| 233 |
|
} |
| 234 |
|
} |
| 235 |
|
|
| 236 |
< |
#endif |
| 237 |
< |
|
| 238 |
< |
// allocate memory for the parallel objects |
| 239 |
< |
atypesLocal.resize(nLocal_); |
| 240 |
< |
|
| 241 |
< |
for (int i = 0; i < nLocal_; i++) |
| 242 |
< |
atypesLocal[i] = ff_->getAtomType(idents[i]); |
| 243 |
< |
|
| 244 |
< |
groupList_.clear(); |
| 245 |
< |
groupList_.resize(nGroups_); |
| 246 |
< |
for (int i = 0; i < nGroups_; i++) { |
| 247 |
< |
int gid = cgLocalToGlobal[i]; |
| 248 |
< |
for (int j = 0; j < nLocal_; j++) { |
| 249 |
< |
int aid = AtomLocalToGlobal[j]; |
| 250 |
< |
if (globalGroupMembership[aid] == gid) { |
| 251 |
< |
groupList_[i].push_back(j); |
| 252 |
< |
} |
| 253 |
< |
} |
| 254 |
< |
} |
| 255 |
< |
|
| 236 |
> |
#else |
| 237 |
|
excludesForAtom.clear(); |
| 238 |
|
excludesForAtom.resize(nLocal_); |
| 239 |
|
toposForAtom.clear(); |
| 247 |
|
for (int j = 0; j < nLocal_; j++) { |
| 248 |
|
int jglob = AtomLocalToGlobal[j]; |
| 249 |
|
|
| 250 |
< |
if (excludes->hasPair(iglob, jglob)) |
| 250 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 251 |
|
excludesForAtom[i].push_back(j); |
| 252 |
|
|
| 253 |
+ |
|
| 254 |
|
if (oneTwo->hasPair(iglob, jglob)) { |
| 255 |
|
toposForAtom[i].push_back(j); |
| 256 |
|
topoDist[i].push_back(1); |
| 267 |
|
} |
| 268 |
|
} |
| 269 |
|
} |
| 270 |
< |
|
| 270 |
> |
#endif |
| 271 |
> |
|
| 272 |
> |
// allocate memory for the parallel objects |
| 273 |
> |
atypesLocal.resize(nLocal_); |
| 274 |
> |
|
| 275 |
> |
for (int i = 0; i < nLocal_; i++) |
| 276 |
> |
atypesLocal[i] = ff_->getAtomType(idents[i]); |
| 277 |
> |
|
| 278 |
> |
groupList_.clear(); |
| 279 |
> |
groupList_.resize(nGroups_); |
| 280 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 281 |
> |
int gid = cgLocalToGlobal[i]; |
| 282 |
> |
for (int j = 0; j < nLocal_; j++) { |
| 283 |
> |
int aid = AtomLocalToGlobal[j]; |
| 284 |
> |
if (globalGroupMembership[aid] == gid) { |
| 285 |
> |
groupList_[i].push_back(j); |
| 286 |
> |
} |
| 287 |
> |
} |
| 288 |
> |
} |
| 289 |
> |
|
| 290 |
> |
|
| 291 |
|
createGtypeCutoffMap(); |
| 292 |
|
|
| 293 |
|
} |
| 685 |
|
} |
| 686 |
|
|
| 687 |
|
AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
| 688 |
< |
for (int i = 0; i < ns; i++) |
| 688 |
> |
for (int i = 0; i < ns; i++) |
| 689 |
|
snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
| 690 |
+ |
|
| 691 |
|
} |
| 692 |
|
|
| 693 |
|
nLocal_ = snap_->getNumberOfAtoms(); |
| 717 |
|
pairwisePot[ii] = ploc2; |
| 718 |
|
} |
| 719 |
|
|
| 720 |
+ |
for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
| 721 |
+ |
RealType ploc1 = embeddingPot[ii]; |
| 722 |
+ |
RealType ploc2 = 0.0; |
| 723 |
+ |
MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
| 724 |
+ |
embeddingPot[ii] = ploc2; |
| 725 |
+ |
} |
| 726 |
+ |
|
| 727 |
|
#endif |
| 728 |
|
|
| 729 |
|
} |
| 865 |
|
* field) must still be handled for these pairs. |
| 866 |
|
*/ |
| 867 |
|
bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { |
| 868 |
< |
int unique_id_2; |
| 869 |
< |
#ifdef IS_MPI |
| 870 |
< |
// in MPI, we have to look up the unique IDs for the row atom. |
| 861 |
< |
unique_id_2 = AtomColToGlobal[atom2]; |
| 862 |
< |
#else |
| 863 |
< |
// in the normal loop, the atom numbers are unique |
| 864 |
< |
unique_id_2 = atom2; |
| 865 |
< |
#endif |
| 868 |
> |
|
| 869 |
> |
// excludesForAtom was constructed to use row/column indices in the MPI |
| 870 |
> |
// version, and to use local IDs in the non-MPI version: |
| 871 |
|
|
| 872 |
|
for (vector<int>::iterator i = excludesForAtom[atom1].begin(); |
| 873 |
|
i != excludesForAtom[atom1].end(); ++i) { |
| 874 |
< |
if ( (*i) == unique_id_2 ) return true; |
| 874 |
> |
if ( (*i) == atom2 ) return true; |
| 875 |
|
} |
| 876 |
|
|
| 877 |
|
return false; |
