| 54 |
|
void ForceMatrixDecomposition::distributeInitialData() { |
| 55 |
|
snap_ = sman_->getCurrentSnapshot(); |
| 56 |
|
storageLayout_ = sman_->getStorageLayout(); |
| 57 |
< |
#ifdef IS_MPI |
| 58 |
< |
int nLocal = snap_->getNumberOfAtoms(); |
| 59 |
< |
int nGroups = snap_->getNumberOfCutoffGroups(); |
| 60 |
< |
|
| 61 |
< |
AtomCommIntRow = new Communicator<Row,int>(nLocal); |
| 62 |
< |
AtomCommRealRow = new Communicator<Row,RealType>(nLocal); |
| 63 |
< |
AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal); |
| 64 |
< |
AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal); |
| 57 |
> |
nLocal_ = snap_->getNumberOfAtoms(); |
| 58 |
> |
nGroups_ = snap_->getNumberOfCutoffGroups(); |
| 59 |
|
|
| 60 |
< |
AtomCommIntColumn = new Communicator<Column,int>(nLocal); |
| 61 |
< |
AtomCommRealColumn = new Communicator<Column,RealType>(nLocal); |
| 62 |
< |
AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal); |
| 63 |
< |
AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal); |
| 60 |
> |
#ifdef IS_MPI |
| 61 |
> |
|
| 62 |
> |
AtomCommIntRow = new Communicator<Row,int>(nLocal_); |
| 63 |
> |
AtomCommRealRow = new Communicator<Row,RealType>(nLocal_); |
| 64 |
> |
AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_); |
| 65 |
> |
AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_); |
| 66 |
|
|
| 67 |
< |
cgCommIntRow = new Communicator<Row,int>(nGroups); |
| 68 |
< |
cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups); |
| 69 |
< |
cgCommIntColumn = new Communicator<Column,int>(nGroups); |
| 70 |
< |
cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups); |
| 67 |
> |
AtomCommIntColumn = new Communicator<Column,int>(nLocal_); |
| 68 |
> |
AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_); |
| 69 |
> |
AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_); |
| 70 |
> |
AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_); |
| 71 |
|
|
| 72 |
< |
int nAtomsInRow = AtomCommIntRow->getSize(); |
| 73 |
< |
int nAtomsInCol = AtomCommIntColumn->getSize(); |
| 74 |
< |
int nGroupsInRow = cgCommIntRow->getSize(); |
| 75 |
< |
int nGroupsInCol = cgCommIntColumn->getSize(); |
| 72 |
> |
cgCommIntRow = new Communicator<Row,int>(nGroups_); |
| 73 |
> |
cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_); |
| 74 |
> |
cgCommIntColumn = new Communicator<Column,int>(nGroups_); |
| 75 |
> |
cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_); |
| 76 |
|
|
| 77 |
+ |
nAtomsInRow_ = AtomCommIntRow->getSize(); |
| 78 |
+ |
nAtomsInCol_ = AtomCommIntColumn->getSize(); |
| 79 |
+ |
nGroupsInRow_ = cgCommIntRow->getSize(); |
| 80 |
+ |
nGroupsInCol_ = cgCommIntColumn->getSize(); |
| 81 |
+ |
|
| 82 |
|
// Modify the data storage objects with the correct layouts and sizes: |
| 83 |
< |
atomRowData.resize(nAtomsInRow); |
| 84 |
< |
atomRowData.setStorageLayout(storageLayout_); |
| 85 |
< |
atomColData.resize(nAtomsInCol); |
| 83 |
> |
atomRowData.resize(nAtomsInRow_); |
| 84 |
> |
atomRowData.setStorageLayout(storageLayout_); |
| 85 |
> |
atomColData.resize(nAtomsInCol_); |
| 86 |
|
atomColData.setStorageLayout(storageLayout_); |
| 87 |
< |
cgRowData.resize(nGroupsInRow); |
| 87 |
> |
cgRowData.resize(nGroupsInRow_); |
| 88 |
|
cgRowData.setStorageLayout(DataStorage::dslPosition); |
| 89 |
< |
cgColData.resize(nGroupsInCol); |
| 89 |
> |
cgColData.resize(nGroupsInCol_); |
| 90 |
|
cgColData.setStorageLayout(DataStorage::dslPosition); |
