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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8357 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-20 16:40:25 +00:00
parent 69f5fbf421
commit 7975177abd
6 changed files with 238 additions and 38 deletions
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8
src/neigh_full.cpp
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@ -163,6 +163,7 @@ void Neighbor::full_nsq_ghost(NeighList *list)
// loop over all atoms, owned and ghost
// skip i = j
// no molecular test when i = ghost atom
if (i < nlocal) {
for (j = 0; j < nall; j++) {
@ -195,8 +196,7 @@ void Neighbor::full_nsq_ghost(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype])
neighptr[n++] = j;
if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
}
}
@ -371,6 +371,7 @@ void Neighbor::full_bin_ghost(NeighList *list)
// loop over all atoms in surrounding bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
// skip i = j
// no molecular test when i = ghost atom
if (i < nlocal) {
ibin = coord2bin(x[i]);
@ -418,8 +419,7 @@ void Neighbor::full_bin_ghost(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype])
neighptr[n++] = j;
if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
}
}
}

4
src/neigh_half_bin.cpp
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@ -187,6 +187,7 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
// stores own/own pairs only once
// stores own/ghost pairs with owned atom only, on both procs
// stores ghost/ghost pairs only once
// no molecular test when i = ghost atom
if (i < nlocal) {
ibin = coord2bin(x[i]);
@ -235,8 +236,7 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype])
neighptr[n++] = j;
if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
}
}
}

118
src/neigh_half_nsq.cpp
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@ -32,8 +32,6 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
@ -59,6 +57,8 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
int npage = 0;
int npnt = 0;
// loop over owned atoms, storing neighbors
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
@ -76,6 +76,7 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
// only store pair if i < j
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
@ -109,6 +110,119 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
list->inum = inum;
}
/* ----------------------------------------------------------------------
N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
include neighbors of ghost atoms, but no "special neighbors" for ghosts
pair stored once if i,j are both owned and i < j
pair stored by me if i owned and j ghost (also stored by proc owning j)
pair stored once if i,j are both ghost and i < j
------------------------------------------------------------------------- */
void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
{
int i,j,n,itype,jtype,which,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
if (includegroup) {
nlocal = atom->nfirst;
bitmask = group->bitmask[includegroup];
}
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int inum = 0;
int npage = 0;
int npnt = 0;
// loop over owned & ghost atoms, storing neighbors
for (i = 0; i < nall; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs with owned atom only, on both procs
// stores ghost/ghost pairs only once
// no molecular test when i = ghost atom
if (i < nlocal) {
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
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) {
which = find_special(special[i],nspecial[i],tag[j]);
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;
}
}
} else {
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
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]) neighptr[n++] = j;
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = atom->nlocal;
list->gnum = inum - atom->nlocal;
}
/* ----------------------------------------------------------------------
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
every pair stored exactly once by some processor

22
src/neigh_stencil.cpp
View File

@ -61,6 +61,28 @@ void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_ghost_bin_2d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;
stencilxyz[nstencil][2] = 0;
stencil[nstencil++] = j*mbinx + i;
}
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_half_bin_3d_no_newton(NeighList *list,
int sx, int sy, int sz)
{

