| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 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 |
| 14 |
< |
* 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)) |
| 17 |
< |
* |
| 18 |
< |
* 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 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* 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, 234107 (2008). |
| 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 oopse { |
| 44 |
> |
namespace OpenMD { |
| 45 |
|
|
| 45 |
– |
|
| 46 |
– |
|
| 46 |
|
IndexFinder::IndexFinder(SimInfo* info) : info_(info){ |
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|
nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 48 |
|
bitSets_.resize(info_->getNGlobalMolecules()); |
| 49 |
|
init(); |
| 50 |
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} |
| 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 |
< |
OOPSEBitSet bs(nStuntDoubles_); |
| 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 |
< |
OOPSEBitSet IndexFinder::find(int molIndex){ |
| 76 |
> |
OpenMDBitSet IndexFinder::find(int molIndex){ |
| 77 |
|
return bitSets_[molIndex]; |
| 78 |
|
} |
| 79 |
|
|
| 80 |
< |
OOPSEBitSet IndexFinder::find(int begMolIndex, int endMolIndex){ |
| 81 |
< |
OOPSEBitSet bs(nStuntDoubles_); |
| 80 |
> |
OpenMDBitSet IndexFinder::find(int begMolIndex, int endMolIndex){ |
| 81 |
> |
OpenMDBitSet bs(nStuntDoubles_); |
| 82 |
|
|
| 83 |
|
for (int i = begMolIndex; i < endMolIndex; ++i) { |
| 84 |
|
bs |= bitSets_[i]; |
| 85 |
< |
} |
| 89 |
< |
|
| 85 |
> |
} |
| 86 |
|
return bs; |
| 87 |
|
} |
| 92 |
– |
|
| 93 |
– |
|
| 88 |
|
} |
| 89 |
|
|