| 91 |
|
|
| 92 |
|
vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, |
| 93 |
< |
vector<RealType> (nAtomsInRow, 0.0)); |
| 93 |
> |
vector<RealType> (nAtomsInRow_, 0.0)); |
| 94 |
|
vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES, |
| 95 |
< |
vector<RealType> (nAtomsInCol, 0.0)); |
| 95 |
> |
vector<RealType> (nAtomsInCol_, 0.0)); |
| 96 |
|
|
| 97 |
|
|
| 98 |
|
vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
| 99 |
|
|
| 100 |
|
// gather the information for atomtype IDs (atids): |
| 101 |
|
vector<int> identsLocal = info_->getIdentArray(); |
| 102 |
< |
identsRow.reserve(nAtomsInRow); |
| 103 |
< |
identsCol.reserve(nAtomsInCol); |
| 102 |
> |
identsRow.reserve(nAtomsInRow_); |
| 103 |
> |
identsCol.reserve(nAtomsInCol_); |
| 104 |
|
|
| 105 |
|
AtomCommIntRow->gather(identsLocal, identsRow); |
| 106 |
|
AtomCommIntColumn->gather(identsLocal, identsCol); |
| 230 |
|
snap_->atomData.torque[i] += trq_tmp[i]; |
| 231 |
|
} |
| 232 |
|
|
| 233 |
< |
int nLocal = snap_->getNumberOfAtoms(); |
| 233 |
> |
nLocal_ = snap_->getNumberOfAtoms(); |
| 234 |
|
|
| 235 |
|
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 236 |
< |
vector<RealType> (nLocal, 0.0)); |
| 236 |
> |
vector<RealType> (nLocal_, 0.0)); |
| 237 |
|
|
| 238 |
|
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 239 |
|
AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); |
| 313 |
|
#else |
| 314 |
|
snap_->atomData.force[atom2] += fg; |
| 315 |
|
#endif |
| 315 |
– |
|
| 316 |
|
} |
| 317 |
|
|
| 318 |
|
// filling interaction blocks with pointers |
| 319 |
|
InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { |
| 320 |
– |
|
| 320 |
|
InteractionData idat; |
| 321 |
+ |
|
| 322 |
|
#ifdef IS_MPI |
| 323 |
|
if (storageLayout_ & DataStorage::dslAmat) { |
| 324 |
|
idat.A1 = &(atomRowData.aMat[atom1]); |
| 325 |
|
idat.A2 = &(atomColData.aMat[atom2]); |
| 326 |
|
} |
| 327 |
< |
|
| 327 |
> |
|
| 328 |
|
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 329 |
|
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 330 |
|
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 370 |
|
idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
| 371 |
|
} |
| 372 |
|
#endif |
| 373 |
< |
|
| 373 |
> |
return idat; |
| 374 |
|
} |
| 375 |
+ |
|
| 376 |
|
InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ |
| 377 |
+ |
|
| 378 |
|
InteractionData idat; |
| 377 |
– |
skippedCharge1 |
| 378 |
– |
skippedCharge2 |
| 379 |
– |
rij |
| 380 |
– |
d |
| 381 |
– |
electroMult |
| 382 |
– |
sw |
| 383 |
– |
f |
| 379 |
|
#ifdef IS_MPI |
| 385 |
– |
|
| 380 |
|
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 381 |
|
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 382 |
|
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 385 |
|
idat.t1 = &(atomRowData.torque[atom1]); |
| 386 |
|
idat.t2 = &(atomColData.torque[atom2]); |
| 387 |
|
} |
| 388 |
< |
|
| 388 |
> |
if (storageLayout_ & DataStorage::dslForce) { |
| 389 |
> |
idat.t1 = &(atomRowData.force[atom1]); |
| 390 |
> |
idat.t2 = &(atomColData.force[atom2]); |
| 391 |
> |
} |
| 392 |
> |
#else |
| 393 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 394 |
> |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 395 |
> |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 396 |
> |
} |
| 397 |
> |
if (storageLayout_ & DataStorage::dslTorque) { |
| 398 |
> |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 399 |
