| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "selection/DistanceFinder.hpp" |
| 44 |
|
#include "primitives/Molecule.hpp" |
| 45 |
< |
namespace OpenMD { |
| 45 |
> |
#ifdef IS_MPI |
| 46 |
> |
#include <mpi.h> |
| 47 |
> |
#endif |
| 48 |
|
|
| 49 |
+ |
namespace OpenMD { |
| 50 |
+ |
|
| 51 |
|
DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) { |
| 52 |
< |
|
| 52 |
> |
|
| 53 |
|
nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 54 |
|
stuntdoubles_.resize(nStuntDoubles_); |
| 55 |
|
|
| 59 |
|
Atom* atom; |
| 60 |
|
Molecule::RigidBodyIterator rbIter; |
| 61 |
|
RigidBody* rb; |
| 57 |
– |
|
| 62 |
|
|
| 63 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 63 |
> |
|
| 64 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 65 |
> |
mol = info_->nextMolecule(mi)) { |
| 66 |
|
|
| 67 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 67 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 68 |
> |
atom = mol->nextAtom(ai)) { |
| 69 |
|
stuntdoubles_[atom->getGlobalIndex()] = atom; |
| 70 |
|
} |
| 71 |
|
|
| 72 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 72 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 73 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 74 |
|
stuntdoubles_[rb->getGlobalIndex()] = rb; |
| 75 |
|
} |
| 76 |
< |
|
| 69 |
< |
} |
| 70 |
< |
|
| 76 |
> |
} |
| 77 |
|
} |
| 78 |
|
|
| 79 |
|
OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) { |
| 80 |
|
StuntDouble * center; |
| 81 |
|
Vector3d centerPos; |
| 82 |
|
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 83 |
< |
OpenMDBitSet bsResult(nStuntDoubles_); |
| 83 |
> |
OpenMDBitSet bsResult(nStuntDoubles_); |
| 84 |
|
assert(bsResult.size() == bs.size()); |
| 85 |
< |
|
| 86 |
< |
for (int j = 0; j < stuntdoubles_.size(); ++j) { |
| 85 |
> |
|
| 86 |
> |
#ifdef IS_MPI |
| 87 |
> |
int mol; |
| 88 |
> |
int proc; |
| 89 |
> |
RealType data[3]; |
| 90 |
> |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 91 |
> |
#endif |
| 92 |
> |
|
| 93 |
> |
for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
| 94 |
|
if (stuntdoubles_[j]->isRigidBody()) { |
| 95 |
|
RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]); |
| 96 |
|
rb->updateAtoms(); |
| 97 |
|
} |
| 98 |
|
} |
| 99 |
< |
|
| 100 |
< |
for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) { |
| 99 |
> |
|
| 100 |
> |
OpenMDBitSet bsTemp(nStuntDoubles_); |
| 101 |
> |
bsTemp = bs; |
| 102 |
> |
bsTemp.parallelReduce(); |
| 103 |
> |
|
| 104 |
> |
for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) { |
| 105 |
> |
|
| 106 |
> |
// Now, if we own stuntdouble i, we can use the position, but in |
| 107 |
> |
// parallel, we'll need to let everyone else know what that |
| 108 |
> |
// position is! |
| 109 |
> |
|
| 110 |
> |
#ifdef IS_MPI |
| 111 |
> |
mol = info_->getGlobalMolMembership(i); |
| 112 |
> |
proc = info_->getMolToProc(mol); |
| 113 |
> |
|
| 114 |
> |
if (proc == worldRank) { |
| 115 |
> |
center = stuntdoubles_[i]; |
| 116 |
> |
centerPos = center->getPos(); |
| 117 |
> |
data[0] = centerPos.x(); |
| 118 |
> |
data[1] = centerPos.y(); |
| 119 |
> |
data[2] = centerPos.z(); |
| 120 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); |
| 121 |
> |
} else { |
| 122 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); |
| 123 |
> |
centerPos = Vector3d(data); |
| 124 |
> |
} |
| 125 |
> |
#else |
| 126 |
|
center = stuntdoubles_[i]; |
| 127 |
|
centerPos = center->getPos(); |
| 128 |
< |
for (int j = 0; j < stuntdoubles_.size(); ++j) { |
| 128 |
> |
#endif |
| 129 |
> |
|
| 130 |
> |
for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
| 131 |
|
Vector3d r =centerPos - stuntdoubles_[j]->getPos(); |
| 132 |
|
currSnapshot->wrapVector(r); |
| 133 |
|
if (r.length() <= distance) { |
| 135 |
|
} |
| 136 |
|
} |
| 137 |
|
} |
| 98 |
– |
|
| 138 |
|
return bsResult; |
| 139 |
|
} |
| 101 |
– |
|
| 140 |
|
} |
