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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* Copyright (c) 2005, 2010 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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* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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, 24107 (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/DistanceFinder.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) { |
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|
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namespace OpenMD { |
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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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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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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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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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for(atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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stuntdoubles_[atom->getGlobalIndex()] = atom; |
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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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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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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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BitSet DistanceFinder::find(const BitSet& bs, double distance) { |
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OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType 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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OpenMDBitSet bsResult(nStuntDoubles_); |
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assert(bsResult.size() == bs.size()); |
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for (int i = bs.nextOnBit(-1); i != -1; i = bs.nextOnBit(i)) { |
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#ifdef IS_MPI |
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int mol; |
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int proc; |
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RealType data[3]; |
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int worldRank = MPI::COMM_WORLD.Get_rank(); |
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#endif |
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|
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for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
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if (stuntdoubles_[j]->isRigidBody()) { |
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RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]); |
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rb->updateAtoms(); |
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} |
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} |
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|
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OpenMDBitSet bsTemp(nStuntDoubles_); |
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bsTemp = bs; |
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bsTemp.parallelReduce(); |
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for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) { |
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// Now, if we own stuntdouble i, we can use the position, but in |
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// parallel, we'll need to let everyone else know what that |
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// position is! |
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#ifdef IS_MPI |
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mol = info_->getGlobalMolMembership(i); |
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proc = info_->getMolToProc(mol); |
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if (proc == worldRank) { |
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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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data[0] = centerPos.x(); |
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data[1] = centerPos.y(); |
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data[2] = centerPos.z(); |
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MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); |
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} else { |
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MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); |
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centerPos = Vector3d(data); |
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} |
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#else |
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center = stuntdoubles_[i]; |
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centerPos = center->getPos(); |
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#endif |
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for (unsigned 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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return bsResult; |
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} |
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} |
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} |
