Adding other npair classes

src/npair_nsq_ghost.cpp

@@ -0,0 +1,176 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, 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_nsq_ghost.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace NeighConst;
+
+/* ---------------------------------------------------------------------- */
+
+template<int HALF>
+NPairNsqGhost<HALF>::NPairNsqGhost(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   Full:
+     N^2 search for all neighbors
+     include neighbors of ghost atoms, but no "special neighbors" for ghosts
+     every neighbor pair appears in list of both atoms i and j
+   Half + Newtoff:
+     N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+     include neighbors of ghost atoms, but no "special neighbors" for ghosts
+     pair stored once if i,j are both owned and i < j
+     pair stored by me if i owned and j ghost (also stored by proc owning j)
+     pair stored once if i,j are both ghost and i < j
+------------------------------------------------------------------------- */
+
+
+template<int HALF>
+void NPairNsqGhost<HALF>::build(NeighList *list)
+{
+  int i,j,jstart,n,itype,jtype,which,bitmask,imol,iatom,moltemplate;
+  tagint tagprev;
+  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+  int *neighptr;
+
+  double **x = atom->x;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  tagint *tag = atom->tag;
+  tagint *molecule = atom->molecule;
+  tagint **special = atom->special;
+  int **nspecial = atom->nspecial;
+  int nlocal = atom->nlocal;
+  int nall = nlocal + atom->nghost;
+  if (includegroup) {
+    nlocal = atom->nfirst;
+    bitmask = group->bitmask[includegroup];
+  }
+
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+  if (molecular == Atom::TEMPLATE) moltemplate = 1;
+  else moltemplate = 0;
+
+  int *ilist = list->ilist;
+  int *numneigh = list->numneigh;
+  int **firstneigh = list->firstneigh;
+  MyPage<int> *ipage = list->ipage;
+
+  int inum = 0;
+  ipage->reset();
+
+  // loop over owned & ghost atoms, storing neighbors
+  for (i = 0; i < nall; i++) {
+    n = 0;
+    neighptr = ipage->vget();
+
+    itype = type[i];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    if (moltemplate) {
+      imol = molindex[i];
+      iatom = molatom[i];
+      tagprev = tag[i] - iatom - 1;
+    }
+
+    // loop over all atoms, owned and ghost
+    // Full:
+    //   skip i = j
+    // Half:
+    //   only store pair if i < j
+    //   stores own/own pairs only once
+    //   stores own/ghost pairs with owned atom only, on both procs
+    //   stores ghost/ghost pairs only once
+    // no molecular test when i = ghost atom
+
+    if (!HALF) jstart = 0;
+    else jstart = i + 1;
+
+    if (i < nlocal) {
+      for (j = jstart; j < nall; j++) {
+        if (includegroup && !(mask[j] & bitmask)) continue; // JTC: missing in original full version
+        if (!HALF) {
+          if (i == j) continue;
+        }
+
+        jtype = type[j];
+        if (exclude && exclusion(i,j,itype,jtype,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;
+
+        if (rsq <= cutneighsq[itype][jtype]) {
+          if (molecular != Atom::ATOMIC) {
+            if (!moltemplate)
+              which = find_special(special[i],nspecial[i],tag[j]);
+            else if (imol >= 0)
+              which = find_special(onemols[imol]->special[iatom],
+                                   onemols[imol]->nspecial[iatom],
+                                   tag[j]-tagprev);
+            else which = 0;
+            if (which == 0) neighptr[n++] = j;
+            else if (domain->minimum_image_check(delx,dely,delz))
+              neighptr[n++] = j;
+            else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
+          } else neighptr[n++] = j;
+        }
+      }
+    } else {
+      for (j = jstart; j < nall; j++) {
+        if (includegroup && !(mask[j] & bitmask)) continue; // JTC: missing in original full version
+        if (!HALF) {
+          if (i == j) continue;
+        }
+
+        jtype = type[j];
+        if (exclude && exclusion(i,j,itype,jtype,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;
+
+        if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
+      }
+    }
+
+    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 = atom->nlocal;
+  list->gnum = inum - atom->nlocal;
+}
+
+namespace LAMMPS_NS {
+template class NPairNsqGhost<0>;
+template class NPairNsqGhost<1>;
+}