new neighbor list changes

src/npair_half_size_nsq_newtoff.cpp

@@ -0,0 +1,169 @@
+/* ----------------------------------------------------------------------
+   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 <string.h>
+#include "npair_half_size_nsq_newtoff.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "molecule.h"
+#include "domain.h"
+#include "fix_shear_history.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalfSizeNsqNewtoff::NPairHalfSizeNsqNewtoff(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   size particles
+   N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+   shear history must be accounted for when a neighbor pair is added
+   pair added to list if atoms i and j are both owned and i < j
+   pair added if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void NPairHalfSizeNsqNewtoff::build(NeighList *list)
+{
+  int i,j,m,n,nn,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 *listgranhistory;
+
+  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 = 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;
+    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();
+  }
+
+  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];
+
+    // loop over remaining atoms, owned and ghost
+
+    for (j = i+1; j < nall; j++) {
+      if (includegroup && !(mask[j] & bitmask)) 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) {
+            for (m = 0; m < npartner[i]; m++)
+              if (partner[i][m] == tag[j]) break;
+            if (m < npartner[i]) {
+              touchptr[n] = 1;
+              memcpy(&shearptr[nn],&shearpartner[i][dnum*m],dnumbytes);
+              nn += dnum;
+            } else {
+              touchptr[n] = 0;
+              memcpy(&shearptr[nn],zeroes,dnumbytes);
+              nn += dnum;
+            }
+          } else {
+            touchptr[n] = 0;
+            memcpy(&shearptr[nn],zeroes,dnumbytes);
+            nn += dnum;
+          }
+        }
+
+        n++;
+      }
+    }
+
+    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");
+
+    if (fix_history) {
+      firsttouch[i] = touchptr;
+      firstshear[i] = shearptr;
+      ipage_touch->vgot(n);
+      dpage_shear->vgot(nn);
+    }
+  }
+
+  list->inum = inum;
+}