new neighbor list changes

src/npair_skip_respa.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 "npair_skip_respa.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;
+
+/* ---------------------------------------------------------------------- */
+
+NPairSkipRespa::NPairSkipRespa(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 respa lists, copy the inner/middle values from parent
+------------------------------------------------------------------------- */
+
+void NPairSkipRespa::build(NeighList *list)
+{
+  int i,j,ii,jj,n,itype,jnum,joriginal,n_inner,n_middle;
+  int *neighptr,*jlist,*neighptr_inner,*neighptr_middle;
+
+  int *type = atom->type;
+
+  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 inum_skip = list->listskip->inum;
+
+  int *iskip = list->iskip;
+  int **ijskip = list->ijskip;
+
+  NeighList *listinner = list->listinner;
+  int *ilist_inner = listinner->ilist;
+  int *numneigh_inner = listinner->numneigh;
+  int **firstneigh_inner = listinner->firstneigh;
+  MyPage<int> *ipage_inner = listinner->ipage;
+
+  int *numneigh_inner_skip = list->listskip->listinner->numneigh;
+  int **firstneigh_inner_skip = list->listskip->listinner->firstneigh;
+
+  NeighList *listmiddle;
+  int *ilist_middle,*numneigh_middle,**firstneigh_middle;
+  MyPage<int> *ipage_middle;
+  int *numneigh_middle_skip,**firstneigh_middle_skip;
+  int respamiddle = list->respamiddle;
+  if (respamiddle) {
+    listmiddle = list->listmiddle;
+    ilist_middle = listmiddle->ilist;
+    numneigh_middle = listmiddle->numneigh;
+    firstneigh_middle = listmiddle->firstneigh;
+    ipage_middle = listmiddle->ipage;
+    numneigh_middle_skip = list->listskip->listmiddle->numneigh;
+    firstneigh_middle_skip = list->listskip->listmiddle->firstneigh;
+  }
+
+  int inum = 0;
+  ipage->reset();
+  ipage_inner->reset();
+  if (respamiddle) ipage_middle->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 < inum_skip; ii++) {
+    i = ilist_skip[ii];
+    itype = type[i];
+    if (iskip[itype]) continue;
+
+    n = n_inner = 0;
+    neighptr = ipage->vget();
+    neighptr_inner = ipage_inner->vget();
+    if (respamiddle) {
+      n_middle = 0;
+      neighptr_middle = ipage_middle->vget();
+    }
+
+    // loop over parent outer rRESPA 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;
+    }
+
+    // loop over parent inner rRESPA list
+
+    jlist = firstneigh_inner_skip[i];
+    jnum = numneigh_inner_skip[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      joriginal = jlist[jj];
+      j = joriginal & NEIGHMASK;
+      if (ijskip[itype][type[j]]) continue;
+      neighptr_inner[n_inner++] = joriginal;
+    }
+
+    // loop over parent middle rRESPA list
+
+    if (respamiddle) {
+      jlist = firstneigh_middle_skip[i];
+      jnum = numneigh_middle_skip[i];
+
+      for (jj = 0; jj < jnum; jj++) {
+        joriginal = jlist[jj];
+        j = joriginal & NEIGHMASK;
+        if (ijskip[itype][type[j]]) continue;
+        neighptr_middle[n_middle++] = 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");
+
+    ilist_inner[inum] = i;
+    firstneigh_inner[i] = neighptr_inner;
+    numneigh_inner[i] = n_inner;
+    ipage_inner->vgot(n);
+    if (ipage_inner->status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+    if (respamiddle) {
+      ilist_middle[inum] = i;
+      firstneigh_middle[i] = neighptr_middle;
+      numneigh_middle[i] = n_middle;
+      ipage_middle->vgot(n);
+      if (ipage_middle->status())
+        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+    }
+
+    inum++;
+  }
+
+  list->inum = inum;
+  listinner->inum = inum;
+  if (respamiddle) listmiddle->inum = inum;
+}