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/* |
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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. 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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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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#include "selection/DistanceFinder.hpp" |
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#include "primitives/Molecule.hpp" |
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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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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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stuntdoubles_.resize(nObjects_[STUNTDOUBLE]); |
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bonds_.resize(nObjects_[BOND]); |
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bends_.resize(nObjects_[BEND]); |
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torsions_.resize(nObjects_[TORSION]); |
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inversions_.resize(nObjects_[INVERSION]); |
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molecules_.resize(nObjects_[MOLECULE]); |
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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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molecules_[mol->getGlobalIndex()] = mol; |
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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; |
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rb = mol->nextRigidBody(rbIter)) { |
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stuntdoubles_[rb->getGlobalIndex()] = rb; |
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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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bonds_[bond->getGlobalIndex()] = bond; |
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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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bends_[bend->getGlobalIndex()] = bend; |
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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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torsions_[torsion->getGlobalIndex()] = torsion; |
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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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inversions_[inversion->getGlobalIndex()] = inversion; |
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} |
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|
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} |
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} |
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|
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SelectionSet DistanceFinder::find(const SelectionSet& 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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SelectionSet bsResult(nObjects_); |
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assert(bsResult.size() == bs.size()); |
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|
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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; |
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MPI_Comm_rank( MPI_COMM_WORLD, &worldRank); |
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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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SelectionSet bsTemp(nObjects_); |
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bsTemp = bs; |
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bsTemp.parallelReduce(); |
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|
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for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1; |
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i = bsTemp.bitsets_[STUNTDOUBLE].nextOnBit(i)) { |
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|
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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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|
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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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|
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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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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_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD); |
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} else { |
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MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD); |
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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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|
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for (unsigned int j = 0; j < molecules_.size(); ++j) { |
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Vector3d r =centerPos - molecules_[j]->getCom(); |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[MOLECULE].setBitOn(j); |
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} |
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} |
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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.bitsets_[STUNTDOUBLE].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < bonds_.size(); ++j) { |
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Vector3d loc = bonds_[j]->getAtomA()->getPos(); |
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loc += bonds_[j]->getAtomB()->getPos(); |
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loc = loc / 2.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[BOND].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < bends_.size(); ++j) { |
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Vector3d loc = bends_[j]->getAtomA()->getPos(); |
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loc += bends_[j]->getAtomB()->getPos(); |
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loc += bends_[j]->getAtomC()->getPos(); |
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loc = loc / 3.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[BEND].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < torsions_.size(); ++j) { |
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Vector3d loc = torsions_[j]->getAtomA()->getPos(); |
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loc += torsions_[j]->getAtomB()->getPos(); |
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loc += torsions_[j]->getAtomC()->getPos(); |
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loc += torsions_[j]->getAtomD()->getPos(); |
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loc = loc / 4.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[TORSION].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < inversions_.size(); ++j) { |
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Vector3d loc = inversions_[j]->getAtomA()->getPos(); |
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loc += inversions_[j]->getAtomB()->getPos(); |
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loc += inversions_[j]->getAtomC()->getPos(); |
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loc += inversions_[j]->getAtomD()->getPos(); |
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loc = loc / 4.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[INVERSION].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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|
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SelectionSet DistanceFinder::find(const SelectionSet& bs, RealType distance, int frame ) { |
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StuntDouble * center; |
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Vector3d centerPos; |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame); |
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SelectionSet bsResult(nObjects_); |
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assert(bsResult.size() == bs.size()); |
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|
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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; |
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MPI_Comm_rank( MPI_COMM_WORLD, &worldRank); |
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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(frame); |
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} |
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} |
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|
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SelectionSet bsTemp(nObjects_); |
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bsTemp = bs; |
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bsTemp.parallelReduce(); |
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|
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for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1; |
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i = bsTemp.bitsets_[STUNTDOUBLE].nextOnBit(i)) { |
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|
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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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|
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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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|
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if (proc == worldRank) { |
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center = stuntdoubles_[i]; |
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centerPos = center->getPos(frame); |
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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_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD); |
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} else { |
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MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD); |
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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(frame); |
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#endif |
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for (unsigned int j = 0; j < molecules_.size(); ++j) { |
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Vector3d r =centerPos - molecules_[j]->getCom(frame); |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[MOLECULE].setBitOn(j); |
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} |
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} |
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|
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for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
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Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame); |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[STUNTDOUBLE].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < bonds_.size(); ++j) { |
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Vector3d loc = bonds_[j]->getAtomA()->getPos(frame); |
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loc += bonds_[j]->getAtomB()->getPos(frame); |
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loc = loc / 2.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[BOND].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < bends_.size(); ++j) { |
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Vector3d loc = bends_[j]->getAtomA()->getPos(frame); |
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loc += bends_[j]->getAtomB()->getPos(frame); |
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loc += bends_[j]->getAtomC()->getPos(frame); |
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loc = loc / 3.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[BEND].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < torsions_.size(); ++j) { |
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Vector3d loc = torsions_[j]->getAtomA()->getPos(frame); |
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loc += torsions_[j]->getAtomB()->getPos(frame); |
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loc += torsions_[j]->getAtomC()->getPos(frame); |
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loc += torsions_[j]->getAtomD()->getPos(frame); |
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loc = loc / 4.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[TORSION].setBitOn(j); |
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} |
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} |
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for (unsigned int j = 0; j < inversions_.size(); ++j) { |
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Vector3d loc = inversions_[j]->getAtomA()->getPos(frame); |
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loc += inversions_[j]->getAtomB()->getPos(frame); |
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loc += inversions_[j]->getAtomC()->getPos(frame); |
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loc += inversions_[j]->getAtomD()->getPos(frame); |
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loc = loc / 4.0; |
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Vector3d r = centerPos - loc; |
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currSnapshot->wrapVector(r); |
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if (r.length() <= distance) { |
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bsResult.bitsets_[INVERSION].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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} |
