forked from lijiext/lammps
587 lines
16 KiB
C++
587 lines
16 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "atom.h"
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#include "group.h"
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#include "fix_shear_history.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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granular particles
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N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
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shear history must be accounted for when a neighbor pair is added
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pair added to list if atoms i and j are both owned and i < j
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pair added if j is ghost (also stored by proc owning j)
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------------------------------------------------------------------------- */
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void Neighbor::granular_nsq_no_newton(NeighList *list)
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{
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int i,j,m,n,nn,bitmask;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double radi,radsum,cutsq;
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int *neighptr,*touchptr;
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double *shearptr;
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NeighList *listgranhistory;
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int *npartner,**partner;
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double (**shearpartner)[3];
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int **firsttouch;
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double **firstshear;
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MyPage<int> *ipage_touch;
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MyPage<double> *dpage_shear;
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double **x = atom->x;
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double *radius = atom->radius;
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int *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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if (includegroup) {
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nlocal = atom->nfirst;
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bitmask = group->bitmask[includegroup];
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}
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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MyPage<int> *ipage = list->ipage;
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FixShearHistory *fix_history = list->fix_history;
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if (fix_history) {
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npartner = fix_history->npartner;
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partner = fix_history->partner;
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shearpartner = fix_history->shearpartner;
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listgranhistory = list->listgranhistory;
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firsttouch = listgranhistory->firstneigh;
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firstshear = listgranhistory->firstdouble;
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ipage_touch = listgranhistory->ipage;
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dpage_shear = listgranhistory->dpage;
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}
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int inum = 0;
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ipage->reset();
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if (fix_history) {
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ipage_touch->reset();
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dpage_shear->reset();
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}
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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if (fix_history) {
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nn = 0;
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touchptr = ipage_touch->vget();
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shearptr = dpage_shear->vget();
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}
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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radi = radius[i];
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// loop over remaining atoms, owned and ghost
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for (j = i+1; j < nall; j++) {
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if (includegroup && !(mask[j] & bitmask)) continue;
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if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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radsum = radi + radius[j];
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cutsq = (radsum+skin) * (radsum+skin);
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if (rsq <= cutsq) {
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neighptr[n] = j;
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if (fix_history) {
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if (rsq < radsum*radsum) {
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for (m = 0; m < npartner[i]; m++)
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if (partner[i][m] == tag[j]) break;
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if (m < npartner[i]) {
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touchptr[n] = 1;
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shearptr[nn++] = shearpartner[i][m][0];
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shearptr[nn++] = shearpartner[i][m][1];
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shearptr[nn++] = shearpartner[i][m][2];
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} else {
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touchptr[n] = 0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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}
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} else {
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touchptr[n] = 0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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}
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}
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n++;
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}
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}
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ilist[inum++] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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ipage->vgot(n);
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if (ipage->status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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if (fix_history) {
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firsttouch[i] = touchptr;
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firstshear[i] = shearptr;
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ipage_touch->vgot(n);
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dpage_shear->vgot(nn);
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}
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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granular particles
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N^2 / 2 search for neighbor pairs with full Newton's 3rd law
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no shear history is allowed for this option
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pair added to list if atoms i and j are both owned and i < j
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if j is ghost only me or other proc adds pair
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decision based on itag,jtag tests
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------------------------------------------------------------------------- */
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void Neighbor::granular_nsq_newton(NeighList *list)
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{
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int i,j,n,itag,jtag,bitmask;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double radi,radsum,cutsq;
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int *neighptr;
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double **x = atom->x;
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double *radius = atom->radius;
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int *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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if (includegroup) {
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nlocal = atom->nfirst;
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bitmask = group->bitmask[includegroup];
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}
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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MyPage<int> *ipage = list->ipage;
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int inum = 0;
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ipage->reset();
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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itag = tag[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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radi = radius[i];
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// loop over remaining atoms, owned and ghost
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for (j = i+1; j < nall; j++) {
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if (includegroup && !(mask[j] & bitmask)) continue;
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if (j >= nlocal) {
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jtag = tag[j];
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if (itag > jtag) {
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if ((itag+jtag) % 2 == 0) continue;
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} else if (itag < jtag) {
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if ((itag+jtag) % 2 == 1) continue;
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} else {
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp) {
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if (x[j][1] < ytmp) continue;
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if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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}
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}
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if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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radsum = radi + radius[j];
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cutsq = (radsum+skin) * (radsum+skin);
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if (rsq <= cutsq) neighptr[n++] = j;
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}
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ilist[inum++] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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ipage->vgot(n);
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if (ipage->status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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granular particles
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binned neighbor list construction with partial Newton's 3rd law
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shear history must be accounted for when a neighbor pair is added
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each owned atom i checks own bin and surrounding bins in non-Newton stencil
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pair stored once if i,j are both owned and i < j
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pair stored by me if j is ghost (also stored by proc owning j)
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------------------------------------------------------------------------- */
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void Neighbor::granular_bin_no_newton(NeighList *list)
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{
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int i,j,k,m,n,nn,ibin;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double radi,radsum,cutsq;
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int *neighptr,*touchptr;
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double *shearptr;
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NeighList *listgranhistory;
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int *npartner,**partner;
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double (**shearpartner)[3];
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int **firsttouch;
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double **firstshear;
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MyPage<int> *ipage_touch;
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MyPage<double> *dpage_shear;
