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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 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). |
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+ |
* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "selection/DistanceFinder.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) { |
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> |
DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) { |
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|
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nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
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stuntdoubles_.resize(nStuntDoubles_); |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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< |
stuntdoubles_[atom->getGlobalIndex()] = atom; |
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< |
} |
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> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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> |
stuntdoubles_[atom->getGlobalIndex()] = atom; |
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> |
} |
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|
|
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< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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< |
stuntdoubles_[rb->getGlobalIndex()] = rb; |
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< |
} |
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> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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> |
stuntdoubles_[rb->getGlobalIndex()] = rb; |
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> |
} |
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|
|
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} |
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|
|
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< |
} |
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> |
} |
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|
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< |
BitSet DistanceFinder::find(const BitSet& bs, double distance) { |
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> |
OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) { |
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StuntDouble * center; |
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Vector3d centerPos; |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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< |
BitSet bsResult(nStuntDoubles_); |
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> |
OpenMDBitSet bsResult(nStuntDoubles_); |
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|
assert(bsResult.size() == bs.size()); |
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|
|
| 80 |
< |
for (int i = bs.nextOnBit(-1); i != -1; i = bs.nextOnBit(i)) { |
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< |
center = stuntdoubles_[i]; |
| 82 |
< |
centerPos = center->getPos(); |
| 83 |
< |
for (int j = 0; j < stuntdoubles_.size(); ++j) { |
| 84 |
< |
Vector3d r =centerPos - stuntdoubles_[j]->getPos(); |
| 85 |
< |
currSnapshot->wrapVector(r); |
| 86 |
< |
if (r.length() <= distance) { |
| 87 |
< |
bsResult.setBitOn(j); |
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< |
} |
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< |
} |
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> |
for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) { |
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> |
center = stuntdoubles_[i]; |
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> |
centerPos = center->getPos(); |
| 83 |
> |
for (int j = 0; j < stuntdoubles_.size(); ++j) { |
| 84 |
> |
Vector3d r =centerPos - stuntdoubles_[j]->getPos(); |
| 85 |
> |
currSnapshot->wrapVector(r); |
| 86 |
> |
if (r.length() <= distance) { |
| 87 |
> |
bsResult.setBitOn(j); |
| 88 |
> |
} |
| 89 |
> |
} |
| 90 |
|
} |
| 91 |
|
|
| 92 |
|
return bsResult; |
| 93 |
< |
} |
| 93 |
> |
} |
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|
| 95 |
|
} |
