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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include "selection/IndexFinder.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace OpenMD { |
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|
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IndexFinder::IndexFinder(SimInfo* info) : info_(info){ |
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nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies()); |
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nObjects_.push_back(info_->getNGlobalBonds()); |
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nObjects_.push_back(info_->getNGlobalBends()); |
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nObjects_.push_back(info_->getNGlobalTorsions()); |
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nObjects_.push_back(info_->getNGlobalInversions()); |
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nObjects_.push_back(info_->getNGlobalMolecules()); |
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|
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selectionSets_.resize(info_->getNGlobalMolecules()); |
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init(); |
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} |
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|
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void IndexFinder::init() { |
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|
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SimInfo::MoleculeIterator mi; |
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Molecule::AtomIterator ai; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::BondIterator bondIter; |
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Molecule::BendIterator bendIter; |
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Molecule::TorsionIterator torsionIter; |
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Molecule::InversionIterator inversionIter; |
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|
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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Inversion* inversion; |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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SelectionSet ss(nObjects_); |
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ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex()); |
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|
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
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} |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); |
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} |
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for (bond = mol->beginBond(bondIter); bond != NULL; |
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bond = mol->nextBond(bondIter)) { |
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ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex()); |
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} |
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for (bend = mol->beginBend(bendIter); bend != NULL; |
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bend = mol->nextBend(bendIter)) { |
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ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex()); |
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} |
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for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
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torsion = mol->nextTorsion(torsionIter)) { |
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ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex()); |
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} |
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for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
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inversion = mol->nextInversion(inversionIter)) { |
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ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex()); |
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} |
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|
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selectionSets_[mol->getGlobalIndex()] = ss; |
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} |
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} |
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|
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SelectionSet IndexFinder::find(int molIndex){ |
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return selectionSets_[molIndex]; |
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} |
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|
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SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex){ |
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SelectionSet ss(nObjects_); |
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|
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for (int i = begMolIndex; i < endMolIndex; ++i) { |
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ss |= selectionSets_[i]; |
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} |
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return ss; |
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} |
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} |
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|
