| 35 |
|
* |
| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 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" |
| 43 |
|
#ifdef IS_MPI |
| 44 |
|
#include <mpi.h> |
| 45 |
|
#endif |
| 46 |
|
|
| 47 |
< |
namespace OpenMD { |
| 47 |
> |
#include "selection/DistanceFinder.hpp" |
| 48 |
> |
#include "primitives/Molecule.hpp" |
| 49 |
|
|
| 50 |
+ |
namespace OpenMD { |
| 51 |
+ |
|
| 52 |
|
DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) { |
| 53 |
< |
|
| 53 |
> |
|
| 54 |
|
nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 55 |
|
stuntdoubles_.resize(nStuntDoubles_); |
| 56 |
|
|
| 60 |
|
Atom* atom; |
| 61 |
|
Molecule::RigidBodyIterator rbIter; |
| 62 |
|
RigidBody* rb; |
| 62 |
– |
|
| 63 |
|
|
| 64 |
+ |
|
| 65 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 66 |
|
mol = info_->nextMolecule(mi)) { |
| 67 |
|
|
| 136 |
|
} |
| 137 |
|
} |
| 138 |
|
} |
| 138 |
– |
|
| 139 |
|
return bsResult; |
| 140 |
|
} |
| 141 |
|
|
| 142 |
+ |
|
| 143 |
+ |
OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) { |
| 144 |
+ |
StuntDouble * center; |
| 145 |
+ |
Vector3d centerPos; |
| 146 |
+ |
Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame); |
| 147 |
+ |
OpenMDBitSet bsResult(nStuntDoubles_); |
| 148 |
+ |
assert(bsResult.size() == bs.size()); |
| 149 |
+ |
|
| 150 |
+ |
#ifdef IS_MPI |
| 151 |
+ |
int mol; |
| 152 |
+ |
int proc; |
| 153 |
+ |
RealType data[3]; |
| 154 |
+ |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 155 |
+ |
#endif |
| 156 |
+ |
|
| 157 |
+ |
for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
| 158 |
+ |
if (stuntdoubles_[j]->isRigidBody()) { |
| 159 |
+ |
RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]); |
| 160 |
+ |
rb->updateAtoms(frame); |
| 161 |
+ |
} |
| 162 |
+ |
} |
| 163 |
+ |
|
| 164 |
+ |
OpenMDBitSet bsTemp(nStuntDoubles_); |
| 165 |
+ |
bsTemp = bs; |
| 166 |
+ |
bsTemp.parallelReduce(); |
| 167 |
+ |
|
| 168 |
+ |
for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) { |
| 169 |
+ |
|
| 170 |
+ |
// Now, if we own stuntdouble i, we can use the position, but in |
| 171 |
+ |
// parallel, we'll need to let everyone else know what that |
| 172 |
+ |
// position is! |
| 173 |
+ |
|
| 174 |
+ |
#ifdef IS_MPI |
| 175 |
+ |
mol = info_->getGlobalMolMembership(i); |
| 176 |
+ |
proc = info_->getMolToProc(mol); |
| 177 |
+ |
|
| 178 |
+ |
if (proc == worldRank) { |
| 179 |
+ |
center = stuntdoubles_[i]; |
| 180 |
+ |
centerPos = center->getPos(frame); |
| 181 |
+ |
data[0] = centerPos.x(); |
| 182 |
+ |
data[1] = centerPos.y(); |
| 183 |
+ |
data[2] = centerPos.z(); |
| 184 |
+ |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); |
| 185 |
+ |
} else { |
| 186 |
+ |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); |
| 187 |
+ |
centerPos = Vector3d(data); |
| 188 |
+ |
} |
| 189 |
+ |
#else |
| 190 |
+ |
center = stuntdoubles_[i]; |
| 191 |
+ |
centerPos = center->getPos(frame); |
| 192 |
+ |
#endif |
| 193 |
+ |
|
| 194 |
+ |
for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { |
| 195 |
+ |
Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame); |
| 196 |
+ |
currSnapshot->wrapVector(r); |
| 197 |
+ |
if (r.length() <= distance) { |
| 198 |
+ |
bsResult.setBitOn(j); |
| 199 |
+ |
} |
| 200 |
+ |
} |
| 201 |
+ |
} |
| 202 |
+ |
return bsResult; |
| 203 |
+ |
} |
| 204 |
|
} |
