tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

USER-DPD: track & use the extent of the local atoms in the bins

Browse Source
This commit is contained in:
Tim Mattox
2017-01-26 16:20:12 -05:00
parent ff2786c86c
commit e42678ed51
4 changed files with 93 additions and 46 deletions
Download Patch File Download Diff File Expand all files Collapse all files

73
src/USER-DPD/nbin_ssa.cpp
View File

@ -30,22 +30,24 @@ using namespace LAMMPS_NS;
NBinSSA::NBinSSA(LAMMPS *lmp) : NBinStandard(lmp)
{
maxbin_ssa = 0;
bins_ssa = NULL;
maxhead_ssa = 0;
binhead_ssa = NULL;
for (int i = 0; i < 9; i++) gairhead_ssa[i] = -1;
binlist_ssa = NULL;
binct_ssa = NULL;
for (int i = 0; i < 9; i++) {
gairhead_ssa[i] = -1;
gairct_ssa[i] = 0;
}
}
NBinSSA::~NBinSSA()
{
memory->destroy(bins_ssa);
memory->destroy(binhead_ssa);
memory->destroy(binlist_ssa);
memory->destroy(binct_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
local atoms are in distinct bins (binhead[]) from the ghosts
ghost atoms are "binned" in gairhead_ssa[] instead
ghosts which are not in an Active Interaction Region (AIR) are skipped
------------------------------------------------------------------------- */
@ -58,6 +60,7 @@ void NBinSSA::bin_atoms()
double **x = atom->x;
int *mask = atom->mask;
int *ssaAIR = atom->ssaAIR;
int xbin,ybin,zbin;
last_bin = update->ntimestep;
@ -66,10 +69,13 @@ void NBinSSA::bin_atoms()
for (i = 0; i < 9; i++) {
gairhead_ssa[i] = -1;
gairct_ssa[i] = 0;
}
for (i = 0; i < mbins; i++) {
binhead_ssa[i] = -1;
binhead[i] = -1;
binlist_ssa[i] = -1;
binct_ssa[i] = 0;
}
// bin in reverse order so linked list will be in forward order
@ -81,23 +87,34 @@ void NBinSSA::bin_atoms()
ibin = ssaAIR[i];
if (ibin < 2) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
bins_ssa[i] = gairhead_ssa[ibin];
bins[i] = gairhead_ssa[ibin];
gairhead_ssa[ibin] = i;
++(gairct_ssa[ibin]);
}
}
} else {
for (i = nall-1; i >= nlocal; i--) {
ibin = ssaAIR[i];
if (ibin < 2) continue; // skip ghost atoms not in AIR
bins_ssa[i] = gairhead_ssa[ibin];
bins[i] = gairhead_ssa[ibin];
gairhead_ssa[ibin] = i;
++(gairct_ssa[ibin]);
}
}
for (i = nlocal-1; i >= 0; i--) {
ibin = coord2bin(x[i][0], x[i][1], x[i][2]);
bins_ssa[i] = binhead_ssa[ibin];
binhead_ssa[ibin] = i;
ibin = coord2bin(x[i][0], x[i][1], x[i][2], xbin, ybin, zbin);
// Find the bounding box of the local atoms in the bins
if (xbin < lbinxlo) lbinxlo = xbin;
if (xbin >= lbinxhi) lbinxhi = xbin + 1;
if (ybin < lbinylo) lbinylo = ybin;
if (ybin >= lbinyhi) lbinyhi = ybin + 1;
if (zbin < lbinzlo) lbinzlo = zbin;
if (zbin >= lbinzhi) lbinzhi = zbin + 1;
bins[i] = binhead[ibin];
binhead[ibin] = i;
++(binct_ssa[ibin]);
}
}
/* ---------------------------------------------------------------------- */
@ -106,17 +123,21 @@ 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(binhead_ssa);
memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa");
if (mbins > maxbin_ssa) {
maxbin_ssa = mbins;
memory->destroy(binlist_ssa);
memory->destroy(binct_ssa);
memory->create(binlist_ssa,maxbin_ssa,"binlist_ssa");
memory->create(binct_ssa,maxbin_ssa,"binct_ssa");
}
if (nall > maxbin_ssa) {
maxbin_ssa = nall;
memory->destroy(bins_ssa);
memory->create(bins_ssa,maxbin_ssa,"bins_ssa");
}
// Clear the local bin extent bounding box.
lbinxlo = mbinx - 1; // Safe to = stencil->sx + 1
lbinylo = mbiny - 1; // Safe to = stencil->sy + 1
lbinzlo = mbinz - 1; // Safe to = stencil->sz + 1
lbinxhi = 0; // Safe to = mbinx - stencil->sx - 1
lbinyhi = 0; // Safe to = mbiny - stencil->sy - 1
lbinzhi = 0; // Safe to = mbinz - stencil->sz - 1
}
/* ---------------------------------------------------------------------- */
@ -125,9 +146,9 @@ 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);
if (maxbin_ssa) {
bytes += memory->usage(binlist_ssa,maxbin_ssa);
bytes += memory->usage(binct_ssa,maxbin_ssa);
}
return bytes;
}

