# | Line 36 | Line 36 | |
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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 | ||
# | Line 54 | Line 59 | namespace OpenMD { | |
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) { | |
# | Line 95 | Line 135 | namespace OpenMD { | |
135 | } | |
136 | } | |
137 | } | |
98 | – | |
138 | return bsResult; | |
139 | } | |
101 | – | |
140 | } |
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