--- trunk/src/selection/SelectionManager.cpp 2005/02/16 19:36:30 353 +++ branches/development/src/selection/SelectionManager.cpp 2011/11/22 20:38:56 1665 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,13 +28,23 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "selection/SelectionManager.hpp" #include "primitives/Molecule.hpp" #include "brains/SimInfo.hpp" -namespace oopse { -SelectionManager::SelectionManager(SimInfo* info) : info_(info){ +namespace OpenMD { + SelectionManager::SelectionManager(SimInfo* info) : info_(info){ int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); @@ -60,60 +61,60 @@ SelectionManager::SelectionManager(SimInfo* info) : in for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { - for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { - stuntdoubles_[atom->getGlobalIndex()] = atom; - } + for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + stuntdoubles_[atom->getGlobalIndex()] = atom; + } - for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { - stuntdoubles_[rb->getGlobalIndex()] = rb; - } + for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { + stuntdoubles_[rb->getGlobalIndex()] = rb; + } } -} + } -StuntDouble* SelectionManager::beginSelected(int& i) { + StuntDouble* SelectionManager::beginSelected(int& i) { i = bsSelection_.firstOnBit(); return i == -1 ? NULL : stuntdoubles_[i]; -} -StuntDouble* SelectionManager::nextSelected(int& i) { + } + StuntDouble* SelectionManager::nextSelected(int& i) { i = bsSelection_.nextOnBit(i); return i == -1 ? NULL : stuntdoubles_[i]; -} + } -StuntDouble* SelectionManager::beginUnselected(int& i){ + StuntDouble* SelectionManager::beginUnselected(int& i){ i = bsSelection_.firstOffBit(); return i == -1 ? NULL : stuntdoubles_[i]; -} -StuntDouble* SelectionManager::nextUnSelected(int& i) { + } + StuntDouble* SelectionManager::nextUnSelected(int& i) { i = bsSelection_.nextOffBit(i); return i == -1 ? NULL : stuntdoubles_[i]; -} + } -SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) { + SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) { SelectionManager result(sman1); result |= sman2; return result; -} -SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) { + } + SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) { SelectionManager result(sman1); result &= sman2; return result; -} -SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) { + } + SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) { SelectionManager result(sman1); result ^= sman2; return result; -} -SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){ + } + SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){ SelectionManager result(sman1); result -= sman2; return result; -} + } }