> |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 400 |
> |
} |
| 401 |
> |
if (storageLayout_ & DataStorage::dslForce) { |
| 402 |
> |
idat.t1 = &(snap_->atomData.force[atom1]); |
| 403 |
> |
idat.t2 = &(snap_->atomData.force[atom2]); |
| 404 |
> |
} |
| 405 |
> |
#endif |
| 406 |
|
|
| 407 |
|
} |
| 397 |
– |
SelfData ForceMatrixDecomposition::fillSelfData(int atom1) { |
| 398 |
– |
} |
| 408 |
|
|
| 409 |
|
|
| 410 |
+ |
|
| 411 |
+ |
|
| 412 |
|
/* |
| 413 |
|
* buildNeighborList |
| 414 |
|
* |
| 415 |
|
* first element of pair is row-indexed CutoffGroup |
| 416 |
|
* second element of pair is column-indexed CutoffGroup |
| 417 |
|
*/ |
| 418 |
< |
vector<pair<int, int> > buildNeighborList() { |
| 419 |
< |
Vector3d dr, invWid, rs, shift; |
| 420 |
< |
Vector3i cc, m1v, m2s; |
| 421 |
< |
RealType rrNebr; |
| 422 |
< |
int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset; |
| 418 |
> |
vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() { |
| 419 |
> |
|
| 420 |
> |
vector<pair<int, int> > neighborList; |
| 421 |
> |
#ifdef IS_MPI |
| 422 |
> |
cellListRow_.clear(); |
| 423 |
> |
cellListCol_.clear(); |
| 424 |
> |
#else |
| 425 |
> |
cellList_.clear(); |
| 426 |
> |
#endif |
| 427 |
|
|
| 428 |
< |
|
| 429 |
< |
vector<pair<int, int> > neighborList; |
| 430 |
< |
Vector3i nCells; |
| 431 |
< |
Vector3d invWid, r; |
| 432 |
< |
|
| 433 |
< |
rList_ = (rCut_ + skinThickness_); |
| 419 |
< |
rl2 = rList_ * rList_; |
| 420 |
< |
|
| 421 |
< |
snap_ = sman_->getCurrentSnapshot(); |
| 428 |
> |
// dangerous to not do error checking. |
| 429 |
> |
RealType rCut_; |
| 430 |
> |
|
| 431 |
> |
RealType rList_ = (rCut_ + skinThickness_); |
| 432 |
> |
RealType rl2 = rList_ * rList_; |
| 433 |
> |
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 434 |
|
Mat3x3d Hmat = snap_->getHmat(); |
| 435 |
|
Vector3d Hx = Hmat.getColumn(0); |
| 436 |
|
Vector3d Hy = Hmat.getColumn(1); |
| 437 |
|
Vector3d Hz = Hmat.getColumn(2); |
| 438 |
|
|
| 439 |
< |
nCells.x() = (int) ( Hx.length() )/ rList_; |
| 440 |
< |
nCells.y() = (int) ( Hy.length() )/ rList_; |
| 441 |
< |
nCells.z() = (int) ( Hz.length() )/ rList_; |
| 439 |
> |
nCells_.x() = (int) ( Hx.length() )/ rList_; |
| 440 |
> |
nCells_.y() = (int) ( Hy.length() )/ rList_; |
| 441 |
> |
nCells_.z() = (int) ( Hz.length() )/ rList_; |
| 442 |
|
|
| 443 |
< |
for (i = 0; i < nGroupsInRow; i++) { |
| 444 |
< |
rs = cgRowData.position[i]; |
| 445 |
< |
snap_->scaleVector(rs); |
| 446 |
< |
} |
| 435 |
< |
|
| 436 |
< |
|
| 437 |
< |
VDiv (invWid, cells, region); |
| 438 |
< |
for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1; |
| 439 |
< |
for (n = 0; n < nMol; n ++) { |
| 440 |
< |
VSAdd (rs, mol[n].r, 0.5, region); |
| 441 |
< |
VMul (cc, rs, invWid); |
| 442 |
< |
c = VLinear (cc, cells) + nMol; |
| 443 |
< |
cellList[n] = cellList[c]; |
| 444 |
< |
cellList[c] = n; |
| 445 |
< |
} |
| 446 |
< |
nebrTabLen = 0; |
| 447 |
< |
for (m1z = 0; m1z < cells.z(); m1z++) { |
| 448 |
< |
for (m1y = 0; m1y < cells.y(); m1y++) { |
| 449 |
< |
for (m1x = 0; m1x < cells.x(); m1x++) { |
| 450 |
< |
Vector3i m1v(m1x, m1y, m1z); |
| 451 |
< |
m1 = VLinear(m1v, cells) + nMol; |
| 452 |
< |
for (offset = 0; offset < nOffset_; offset++) { |
| 453 |
< |
m2v = m1v + cellOffsets_[offset]; |
| 454 |
< |
shift = V3Zero(); |
| 443 |
> |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 444 |
> |
