| 154 |
|
AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 155 |
|
AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 156 |
|
|
| 157 |
– |
cerr << "Atoms in Local:\n"; |
| 158 |
– |
for (int i = 0; i < AtomLocalToGlobal.size(); i++) { |
| 159 |
– |
cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n"; |
| 160 |
– |
} |
| 161 |
– |
cerr << "Atoms in Row:\n"; |
| 162 |
– |
for (int i = 0; i < AtomRowToGlobal.size(); i++) { |
| 163 |
– |
cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n"; |
| 164 |
– |
} |
| 165 |
– |
cerr << "Atoms in Col:\n"; |
| 166 |
– |
for (int i = 0; i < AtomColToGlobal.size(); i++) { |
| 167 |
– |
cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n"; |
| 168 |
– |
} |
| 169 |
– |
|
| 157 |
|
cgRowToGlobal.resize(nGroupsInRow_); |
| 158 |
|
cgColToGlobal.resize(nGroupsInCol_); |
| 159 |
|
cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 160 |
|
cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 174 |
– |
|
| 175 |
– |
cerr << "Gruops in Local:\n"; |
| 176 |
– |
for (int i = 0; i < cgLocalToGlobal.size(); i++) { |
| 177 |
– |
cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n"; |
| 178 |
– |
} |
| 179 |
– |
cerr << "Groups in Row:\n"; |
| 180 |
– |
for (int i = 0; i < cgRowToGlobal.size(); i++) { |
| 181 |
– |
cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n"; |
| 182 |
– |
} |
| 183 |
– |
cerr << "Groups in Col:\n"; |
| 184 |
– |
for (int i = 0; i < cgColToGlobal.size(); i++) { |
| 185 |
– |
cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n"; |
| 186 |
– |
} |
| 187 |
– |
|
| 161 |
|
|
| 162 |
|
massFactorsRow.resize(nAtomsInRow_); |
| 163 |
|
massFactorsCol.resize(nAtomsInCol_); |
| 548 |
|
atomColData.position); |
| 549 |
|
|
| 550 |
|
// gather up the cutoff group positions |
| 578 |
– |
|
| 579 |
– |
cerr << "before gather\n"; |
| 580 |
– |
for (int i = 0; i < snap_->cgData.position.size(); i++) { |
| 581 |
– |
cerr << "cgpos = " << snap_->cgData.position[i] << "\n"; |
| 582 |
– |
} |
| 551 |
|
|
| 552 |
|
cgPlanVectorRow->gather(snap_->cgData.position, |
| 553 |
|
cgRowData.position); |
| 554 |
|
|
| 587 |
– |
cerr << "after gather\n"; |
| 588 |
– |
for (int i = 0; i < cgRowData.position.size(); i++) { |
| 589 |
– |
cerr << "cgRpos = " << cgRowData.position[i] << "\n"; |
| 590 |
– |
} |
| 591 |
– |
|
| 555 |
|
cgPlanVectorColumn->gather(snap_->cgData.position, |
| 556 |
|
cgColData.position); |
| 594 |
– |
for (int i = 0; i < cgColData.position.size(); i++) { |
| 595 |
– |
cerr << "cgCpos = " << cgColData.position[i] << "\n"; |
| 596 |
– |
} |
| 557 |
|
|
| 558 |
|
|
| 559 |
|
// if needed, gather the atomic rotation matrices |
| 691 |
|
|
| 692 |
|
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
| 693 |
|
pairwisePot += pot_temp[ii]; |
| 694 |
+ |
|
| 695 |
+ |
for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { |
| 696 |
+ |
RealType ploc1 = pairwisePot[ii]; |
| 697 |
+ |
RealType ploc2 = 0.0; |
| 698 |
+ |
MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); |
| 699 |
+ |
pairwisePot[ii] = ploc2; |
| 700 |
+ |
} |
| 701 |
+ |
|
| 702 |
|
#endif |
| 703 |
|
|
| 736 |
– |
cerr << "pairwisePot = " << pairwisePot << "\n"; |
| 704 |
|
} |
| 705 |
|
|
| 706 |
|
int ForceMatrixDecomposition::getNAtomsInRow() { |
| 735 |
|
|
| 736 |
|
#ifdef IS_MPI |
| 737 |
|
d = cgColData.position[cg2] - cgRowData.position[cg1]; |
| 771 |
– |
cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n"; |
| 772 |
– |
cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n"; |
| 738 |
|
#else |
| 739 |
|
d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1]; |
| 775 |
– |
cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n"; |
| 776 |
– |
cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n"; |
| 740 |
|
#endif |
| 741 |
|
|
| 742 |
|
snap_->wrapVector(d); |
| 812 |
|
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
| 813 |
|
int unique_id_1, unique_id_2; |
| 814 |
|
|
| 852 |
– |
|
| 853 |
– |
cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n"; |
| 815 |
|
#ifdef IS_MPI |
| 816 |
|
// in MPI, we have to look up the unique IDs for each atom |
| 817 |
|
unique_id_1 = AtomRowToGlobal[atom1]; |
| 818 |
|
unique_id_2 = AtomColToGlobal[atom2]; |
| 819 |
|
|
| 859 |
– |
cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n"; |
| 820 |
|
// this situation should only arise in MPI simulations |
| 821 |
|
if (unique_id_1 == unique_id_2) return true; |
| 822 |
|
|
