From ea39843564417b2905e31c9c5f9a58f24d7692ee Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 15 Jul 2016 23:14:13 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15329
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/neigh_list.cpp | 26 ++++++++++
src/neigh_list.h | 10 ++++
src/neigh_shardlow.cpp | 107 ++++++++++++++++++++++++++++++-----------
src/neighbor.cpp | 27 ++---------
src/neighbor.h | 8 ---
5 files changed, 117 insertions(+), 61 deletions(-)
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 9be7c33a81..dfdd0f33a8 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -57,6 +57,14 @@ NeighList::NeighList(LAMMPS *lmp) :
listcopy = NULL;
listskip = NULL;
+ // USER-DPD package
+ ndxAIR_ssa = NULL;
+ maxbin_ssa = 0;
+ bins_ssa = NULL;
+ maxhead_ssa = 0;
+ binhead_ssa = NULL;
+ gbinhead_ssa = NULL;
+
maxstencil = ghostflag = 0;
stencil = NULL;
stencilxyz = NULL;
@@ -89,6 +97,12 @@ NeighList::~NeighList()
if (maxstencil) memory->destroy(stencil);
if (ghostflag) memory->destroy(stencilxyz);
+ if (ndxAIR_ssa) memory->sfree(ndxAIR_ssa);
+ if (maxbin_ssa) memory->destroy(bins_ssa);
+ if (maxhead_ssa) {
+ memory->destroy(binhead_ssa);
+ memory->destroy(gbinhead_ssa);
+ }
if (maxstencil_multi) {
for (int i = 1; i <= atom->ntypes; i++) {
@@ -148,6 +162,11 @@ void NeighList::grow(int nmax)
if (dnum)
firstdouble = (double **) memory->smalloc(maxatoms*sizeof(double *),
"neighlist:firstdouble");
+ if (ssaflag) {
+ if (ndxAIR_ssa) memory->sfree(ndxAIR_ssa);
+ ndxAIR_ssa = (uint16_t (*)[8]) memory->smalloc(sizeof(uint16_t)*8*maxatoms,
+ "neighlist:ndxAIR_ssa");
+ }
}
/* ----------------------------------------------------------------------
@@ -229,6 +248,7 @@ void NeighList::print_attributes()
printf(" %d = grow flag\n",growflag);
printf(" %d = stencil flag\n",stencilflag);
printf(" %d = ghost flag\n",ghostflag);
+ printf(" %d = ssa flag\n",ssaflag);
printf("\n");
printf(" %d = pair\n",rq->pair);
printf(" %d = fix\n",rq->fix);
@@ -290,6 +310,12 @@ bigint NeighList::memory_usage()
if (maxstencil) bytes += memory->usage(stencil,maxstencil);
if (ghostflag) bytes += memory->usage(stencilxyz,maxstencil,3);
+ if (ndxAIR_ssa) bytes += sizeof(uint16_t) * 8 * maxatoms;
+ 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);
+ }
if (maxstencil_multi) {
bytes += memory->usage(stencil_multi,atom->ntypes,maxstencil_multi);
diff --git a/src/neigh_list.h b/src/neigh_list.h
index a268dee468..d76682dfc4 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -65,6 +65,16 @@ class NeighList : protected Pointers {
NeighList *listcopy; // me = copy list, point to list I copy from
NeighList *listskip; // me = skip list, point to list I skip from
+ // USER-DPD package and Shardlow Splitting Algorithm (SSA) support
+
+ int ssaflag; // 1 if the list has the ndxAIR_ssa array
+ 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
+
// stencils of bin indices for neighbor finding
int maxstencil; // max size of stencil
diff --git a/src/neigh_shardlow.cpp b/src/neigh_shardlow.cpp
