diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/USER-DPD/nbin_ssa.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d55acb6040cf2fc3e9e0d4b1605449c2e510d326
--- /dev/null
+++ b/src/USER-DPD/nbin_ssa.cpp
@@ -0,0 +1,129 @@
+/* ----------------------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ James Larentzos (ARL) and Timothy I. Mattox (Engility Corporation)
+------------------------------------------------------------------------- */
+
+#include "nbin_ssa.h"
+#include "atom.h"
+#include "group.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NBinSSA::NBinSSA(LAMMPS *lmp) : NBinStandard(lmp)
+{
+ maxbin_ssa = 0;
+ bins_ssa = NULL;
+ maxhead_ssa = 0;
+ binhead_ssa = NULL;
+ gbinhead_ssa = NULL;
+}
+
+NBinSSA::~NBinSSA()
+{
+ memory->destroy(bins_ssa);
+ memory->destroy(binhead_ssa);
+ memory->destroy(gbinhead_ssa);
+}
+
+/* ----------------------------------------------------------------------
+ bin owned and ghost atoms for the Shardlow Splitting Algorithm (SSA)
+ local atoms are in distinct bins (binhead_ssa) from the ghosts
+ ghost atoms are in distinct bins (gbinhead_ssa) from the locals
+ ghosts which are not in an Active Interaction Region (AIR) are skipped
+------------------------------------------------------------------------- */
+
+void NBinSSA::bin_atoms()
+{
+ int i,ibin;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ if (includegroup) nlocal = atom->nfirst;
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int *ssaAIR = atom->ssaAIR;
+
+ for (i = 0; i < mbins; i++) {
+ gbinhead_ssa[i] = -1;
+ binhead_ssa[i] = -1;
+ }
+
+ // bin in reverse order so linked list will be in forward order
+
+ if (includegroup) {
+ int bitmask = group->bitmask[includegroup];
+ int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
+ for (i = nall-1; i >= nowned; i--) {
+ if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
+ if (mask[i] & bitmask) {
+ ibin = coord2bin(x[i]);
+ bins_ssa[i] = gbinhead_ssa[ibin];
+ gbinhead_ssa[ibin] = i;
+ }
+ }
+ } else {
+ for (i = nall-1; i >= nlocal; i--) {
+ if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
+ ibin = coord2bin(x[i]);
+ bins_ssa[i] = gbinhead_ssa[ibin];
+ gbinhead_ssa[ibin] = i;
+ }
+ }
+ for (i = nlocal-1; i >= 0; i--) {
+ ibin = coord2bin(x[i]);
+ bins_ssa[i] = binhead_ssa[ibin];
+ binhead_ssa[ibin] = i;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NBinSSA::bin_atoms_setup(int nall)
+{
+ NBinStandard::bin_atoms_setup(nall); // Setup the parent class's data too
+
+ if (mbins > maxhead_ssa) {
+ maxhead_ssa = mbins;
+ memory->destroy(gbinhead_ssa);
+ memory->destroy(binhead_ssa);
+ memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa");
+ memory->create(gbinhead_ssa,maxhead_ssa,"gbinhead_ssa");
+ }
+
+ if (nall > maxbin_ssa) {
+ maxbin_ssa = nall;
+ memory->destroy(bins_ssa);
+ memory->create(bins_ssa,maxbin_ssa,"bins_ssa");
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint NBinSSA::memory_usage()
+{
+ bigint bytes = NBinStandard::memory_usage(); // Count the parent's usage too
+
+ if (maxbin_ssa) bytes += memory->usage(bins_ssa,maxbin_ssa);
+ if (maxhead_ssa) {
+ bytes += memory->usage(binhead_ssa,maxhead_ssa);
+ bytes += memory->usage(gbinhead_ssa,maxhead_ssa);
+ }
+ return bytes;
+}
+
diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h
new file mode 100644
index 0000000000000000000000000000000000000000..f0699b3a7ae2298204cacb769b9d9bb6d53e39cf
--- /dev/null
+++ b/src/USER-DPD/nbin_ssa.h
@@ -0,0 +1,54 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+#ifdef NBIN_CLASS
+
+NBinStyle(ssa,
+ NBinSSA,
+ NB_SSA)
+
+#else
+
+#ifndef LMP_NBIN_SSA_H
+#define LMP_NBIN_SSA_H
+
+#include "nbin_standard.h"
+
+namespace LAMMPS_NS {
+
+class NBinSSA : public NBinStandard {
+ public:
+
+ int *bins_ssa; // index of next atom in each bin
+ int maxbin_ssa; // size of bins_ssa array
+ int *binhead_ssa; // index of 1st local atom in each bin
+ int *gbinhead_ssa; // index of 1st ghost atom in each bin
+ int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays
+
+ NBinSSA(class LAMMPS *);
+ ~NBinSSA();
+
+ void bin_atoms_setup(int);
+ void bin_atoms();
+
+ bigint memory_usage();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
index b529121a0ac301971da48095b7c751dbcac79e0b..e41b9d4276180b4f9e58e60723d00b64c417ab57 100644
--- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp
+++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
@@ -18,6 +18,7 @@
#include "npair_half_bin_newton_ssa.h"
#include "neighbor.h"
+#include "nbin_ssa.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
@@ -78,71 +79,13 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
- int inum = 0;
-
- // bin owned and ghost atoms for use by Shardlow Splitting Algorithm
- // exclude ghost atoms that are not in the Active Interaction Regions (AIR)
-
- // NOTE to Tim: this binatomflag no longer exists
- // the logic up higher assures that binning has been done
- // before this build() method is called
- // maybe this code below needs to be in a new NBinShardlow class?
