new neighbor list changes

2016-09-07 13:42:58 -06:00
parent 0252347d43
commit c9c2ae6c61
259 changed files with 23076 additions and 14650 deletions
--- a/src/npair_skip.cpp
+++ b/src/npair_skip.cpp
@ -0,0 +1,103 @@
+/* ----------------------------------------------------------------------
+   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 "npair_skip.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairSkip::NPairSkip(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   build skip list for subset of types from parent list
+   iskip and ijskip flag which atom types and type pairs to skip
+   this is for half and full lists
+   if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
+------------------------------------------------------------------------- */
+
+void NPairSkip::build(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->ghost) 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->ghost) {
+    int num = 0;
+    for (i = 0; i < inum; i++)
+      if (ilist[i] < nlocal) num++;
+      else break;
+    list->inum = num;
+    list->gnum = inum - num;
+  }
+}