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Changing logic for self-bin check, newton+ortho

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This commit is contained in:
jtclemm
2023-11-01 12:22:30 -06:00
parent 8f14cdcb34
commit 745f2e6c54
18 changed files with 85 additions and 89 deletions
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2
src/OPENMP/npair_bin_ghost_omp.cpp
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@ -185,7 +185,7 @@ void NPairBinGhostOmp<HALF>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;
list->inum = nlocal; list->inum = nlocal;

8
src/OPENMP/npair_bin_omp.cpp
View File

@ -117,7 +117,7 @@ void NPairBinOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
for (k = 0; k < nstencil; k++) { for (k = 0; k < nstencil; k++) {
bin_start = binhead[ibin + stencil[k]]; bin_start = binhead[ibin + stencil[k]];
if (HALF && NEWTON && (!TRI)) { if (HALF && NEWTON && (!TRI)) {
if (stencil[k] == 0) { if (k == 0) {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// loop over rest of atoms in i's bin, ghosts are at end of linked list // loop over rest of atoms in i's bin, ghosts are at end of linked list
bin_start = bins[i]; bin_start = bins[i];
@ -163,7 +163,7 @@ void NPairBinOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// store every pair for every bin in stencil, except for i's bin // store every pair for every bin in stencil, except for i's bin
if (stencil[k] == 0) { if (k == 0) {
// if j is owned atom, store it, since j is beyond i in linked list // if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the "right" of i // if j is ghost, only store if j coords are "above and to the "right" of i
if (j >= nlocal) { if (j >= nlocal) {
@ -229,7 +229,7 @@ void NPairBinOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
if (!moltemplate) if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]); which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0) else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols[imol] ->nspecial[iatom], which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev); tag[j] - tagprev);
else which = 0; else which = 0;
if (which == 0) if (which == 0)
@ -250,7 +250,7 @@ void NPairBinOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;
list->inum = nlocal; list->inum = nlocal;

6
src/OPENMP/npair_halffull_omp.cpp
View File

@ -106,9 +106,9 @@ void NPairHalffullOmp<NEWTON, TRI, TRIM>::build(NeighList *list)
if (j < nlocal) { if (j < nlocal) {
if (i > j) continue; if (i > j) continue;
} else if (TRI) { } else if (TRI) {
if (fabs(x[j][2]-ztmp) > delta) { if (fabs(x[j][2] - ztmp) > delta) {
if (x[j][2] < ztmp) continue; if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) { } else if (fabs(x[j][1] - ytmp) > delta) {
if (x[j][1] < ytmp) continue; if (x[j][1] < ytmp) continue;
} else { } else {
if (x[j][0] < xtmp) continue; if (x[j][0] < xtmp) continue;
@ -149,7 +149,7 @@ void NPairHalffullOmp<NEWTON, TRI, TRIM>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;
list->inum = inum_full; list->inum = inum_full;

4
src/OPENMP/npair_multi_old_omp.cpp
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@ -119,7 +119,7 @@ void NPairMultiOldOmp<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
ns = nstencil_multi_old[itype]; ns = nstencil_multi_old[itype];
for (k = 0; k < ns; k++) { for (k = 0; k < ns; k++) {
bin_start = binhead[ibin+s[k]]; bin_start = binhead[ibin+s[k]];
if (s[k] == 0) { if (k == 0) {
if (HALF && NEWTON && (!TRI)) { if (HALF && NEWTON && (!TRI)) {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// loop over rest of atoms in i's bin, ghosts are at end of linked list // loop over rest of atoms in i's bin, ghosts are at end of linked list
@ -166,7 +166,7 @@ void NPairMultiOldOmp<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// store every pair for every bin in stencil,except for i's bin // store every pair for every bin in stencil,except for i's bin
if (s[k] == 0) { if (k == 0) {
// if j is owned atom, store it, since j is beyond i in linked list // if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the "right" of i // if j is ghost, only store if j coords are "above and to the "right" of i
if (j >= nlocal) { if (j >= nlocal) {

