new neighbor list changes

src/nbin.cpp

@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+   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 "nbin.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "update.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NBin::NBin(LAMMPS *lmp) : Pointers(lmp)
+{
+  last_setup = last_bin = last_bin_memory = -1;
+  maxbin = maxatom = 0;
+  binhead = NULL;
+  bins = NULL;
+
+  // geometry settings
+
+  dimension = domain->dimension;
+  triclinic = domain->triclinic;
+}
+
+/* ---------------------------------------------------------------------- */
+
+NBin::~NBin()
+{
+  memory->destroy(binhead);
+  memory->destroy(bins);
+}
+
+/* ----------------------------------------------------------------------
+   copy needed info from Neighbor class
+------------------------------------------------------------------------- */
+
+void NBin::copy_neighbor_info()
+{
+  includegroup = neighbor->includegroup;
+  cutneighmin = neighbor->cutneighmin;
+  cutneighmax = neighbor->cutneighmax;
+  binsizeflag = neighbor->binsizeflag;
+  binsize_user = neighbor->binsize_user;
+  bboxlo = neighbor->bboxlo;
+  bboxhi = neighbor->bboxhi;
+}
+
+/* ----------------------------------------------------------------------
+   setup for bin_atoms()
+------------------------------------------------------------------------- */
+
+void NBin::bin_atoms_setup(int nall)
+{
+  // binhead = per-bin vector, mbins in length
+  // add 1 bin for USER-INTEL package
+
+  if (mbins > maxbin) {
+    maxbin = mbins;
+    memory->destroy(binhead);
+    memory->create(binhead,maxbin,"neigh:binhead");
+    last_bin_memory = update->ntimestep;
+  }
+
+  // bins = per-atom vector
+
+  if (nall > maxatom) {
+    maxatom = nall;
+    memory->destroy(bins);
+    memory->create(bins,maxatom,"neigh:bins");
+    last_bin_memory = update->ntimestep;
+  }
+
+  last_bin = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+   convert atom coords into local bin #
+   for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
+     take special care to insure ghosts are in correct bins even w/ roundoff
+     hi ghost atoms = nbin,nbin+1,etc
+     owned atoms = 0 to nbin-1
+     lo ghost atoms = -1,-2,etc
+     this is necessary so that both procs on either side of PBC
+       treat a pair of atoms straddling the PBC in a consistent way
+   for triclinic, doesn't matter since stencil & neigh list built differently
+------------------------------------------------------------------------- */
+
+int NBin::coord2bin(double *x)
+{
+  int ix,iy,iz;
+
+  if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
+    error->one(FLERR,"Non-numeric positions - simulation unstable");
+
+  if (x[0] >= bboxhi[0])
+    ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
+  else if (x[0] >= bboxlo[0]) {
+    ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
+    ix = MIN(ix,nbinx-1);
+  } else
+    ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
+
+  if (x[1] >= bboxhi[1])
+    iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
+  else if (x[1] >= bboxlo[1]) {
+    iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
+    iy = MIN(iy,nbiny-1);
+  } else
+    iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
+
+  if (x[2] >= bboxhi[2])
+    iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
+  else if (x[2] >= bboxlo[2]) {
+    iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
+    iz = MIN(iz,nbinz-1);
+  } else
+    iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
+
+  return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint NBin::memory_usage()
+{
+  bigint bytes = 0;
+  bytes += maxbin*sizeof(int);
+  bytes += maxatom*sizeof(int);
+  return bytes;
+}