122
src/neighbor.cpp
View File

@ -826,24 +826,48 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (rq->half) {
if (style == NSQ) {
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton;
else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton;
if (newton_pair == 0) {
if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
else pb = &Neighbor::half_nsq_no_newton_ghost;
} else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton;
} else if (rq->newton == 1) {
pb = &Neighbor::half_nsq_newton;
} else if (rq->newton == 2) pb = &Neighbor::half_nsq_no_newton;
} else if (rq->newton == 2) {
if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
else pb = &Neighbor::half_nsq_no_newton_ghost;
}
} else if (style == BIN) {
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton;
else if (triclinic == 0) pb = &Neighbor::half_bin_newton;
else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
if (newton_pair == 0) {
if (rq->ghost == 0) pb = &Neighbor::half_bin_no_newton;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
else pb = &Neighbor::half_bin_no_newton_ghost;
} else if (triclinic == 0) {
pb = &Neighbor::half_bin_newton;
} else if (triclinic == 1)
pb = &Neighbor::half_bin_newton_tri;
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_bin_newton;
else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
} else if (rq->newton == 2) {
if (rq->ghost) pb = &Neighbor::half_bin_no_newton_ghost;
else pb = &Neighbor::half_bin_no_newton;
if (rq->ghost == 0) pb = &Neighbor::half_bin_no_newton;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
else pb = &Neighbor::half_bin_no_newton_ghost;
}
} else if (style == MULTI) {
if (rq->ghost == 1)
error->all(FLERR,
"Neighbor multi not yet enabled for ghost neighbors");
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton;
else if (triclinic == 0) pb = &Neighbor::half_multi_newton;
@ -860,17 +884,18 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (includegroup)
error->all(FLERR,
"Neighbor include group not allowed with ghost neighbors");
else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost;
else pb = &Neighbor::full_nsq_ghost;
} else if (style == BIN) {
if (rq->ghost == 0) pb = &Neighbor::full_bin;
else if (includegroup)
error->all(FLERR,
"Neighbor include group not allowed with ghost neighbors");
else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost;
else pb = &Neighbor::full_bin_ghost;
} else if (style == MULTI) {
if (rq->ghost == 0) pb = &Neighbor::full_multi;
else error->all(FLERR,
"Neighbor multi not yet enabled for ghost neighbors");
if (rq->ghost == 1)
error->all(FLERR,
"Neighbor multi not yet enabled for ghost neighbors");
pb = &Neighbor::full_multi;
}
} else if (rq->gran) {
@ -895,6 +920,9 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (style == MULTI)
error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
}
// OMP versions of build methods
} else {
if (rq->copy) pb = &Neighbor::copy_from;
@ -912,23 +940,52 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (rq->half) {
if (style == NSQ) {
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton_omp;
else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton_omp;
if (newton_pair == 0) {
if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton_omp;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_nsq_no_newton_ghost;
} else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton_omp;
} else if (rq->newton == 1) {
pb = &Neighbor::half_nsq_newton_omp;
} else if (rq->newton == 2) {
pb = &Neighbor::half_nsq_no_newton_omp;
if (rq->ghost == 0) pb = &Neighbor::half_nsq_no_newton_omp;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_nsq_no_newton_ghost;
}
} else if (style == BIN) {
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton_omp;
else if (triclinic == 0) pb = &Neighbor::half_bin_newton_omp;
else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri_omp;
if (newton_pair == 0) {
if (rq->ghost == 0) pb = &Neighbor::half_bin_no_newton_omp;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_bin_no_newton_ghost;
} else if (triclinic == 0) {
pb = &Neighbor::half_bin_newton_omp;
} else if (triclinic == 1)
pb = &Neighbor::half_bin_newton_tri_omp;
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_bin_newton_omp;
else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri_omp;
} else if (rq->newton == 2) pb = &Neighbor::half_bin_no_newton_omp;
} else if (rq->newton == 2) {
if (rq->ghost == 0) pb = &Neighbor::half_bin_no_newton_omp;
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_bin_no_newton_ghost;
}
} else if (style == MULTI) {
if (rq->ghost == 1)
error->all(FLERR,
"Neighbor multi not yet enabled for ghost neighbors");
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton_omp;
else if (triclinic == 0) pb = &Neighbor::half_multi_newton_omp;
@ -945,17 +1002,18 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (includegroup)
error->all(FLERR,
"Neighbor include group not allowed with ghost neighbors");
else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost_omp;
else pb = &Neighbor::full_nsq_ghost_omp;
} else if (style == BIN) {
if (rq->ghost == 0) pb = &Neighbor::full_bin_omp;
else if (includegroup)
error->all(FLERR,
"Neighbor include group not allowed with ghost neighbors");
else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost_omp;
else pb = &Neighbor::full_bin_ghost_omp;
} else if (style == MULTI) {
if (rq->ghost == 0) pb = &Neighbor::full_multi_omp;
else error->all(FLERR,
"Neighbor multi not yet enabled for ghost neighbors");
if (rq->ghost == 1)
error->all(FLERR,
"Neighbor multi not yet enabled for ghost neighbors");
pb = &Neighbor::full_multi_omp;
}
} else if (rq->gran) {
@ -1004,10 +1062,13 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq)
if (style == BIN) {
if (rq->newton == 0) {
if (newton_pair == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_no_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_bin_3d_no_newton;
if (dimension == 2) {
if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_2d_no_newton;
else sc = &Neighbor::stencil_half_bin_2d_no_newton;
} else if (dimension == 3) {
if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_3d_no_newton;
else sc = &Neighbor::stencil_half_bin_3d_no_newton;
}
} else if (triclinic == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_newton;
@ -1033,7 +1094,8 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq)
}
} else if (rq->newton == 2) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_no_newton;
if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_2d_no_newton;
else sc = &Neighbor::stencil_half_bin_2d_no_newton;
else if (dimension == 3) {
if (rq->ghost) sc = &Neighbor::stencil_half_ghost_bin_3d_no_newton;
else sc = &Neighbor::stencil_half_bin_3d_no_newton;

2
src/neighbor.h
View File

@ -177,6 +177,7 @@ class Neighbor : protected Pointers {
PairPtr *pair_build;
void half_nsq_no_newton(class NeighList *);
void half_nsq_no_newton_ghost(class NeighList *);
void half_nsq_newton(class NeighList *);
void half_bin_no_newton(class NeighList *);
@ -223,6 +224,7 @@ class Neighbor : protected Pointers {
StencilPtr *stencil_create;
void stencil_half_bin_2d_no_newton(class NeighList *, int, int, int);
void stencil_half_ghost_bin_2d_no_newton(class NeighList *, int, int, int);
void stencil_half_bin_3d_no_newton(class NeighList *, int, int, int);
void stencil_half_ghost_bin_3d_no_newton(class NeighList *, int, int, int);
void stencil_half_bin_2d_newton(class NeighList *, int, int, int);