36
src/OPENMP/npair_multi_omp.cpp
View File

@ -131,7 +131,7 @@ void NPairMultiOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
// own-bin for half stencil // own-bin for half stencil
if (HALF && !TRI) if (HALF && !TRI)
if (flag_half_multi[icollection][jcollection] && s[k] == 0) js = bins[i]; if (k == 0 && flag_half_multi[icollection][jcollection]) js = bins[i];
for (j = js; j >= 0; j = bins[j]) { for (j = js; j >= 0; j = bins[j]) {
if (!HALF) { if (!HALF) {
@ -180,24 +180,22 @@ void NPairMultiOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
} else { } else {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// if same size: uses half stencil so includes a check of the central bin // if same size: uses half stencil so includes a check of the central bin
if (flag_half_multi[icollection][jcollection]){ if (k == 0 && flag_half_multi[icollection][jcollection]) {
if (s[k] == 0) { // if same collection,
// if same collection, // if j is owned atom, store it, since j is beyond i in linked list
// if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i
// if j is ghost, only store if j coords are "above and to the right" of i
// if different collections, // if different collections,
// if j is owned atom, store it if j > i // if j is owned atom, store it if j > i
// if j is ghost, only store if j coords are "above and to the right" of i // if j is ghost, only store if j coords are "above and to the right" of i
if ((icollection != jcollection) && (j < i)) continue; if ((icollection != jcollection) && (j < i)) continue;
if (j >= nlocal) { if (j >= nlocal) {
if (x[j][2] < ztmp) continue; if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) { if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue; if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue; if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
} }
} }
} }
@ -233,7 +231,7 @@ void NPairMultiOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
if (!moltemplate) if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]); which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0) else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom], which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev); tag[j] - tagprev);
else else
which = 0; which = 0;
@ -256,7 +254,7 @@ void NPairMultiOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
if (!moltemplate) if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]); which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0) else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom], which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev); tag[j] - tagprev);
else else
which = 0; which = 0;
@ -279,7 +277,7 @@ void NPairMultiOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;
list->inum = nlocal; list->inum = nlocal;

2
src/OPENMP/npair_nsq_ghost_omp.cpp
View File

@ -172,7 +172,7 @@ void NPairNsqGhostOmp<HALF>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;
list->inum = nlocal; list->inum = nlocal;

6
src/OPENMP/npair_nsq_omp.cpp
View File

@ -137,9 +137,9 @@ void NPairNsqOmp<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
if (j >= nlocal) { if (j >= nlocal) {
jtag = tag[j]; jtag = tag[j];
if (itag > jtag) { if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue; if ((itag + jtag) % 2 == 0) continue;
} else if (itag < jtag) { } else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue; if ((itag + jtag) % 2 == 1) continue;
} else if (TRI) { } else if (TRI) {
if (fabs(x[j][2] - ztmp) > delta) { if (fabs(x[j][2] - ztmp) > delta) {
if (x[j][2] < ztmp) continue; if (x[j][2] < ztmp) continue;
@ -219,7 +219,7 @@ void NPairNsqOmp<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;
list->inum = nlocal; list->inum = nlocal;

14
src/OPENMP/npair_respa_bin_omp.cpp
View File

@ -88,7 +88,7 @@ void NPairRespaBinOmp<NEWTON, TRI>::build(NeighList *list)
int *numneigh_inner = list->numneigh_inner; int *numneigh_inner = list->numneigh_inner;
int **firstneigh_inner = list->firstneigh_inner; int **firstneigh_inner = list->firstneigh_inner;
int *ilist_middle,*numneigh_middle,**firstneigh_middle; int *ilist_middle, *numneigh_middle, **firstneigh_middle;
if (respamiddle) { if (respamiddle) {
ilist_middle = list->ilist_middle; ilist_middle = list->ilist_middle;
numneigh_middle = list->numneigh_middle; numneigh_middle = list->numneigh_middle;
@ -133,9 +133,9 @@ void NPairRespaBinOmp<NEWTON, TRI>::build(NeighList *list)
} }
for (k = 0; k < nstencil; k++) { for (k = 0; k < nstencil; k++) {
bin_start = binhead[ibin+stencil[k]]; bin_start = binhead[ibin + stencil[k]];
if (NEWTON && (!TRI)) { if (NEWTON && (!TRI)) {
if (stencil[k] == 0) { if (k == 0) {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// loop over rest of atoms in i's bin, ghosts are at end of linked list // loop over rest of atoms in i's bin, ghosts are at end of linked list
bin_start = bins[i]; bin_start = bins[i];
@ -177,7 +177,7 @@ void NPairRespaBinOmp<NEWTON, TRI>::build(NeighList *list)
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// store every pair for every bin in stencil,except for i's bin // store every pair for every bin in stencil,except for i's bin
if (stencil[k] == 0) { if (k == 0) {
// if j is owned atom, store it, since j is beyond i in linked list // if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the "right" of i // if j is ghost, only store if j coords are "above and to the "right" of i
if (j >= nlocal) { if (j >= nlocal) {
@ -242,20 +242,20 @@ void NPairRespaBinOmp<NEWTON, TRI>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i; ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner; firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner; numneigh_inner[i] = n_inner;
ipage.vgot(n_inner); ipage.vgot(n_inner);
if (ipage_inner.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_inner.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
if (respamiddle) { if (respamiddle) {
ilist_middle[i] = i; ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle; firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle; numneigh_middle[i] = n_middle;
ipage_middle->vgot(n_middle); ipage_middle->vgot(n_middle);
if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_middle->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;

