| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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, 24107 (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 OpenMD { |
| 45 |
|
| 46 |
IndexFinder::IndexFinder(SimInfo* info) : info_(info){ |
| 47 |
nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 48 |
bitSets_.resize(info_->getNGlobalMolecules()); |
| 49 |
init(); |
| 50 |
} |
| 51 |
|
| 52 |
void IndexFinder::init() { |
| 53 |
|
| 54 |
SimInfo::MoleculeIterator mi; |
| 55 |
Molecule* mol; |
| 56 |
Molecule::AtomIterator ai; |
| 57 |
Atom* atom; |
| 58 |
Molecule::RigidBodyIterator rbIter; |
| 59 |
RigidBody* rb; |
| 60 |
|
| 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 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 69 |
rb = mol->nextRigidBody(rbIter)) { |
| 70 |
bs.setBitOn(rb->getGlobalIndex()); |
| 71 |
} |
| 72 |
bitSets_[mol->getGlobalIndex()] = bs; |
| 73 |
} |
| 74 |
} |
| 75 |
|
| 76 |
OpenMDBitSet IndexFinder::find(int molIndex){ |
| 77 |
return bitSets_[molIndex]; |
| 78 |
} |
| 79 |
|
| 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 |
} |
| 86 |
return bs; |
| 87 |
} |
| 88 |
} |
| 89 |
|
