| 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(); |
| 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; |
| 427 |
|
if (iLoop == PREPAIR_LOOP) { |
| 428 |
|
if (info_->requiresPrepair()) { |
| 429 |
|
fDecomp_->collectIntermediateData(); |
| 430 |
< |
atomListLocal = fDecomp_->getAtomList(); |
| 431 |
< |
for (vector<int>::iterator ia = atomListLocal.begin(); |
| 432 |
< |
ia != atomListLocal.end(); ++ia) { |
| 433 |
< |
atom1 = (*ia); |
| 430 |
> |
|
| 431 |
> |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 432 |
|
sdat = fDecomp_->fillSelfData(atom1); |
| 433 |
|
interactionMan_->doPreForce(sdat); |
| 434 |
|
} |
| 435 |
+ |
|
| 436 |
|
fDecomp_->distributeIntermediateData(); |
| 437 |
|
} |
| 438 |
|
} |
| 441 |
|
|
| 442 |
|
fDecomp_->collectData(); |
| 443 |
|
|
| 444 |
< |
if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) { |
| 445 |
< |
atomListLocal = fDecomp_->getAtomList(); |
| 446 |
< |
for (vector<int>::iterator ia = atomListLocal.begin(); |
| 448 |
< |
ia != atomListLocal.end(); ++ia) { |
| 449 |
< |
atom1 = (*ia); |
| 444 |
> |
if ( info_->requiresSkipCorrection() ) { |
| 445 |
> |
|
| 446 |
> |
for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) { |
| 447 |
|
|
| 448 |
< |
if (info_->requiresSkipCorrection()) { |
| 449 |
< |
vector<int> skipList = fDecomp_->getSkipsForAtom(atom1); |
| 450 |
< |
for (vector<int>::iterator jb = skipList.begin(); |
| 451 |
< |
jb != skipList.end(); ++jb) { |
| 452 |
< |
atom2 = (*jb); |
| 453 |
< |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 454 |
< |
interactionMan_->doSkipCorrection(idat); |
| 455 |
< |
} |
| 448 |
> |
vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 ); |
| 449 |
> |
|
| 450 |
> |
for (vector<int>::iterator jb = skipList.begin(); |
| 451 |
> |
jb != skipList.end(); ++jb) { |
| 452 |
> |
|
| 453 |
> |
atom2 = (*jb); |
| 454 |
> |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 455 |
> |
interactionMan_->doSkipCorrection(idat); |
| 456 |
> |
|
| 457 |
|
} |
| 460 |
– |
|
| 461 |
– |
if (info_->requiresSelfCorrection()) { |
| 462 |
– |
sdat = fDecomp_->fillSelfData(atom1); |
| 463 |
– |
interactionMan_->doSelfCorrection(sdat); |
| 464 |
– |
} |
| 458 |
|
} |
| 459 |
|
} |
| 460 |
+ |
|
| 461 |
+ |
if (info_->requiresSelfCorrection()) { |
| 462 |
|
|
| 463 |
+ |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 464 |
+ |
sdat = fDecomp_->fillSelfData(atom1); |
| 465 |
+ |
interactionMan_->doSelfCorrection(sdat); |
| 466 |
+ |
} |
| 467 |
+ |
|
| 468 |
+ |
} |
| 469 |
+ |
|
| 470 |
|
// dangerous to iterate over enums, but we'll live on the edge: |
| 471 |
|
for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){ |
| 472 |
|
lrPot += longRangePotential[i]; //Quick hack |
