| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "selection/DistanceFinder.hpp" |
| 57 |
|
RigidBody* rb; |
| 58 |
|
|
| 59 |
|
|
| 60 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 60 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 61 |
> |
mol = info_->nextMolecule(mi)) { |
| 62 |
|
|
| 63 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 63 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 64 |
> |
atom = mol->nextAtom(ai)) { |
| 65 |
|
stuntdoubles_[atom->getGlobalIndex()] = atom; |
| 66 |
|
} |
| 67 |
|
|
| 68 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 68 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 69 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 70 |
|
stuntdoubles_[rb->getGlobalIndex()] = rb; |
| 71 |
|
} |
| 72 |
< |
|
| 69 |
< |
} |
| 70 |
< |
|
| 72 |
> |
} |
| 73 |
|
} |
| 74 |
|
|
| 75 |
|
OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) { |
| 79 |
|
OpenMDBitSet bsResult(nStuntDoubles_); |
| 80 |
|
assert(bsResult.size() == bs.size()); |
| 81 |
|
|
| 82 |
< |
for (int j = 0; j < stuntdoubles_.size(); ++j) { |
| 82 |
> |
for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
| 83 |
|
if (stuntdoubles_[j]->isRigidBody()) { |
| 84 |
|
RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]); |
| 85 |
|
rb->updateAtoms(); |
| 86 |
|
} |
| 87 |
|
} |
| 88 |
|
|
| 89 |
+ |
// This will fail in parallel because i might not be on this processor. |
| 90 |
+ |
|
| 91 |
|
for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) { |
| 92 |
|
center = stuntdoubles_[i]; |
| 93 |
|
centerPos = center->getPos(); |
| 94 |
< |
for (int j = 0; j < stuntdoubles_.size(); ++j) { |
| 94 |
> |
for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
| 95 |
|
Vector3d r =centerPos - stuntdoubles_[j]->getPos(); |
| 96 |
|
currSnapshot->wrapVector(r); |
| 97 |
|
if (r.length() <= distance) { |