- // this class also inherits NPair::nb from its parent
- // which points to the NBin class that did the binning
- // there are last_step variables stored there which indicate
- // the last time binning was done
- // the basic question is what data is created/stored by SSA binning
- // and in what class should it live?
- // if it is created by the binning operation, then I think
- // it should be in a new NBinShardlow class
-
- if (true /* binatomflag */) { // only false in Neighbor::build_one
-
- if (mbins > list->maxhead_ssa) {
- list->maxhead_ssa = mbins;
- memory->destroy(list->gbinhead_ssa);
- memory->destroy(list->binhead_ssa);
- memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa");
- memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa");
- }
- for (i = 0; i < mbins; i++) {
- list->gbinhead_ssa[i] = -1;
- list->binhead_ssa[i] = -1;
- }
-
- if (nall > list->maxbin_ssa) {
- list->maxbin_ssa = nall;
- memory->destroy(list->bins_ssa);
- memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
- }
+ NBinSSA *nb_ssa = dynamic_cast<NBinSSA*>(nb);
+ if (!nb_ssa) error->one(FLERR, "NBin wasn't a NBinSSA object");
+ int *bins_ssa = nb_ssa->bins_ssa;
+ int *binhead_ssa = nb_ssa->binhead_ssa;
+ int *gbinhead_ssa = nb_ssa->gbinhead_ssa;
- // bin in reverse order so linked list will be in forward order
-
- if (includegroup) {
- int bitmask = group->bitmask[includegroup];
- int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
- for (i = nall-1; i >= nowned; i--) {
- if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
- if (mask[i] & bitmask) {
- ibin = coord2bin(x[i]);
- list->bins_ssa[i] = list->gbinhead_ssa[ibin];
- list->gbinhead_ssa[ibin] = i;
- }
- }
- } else {
- for (i = nall-1; i >= nlocal; i--) {
- if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
- ibin = coord2bin(x[i]);
- list->bins_ssa[i] = list->gbinhead_ssa[ibin];
- list->gbinhead_ssa[ibin] = i;
- }
- }
- for (i = nlocal-1; i >= 0; i--) {
- ibin = coord2bin(x[i]);
- list->bins_ssa[i] = list->binhead_ssa[ibin];
- list->binhead_ssa[ibin] = i;
- }
- } // else reuse previous binning. See Neighbor::build_one comment
+ int inum = 0;
ipage->reset();
@@ -166,7 +109,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
// loop over rest of local atoms in i's bin
// just store them, since j is beyond i in linked list
- for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) {
+ for (j = bins_ssa[i]; j >= 0; j = bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -198,8 +141,8 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
// loop over all local atoms in other bins in "half" stencil
for (k = 0; k < nstencil; k++) {
- for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0;
- j = list->bins_ssa[j]) {
+ for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -234,8 +177,8 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
// Note2: only non-pure locals can have ghosts as neighbors
if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) {
- for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0;
- j = list->bins_ssa[j]) {
+ for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
+ j = bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 2a29c34565d1bb16c121a58b36dc3a5145622518..dfab9b023ac6c3b1606886fd30bd2cb2e8bf78f6 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -70,11 +70,6 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
// USER-DPD package
ndxAIR_ssa = NULL;
- maxbin_ssa = 0;
- bins_ssa = NULL;
- maxhead_ssa = 0;
- binhead_ssa = NULL;
- gbinhead_ssa = NULL;
}
/* ---------------------------------------------------------------------- */
@@ -96,9 +91,6 @@ NeighList::~NeighList()
if (ssa) {
memory->sfree(ndxAIR_ssa);
- memory->destroy(bins_ssa);
- memory->destroy(binhead_ssa);
- memory->destroy(gbinhead_ssa);
}
}
@@ -308,11 +300,6 @@ bigint NeighList::memory_usage()
}
if (ndxAIR_ssa) bytes += sizeof(uint16_t) * 8 * maxatom;
- if (maxbin_ssa) bytes += memory->usage(bins_ssa,maxbin_ssa);
- if (maxhead_ssa) {
- bytes += memory->usage(binhead_ssa,maxhead_ssa);
- bytes += memory->usage(gbinhead_ssa,maxhead_ssa);
- }
return bytes;
}
diff --git a/src/neigh_list.h b/src/neigh_list.h
index 232892f8b407ec0d68b5cda22f2c9282558240b3..d3bde212c25c1294686eb0a48ed1fdfc4c071a7a 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -72,11 +72,6 @@ class NeighList : protected Pointers {
// USER-DPD package and Shardlow Splitting Algorithm (SSA) support
uint16_t (*ndxAIR_ssa)[8]; // for each atom, last neighbor index of each AIR
- int *bins_ssa; // index of next atom in each bin
- int maxbin_ssa; // size of bins_ssa array
- int *binhead_ssa; // index of 1st local atom in each bin
- int *gbinhead_ssa; // index of 1st ghost atom in each bin
- int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays
// methods