Adding other nstencil classes

src/nstencil_bin.cpp

@@ -28,8 +28,7 @@ NStencilBin<HALF, DIM_3D, TRI>::NStencilBin(LAMMPS *lmp) : NStencil(lmp) {}
 template<int HALF, int DIM_3D, int TRI>
 void NStencilBin<HALF, DIM_3D, TRI>::create()
 {
-  int i,j,k;
+  int i, j, k;
-  bool bin_include;
 
   // For half stencils, only the upper plane is needed
   int sy_min = sy;
@@ -55,7 +54,7 @@ void NStencilBin<HALF, DIM_3D, TRI>::create()
           if (! (k > 0 || j > 0 || (j == 0 && i > 0))) continue;
 
         if (bin_distance(i,j,k) < cutneighmaxsq)
-          stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+          stencil[nstencil++] = k * mbiny * mbinx + j * mbinx + i;
       }
     }
   }

src/nstencil_ghost_bin.cpp

@@ -0,0 +1,73 @@
+// 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 "nstencil_ghost_bin.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+template<int HALF, int DIM_3D, int TRI>
+NStencilGhostBin<HALF, DIM_3D, TRI>::NStencilGhostBin(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+   create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+template<int HALF, int DIM_3D, int TRI>
+void NStencilGhostBin<HALF, DIM_3D, TRI>::create()
+{
+  int i, j, k;
+
+  // For half stencils, only the upper plane is needed
+  int sy_min = sy;
+  int sz_min = sz;
+  if (HALF && (!DIM_3D)) sy_min = 0;
+  if (HALF && DIM_3D) sz_min = 0;
+
+  nstencil = 0;
+
+  // Half and ortho stencils include central bin first
+  // This preserves the historical order of the neighbor list
+  // as the old npair classes used to separately parse the central bin first
+  if (HALF && (!TRI)) stencil[nstencil++] = 0;
+
+  for (k = -sz_min; k <= sz; k++) {
+    for (j = -sy_min; j <= sy; j++) {
+      for (i = -sx; i <= sx; i++) {
+
+        // Now only include "upper right" bins for half and ortho stencils
+        if (HALF && (!DIM_3D) && (!TRI))
+          if (! (j > 0 || (j == 0 && i > 0))) continue;
+        if (HALF && DIM_3D && (!TRI))
+          if (! (k > 0 || j > 0 || (j == 0 && i > 0))) continue;
+
+        if (bin_distance(i,j,k) < cutneighmaxsq)
+          stencilxyz[nstencil][0] = i;
+          stencilxyz[nstencil][1] = j;
+          stencilxyz[nstencil][2] = k;
+          stencil[nstencil++] = k * mbiny * mbinx + j * mbinx + i;
+      }
+    }
+  }
+}
+
+namespace LAMMPS_NS {
+template class NStencilGhostBin<0,0,0>;
+template class NStencilGhostBin<0,1,0>;
+template class NStencilGhostBin<1,0,0>;
+template class NStencilGhostBin<1,0,1>;
+template class NStencilGhostBin<1,1,0>;
+template class NStencilGhostBin<1,1,1>;
+}

src/nstencil_ghost_bin.h

@@ -0,0 +1,69 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+// clang-format off
+typedef NStencilGhostBin<0, 0, 0> NStencilFullGhostBin2d;
+NStencilStyle(full/ghost/bin/2d,
+              NStencilFullGhostBin2d,
+              NS_FULL | NS_GhostBin | NS_2D | NS_ORTHO | NS_TRI);
+
+typedef NStencilGhostBin<0, 1, 0> NStencilFullGhostBin3d;
+NStencilStyle(full/ghost/bin/3d,
+              NStencilFullGhostBin3d,
+              NS_FULL | NS_GhostBin | NS_3D | NS_ORTHO | NS_TRI);
+
+typedef NStencilGhostBin<1, 0, 0> NStencilHalfGhostBin2d;
+NStencilStyle(half/ghost/bin/2d,
+              NStencilHalfGhostBin2d,
+              NS_HALF | NS_GhostBin | NS_2D | NS_ORTHO);
+
+typedef NStencilGhostBin<1, 0, 1> NStencilHalfGhostBin2dTri;
+NStencilStyle(half/ghost/bin/2d/tri,
+              NStencilHalfGhostBin2dTri,
+              NS_HALF | NS_GhostBin | NS_2D | NS_TRI);
+
+typedef NStencilGhostBin<1, 1, 0> NStencilHalfGhostBin3d;
+NStencilStyle(half/ghost/bin/3d,
+              NStencilHalfGhostBin3d,
+              NS_HALF | NS_GhostBin | NS_3D | NS_ORTHO);
+
+typedef NStencilGhostBin<1, 1, 1> NStencilHalfGhostBin3dTri;
+NStencilStyle(half/ghost/bin/3d/tri,
+              NStencilHalfGhostBin3dTri,
+              NS_HALF | NS_GhostBin | NS_3D | NS_TRI);
+// clang-format on
+#else
+
+#ifndef LMP_NSTENCIL_GHOST_BIN_H
+#define LMP_NSTENCIL_GHOST_BIN_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+template<int HALF, int DIM_3D, int TRI>
+class NStencilGhostBin : public NStencil {
+ public:
+  NStencilGhostBin(class LAMMPS *);
+  void create() override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/