index 3a1246684b..1b87ab65d7 100644
--- a/src/neigh_shardlow.cpp
+++ b/src/neigh_shardlow.cpp
@@ -107,6 +107,20 @@ void Neighbor::stencil_half_bin_3d_ssa(NeighList *list,
}
}
+// space for static variable ssaAIRptr so it
+// can be used in qsort's compair function "cmp_ssaAIR()"
+static int *ssaAIRptr;
+
+static int cmp_ssaAIR(const void *iptr, const void *jptr)
+{
+ int i = *((int *) iptr);
+ int j = *((int *) jptr);
+ if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
+ if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
+ return 0;
+}
+
+
/* ----------------------------------------------------------------------
build half list from full list for use by Shardlow Spliting Algorithm
pair stored once if i,j are both owned and i < j
@@ -138,6 +152,7 @@ void Neighbor::half_from_full_newton_ssa(NeighList *list)
// loop over parent full list
for (ii = 0; ii < inum_full; ii++) {
+ int AIRct[8] = { 0 };
n = 0;
neighptr = ipage->vget();
@@ -153,8 +168,10 @@ void Neighbor::half_from_full_newton_ssa(NeighList *list)
j = joriginal & NEIGHMASK;
if (j < nlocal) {
if (i > j) continue;
+ ++(AIRct[0]);
} else {
- if (ssaAIR[j] <= 0) continue;
+ if (ssaAIR[j] < 2) continue; // skip ghost atoms not in AIR
+ ++(AIRct[ssaAIR[j] - 1]);
}
neighptr[n++] = joriginal;
}
@@ -165,6 +182,16 @@ void Neighbor::half_from_full_newton_ssa(NeighList *list)
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ // sort the locals+ghosts in the neighbor list by their ssaAIR number
+ ssaAIRptr = atom->ssaAIR;
+ qsort(&(neighptr[0]), n, sizeof(int), cmp_ssaAIR);
+
+ // Do a prefix sum on the counts to turn them into indexes.
+ list->ndxAIR_ssa[i][0] = AIRct[0];
+ for (int ndx = 1; ndx < 8; ++ndx) {
+ list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
+ }
}
list->inum = inum;
@@ -218,22 +245,22 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
exclude ghost atoms that are not in the Active Interaction Regions (AIR)
------------------------------------------------------------------------- */
- 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 (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++) {
- gbinhead_ssa[i] = -1;
- binhead_ssa[i] = -1;
+ list->gbinhead_ssa[i] = -1;
+ list->binhead_ssa[i] = -1;
}
- if (maxbin > maxbin_ssa) {
- maxbin_ssa = maxbin;
- memory->destroy(bins_ssa);
- memory->create(bins_ssa,maxbin_ssa,"bins_ssa");
+ if (maxbin > list->maxbin_ssa) {
+ list->maxbin_ssa = maxbin;
+ memory->destroy(list->bins_ssa);
+ memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
}
// bin in reverse order so linked list will be in forward order
@@ -241,26 +268,26 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
if (includegroup) {
int bitmask = group->bitmask[includegroup];
for (i = nall-1; i >= nlocal; i--) {
- if (ssaAIR[i] <= 0) continue; // skip ghost atoms not in AIR
+ 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;
+ list->bins_ssa[i] = list->gbinhead_ssa[ibin];
+ list->gbinhead_ssa[ibin] = i;
}
}
nlocal = atom->nfirst; // This is important for the code that follows!