8
src/OPENMP/npair_respa_nsq_omp.cpp
View File

@ -99,7 +99,7 @@ void NPairRespaNsqOmp<NEWTON, TRI>::build(NeighList *list)
int *numneigh_inner = list->numneigh_inner; int *numneigh_inner = list->numneigh_inner;
int **firstneigh_inner = list->firstneigh_inner; int **firstneigh_inner = list->firstneigh_inner;
int *ilist_middle,*numneigh_middle,**firstneigh_middle; int *ilist_middle, *numneigh_middle, **firstneigh_middle;
if (respamiddle) { if (respamiddle) {
ilist_middle = list->ilist_middle; ilist_middle = list->ilist_middle;
numneigh_middle = list->numneigh_middle; numneigh_middle = list->numneigh_middle;
@ -222,20 +222,20 @@ void NPairRespaNsqOmp<NEWTON, TRI>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
ilist_inner[i] = i; ilist_inner[i] = i;
firstneigh_inner[i] = neighptr_inner; firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner; numneigh_inner[i] = n_inner;
ipage.vgot(n_inner); ipage.vgot(n_inner);
if (ipage_inner.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_inner.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
if (respamiddle) { if (respamiddle) {
ilist_middle[i] = i; ilist_middle[i] = i;
firstneigh_middle[i] = neighptr_middle; firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle; numneigh_middle[i] = n_middle;
ipage_middle->vgot(n_middle); ipage_middle->vgot(n_middle);
if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_middle->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;

2
src/OPENMP/npair_trim_omp.cpp
View File

@ -98,7 +98,7 @@ void NPairTrimOmp::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage.vgot(n); ipage.vgot(n);
if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage.status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
NPAIR_OMP_CLOSE; NPAIR_OMP_CLOSE;
list->inum = inum_copy; list->inum = inum_copy;

10
src/npair_bin.cpp
View File

@ -110,7 +110,7 @@ void NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
for (k = 0; k < nstencil; k++) { for (k = 0; k < nstencil; k++) {
bin_start = binhead[ibin + stencil[k]]; bin_start = binhead[ibin + stencil[k]];
if (HALF && NEWTON && (!TRI)) { if (HALF && NEWTON && (!TRI)) {
if (stencil[k] == 0) { if (k == 0) {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// loop over rest of atoms in i's bin, ghosts are at end of linked list // loop over rest of atoms in i's bin, ghosts are at end of linked list
bin_start = bins[i]; bin_start = bins[i];
@ -155,7 +155,7 @@ void NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// store every pair for every bin in stencil, except for i's bin // store every pair for every bin in stencil, except for i's bin
if (stencil[k] == 0) { if (k == 0) {
// if j is owned atom, store it, since j is beyond i in linked list // if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the "right" of i // if j is ghost, only store if j coords are "above and to the "right" of i
if (j >= nlocal) { if (j >= nlocal) {
@ -198,7 +198,7 @@ void NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
if (!moltemplate) if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]); which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0) else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom], which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev); tag[j] - tagprev);
else else
which = 0; which = 0;
@ -221,7 +221,7 @@ void NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
if (!moltemplate) if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]); which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0) else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom], which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev); tag[j] - tagprev);
else else
which = 0; which = 0;
@ -243,7 +243,7 @@ void NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage->vgot(n); ipage->vgot(n);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
list->inum = inum; list->inum = inum;