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// bin local & ghost atoms
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bin_atoms();
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// loop over each atom, storing neighbors
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double **x = atom->x;
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double *radius = atom->radius;
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int *tag = atom->tag;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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if (includegroup) nlocal = atom->nfirst;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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MyPage<int> *ipage = list->ipage;
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FixShearHistory *fix_history = list->fix_history;
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if (fix_history) {
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npartner = fix_history->npartner;
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partner = fix_history->partner;
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shearpartner = fix_history->shearpartner;
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listgranhistory = list->listgranhistory;
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firsttouch = listgranhistory->firstneigh;
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firstshear = listgranhistory->firstdouble;
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ipage_touch = listgranhistory->ipage;
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dpage_shear = listgranhistory->dpage;
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}
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int inum = 0;
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ipage->reset();
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if (fix_history) {
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ipage_touch->reset();
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dpage_shear->reset();
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}
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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if (fix_history) {
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nn = 0;
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touchptr = ipage_touch->vget();
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shearptr = dpage_shear->vget();
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}
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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radi = radius[i];
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ibin = coord2bin(x[i]);
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// loop over all atoms in surrounding bins in stencil including self
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// only store pair if i < j
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// stores own/own pairs only once
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// stores own/ghost pairs on both procs
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for (k = 0; k < nstencil; k++) {
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for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
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if (j <= i) continue;
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if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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radsum = radi + radius[j];
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cutsq = (radsum+skin) * (radsum+skin);
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if (rsq <= cutsq) {
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neighptr[n] = j;
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if (fix_history) {
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if (rsq < radsum*radsum) {
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for (m = 0; m < npartner[i]; m++)
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if (partner[i][m] == tag[j]) break;
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if (m < npartner[i]) {
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touchptr[n] = 1;
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shearptr[nn++] = shearpartner[i][m][0];
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shearptr[nn++] = shearpartner[i][m][1];
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shearptr[nn++] = shearpartner[i][m][2];
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} else {
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touchptr[n] = 0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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}
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} else {
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touchptr[n] = 0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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shearptr[nn++] = 0.0;
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}
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}
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n++;
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}
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}
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}
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ilist[inum++] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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ipage->vgot(n);
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if (ipage->status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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if (fix_history) {
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firsttouch[i] = touchptr;
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firstshear[i] = shearptr;
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ipage_touch->vgot(n);
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dpage_shear->vgot(nn);
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}
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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granular particles
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binned neighbor list construction with full Newton's 3rd law
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no shear history is allowed for this option
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each owned atom i checks its own bin and other bins in Newton stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void Neighbor::granular_bin_newton(NeighList *list)
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{
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int i,j,k,n,ibin;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double radi,radsum,cutsq;
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int *neighptr;
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// bin local & ghost atoms
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bin_atoms();
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// loop over each atom, storing neighbors
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double **x = atom->x;
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double *radius = atom->radius;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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if (includegroup) nlocal = atom->nfirst;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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MyPage<int> *ipage = list->ipage;
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int inum = 0;
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ipage->reset();
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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radi = radius[i];
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// loop over rest of atoms in i's bin, ghosts are at end of linked list
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// if j is owned atom, store it, since j is beyond i in linked list
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// if j is ghost, only store if j coords are "above and to the right" of i
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for (j = bins[i]; j >= 0; j = bins[j]) {
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if (j >= nlocal) {
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp) {
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if (x[j][1] < ytmp) continue;
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if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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}
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if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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radsum = radi + radius[j];
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cutsq = (radsum+skin) * (radsum+skin);
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if (rsq <= cutsq) neighptr[n++] = j;
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}
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// loop over all atoms in other bins in stencil, store every pair
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ibin = coord2bin(x[i]);
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for (k = 0; k < nstencil; k++) {
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for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
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if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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radsum = radi + radius[j];
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cutsq = (radsum+skin) * (radsum+skin);
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if (rsq <= cutsq) neighptr[n++] = j;
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}
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}
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ilist[inum++] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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ipage->vgot(n);
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if (ipage->status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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}
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list->inum = inum;
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}
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/* ----------------------------------------------------------------------
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granular particles
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binned neighbor list construction with Newton's 3rd law for triclinic
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no shear history is allowed for this option
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each owned atom i checks its own bin and other bins in triclinic stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void Neighbor::granular_bin_newton_tri(NeighList *list)
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{
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int i,j,k,n,ibin;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double radi,radsum,cutsq;
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int *neighptr;
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|
|
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// bin local & ghost atoms
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|
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bin_atoms();
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|
|
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// loop over each atom, storing neighbors
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|
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double **x = atom->x;
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double *radius = atom->radius;
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int *type = atom->type;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int nlocal = atom->nlocal;
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if (includegroup) nlocal = atom->nfirst;
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|
|
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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int nstencil = list->nstencil;
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int *stencil = list->stencil;
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MyPage<int> *ipage = list->ipage;
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|
|
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int inum = 0;
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ipage->reset();
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|
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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|
|
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
|
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radi = radius[i];
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|
|
|
// 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]) {
|
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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;
|
|
}
|
|
}
|
|
|
|
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;
|
|
}
|