new neighbor list changes

src/nstencil.cpp

@@ -0,0 +1,230 @@
+/* ----------------------------------------------------------------------
+   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 "nstencil.h"
+#include "neighbor.h"
+#include "nbin.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "memory.h"
+
+using namespace LAMMPS_NS;
+
+enum{NSQ,BIN,MULTI};     // also in Neighbor
+
+/* ----------------------------------------------------------------------
+   NStencil classes
+   each has method to create a stencil = list of bin offsets
+     invoked each time simulation box size/shape changes
+     since induces change in bins
+   stencil = bins whose closest corner to central bin is within cutoff
+   sx,sy,sz = bin bounds = furthest the stencil could possibly extend
+     calculated below in create_setup()
+   3d creates xyz stencil, 2d creates xy stencil
+   for half list with newton off:
+     stencil is all surrounding bins including self
+     regardless of triclinic
+   for half list with newton on:
+     stencil is bins to the "upper right" of central bin
+     stencil does not include self
+     no versions that allow ghost on (no callers need it?)
+   for half list with newton on and triclinic:
+     stencil is all bins in z-plane of self and above, but not below
+     in 2d is all bins in y-plane of self and above, but not below
+     stencil includes self
+     no versions that allow ghost on (no callers need it?)
+   for full list:
+     stencil is all surrounding bins including self
+     regardless of newton on/off or triclinic
+   for multi:
+     create one stencil for each atom type
+     stencil follows same rules for half/full, newton on/off, triclinic
+     cutoff is not cutneighmaxsq, but max cutoff for that atom type
+     no versions that allow ghost on (any need for it?)
+------------------------------------------------------------------------- */
+
+NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
+{
+  last_create = last_stencil_memory = -1;
+  last_copy_bin = -1;
+
+  xyzflag = 0;
+
+  maxstencil = maxstencil_multi = 0;
+  stencil = NULL;
+  stencilxyz = NULL;
+  nstencil_multi = NULL;
+  stencil_multi = NULL;
+  distsq_multi = NULL;
+
+  dimension = domain->dimension;
+}
+
+/* ---------------------------------------------------------------------- */
+
+NStencil::~NStencil()
+{
+  memory->destroy(stencil);
+  memory->destroy(stencilxyz);
+  memory->destroy(nstencil_multi);
+
+  if (!stencil_multi) return;
+
+  int n = atom->ntypes;
+  for (int i = 1; i <= n; i++) {
+    memory->destroy(stencil_multi[i]);
+    memory->destroy(distsq_multi[i]);
+  }
+  delete [] stencil_multi;
+  delete [] distsq_multi;
+}
+
+/* ----------------------------------------------------------------------
+   copy needed info from Neighbor class to this stencil class
+------------------------------------------------------------------------- */
+
+void NStencil::copy_neighbor_info()
+{
+  neighstyle = neighbor->style;
+  cutneighmax = neighbor->cutneighmax;
+  cutneighmaxsq = neighbor->cutneighmaxsq;
+  cuttypesq = neighbor->cuttypesq;
+}
+
+/* ----------------------------------------------------------------------
+   copy needed info from NBin class to this stencil class
+------------------------------------------------------------------------- */
+
+void NStencil::copy_bin_info()
+{
+  mbinx = nb->mbinx;
+  mbiny = nb->mbiny;
+  mbinz = nb->mbinz;
+  binsizex = nb->binsizex;
+  binsizey = nb->binsizey;
+  binsizez = nb->binsizez;
+  bininvx = nb->bininvx;
+  bininvy = nb->bininvy;
+  bininvz = nb->bininvz;
+}
+
+/* ----------------------------------------------------------------------
+   insure NBin data is current
+   insure stencils are allocated large enough
+------------------------------------------------------------------------- */
+
+void NStencil::create_setup()
+{
+  if (nb && last_copy_bin < nb->last_setup) {
+    copy_bin_info();
+    last_copy_bin = update->ntimestep;
+  }
+
+  // sx,sy,sz = max range of stencil in each dim
+  // smax = max possible size of entire 3d stencil
+  // stencil will be empty if cutneighmax = 0.0
+
+  sx = static_cast<int> (cutneighmax*bininvx);
+  if (sx*binsizex < cutneighmax) sx++;
+  sy = static_cast<int> (cutneighmax*bininvy);
+  if (sy*binsizey < cutneighmax) sy++;
+  sz = static_cast<int> (cutneighmax*bininvz);
+  if (sz*binsizez < cutneighmax) sz++;
+  if (dimension == 2) sz = 0;
+
+  int smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
+
+  // reallocate stencil structs if necessary
+  // for BIN and MULTI styles
+
+  if (neighstyle == BIN) {
+    if (smax > maxstencil) {
+      maxstencil = smax;
+      memory->destroy(stencil);
+      memory->create(stencil,maxstencil,"neighstencil:stencil");
+      if (xyzflag) {
+        memory->destroy(stencilxyz);
+        memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
+      }
+      last_stencil_memory = update->ntimestep;
+    }
+
+  } else {
+    int i;
+    int n = atom->ntypes;
+    if (maxstencil_multi == 0) {
+      nstencil_multi = new int[n+1];
+      stencil_multi = new int*[n+1];
+      distsq_multi = new double*[n+1];
+      for (i = 1; i <= n; i++) {
+        nstencil_multi[i] = 0;
+        stencil_multi[i] = NULL;
+        distsq_multi[i] = NULL;
+      }
+      last_stencil_memory = update->ntimestep;
+    }
+    if (smax > maxstencil_multi) {
+      maxstencil_multi = smax;
+      for (i = 1; i <= n; i++) {
+        memory->destroy(stencil_multi[i]);
+        memory->destroy(distsq_multi[i]);
+        memory->create(stencil_multi[i],maxstencil_multi,
+                       "neighstencil:stencil_multi");
+        memory->create(distsq_multi[i],maxstencil_multi,
+                       "neighstencil:distsq_multi");
+        last_stencil_memory = update->ntimestep;
+      }
+    }
+  }
+
+  last_create = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+   compute closest distance between central bin (0,0,0) and bin (i,j,k)
+------------------------------------------------------------------------- */
+
+double NStencil::bin_distance(int i, int j, int k)
+{
+  double delx,dely,delz;
+
+  if (i > 0) delx = (i-1)*binsizex;
+  else if (i == 0) delx = 0.0;
+  else delx = (i+1)*binsizex;
+
+  if (j > 0) dely = (j-1)*binsizey;
+  else if (j == 0) dely = 0.0;
+  else dely = (j+1)*binsizey;
+
+  if (k > 0) delz = (k-1)*binsizez;
+  else if (k == 0) delz = 0.0;
+  else delz = (k+1)*binsizez;
+
+  return (delx*delx + dely*dely + delz*delz);
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint NStencil::memory_usage()
+{
+  bigint bytes = 0;
+  if (neighstyle == BIN) {
+    bytes += memory->usage(stencil,maxstencil);
+    bytes += memory->usage(stencilxyz,maxstencil,3);
+  } else if (neighstyle == MULTI) {
+    bytes += atom->ntypes*maxstencil_multi * sizeof(int);
+    bytes += atom->ntypes*maxstencil_multi * sizeof(double);
+  }
+  return bytes;
+}