--- branches/development/src/selection/DistanceFinder.cpp 2010/07/09 23:08:25 1465 +++ branches/development/src/selection/DistanceFinder.cpp 2012/10/03 14:20:07 1803 @@ -36,11 +36,16 @@ * [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] Vardeman & Gezelter, in progress (2009). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "selection/DistanceFinder.hpp" #include "primitives/Molecule.hpp" +#ifdef IS_MPI +#include +#endif + namespace OpenMD { DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) { @@ -56,38 +61,73 @@ namespace OpenMD { RigidBody* rb; - for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { + for (mol = info_->beginMolecule(mi); mol != NULL; + mol = info_->nextMolecule(mi)) { - for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + 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)) { + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { stuntdoubles_[rb->getGlobalIndex()] = rb; } - - } - + } } OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) { StuntDouble * center; Vector3d centerPos; Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); - OpenMDBitSet bsResult(nStuntDoubles_); + OpenMDBitSet bsResult(nStuntDoubles_); assert(bsResult.size() == bs.size()); - - for (int j = 0; j < stuntdoubles_.size(); ++j) { + +#ifdef IS_MPI + int mol; + int proc; + RealType data[3]; + int worldRank = MPI::COMM_WORLD.Get_rank(); +#endif + + for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { if (stuntdoubles_[j]->isRigidBody()) { RigidBody* rb = static_cast(stuntdoubles_[j]); rb->updateAtoms(); } } - - for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) { + + OpenMDBitSet bsTemp(nStuntDoubles_); + bsTemp = bs; + bsTemp.parallelReduce(); + + for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) { + + // Now, if we own stuntdouble i, we can use the position, but in + // parallel, we'll need to let everyone else know what that + // position is! + +#ifdef IS_MPI + mol = info_->getGlobalMolMembership(i); + proc = info_->getMolToProc(mol); + + if (proc == worldRank) { + center = stuntdoubles_[i]; + centerPos = center->getPos(); + data[0] = centerPos.x(); + data[1] = centerPos.y(); + data[2] = centerPos.z(); + MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); + } else { + MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); + centerPos = Vector3d(data); + } +#else center = stuntdoubles_[i]; centerPos = center->getPos(); - for (int j = 0; j < stuntdoubles_.size(); ++j) { +#endif + + for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { Vector3d r =centerPos - stuntdoubles_[j]->getPos(); currSnapshot->wrapVector(r); if (r.length() <= distance) {