

    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;
    if (includegroup) nlocal = atom->nfirst;
    int molecular = atom->molecular;

    int *ilist = list->ilist;
    int *numneigh = list->numneigh;
    int **firstneigh = list->firstneigh;
    int nstencil = list->nstencil;
    int *stencil = list->stencil;
    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];

        // 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]);
                        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;
}

void NPairSkipRespa::build(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;
  MyPage<int> *ipage = list->ipage;

  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 *ilist_inner = listinner->ilist;
  int *numneigh_inner = listinner->numneigh;
  int **firstneigh_inner = listinner->firstneigh;
  MyPage<int> *ipage_inner = listinner->ipage;

  int *numneigh_inner_skip = list->listskip->listinner->numneigh;
  int **firstneigh_inner_skip = list->listskip->listinner->firstneigh;

  NeighList *listmiddle;
  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
  MyPage<int> *ipage_middle;
  int *numneigh_middle_skip,**firstneigh_middle_skip;
  int respamiddle = list->respamiddle;
  if (respamiddle) {
    listmiddle = list->listmiddle;
    ilist_middle = listmiddle->ilist;
    numneigh_middle = listmiddle->numneigh;
    firstneigh_middle = listmiddle->firstneigh;
    ipage_middle = listmiddle->ipage;
    numneigh_middle_skip = list->listskip->listmiddle->numneigh;
    firstneigh_middle_skip = list->listskip->listmiddle->firstneigh;
  }

  int inum = 0;
  ipage->reset();
  ipage_inner->reset();
  if (respamiddle) ipage_middle->reset();

  // 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;

    n = n_inner = 0;
    neighptr = ipage->vget();
    neighptr_inner = ipage_inner->vget();
    if (respamiddle) {
      n_middle = 0;
      neighptr_middle = ipage_middle->vget();
    }

    // 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;
//.........这里部分代码省略.........

void Neighbor::half_multi_no_newton(NeighList *list)
{
  int i,j,k,n,itype,jtype,ibin,which,ns;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *neighptr,*s;
  double *cutsq,*distsq;

  // 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 molecular = atom->molecular;
  if (includegroup) nlocal = atom->nfirst;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  int *nstencil_multi = list->nstencil_multi;
  int **stencil_multi = list->stencil_multi;
  double **distsq_multi = list->distsq_multi;
  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];

    // loop over all atoms in other bins in stencil including self
    // only store pair if i < j
    // skip if i,j neighbor cutoff is less than bin distance
    // stores own/own pairs only once
    // stores own/ghost pairs on both procs

    ibin = coord2bin(x[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]) {
        if (j <= i) continue;
        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) {
            which = find_special(special[i],nspecial[i],tag[j]);
            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;
}