36
src/npair_multi.cpp
View File

@ -128,7 +128,7 @@ void NPairMulti<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
// own-bin for half stencil // own-bin for half stencil
if (HALF && !TRI) if (HALF && !TRI)
if (flag_half_multi[icollection][jcollection] && s[k] == 0) js = bins[i]; if (k == 0 && flag_half_multi[icollection][jcollection]) js = bins[i];
for (j = js; j >= 0; j = bins[j]) { for (j = js; j >= 0; j = bins[j]) {
if (!HALF) { if (!HALF) {
@ -177,24 +177,22 @@ void NPairMulti<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
} else { } else {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// if same size: uses half stencil so includes a check of the central bin // if same size: uses half stencil so includes a check of the central bin
if (flag_half_multi[icollection][jcollection]) { if (k == 0 && flag_half_multi[icollection][jcollection]) {
if (s[k] == 0) { // if same collection,
// if same collection, // if j is owned atom, store it, since j is beyond i in linked list
// if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i
// if j is ghost, only store if j coords are "above and to the right" of i
// if different collections, // if different collections,
// if j is owned atom, store it if j > i // if j is owned atom, store it if j > i
// if j is ghost, only store if j coords are "above and to the right" of i // if j is ghost, only store if j coords are "above and to the right" of i
if ((icollection != jcollection) && (j < i)) continue; if ((icollection != jcollection) && (j < i)) continue;
if (j >= nlocal) { if (j >= nlocal) {
if (x[j][2] < ztmp) continue; if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) { if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue; if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue; if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
} }
} }
} }
@ -230,7 +228,7 @@ void NPairMulti<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
if (!moltemplate) if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]); which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0) else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom], which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev); tag[j] - tagprev);
else else
which = 0; which = 0;
@ -253,7 +251,7 @@ void NPairMulti<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
if (!moltemplate) if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]); which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0) else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom], which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev); tag[j] - tagprev);
else else
which = 0; which = 0;
@ -276,7 +274,7 @@ void NPairMulti<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage->vgot(n); ipage->vgot(n);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
list->inum = inum; list->inum = inum;

6
src/npair_multi_old.cpp
View File

@ -113,7 +113,7 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
for (k = 0; k < ns; k++) { for (k = 0; k < ns; k++) {
bin_start = binhead[ibin + s[k]]; bin_start = binhead[ibin + s[k]];
if (HALF && NEWTON && (!TRI)) { if (HALF && NEWTON && (!TRI)) {
if (s[k] == 0) { if (k == 0) {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// loop over rest of atoms in i's bin, ghosts are at end of linked list // loop over rest of atoms in i's bin, ghosts are at end of linked list
bin_start = bins[i]; bin_start = bins[i];
@ -159,7 +159,7 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// store every pair for every bin in stencil,except for i's bin // store every pair for every bin in stencil,except for i's bin
if (s[k] == 0) { if (k == 0) {
// if j is owned atom, store it, since j is beyond i in linked list // if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the "right" of i // if j is ghost, only store if j coords are "above and to the "right" of i
if (j >= nlocal) { if (j >= nlocal) {
@ -236,7 +236,7 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage->vgot(n); ipage->vgot(n);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
list->inum = inum; list->inum = inum;

2
src/npair_nsq.cpp
View File

@ -211,7 +211,7 @@ void NPairNsq<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage->vgot(n); ipage->vgot(n);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
list->inum = inum; list->inum = inum;

12
src/npair_respa_bin.cpp
View File

@ -81,7 +81,7 @@ void NPairRespaBin<NEWTON, TRI>::build(NeighList *list)
int **firstneigh_inner = list->firstneigh_inner; int **firstneigh_inner = list->firstneigh_inner;
MyPage<int> *ipage_inner = list->ipage_inner; MyPage<int> *ipage_inner = list->ipage_inner;
int *ilist_middle,*numneigh_middle,**firstneigh_middle; int *ilist_middle, *numneigh_middle, **firstneigh_middle;
MyPage<int> *ipage_middle; MyPage<int> *ipage_middle;
int respamiddle = list->respamiddle; int respamiddle = list->respamiddle;
if (respamiddle) { if (respamiddle) {
@ -123,7 +123,7 @@ void NPairRespaBin<NEWTON, TRI>::build(NeighList *list)
for (k = 0; k < nstencil; k++) { for (k = 0; k < nstencil; k++) {
bin_start = binhead[ibin+stencil[k]]; bin_start = binhead[ibin+stencil[k]];
if (NEWTON && (!TRI)) { if (NEWTON && (!TRI)) {
if (stencil[k] == 0) { if (k == 0) {
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// loop over rest of atoms in i's bin, ghosts are at end of linked list // loop over rest of atoms in i's bin, ghosts are at end of linked list
bin_start = bins[i]; bin_start = bins[i];
@ -165,7 +165,7 @@ void NPairRespaBin<NEWTON, TRI>::build(NeighList *list)
// Half neighbor list, newton on, orthonormal // Half neighbor list, newton on, orthonormal
// store every pair for every bin in stencil,except for i's bin // store every pair for every bin in stencil,except for i's bin
if (stencil[k] == 0) { if (k == 0) {
// if j is owned atom, store it, since j is beyond i in linked list // if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the "right" of i // if j is ghost, only store if j coords are "above and to the "right" of i
if (j >= nlocal) { if (j >= nlocal) {
@ -230,20 +230,20 @@ void NPairRespaBin<NEWTON, TRI>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage->vgot(n); ipage->vgot(n);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
ilist_inner[inum] = i; ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner; firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner; numneigh_inner[i] = n_inner;
ipage_inner->vgot(n_inner); ipage_inner->vgot(n_inner);
if (ipage_inner->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_inner->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
if (respamiddle) { if (respamiddle) {
ilist_middle[inum] = i; ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle; firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle; numneigh_middle[i] = n_middle;
ipage_middle->vgot(n_middle); ipage_middle->vgot(n_middle);
if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_middle->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
inum++; inum++;

