| 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 |
|
#include "selection/IndexFinder.hpp" |
| 43 |
|
#include "primitives/Molecule.hpp" |
| 44 |
|
namespace OpenMD { |
| 45 |
|
|
| 45 |
– |
|
| 46 |
– |
|
| 46 |
|
IndexFinder::IndexFinder(SimInfo* info) : info_(info){ |
| 47 |
|
nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 48 |
|
bitSets_.resize(info_->getNGlobalMolecules()); |
| 49 |
|
init(); |
| 50 |
|
} |
| 51 |
|
|
| 53 |
– |
|
| 52 |
|
void IndexFinder::init() { |
| 53 |
|
|
| 54 |
|
SimInfo::MoleculeIterator mi; |
| 58 |
|
Molecule::RigidBodyIterator rbIter; |
| 59 |
|
RigidBody* rb; |
| 60 |
|
|
| 61 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 61 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 62 |
> |
mol = info_->nextMolecule(mi)) { |
| 63 |
|
|
| 64 |
|
OpenMDBitSet bs(nStuntDoubles_); |
| 65 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 66 |
|
bs.setBitOn(atom->getGlobalIndex()); |
| 67 |
|
} |
| 68 |
< |
|
| 69 |
< |
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 |
|
bs.setBitOn(rb->getGlobalIndex()); |
| 71 |
|
} |
| 73 |
– |
|
| 72 |
|
bitSets_[mol->getGlobalIndex()] = bs; |
| 73 |
< |
} |
| 76 |
< |
|
| 73 |
> |
} |
| 74 |
|
} |
| 75 |
|
|
| 76 |
|
OpenMDBitSet IndexFinder::find(int molIndex){ |
| 82 |
|
|
| 83 |
|
for (int i = begMolIndex; i < endMolIndex; ++i) { |
| 84 |
|
bs |= bitSets_[i]; |
| 85 |
< |
} |
| 89 |
< |
|
| 85 |
> |
} |
| 86 |
|
return bs; |
| 87 |
|
} |
| 92 |
– |
|
| 93 |
– |
|
| 88 |
|
} |
| 89 |
|
|
