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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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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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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* 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 |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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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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|
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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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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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|
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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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|
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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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BitSet DistanceFinder::find(const BitSet& bs, double 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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assert(bsResult.size() == bs.size()); |
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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(); |
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for (int j = 0; j < stuntdoubles_.size(); ++j) { |
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Vector3d r =centerPos - stuntdoubles_[j]->getPos(); |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.setBitOn(j); |
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} |
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} |
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} |
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|
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return bsResult; |
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} |
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|
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} |