src/nstencil_multi.cpp

@@ -0,0 +1,133 @@
+// 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 "nstencil_multi.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+template<int HALF, int DIM_3D, int TRI>
+NStencilMulti<HALF, DIM_3D, TRI>::NStencilMulti(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+template<int HALF, int DIM_3D, int TRI>
+void NStencilMulti<HALF, DIM_3D, TRI>::set_stencil_properties()
+{
+  int n = ncollections;
+  int i, j;
+
+  // FULL
+  // Always look up neighbor using full stencil and neighbor's bin
+  // Stencil cutoff set by i-j cutoff
+
+  // HALF
+  // Cross collections: use full stencil, looking one way through hierarchy
+  // smaller -> larger => use full stencil in larger bin
+  // larger -> smaller => no nstencil required
+  // If cut offs are same, use half stencil
+
+  for (i = 0; i < n; i++) {
+    for (j = 0; j < n; j++) {
+      if (HALF)
+        if (cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue;
+
+      flag_skip_multi[i][j] = false;
+      flag_half_multi[i][j] = false;
+      bin_collection_multi[i][j] = j;
+
+      if (HALF) {
+        if (cutcollectionsq[i][i] == cutcollectionsq[j][j]) {
+          flag_half_multi[i][j] = true;
+          bin_collection_multi[i][j] = i;
+        }
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+template<int HALF, int DIM_3D, int TRI>
+void NStencilMulti<HALF, DIM_3D, TRI>::create()
+{
+  int icollection, jcollection, bin_collection, i, j, k, ns, half_flag;
+  int n = ncollections;
+  double cutsq;
+
+  // For half stencils, only the upper plane is needed
+  int sy_min = sy;
+  int sz_min = sz;
+  if (HALF && (!DIM_3D)) sy_min = 0;
+  if (HALF && DIM_3D) sz_min = 0;
+
+  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];
+
+      half_flag = flag_half_multi[icollection][jcollection];
+
+      // Half and ortho stencils include central bin first
+      // This preserves the historical order of the neighbor list
+      // as the old npair classes used to separately parse the central bin first
+      if (half_flag && (!TRI)) stencil[nstencil++] = 0;
+
+      for (k = -sz_min; k <= sz; k++) {
+        for (j = -sy_min; j <= sy; j++) {
+          for (i = -sx; i <= sx; i++) {
+
+            // Now only include "upper right" bins for half and ortho stencils
+            if (half_flag && (!DIM_3D) && (!TRI))
+              if (! (j > 0 || (j == 0 && i > 0))) continue;
+            if (half_flag && DIM_3D && (!TRI))
+              if (! (k > 0 || j > 0 || (j == 0 && i > 0))) continue;
+
+            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;
+    }
+  }
+}
+
+namespace LAMMPS_NS {
+template class NStencilMulti<0,0,0>;
+template class NStencilMulti<0,1,0>;
+template class NStencilMulti<1,0,0>;
+template class NStencilMulti<1,0,1>;
+template class NStencilMulti<1,1,0>;
+template class NStencilMulti<1,1,1>;
+}

src/nstencil_multi.h

@@ -0,0 +1,72 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+// clang-format off
+typedef NStencilMulti<0, 0, 0> NStencilFullMulti2d;
+NStencilStyle(full/multi/2d,
+              NStencilFullMulti2d,
+              NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI);
+
+typedef NStencilMulti<0, 1, 0> NStencilFullMulti3d;
+NStencilStyle(full/multi/3d,
+              NStencilFullMulti3d,
+              NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI);
+
+typedef NStencilMulti<1, 0, 0> NStencilHalfMulti2d;
+NStencilStyle(half/multi/2d,
+              NStencilHalfMulti2d,
+              NS_HALF | NS_MULTI | NS_2D | NS_ORTHO);
+
+typedef NStencilMulti<1, 0, 1> NStencilHalfMulti2dTri;
+NStencilStyle(half/multi/2d/tri,
+              NStencilHalfMulti2dTri,
+              NS_HALF | NS_MULTI | NS_2D | NS_TRI);
+
+typedef NStencilMulti<1, 1, 0> NStencilHalfMulti3d;
+NStencilStyle(half/multi/3d,
+              NStencilHalfMulti3d,
+              NS_HALF | NS_MULTI | NS_3D | NS_ORTHO);
+
+typedef NStencilMulti<1, 1, 1> NStencilHalfMulti3dTri;
+NStencilStyle(half/multi/3d/tri,
+              NStencilHalfMulti3dTri,
+              NS_HALF | NS_MULTI | NS_3D | NS_TRI);
+// clang-format on
+#else
+
+#ifndef LMP_NSTENCIL_MULTI_H
+#define LMP_NSTENCIL_MULTI_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+template<int HALF, int DIM_3D, int TRI>
+class NStencilMulti : public NStencil {
+ public:
+  NStencilMulti(class LAMMPS *);
+  void create() override;
+
+ protected:
+  void set_stencil_properties() override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/