16
src/USER-DPD/nbin_ssa.h
View File

@ -29,11 +29,19 @@ 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 *binlist_ssa; // index in neighlist of 1st local atom in each bin
int *binct_ssa; // count of local atoms in each bin
int gairhead_ssa[9]; // index of 1st ghost atom in each AIR
int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays
int gairct_ssa[9]; // count of ghost atoms in each AIR
int maxbin_ssa; // size of binlist_ssa and binct_ssa arrays
// Bounds of the local atoms in the binhead array
int lbinxlo; // lowest local bin x-dim coordinate
int lbinylo; // lowest local bin y-dim coordinate
int lbinzlo; // lowest local bin z-dim coordinate
int lbinxhi; // highest local bin x-dim coordinate
int lbinyhi; // highest local bin y-dim coordinate
int lbinzhi; // highest local bin z-dim coordinate
NBinSSA(class LAMMPS *);
~NBinSSA();

49
src/USER-DPD/npair_half_bin_newton_ssa.cpp
View File

@ -79,20 +79,32 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
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 *bins = nb_ssa->bins;
int *binhead = nb_ssa->binhead;
int *binlist_ssa = nb_ssa->binlist_ssa;
int *binct_ssa = nb_ssa->binct_ssa;
int *gairhead_ssa = &(nb_ssa->gairhead_ssa[0]);
int inum = 0;
int gnum = 0;
int xbin,ybin,zbin,xbin2,ybin2,zbin2;
int **stencilxyz = ns_ssa->stencilxyz;
int lbinxlo = nb_ssa->lbinxlo;
int lbinxhi = nb_ssa->lbinxhi;
int lbinylo = nb_ssa->lbinylo;
int lbinyhi = nb_ssa->lbinyhi;
int lbinzlo = nb_ssa->lbinzlo;
int lbinzhi = nb_ssa->lbinzhi;
ipage->reset();
// loop over owned atoms, storing half of the neighbors
for (i = 0; i < nlocal; i++) {
// loop over bins with local atoms, storing half of the neighbors
for (zbin = lbinzlo; zbin < lbinzhi; zbin++) {
for (ybin = lbinylo; ybin < lbinyhi; ybin++) {
for (xbin = lbinxlo; xbin < lbinxhi; xbin++) {
ibin = zbin*mbiny*mbinx + ybin*mbinx + xbin;
binlist_ssa[ibin] = inum; // record where ibin starts in ilist
for (i = binhead[ibin]; i >= 0; i = bins[i]) {
n = 0;
neighptr = ipage->vget();
@ -109,7 +121,7 @@ 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 = bins_ssa[i]; j >= 0; j = bins_ssa[j]) {
for (j = bins[i]; j >= 0; j = bins[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@ -136,13 +148,11 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
}
}
ibin = coord2bin(x[i]);
// loop over all local atoms in other bins in "half" stencil
for (k = 0; k < nstencil_half; k++) {
for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
j = bins_ssa[j]) {
for (j = binhead[ibin+stencil[k]]; j >= 0;
j = bins[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@ -177,13 +187,20 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
// verify count of atoms in ibin
if (binct_ssa[ibin] != (inum - binlist_ssa[ibin]))
error->one(FLERR,"binct_ssa didn't agree with lenght in ilist");
}
}
}
list->inum = inum;
// loop over AIR ghost atoms, storing their local neighbors
// since these are ghosts, must check if stencil bin is out of bounds
for (int airnum = 2; airnum <= 8; airnum++) {
for (i = gairhead_ssa[airnum]; i >= 0; i = bins_ssa[i]) {
list->AIRct_ssa[airnum - 1] = nb_ssa->gairct_ssa[airnum];
for (i = gairhead_ssa[airnum]; i >= 0; i = bins[i]) {
n = 0;
neighptr = ipage->vget();
@ -205,11 +222,11 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
xbin2 = xbin + stencilxyz[k][0];
ybin2 = ybin + stencilxyz[k][1];
zbin2 = zbin + stencilxyz[k][2];
// since we only care about ghost to local neighbors, these "bounds" could be inset
if (xbin2 < 0 || xbin2 >= mbinx ||
ybin2 < 0 || ybin2 >= mbiny ||
zbin2 < 0 || zbin2 >= mbinz) continue;
for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) {
// Skip it if this bin is outside the extent of local bins
if (xbin2 < lbinxlo || xbin2 >= lbinxhi ||
ybin2 < lbinylo || ybin2 >= lbinyhi ||
zbin2 < lbinzlo || zbin2 >= lbinzhi) continue;
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;

1
src/neigh_list.h
View File

@ -80,6 +80,7 @@ class NeighList : protected Pointers {
// USER-DPD package and Shardlow Splitting Algorithm (SSA) support
int AIRct_ssa[8]; // count of how many atoms in each AIR
uint16_t (*ndxAIR_ssa)[8]; // for each atom, last neighbor index of each AIR
// methods