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USER-DPD: new neighbor list code for SSA that gives neighbors to ghosts.

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This simplifies the processing of the neighbor list in fix_shardlow.
NOTE: pair evaluation order changes, causing numerical differences!
This commit is contained in:
Tim Mattox
2016-12-30 14:42:21 -05:00
parent 2db66e49b4
commit 0512e78860
11 changed files with 129 additions and 113 deletions
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18
src/USER-DPD/fix_shardlow.cpp
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@ -148,6 +148,7 @@ void FixShardlow::init()
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->ghost= 1;
neighbor->requests[irequest]->ssa = 1;
}
@ -498,7 +499,7 @@ void FixShardlow::ssa_update_dpde(
void FixShardlow::initial_integrate(int vflag)
{
int i,ii,inum;
int i,ii,inum,anum;
int *ilist;
int nlocal = atom->nlocal;
@ -531,10 +532,12 @@ void FixShardlow::initial_integrate(int vflag)
v_t0 = (double (*)[3]) memory->smalloc(sizeof(double)*3*nghost, "FixShardlow:v_t0");
inum = list->inum;
anum = inum + list->gnum;
ilist = list->ilist;
dtsqrt = sqrt(update->dt);
ii = 0;
//Loop over all 14 directions (8 stages)
for (airnum = 1; airnum <=8; airnum++){
@ -549,15 +552,16 @@ void FixShardlow::initial_integrate(int vflag)
}
}
// Loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
// process neighbors in this AIR
while (ii < anum) {
i = ilist[ii];
int start = (airnum < 2) ? 0 : list->ndxAIR_ssa[i][airnum - 2];
int len = list->ndxAIR_ssa[i][airnum - 1] - start;
if (atom->ssaAIR[i] > airnum) break; /* done with curent AIR */
int len = list->numneigh[i];
if (len > 0) {
if (useDPDE) ssa_update_dpde(i, &(list->firstneigh[i][start]), len);
else ssa_update_dpd(i, &(list->firstneigh[i][start]), len);
if (useDPDE) ssa_update_dpde(i, &(list->firstneigh[i][0]), len);
else ssa_update_dpd(i, &(list->firstneigh[i][0]), len);
}
ii++;
}
// Communicate the ghost deltas to the atom owners

27
src/USER-DPD/nbin_ssa.cpp
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@ -33,14 +33,13 @@ NBinSSA::NBinSSA(LAMMPS *lmp) : NBinStandard(lmp)
bins_ssa = NULL;
maxhead_ssa = 0;
binhead_ssa = NULL;
gbinhead_ssa = NULL;
for (int i = 0; i < 9; i++) gairhead_ssa[i] = -1;
}
NBinSSA::~NBinSSA()
{
memory->destroy(bins_ssa);
memory->destroy(binhead_ssa);
memory->destroy(gbinhead_ssa);
}
/* ----------------------------------------------------------------------
@ -62,8 +61,11 @@ void NBinSSA::bin_atoms()
last_bin = update->ntimestep;
for (i = 0; i < 9; i++) {
gairhead_ssa[i] = -1;
}
for (i = 0; i < mbins; i++) {
gbinhead_ssa[i] = -1;
binhead_ssa[i] = -1;
}
@ -73,19 +75,19 @@ void NBinSSA::bin_atoms()
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
ibin = ssaAIR[i];
if (ibin < 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;
bins_ssa[i] = gairhead_ssa[ibin];
gairhead_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;
ibin = ssaAIR[i];
if (ibin < 2) continue; // skip ghost atoms not in AIR
bins_ssa[i] = gairhead_ssa[ibin];
gairhead_ssa[ibin] = i;
}
}
for (i = nlocal-1; i >= 0; i--) {
@ -103,10 +105,8 @@ void NBinSSA::bin_atoms_setup(int nall)
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) {
@ -125,7 +125,6 @@ bigint NBinSSA::memory_usage()
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;
}

2
src/USER-DPD/nbin_ssa.h
View File

@ -32,7 +32,7 @@ class NBinSSA : public NBinStandard {
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 gairhead_ssa[9]; // index of 1st ghost atom in each AIR
int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays
NBinSSA(class LAMMPS *);

