| 1324 |
|
|
| 1325 |
|
RealType rList_ = (largestRcut_ + skinThickness_); |
| 1326 |
|
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 1327 |
< |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 1327 |
> |
Mat3x3d box; |
| 1328 |
> |
Mat3x3d invBox; |
| 1329 |
> |
|
| 1330 |
|
Vector3d rs, scaled, dr; |
| 1331 |
|
Vector3i whichCell; |
| 1332 |
|
int cellIndex; |
| 1337 |
|
#else |
| 1338 |
|
cellList_.clear(); |
| 1339 |
|
#endif |
| 1340 |
< |
|
| 1340 |
> |
|
| 1341 |
|
if (!usePeriodicBoundaryConditions_) { |
| 1342 |
< |
doAllPairs = true; |
| 1342 |
> |
box = snap_->getBoundingBox(); |
| 1343 |
> |
invBox = snap_->getInvBoundingBox(); |
| 1344 |
|
} else { |
| 1345 |
< |
|
| 1346 |
< |
Mat3x3d Hmat = snap_->getHmat(); |
| 1344 |
< |
Vector3d Hx = Hmat.getColumn(0); |
| 1345 |
< |
Vector3d Hy = Hmat.getColumn(1); |
| 1346 |
< |
Vector3d Hz = Hmat.getColumn(2); |
| 1347 |
< |
|
| 1348 |
< |
nCells_.x() = (int) ( Hx.length() )/ rList_; |
| 1349 |
< |
nCells_.y() = (int) ( Hy.length() )/ rList_; |
| 1350 |
< |
nCells_.z() = (int) ( Hz.length() )/ rList_; |
| 1351 |
< |
|
| 1352 |
< |
// handle small boxes where the cell offsets can end up repeating cells |
| 1353 |
< |
|
| 1354 |
< |
if (nCells_.x() < 3) doAllPairs = true; |
| 1355 |
< |
if (nCells_.y() < 3) doAllPairs = true; |
| 1356 |
< |
if (nCells_.z() < 3) doAllPairs = true; |
| 1357 |
< |
|
| 1358 |
< |
int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); |
| 1359 |
< |
|
| 1360 |
< |
#ifdef IS_MPI |
| 1361 |
< |
cellListRow_.resize(nCtot); |
| 1362 |
< |
cellListCol_.resize(nCtot); |
| 1363 |
< |
#else |
| 1364 |
< |
cellList_.resize(nCtot); |
| 1365 |
< |
#endif |
| 1345 |
> |
box = snap_->getHmat(); |
| 1346 |
> |
invBox = snap_->getInvHmat(); |
| 1347 |
|
} |
| 1348 |
< |
|
| 1348 |
> |
|
| 1349 |
> |
Vector3d boxX = box.getColumn(0); |
| 1350 |
> |
Vector3d boxY = box.getColumn(1); |
| 1351 |
> |
Vector3d boxZ = box.getColumn(2); |
| 1352 |
> |
|
| 1353 |
> |
nCells_.x() = (int) ( boxX.length() )/ rList_; |
| 1354 |
> |
nCells_.y() = (int) ( boxY.length() )/ rList_; |
| 1355 |
> |
nCells_.z() = (int) ( boxZ.length() )/ rList_; |
| 1356 |
> |
|
| 1357 |
> |
// handle small boxes where the cell offsets can end up repeating cells |
| 1358 |
> |
|
| 1359 |
> |
if (nCells_.x() < 3) doAllPairs = true; |
| 1360 |
> |
if (nCells_.y() < 3) doAllPairs = true; |
| 1361 |
> |
if (nCells_.z() < 3) doAllPairs = true; |
| 1362 |
> |
|
| 1363 |
> |
int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); |
| 1364 |
> |
|
| 1365 |
> |
#ifdef IS_MPI |
| 1366 |
> |
cellListRow_.resize(nCtot); |
| 1367 |
> |
cellListCol_.resize(nCtot); |
| 1368 |
> |
#else |
| 1369 |
> |
cellList_.resize(nCtot); |
| 1370 |
> |
#endif |
| 1371 |
> |
|
| 1372 |
|
if (!doAllPairs) { |
| 1373 |
|
#ifdef IS_MPI |
| 1374 |
< |
|
| 1374 |
> |
|
| 1375 |
|
for (int i = 0; i < nGroupsInRow_; i++) { |
| 1376 |
|
rs = cgRowData.position[i]; |
| 1377 |
|
|
| 1378 |
|
// scaled positions relative to the box vectors |
| 1379 |
< |
scaled = invHmat * rs; |
| 1379 |
> |
scaled = invBox * rs; |
| 1380 |
|
|
| 1381 |
|
// wrap the vector back into the unit box by subtracting integer box |
| 1382 |
|
// numbers |
| 1404 |
|
rs = cgColData.position[i]; |
| 1405 |
|
|
| 1406 |
|
// scaled positions relative to the box vectors |
| 1407 |
< |
scaled = invHmat * rs; |
| 1407 |
> |
scaled = invBox * rs; |
| 1408 |
|
|
| 1409 |
|
// wrap the vector back into the unit box by subtracting integer box |
| 1410 |
|
// numbers |
| 1428 |
|
// add this cutoff group to the list of groups in this cell; |
| 1429 |
|
cellListCol_[cellIndex].push_back(i); |
| 1430 |
|
} |
| 1431 |
< |
|
| 1431 |
> |
|
| 1432 |
|
#else |
| 1433 |
|
for (int i = 0; i < nGroups_; i++) { |
| 1434 |
|
rs = snap_->cgData.position[i]; |
| 1435 |
|
|
| 1436 |
|
// scaled positions relative to the box vectors |
| 1437 |
< |
scaled = invHmat * rs; |
| 1437 |
> |
scaled = invBox * rs; |
| 1438 |
|
|
| 1439 |
|
// wrap the vector back into the unit box by subtracting integer box |
| 1440 |
|
// numbers |
| 1527 |
|
// allows atoms within a single cutoff group to |
| 1528 |
|
// interact with each other. |
| 1529 |
|
|
| 1526 |
– |
|
| 1527 |
– |
|
| 1530 |
|
if (m2 != m1 || (*j2) >= (*j1) ) { |
| 1531 |
|
|
| 1532 |
|
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
