| 72 |
|
|
| 73 |
|
void ForceManager::calcForces() { |
| 74 |
|
|
| 75 |
< |
if (!info_->isFortranInitialized()) { |
| 75 |
> |
if (!info_->isTopologyDone()) { |
| 76 |
|
info_->update(); |
| 77 |
|
interactionMan_->setSimInfo(info_); |
| 78 |
|
interactionMan_->initialize(); |
| 79 |
|
swfun_ = interactionMan_->getSwitchingFunction(); |
| 80 |
|
fDecomp_->distributeInitialData(); |
| 81 |
< |
info_->setupFortran(); |
| 81 |
> |
info_->prepareTopology(); |
| 82 |
|
} |
| 83 |
|
|
| 84 |
|
preCalculation(); |
| 323 |
|
rCutSq = groupCutoffMap[gtypes].first; |
| 324 |
|
|
| 325 |
|
if (rgrpsq < rCutSq) { |
| 326 |
< |
idat.rcut = groupCutoffMap[gtypes].second; |
| 326 |
> |
*(idat.rcut) = groupCutoffMap[gtypes].second; |
| 327 |
|
if (iLoop == PAIR_LOOP) { |
| 328 |
|
vij *= 0.0; |
| 329 |
|
fij = V3Zero; |
| 330 |
|
} |
| 331 |
|
|
| 332 |
< |
in_switching_region = swfun_->getSwitch(rgrpsq, idat.sw, dswdr, rgrp); |
| 332 |
> |
in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr, |
| 333 |
> |
rgrp); |
| 334 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 335 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 336 |
|
|
| 347 |
|
idat = fDecomp_->fillInteractionData(atom1, atom2); |
| 348 |
|
|
| 349 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 350 |
< |
idat.d = d_grp; |
| 351 |
< |
idat.r2 = rgrpsq; |
| 350 |
> |
*(idat.d) = d_grp; |
| 351 |
> |
*(idat.r2) = rgrpsq; |
| 352 |
|
} else { |
| 353 |
< |
idat.d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 354 |
< |
curSnapshot->wrapVector(idat.d); |
| 355 |
< |
idat.r2 = idat.d.lengthSquare(); |
| 353 |
> |
*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2); |
| 354 |
> |
curSnapshot->wrapVector( *(idat.d) ); |
| 355 |
> |
*(idat.r2) = idat.d->lengthSquare(); |
| 356 |
|
} |
| 357 |
|
|
| 358 |
< |
idat.rij = sqrt(idat.r2); |
| 358 |
> |
*(idat.rij) = sqrt( *(idat.r2) ); |
| 359 |
|
|
| 360 |
|
if (iLoop == PREPAIR_LOOP) { |
| 361 |
|
interactionMan_->doPrePair(idat); |
| 362 |
|
} else { |
| 363 |
|
interactionMan_->doPair(idat); |
| 364 |
< |
vij += idat.vpair; |
| 365 |
< |
fij += idat.f1; |
| 366 |
< |
tau -= outProduct(idat.d, idat.f1); |
| 364 |
> |
vij += *(idat.vpair); |
| 365 |
> |
fij += *(idat.f1); |
| 366 |
> |
tau -= outProduct( *(idat.d), *(idat.f1)); |
| 367 |
|
} |
| 368 |
|
} |
| 369 |
|
} |
| 377 |
|
fij += fg; |
| 378 |
|
|
| 379 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 380 |
< |
tau -= outProduct(idat.d, fg); |
| 380 |
> |
tau -= outProduct( *(idat.d), fg); |
| 381 |
|
} |
| 382 |
|
|
| 383 |
|
for (vector<int>::iterator ia = atomListRow.begin(); |
| 384 |
|
ia != atomListRow.end(); ++ia) { |
| 385 |
|
atom1 = (*ia); |
| 386 |
< |
mf = fDecomp_->getMfactRow(atom1); |
| 386 |
> |
mf = fDecomp_->getMassFactorRow(atom1); |
| 387 |
|
// fg is the force on atom ia due to cutoff group's |
| 388 |
|
// presence in switching region |
| 389 |
|
fg = swderiv * d_grp * mf; |
| 401 |
|
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 402 |
|
jb != atomListColumn.end(); ++jb) { |
| 403 |
|
atom2 = (*jb); |
| 404 |
< |
mf = fDecomp_->getMfactColumn(atom2); |
| 404 |
> |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 405 |
|
// fg is the force on atom jb due to cutoff group's |
| 406 |
|
// presence in switching region |
| 407 |
|
fg = -swderiv * d_grp * mf; |