153
src/USER-DPD/npair_half_bin_newton_ssa.cpp
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@ -32,12 +32,6 @@
using namespace LAMMPS_NS;
// allocate space for static class variable
// prototype for non-class function
static int *ssaAIRptr;
static int cmp_ssaAIR(const void *, const void *);
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
@ -64,9 +58,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) nlocal = atom->nfirst;
int *ssaAIR = atom->ssaAIR;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
@ -89,16 +81,18 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
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;
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;
ipage->reset();
// loop over owned atoms, storing half of the neighbors
for (i = 0; i < nlocal; i++) {
int AIRct[8] = { 0 };
n = 0;
neighptr = ipage->vget();
@ -175,51 +169,6 @@ void NPairHalfBinNewtonSSA::build(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
// Note2: only non-pure locals can have ghosts as neighbors
if (ssaAIR[i] == 1) for (k = 0; k < nstencil_full; k++) {
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;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) {
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]);
}
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
@ -227,34 +176,74 @@ void NPairHalfBinNewtonSSA::build(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;
// 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]) {
n = 0;
neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
ibin = coord2bin(x[i],xbin,ybin,zbin);
// loop over AIR ghost atoms in all bins in "full" stencil
// Note: the non-AIR ghost atoms have already been filtered out
for (k = 0; k < nstencil_full; k++) {
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]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
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))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
if (n > 0) ilist[inum + (gnum++)] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor (ghost) list overflow, boost neigh_modify one");
}
}
list->gnum = gnum;
}
/* ----------------------------------------------------------------------
comparison function invoked by qsort()
accesses static class member ssaAIRptr, set before call to qsort()
------------------------------------------------------------------------- */
static int cmp_ssaAIR(const void *iptr, const void *jptr)
{
int i = NEIGHMASK & *((int *) iptr);
int j = NEIGHMASK & *((int *) jptr);
if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
return 0;
}

2
src/USER-DPD/npair_half_bin_newton_ssa.h
View File

@ -15,7 +15,7 @@
NPairStyle(half/bin/newton/ssa,
NPairHalfBinNewtonSSA,
NP_HALF | NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA)
NP_HALF | NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA | NP_GHOST)
#else

4
src/USER-DPD/npair_halffull_newton_ssa.cpp
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@ -64,6 +64,10 @@ void NPairHalffullNewtonSSA::build(NeighList *list)
int inum_full = list->listfull->inum;
int inum = 0;
error->one(FLERR,"NPairHalffullNewtonSSA not yet implemented for ghosts with neighbors.");
return;
ipage->reset();
// loop over parent full list

12
src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
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@ -46,8 +46,12 @@ void NStencilHalfBin2dNewtonSSA::create()
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (j > 0 || (j == 0 && i > 0))
if (bin_distance(i,j,0) < cutneighmaxsq)
if (bin_distance(i,j,0) < cutneighmaxsq) {
stencilxyz[pos][0] = i;
stencilxyz[pos][1] = j;
stencilxyz[pos][2] = 0;
stencil[pos++] = j*mbinx + i;
}
nstencil_half = pos; // record where normal half stencil ends
@ -56,8 +60,12 @@ void NStencilHalfBin2dNewtonSSA::create()
for (j = -sy; j <= 0; j++)
for (i = -sx; i <= sx; i++) {
if (j == 0 && i > 0) continue;
if (bin_distance(i,j,0) < cutneighmaxsq)
if (bin_distance(i,j,0) < cutneighmaxsq) {
stencilxyz[pos][0] = i;
stencilxyz[pos][1] = j;
stencilxyz[pos][2] = 0;
stencil[pos++] = j*mbinx + i;
}
}
nstencil = pos; // record where full stencil ends

2
src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h
View File

@ -15,7 +15,7 @@
NStencilStyle(half/bin/2d/newton/ssa,
NStencilHalfBin2dNewtonSSA,
NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO)
NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST)
#else

18
src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
View File

@ -47,8 +47,12 @@ void NStencilHalfBin3dNewtonSSA::create()
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (k > 0 || j > 0 || (j == 0 && i > 0))
if (bin_distance(i,j,k) < cutneighmaxsq)
if (bin_distance(i,j,k) < cutneighmaxsq) {
stencilxyz[pos][0] = i;
stencilxyz[pos][1] = j;
stencilxyz[pos][2] = k;
stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
}
nstencil_half = pos; // record where normal half stencil ends
@ -57,8 +61,12 @@ void NStencilHalfBin3dNewtonSSA::create()
for (k = -sz; k < 0; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,k) < cutneighmaxsq)
if (bin_distance(i,j,k) < cutneighmaxsq) {
stencilxyz[pos][0] = i;
stencilxyz[pos][1] = j;
stencilxyz[pos][2] = k;
stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
}
// For k==0, make sure to skip already included bins
@ -66,8 +74,12 @@ void NStencilHalfBin3dNewtonSSA::create()
for (j = -sy; j <= 0; j++)
for (i = -sx; i <= sx; i++) {
if (j == 0 && i > 0) continue;
if (bin_distance(i,j,k) < cutneighmaxsq)
if (bin_distance(i,j,k) < cutneighmaxsq) {
stencilxyz[pos][0] = i;
stencilxyz[pos][1] = j;
stencilxyz[pos][2] = k;
stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
}
}
nstencil = pos; // record where full stencil ends

2
src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h
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@ -15,7 +15,7 @@
NStencilStyle(half/bin/3d/newton/ssa,
NStencilHalfBin3dNewtonSSA,
NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO)
NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST)
#else

2
src/USER-DPD/nstencil_ssa.h
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@ -20,7 +20,7 @@ namespace LAMMPS_NS {
class NStencilSSA : public NStencil {
public:
NStencilSSA(class LAMMPS *lmp) : NStencil(lmp) { }
NStencilSSA(class LAMMPS *lmp) : NStencil(lmp) { xyzflag = 1; }
~NStencilSSA() {}
virtual void create() = 0;