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This commit is contained in:
Axel Kohlmeyer
2021-08-19 10:06:34 -04:00
parent 11b4ae641f
commit 7046b75861
24 changed files with 412 additions and 412 deletions
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110
src/npair_half_multi_newton.cpp
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@ -90,7 +90,7 @@ void NPairHalfMultiNewton::build(NeighList *list)
// if same collection use own bin
if(icollection == jcollection) jbin = ibin;
else jbin = coord2bin(x[i], jcollection);
else jbin = coord2bin(x[i], jcollection);
// if same size: uses half stencil so check central bin
if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
@ -106,41 +106,41 @@ void NPairHalfMultiNewton::build(NeighList *list)
// 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
for (j = js; j >= 0; j = bins[j]) {
for (j = js; j >= 0; j = bins[j]) {
if((icollection != jcollection) && (j < i)) continue;
if (j >= nlocal) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
if (j >= nlocal) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) 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;
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 (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;
}
}
}
// for all collections, loop over all atoms in other bins in stencil, store every pair
@ -148,38 +148,38 @@ void NPairHalfMultiNewton::build(NeighList *list)
// stencil is half if i same size as j
// stencil is full if i smaller than j
s = stencil_multi[icollection][jcollection];
ns = nstencil_multi[icollection][jcollection];
s = stencil_multi[icollection][jcollection];
ns = nstencil_multi[icollection][jcollection];
for (k = 0; k < ns; k++) {
js = binhead_multi[jcollection][jbin + s[k]];
for (j = js; j >= 0; j = bins[j]) {
for (k = 0; k < ns; k++) {
js = binhead_multi[jcollection][jbin + s[k]];
for (j = js; j >= 0; j = bins[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;
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 != Atom::ATOMIC) {
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 (rsq <= cutneighsq[itype][jtype]) {
if (molecular != Atom::ATOMIC) {
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;
}
}
}
}
ilist[inum++] = i;