| 449 |
|
Molecule::CutoffGroupIterator ci; |
| 450 |
|
CutoffGroup* cg; |
| 451 |
|
|
| 452 |
< |
// forces are zeroed here, before any are accumulated. |
| 452 |
> |
// forces and potentials are zeroed here, before any are |
| 453 |
> |
// accumulated. |
| 454 |
|
|
| 455 |
+ |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 456 |
+ |
|
| 457 |
+ |
snap->setBondPotential(0.0); |
| 458 |
+ |
snap->setBendPotential(0.0); |
| 459 |
+ |
snap->setTorsionPotential(0.0); |
| 460 |
+ |
snap->setInversionPotential(0.0); |
| 461 |
+ |
|
| 462 |
+ |
potVec zeroPot(0.0); |
| 463 |
+ |
snap->setLongRangePotential(zeroPot); |
| 464 |
+ |
snap->setExcludedPotentials(zeroPot); |
| 465 |
+ |
|
| 466 |
+ |
snap->setRestraintPotential(0.0); |
| 467 |
+ |
snap->setRawPotential(0.0); |
| 468 |
+ |
|
| 469 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 470 |
|
mol = info_->nextMolecule(mi)) { |
| 471 |
|
for(atom = mol->beginAtom(ai); atom != NULL; |
| 623 |
|
curSnapshot->setTorsionPotential(torsionPotential); |
| 624 |
|
curSnapshot->setInversionPotential(inversionPotential); |
| 625 |
|
|
| 626 |
< |
RealType shortRangePotential = bondPotential + bendPotential + |
| 627 |
< |
torsionPotential + inversionPotential; |
| 626 |
> |
// RealType shortRangePotential = bondPotential + bendPotential + |
| 627 |
> |
// torsionPotential + inversionPotential; |
| 628 |
|
|
| 629 |
< |
curSnapshot->setShortRangePotential(shortRangePotential); |
| 629 |
> |
// curSnapshot->setShortRangePotential(shortRangePotential); |
| 630 |
|
} |
| 631 |
|
|
| 632 |
|
void ForceManager::longRangeInteractions() { |
| 691 |
|
idat.pot = &workPot; |
| 692 |
|
idat.excludedPot = &exPot; |
| 693 |
|
sdat.pot = fDecomp_->getEmbeddingPotential(); |
| 694 |
+ |
sdat.excludedPot = fDecomp_->getExcludedSelfPotential(); |
| 695 |
|
idat.vpair = &vpair; |
| 696 |
|
idat.dVdFQ1 = &dVdFQ1; |
| 697 |
|
idat.dVdFQ2 = &dVdFQ2; |
| 896 |
|
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 897 |
|
*(fDecomp_->getPairwisePotential()); |
| 898 |
|
|
| 899 |
< |
curSnapshot->setLongRangePotentialFamilies(longRangePotential); |
| 899 |
> |
curSnapshot->setLongRangePotential(longRangePotential); |
| 900 |
|
|
| 901 |
< |
lrPot = longRangePotential.sum(); |
| 901 |
> |
// lrPot = longRangePotential.sum(); |
| 902 |
|
|
| 903 |
< |
//store the long range potential |
| 904 |
< |
curSnapshot->setLongRangePotential(lrPot); |
| 905 |
< |
|
| 906 |
< |
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedPotential())); |
| 903 |
> |
// //store the long range potential |
| 904 |
> |
// curSnapshot->setLongRangePotential(lrPot); |
| 905 |
> |
|
| 906 |
> |
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 907 |
> |
*(fDecomp_->getExcludedPotential())); |
| 908 |
|
|
| 909 |
|
} |
| 910 |
|
|
| 915 |
|
Molecule::RigidBodyIterator rbIter; |
| 916 |
|
RigidBody* rb; |
| 917 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 918 |
< |
|
| 918 |
> |
|
| 919 |
|
// collect the atomic forces onto rigid bodies |
| 920 |
|
|
| 921 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
