Merge branch 'master' into prepare-clang-format

# Conflicts:
#	src/KOKKOS/nbin_kokkos.h
#	src/KOKKOS/nbin_ssa_kokkos.h
#	src/MOLECULE/bond_fene_expand.h
#	src/USER-DPD/nbin_ssa.h
#	src/USER-DPD/nstencil_half_bin_2d_ssa.h
#	src/USER-DPD/nstencil_half_bin_3d_ssa.h
#	src/USER-INTEL/nbin_intel.h
#	src/USER-MISC/fix_propel_self.cpp
#	src/USER-OMP/npair_full_multi_old_omp.h
#	src/USER-OMP/npair_half_multi_old_newton_omp.h
#	src/USER-OMP/npair_half_size_multi_newtoff_omp.h
#	src/USER-OMP/npair_halffull_newtoff_omp.h
#	src/USER-OMP/npair_halffull_newton_omp.h
#	src/USER-OMP/npair_skip_omp.h
#	src/main.cpp
#	src/nbin_standard.h
#	src/npair_full_multi_old.h
#	src/npair_halffull_newtoff.h
#	src/npair_halffull_newton.h
#	src/npair_skip.h
#	src/npair_skip_respa.h
#	src/npair_skip_size.h
#	src/npair_skip_size_off2on.h
#	src/npair_skip_size_off2on_oneside.h
#	src/nstencil_full_bin_2d.h
#	src/nstencil_full_bin_3d.h
#	src/nstencil_full_ghost_bin_2d.h
#	src/nstencil_full_ghost_bin_3d.h
#	src/nstencil_full_multi_2d.h
#	src/nstencil_full_multi_3d.h
#	src/nstencil_full_multi_old_2d.h
#	src/nstencil_full_multi_old_3d.h
#	src/nstencil_half_bin_2d_newtoff.cpp
#	src/nstencil_half_bin_3d_newtoff.cpp
#	src/nstencil_half_bin_3d_newton_tri.h
#	src/nstencil_half_ghost_bin_2d_newtoff.cpp
#	src/nstencil_half_ghost_bin_2d_newtoff.h
#	src/nstencil_half_ghost_bin_3d_newtoff.cpp
#	src/nstencil_half_ghost_bin_3d_newtoff.h
#	src/nstencil_half_multi_2d.h
#	src/nstencil_half_multi_2d_newtoff.h
#	src/nstencil_half_multi_2d_newton_tri.h
#	src/nstencil_half_multi_2d_tri.h
#	src/nstencil_half_multi_3d_newtoff.h
#	src/nstencil_half_multi_3d_newton_tri.h

src/nstencil_full_multi_3d.cpp

@@ -13,7 +13,12 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_full_multi_3d.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "nbin.h"
+#include "memory.h"
 #include "atom.h"
+#include <math.h>
 
 using namespace LAMMPS_NS;
 
@@ -21,32 +26,65 @@ using namespace LAMMPS_NS;
 
 NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {}
 
+/* ---------------------------------------------------------------------- */
+
+void NStencilFullMulti3d::set_stencil_properties()
+{
+  int n = ncollections;
+  int i, j;
+
+  // Always look up neighbor using full stencil and neighbor's bin
+  // Stencil cutoff set by i-j cutoff
+
+  for (i = 0; i < n; i++) {
+    for (j = 0; j < n; j++) {
+      flag_half_multi[i][j] = 0;
+      flag_skip_multi[i][j] = 0;
+      bin_collection_multi[i][j] = j;
+    }
+  }
+}
+
 /* ----------------------------------------------------------------------
-   create stencil based on bin geometry and cutoff
+   create stencils based on bin geometry and cutoff
 ------------------------------------------------------------------------- */
 
 void NStencilFullMulti3d::create()
 {
-  int i,j,k,n;
-  double rsq,typesq;
-  int *s;
-  double *distsq;
+  int icollection, jcollection, bin_collection, i, j, k, ns;
+  int n = ncollections;
+  double cutsq;
 
-  int ntypes = atom->ntypes;
-  for (int itype = 1; itype <= ntypes; itype++) {
-    typesq = cuttypesq[itype];
-    s = stencil_multi[itype];
-    distsq = distsq_multi[itype];
-    n = 0;
-    for (k = -sz; k <= sz; k++)
-      for (j = -sy; j <= sy; j++)
-        for (i = -sx; i <= sx; i++) {
-          rsq = bin_distance(i,j,k);
-          if (rsq < typesq) {
-            distsq[n] = rsq;
-            s[n++] = k*mbiny*mbinx + j*mbinx + i;
-          }
-        }
-    nstencil_multi[itype] = n;
+
+  for (icollection = 0; icollection < n; icollection++) {
+    for (jcollection = 0; jcollection < n; jcollection++) {
+      if (flag_skip_multi[icollection][jcollection]) {
+        nstencil_multi[icollection][jcollection] = 0;
+        continue;
+      }
+
+      ns = 0;
+
+      sx = stencil_sx_multi[icollection][jcollection];
+      sy = stencil_sy_multi[icollection][jcollection];
+      sz = stencil_sz_multi[icollection][jcollection];
+
+      mbinx = stencil_mbinx_multi[icollection][jcollection];
+      mbiny = stencil_mbiny_multi[icollection][jcollection];
+      mbinz = stencil_mbinz_multi[icollection][jcollection];
+
+      bin_collection = bin_collection_multi[icollection][jcollection];
+
+      cutsq = cutcollectionsq[icollection][jcollection];
+
+      for (k = -sz; k <= sz; k++)
+        for (j = -sy; j <= sy; j++)
+          for (i = -sx; i <= sx; i++)
+	        if (bin_distance_multi(i,j,k,bin_collection) < cutsq)
+	          stencil_multi[icollection][jcollection][ns++] =
+                      k*mbiny*mbinx + j*mbinx + i;
+
+      nstencil_multi[icollection][jcollection] = ns;
+    }
   }
 }