src/nstencil_multi_old.cpp

@@ -0,0 +1,85 @@
+// 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 "nstencil_multi_old.h"
+#include "atom.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+template<int HALF, int DIM_3D, int TRI>
+NStencilMultiOld<HALF, DIM_3D, TRI>::NStencilMultiOld(LAMMPS *lmp) : NStencil(lmp) {}
+
+/* ----------------------------------------------------------------------
+   create stencil based on bin geometry and cutoff
+------------------------------------------------------------------------- */
+
+template<int HALF, int DIM_3D, int TRI>
+void NStencilMultiOld<HALF, DIM_3D, TRI>::create()
+{
+  int i, j, k, n, itype;
+  double rsq, typesq;
+  int *s;
+  double *distsq;
+  int ntypes = atom->ntypes;
+
+  // For half stencils, only the upper plane is needed
+  int sy_min = sy;
+  int sz_min = sz;
+  if (HALF && (!DIM_3D)) sy_min = 0;
+  if (HALF && DIM_3D) sz_min = 0;
+
+  for (itype = 1; itype <= ntypes; itype++) {
+
+    typesq = cuttypesq[itype];
+    s = stencil_multi_old[itype];
+    distsq = distsq_multi_old[itype];
+    n = 0;
+
+    // Half and ortho stencils include central bin first
+    // This preserves the historical order of the neighbor list
+    // as the old npair classes used to separately parse the central bin first
+    if (HALF && (!TRI)) s[n++] = 0;
+
+    for (k = -sz_min; k <= sz; k++) {
+      for (j = -sy_min; j <= sy; j++) {
+        for (i = -sx; i <= sx; i++) {
+
+          // Now only include "upper right" bins for half and ortho stencils
+          if (HALF && (!DIM_3D) && (!TRI))
+            if (! (j > 0 || (j == 0 && i > 0))) continue;
+          if (HALF && DIM_3D && (!TRI))
+            if (! (k > 0 || j > 0 || (j == 0 && i > 0))) continue;
+
+          rsq = bin_distance(i, j, 0);
+          if (rsq < typesq) {
+            distsq[n] = rsq;
+            s[n++] = k * mbiny * mbinx + j * mbinx + i;
+          }
+        }
+      }
+    }
+    nstencil_multi_old[itype] = n;
+  }
+}
+
+namespace LAMMPS_NS {
+template class NStencilMultiOld<0,0,0>;
+template class NStencilMultiOld<0,1,0>;
+template class NStencilMultiOld<1,0,0>;
+template class NStencilMultiOld<1,0,1>;
+template class NStencilMultiOld<1,1,0>;
+template class NStencilMultiOld<1,1,1>;
+}

src/nstencil_multi_old.h

@@ -0,0 +1,69 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef NSTENCIL_CLASS
+// clang-format off
+typedef NStencilMultiOld<0, 0, 0> NStencilFullMultiOld2d;
+NStencilStyle(full/multi/old/2d,
+              NStencilFullMultiOld2d,
+              NS_FULL | NS_MULTI_OLD | NS_2D | NS_ORTHO | NS_TRI);
+
+typedef NStencilMultiOld<0, 1, 0> NStencilFullMultiOld3d;
+NStencilStyle(full/multi/old/3d,
+              NStencilFullMultiOld3d,
+              NS_FULL | NS_MULTI_OLD | NS_3D | NS_ORTHO | NS_TRI);
+
+typedef NStencilMultiOld<1, 0, 0> NStencilHalfMultiOld2d;
+NStencilStyle(half/multi/old/2d,
+              NStencilHalfMultiOld2d,
+              NS_HALF | NS_MULTI_OLD | NS_2D | NS_ORTHO);
+
+typedef NStencilMultiOld<1, 0, 1> NStencilHalfMultiOld2dTri;
+NStencilStyle(half/multi/old/2d/tri,
+              NStencilHalfMultiOld2dTri,
+              NS_HALF | NS_MULTI_OLD | NS_2D | NS_TRI);
+
+typedef NStencilMultiOld<1, 1, 0> NStencilHalfMultiOld3d;
+NStencilStyle(half/multi/old/3d,
+              NStencilHalfMultiOld3d,
+              NS_HALF | NS_MULTI_OLD | NS_3D | NS_ORTHO);
+
+typedef NStencilMultiOld<1, 1, 1> NStencilHalfMultiOld3dTri;
+NStencilStyle(half/multi/old/3d/tri,
+              NStencilHalfMultiOld3dTri,
+              NS_HALF | NS_MULTI_OLD | NS_3D | NS_TRI);
+// clang-format on
+#else
+
+#ifndef LMP_NSTENCIL_MULTI_OLD_H
+#define LMP_NSTENCIL_MULTI_OLD_H
+
+#include "nstencil.h"
+
+namespace LAMMPS_NS {
+
+template<int HALF, int DIM_3D, int TRI>
+class NStencilMultiOld : public NStencil {
+ public:
+  NStencilMultiOld(class LAMMPS *);
+  void create() override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/