Vector3d rs, scaled, dr; |
| 445 |
> |
Vector3i whichCell; |
| 446 |
> |
int cellIndex; |
| 447 |
|
|
| 448 |
< |
if (m2v.x() >= cells.x) { |
| 448 |
> |
#ifdef IS_MPI |
| 449 |
> |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 450 |
> |
rs = cgRowData.position[i]; |
| 451 |
> |
// scaled positions relative to the box vectors |
| 452 |
> |
scaled = invHmat * rs; |
| 453 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 454 |
> |
// numbers |
| 455 |
> |
for (int j = 0; j < 3; j++) |
| 456 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 457 |
> |
|
| 458 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 459 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 460 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 461 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 462 |
> |
|
| 463 |
> |
// find single index of this cell: |
| 464 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 465 |
> |
// add this cutoff group to the list of groups in this cell; |
| 466 |
> |
cellListRow_[cellIndex].push_back(i); |
| 467 |
> |
} |
| 468 |
> |
|
| 469 |
> |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 470 |
> |
rs = cgColData.position[i]; |
| 471 |
> |
// scaled positions relative to the box vectors |
| 472 |
> |
scaled = invHmat * rs; |
| 473 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 474 |
> |
// numbers |
| 475 |
> |
for (int j = 0; j < 3; j++) |
| 476 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 477 |
> |
|
| 478 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 479 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 480 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 481 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 482 |
> |
|
| 483 |
> |
// find single index of this cell: |
| 484 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 485 |
> |
// add this cutoff group to the list of groups in this cell; |
| 486 |
> |
cellListCol_[cellIndex].push_back(i); |
| 487 |
> |
} |
| 488 |
> |
#else |
| 489 |
> |
for (int i = 0; i < nGroups_; i++) { |
| 490 |
> |
rs = snap_->cgData.position[i]; |
| 491 |
> |
// scaled positions relative to the box vectors |
| 492 |
> |
scaled = invHmat * rs; |
| 493 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 494 |
> |
// numbers |
| 495 |
> |
for (int j = 0; j < 3; j++) |
| 496 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 497 |
> |
|
| 498 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 499 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 500 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 501 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 502 |
> |
|
| 503 |
> |
// find single index of this cell: |
| 504 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 505 |
> |
// add this cutoff group to the list of groups in this cell; |
| 506 |
> |
cellList_[cellIndex].push_back(i); |
| 507 |
> |
} |
| 508 |
> |
#endif |
| 509 |
> |
|
| 510 |
> |
|
| 511 |
> |
|
| 512 |
> |
for (int m1z = 0; m1z < nCells_.z(); m1z++) { |
| 513 |
> |
for (int m1y = 0; m1y < nCells_.y(); m1y++) { |
| 514 |
> |
for (int m1x = 0; m1x < nCells_.x(); m1x++) { |
| 515 |
> |
Vector3i m1v(m1x, m1y, m1z); |
| 516 |
> |
int m1 = Vlinear(m1v, nCells_); |
| 517 |
> |
|
| 518 |
> |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); |
| 519 |
> |
os != cellOffsets_.end(); ++os) { |
| 520 |
> |
|
| 521 |
> |
Vector3i m2v = m1v + (*os); |
| 522 |
> |
|
| 523 |
> |