8
src/npair_respa_nsq.cpp
View File

@ -92,7 +92,7 @@ void NPairRespaNsq<NEWTON, TRI>::build(NeighList *list)
int **firstneigh_inner = list->firstneigh_inner; int **firstneigh_inner = list->firstneigh_inner;
MyPage<int> *ipage_inner = list->ipage_inner; MyPage<int> *ipage_inner = list->ipage_inner;
int *ilist_middle,*numneigh_middle,**firstneigh_middle; int *ilist_middle, *numneigh_middle, **firstneigh_middle;
MyPage<int> *ipage_middle; MyPage<int> *ipage_middle;
int respamiddle = list->respamiddle; int respamiddle = list->respamiddle;
if (respamiddle) { if (respamiddle) {
@ -215,20 +215,20 @@ void NPairRespaNsq<NEWTON, TRI>::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage->vgot(n); ipage->vgot(n);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
ilist_inner[inum] = i; ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner; firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner; numneigh_inner[i] = n_inner;
ipage_inner->vgot(n_inner); ipage_inner->vgot(n_inner);
if (ipage_inner->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_inner->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
if (respamiddle) { if (respamiddle) {
ilist_middle[inum] = i; ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle; firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle; numneigh_middle[i] = n_middle;
ipage_middle->vgot(n_middle); ipage_middle->vgot(n_middle);
if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_middle->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
inum++; inum++;

10
src/npair_skip_respa.cpp
View File

@ -58,9 +58,9 @@ void NPairSkipRespa::build(NeighList *list)
int *numneigh_inner_skip = list->listskip->numneigh_inner; int *numneigh_inner_skip = list->listskip->numneigh_inner;
int **firstneigh_inner_skip = list->listskip->firstneigh_inner; int **firstneigh_inner_skip = list->listskip->firstneigh_inner;
int *ilist_middle,*numneigh_middle,**firstneigh_middle; int *ilist_middle, *numneigh_middle, **firstneigh_middle;
MyPage<int> *ipage_middle; MyPage<int> *ipage_middle;
int *numneigh_middle_skip,**firstneigh_middle_skip; int *numneigh_middle_skip, **firstneigh_middle_skip;
int respamiddle = list->respamiddle; int respamiddle = list->respamiddle;
if (respamiddle) { if (respamiddle) {
ilist_middle = list->ilist_middle; ilist_middle = list->ilist_middle;
@ -135,20 +135,20 @@ void NPairSkipRespa::build(NeighList *list)
firstneigh[i] = neighptr; firstneigh[i] = neighptr;
numneigh[i] = n; numneigh[i] = n;
ipage->vgot(n); ipage->vgot(n);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
ilist_inner[inum] = i; ilist_inner[inum] = i;
firstneigh_inner[i] = neighptr_inner; firstneigh_inner[i] = neighptr_inner;
numneigh_inner[i] = n_inner; numneigh_inner[i] = n_inner;
ipage_inner->vgot(n); ipage_inner->vgot(n);
if (ipage_inner->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_inner->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
if (respamiddle) { if (respamiddle) {
ilist_middle[inum] = i; ilist_middle[inum] = i;
firstneigh_middle[i] = neighptr_middle; firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle; numneigh_middle[i] = n_middle;
ipage_middle->vgot(n); ipage_middle->vgot(n);
if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage_middle->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
inum++; inum++;

2
src/npair_skip_size_off2on_oneside.cpp
View File

@ -107,7 +107,7 @@ void NPairSkipSizeOff2onOneside::build(NeighList *list)
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
if (numneigh[i] == 0) continue; if (numneigh[i] == 0) continue;
firstneigh[i] = ipage->get(numneigh[i]); firstneigh[i] = ipage->get(numneigh[i]);
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
} }
// second loop over atoms in other list to store neighbors // second loop over atoms in other list to store neighbors