} else {
for (i = nall-1; i >= nlocal; i--) {
- if (ssaAIR[i] <= 0) continue; // skip ghost atoms not in AIR
+ 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;
+ list->bins_ssa[i] = list->gbinhead_ssa[ibin];
+ list->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;
+ list->bins_ssa[i] = list->binhead_ssa[ibin];
+ list->binhead_ssa[ibin] = i;
}
} /* else reuse previous binning. See Neighbor::build_one comment. */
@@ -269,6 +296,7 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
// loop over owned atoms, storing half of the neighbors
for (i = 0; i < nlocal; i++) {
+ int AIRct[8] = { 0 };
n = 0;
neighptr = ipage->vget();
@@ -285,7 +313,7 @@ void Neighbor::half_bin_newton_ssa(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 = bins_ssa[i]; j >= 0; j = bins_ssa[j]) {
+ for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -316,7 +344,7 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
// loop over all local atoms in other bins in "half" stencil
for (k = 0; k < nstencil; k++) {
- for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) {
+ for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -343,13 +371,15 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
}
}
}
+ AIRct[0] = n;
// loop over AIR ghost atoms in all bins in "full" stencil
// Note: the non-AIR ghost atoms have already been filtered out
// That is a significant time savings because of the "full" stencil
- for (k = 0; k < maxstencil; k++) {
+ // Note2: only non-pure locals can have ghosts as neighbors
+ if (ssaAIR[i] == 1) for (k = 0; k < maxstencil; k++) {
if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */
- for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) {
+ for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -368,11 +398,20 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
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))
+ if (which == 0) {
neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
- } else neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ } else if (domain->minimum_image_check(delx,dely,delz)) {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ } else if (which > 0) {
+ neighptr[n++] = j ^ (which << SBBITS);
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
+ } else {
+ neighptr[n++] = j;
+ ++(AIRct[ssaAIR[j] - 1]);
+ }
}
}
}
@@ -383,6 +422,16 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+
+ // sort the ghosts in the neighbor list by their ssaAIR number
+ ssaAIRptr = atom->ssaAIR;
+ qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
+
+ // Do a prefix sum on the counts to turn them into indexes.
+ list->ndxAIR_ssa[i][0] = AIRct[0];
+ for (int ndx = 1; ndx < 8; ++ndx) {
+ list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
+ }
}
list->inum = inum;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 307ea10dd8..5aad5bfd6f 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -104,14 +104,6 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
maxbin = 0;
bins = NULL;
- // USER-DPD SSA AIR binning
-
- maxbin_ssa = 0;
- bins_ssa = NULL;
- binhead_ssa = NULL;
- gbinhead_ssa = NULL;
- maxhead_ssa = 0;
-
// pair exclusion list info
includegroup = 0;
@@ -186,10 +178,6 @@ Neighbor::~Neighbor()
memory->destroy(binhead);
memory->destroy(bins);
- memory->destroy(gbinhead_ssa);
- memory->destroy(binhead_ssa);
- memory->destroy(bins_ssa);
-
memory->destroy(ex1_type);
memory->destroy(ex2_type);
memory->destroy(ex_type);
@@ -391,15 +379,6 @@ void Neighbor::init()
maxbin = maxhead = 0;
binhead = NULL;
bins = NULL;
-
- // for USER-DPD Shardlow Splitting Algorithm (SSA)
- memory->destroy(bins_ssa);
- memory->destroy(binhead_ssa);
- memory->destroy(gbinhead_ssa);
- maxbin_ssa = maxhead_ssa = 0;
- bins_ssa = NULL;
- binhead_ssa = NULL;
- gbinhead_ssa = NULL;
}
// 1st time allocation of xhold and bins
@@ -724,6 +703,9 @@ void Neighbor::init()
lists[i]->ghostflag = 0;
if (requests[i]->ghost) lists[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
+
+ lists[i]->ssaflag = 0;
+ if (requests[i]->ssa) lists[i]->ssaflag = 1;
} else init_list_flags1_kokkos(i);
}
@@ -2254,9 +2236,6 @@ bigint Neighbor::memory_usage()
if (style != NSQ) {
bytes += memory->usage(bins,maxbin);
bytes += memory->usage(binhead,maxhead);
- bytes += memory->usage(bins_ssa,maxbin_ssa);
- bytes += memory->usage(binhead_ssa,maxhead_ssa);
- bytes += memory->usage(gbinhead_ssa,maxhead_ssa);
}
for (int i = 0; i < nrequest; i++)
diff --git a/src/neighbor.h b/src/neighbor.h
index ceec3249ef..7a098e9be2 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -176,14 +176,6 @@ class Neighbor : protected Pointers {
double *zeroes; // vector of zeroes for shear history init
- // USER-DPD package
-
- int *bins_ssa; // ptr to next atom in each bin used by SSA
- int maxbin_ssa; // size of bins array used by SSA
- int *binhead_ssa; // ptr to 1st atom in each bin used by SSA
- int *gbinhead_ssa; // ptr to 1st ghost atom in each bin used by SSA
- int maxhead_ssa; // size of binhead array used by SSA
-
// methods
void bin_atoms(); // bin all atoms
--
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