if (m2v.x() >= nCells_.x()) { |
| 524 |
|
m2v.x() = 0; |
| 458 |
– |
shift.x() = region.x(); |
| 525 |
|
} else if (m2v.x() < 0) { |
| 526 |
< |
m2v.x() = cells.x() - 1; |
| 461 |
< |
shift.x() = - region.x(); |
| 526 |
> |
m2v.x() = nCells_.x() - 1; |
| 527 |
|
} |
| 528 |
< |
|
| 529 |
< |
if (m2v.y() >= cells.y()) { |
| 528 |
> |
|
| 529 |
> |
if (m2v.y() >= nCells_.y()) { |
| 530 |
|
m2v.y() = 0; |
| 466 |
– |
shift.y() = region.y(); |
| 531 |
|
} else if (m2v.y() < 0) { |
| 532 |
< |
m2v.y() = cells.y() - 1; |
| 469 |
< |
shift.y() = - region.y(); |
| 532 |
> |
m2v.y() = nCells_.y() - 1; |
| 533 |
|
} |
| 534 |
+ |
|
| 535 |
+ |
if (m2v.z() >= nCells_.z()) { |
| 536 |
+ |
m2v.z() = 0; |
| 537 |
+ |
} else if (m2v.z() < 0) { |
| 538 |
+ |
m2v.z() = nCells_.z() - 1; |
| 539 |
+ |
} |
| 540 |
+ |
|
| 541 |
+ |
int m2 = Vlinear (m2v, nCells_); |
| 542 |
|
|
| 543 |
< |
m2 = VLinear (m2v, cells) + nMol; |
| 544 |
< |
for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) { |
| 545 |
< |
for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) { |
| 546 |
< |
if (m1 != m2 || j2 < j1) { |
| 547 |
< |
dr = mol[j1].r - mol[j2].r; |
| 548 |
< |
VSub (dr, mol[j1].r, mol[j2].r); |
| 549 |
< |
VVSub (dr, shift); |
| 550 |
< |
if (VLenSq (dr) < rrNebr) { |
| 551 |
< |
neighborList.push_back(make_pair(j1, j2)); |
| 543 |
> |
#ifdef IS_MPI |
| 544 |
> |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 545 |
> |
j1 != cellListRow_[m1].end(); ++j1) { |
| 546 |
> |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 547 |
> |
j2 != cellListCol_[m2].end(); ++j2) { |
| 548 |
> |
|
| 549 |
> |
// Always do this if we're in different cells or if |
| 550 |
> |
// we're in the same cell and the global index of the |
| 551 |
> |
// j2 cutoff group is less than the j1 cutoff group |
| 552 |
> |
|
| 553 |
> |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 554 |
> |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 555 |
> |
snap_->wrapVector(dr); |
| 556 |
> |
if (dr.lengthSquare() < rl2) { |
| 557 |
> |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 558 |
|
} |
| 559 |
|
} |
| 560 |
|
} |
| 561 |
|
} |
| 562 |
+ |
#else |
| 563 |
+ |
for (vector<int>::iterator j1 = cellList_[m1].begin(); |
| 564 |
+ |
j1 != cellList_[m1].end(); ++j1) { |
| 565 |
+ |
for (vector<int>::iterator j2 = cellList_[m2].begin(); |
| 566 |
+ |
j2 != cellList_[m2].end(); ++j2) { |
| 567 |
+ |
|
| 568 |
+ |
// Always do this if we're in different cells or if |
| 569 |
+ |
// we're in the same cell and the global index of the |
| 570 |
+ |
// j2 cutoff group is less than the j1 cutoff group |
| 571 |
+ |
|
| 572 |
+ |
if (m2 != m1 || (*j2) < (*j1)) { |
| 573 |
+ |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 574 |
+ |
snap_->wrapVector(dr); |
| 575 |
+ |
if (dr.lengthSquare() < rl2) { |
| 576 |
+ |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 577 |
+ |
} |
| 578 |
+ |
} |
| 579 |
+ |
} |
| 580 |
+ |
} |
| 581 |
+ |
#endif |
| 582 |
|
} |
| 583 |
|
} |
| 584 |
|
} |
| 585 |
|
} |
| 489 |
– |
} |
| 586 |
|
|
| 587 |
< |
|
| 587 |
> |
// save the local cutoff group positions for the check that is |
| 588 |
> |
// done on each loop: |
| 589 |
> |
saved_CG_positions_.clear(); |
| 590 |
> |
for (int i = 0; i < nGroups_; i++) |
| 591 |
> |
saved_CG_positions_.push_back(snap_->cgData.position[i]); |
| 592 |
> |
|
| 593 |
> |
return neighborList; |
| 594 |
> |
} |
| 595 |
|
} //end namespace OpenMD |
