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Comparing branches/development/src/selection/DistanceFinder.cpp (file contents):
Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

# Line 35 | Line 35
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   */
# Line 47 | Line 47 | namespace OpenMD {
47   #endif
48  
49   namespace OpenMD {
50 <
50 >  
51    DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
52 <
52 >    
53      nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
54      stuntdoubles_.resize(nStuntDoubles_);
55      
# Line 59 | Line 59 | namespace OpenMD {
59      Atom* atom;
60      Molecule::RigidBodyIterator rbIter;
61      RigidBody* rb;
62 –
62      
63 +    
64      for (mol = info_->beginMolecule(mi); mol != NULL;
65           mol = info_->nextMolecule(mi)) {
66          
# Line 135 | Line 135 | namespace OpenMD {
135          }
136        }
137      }
138 –
138      return bsResult;
139    }
140  
141 +
142 + OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) {
143 +    StuntDouble * center;
144 +    Vector3d centerPos;
145 +    Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
146 +    OpenMDBitSet bsResult(nStuntDoubles_);  
147 +    assert(bsResult.size() == bs.size());
148 +
149 + #ifdef IS_MPI
150 +    int mol;
151 +    int proc;
152 +    RealType data[3];
153 +    int worldRank = MPI::COMM_WORLD.Get_rank();
154 + #endif
155 +
156 +    for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
157 +      if (stuntdoubles_[j]->isRigidBody()) {
158 +        RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
159 +        rb->updateAtoms(frame);
160 +      }
161 +    }
162 +      
163 +    OpenMDBitSet bsTemp(nStuntDoubles_);
164 +    bsTemp = bs;
165 +    bsTemp.parallelReduce();
166 +
167 +    for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
168 +
169 +      // Now, if we own stuntdouble i, we can use the position, but in
170 +      // parallel, we'll need to let everyone else know what that
171 +      // position is!
172 +
173 + #ifdef IS_MPI
174 +      mol = info_->getGlobalMolMembership(i);
175 +      proc = info_->getMolToProc(mol);
176 +    
177 +      if (proc == worldRank) {
178 +        center = stuntdoubles_[i];
179 +        centerPos = center->getPos(frame);
180 +        data[0] = centerPos.x();
181 +        data[1] = centerPos.y();
182 +        data[2] = centerPos.z();          
183 +        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
184 +      } else {
185 +        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
186 +        centerPos = Vector3d(data);
187 +      }
188 + #else
189 +      center = stuntdoubles_[i];
190 +      centerPos = center->getPos(frame);
191 + #endif
192 +      
193 +      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
194 +        Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
195 +        currSnapshot->wrapVector(r);
196 +        if (r.length() <= distance) {
197 +          bsResult.setBitOn(j);
198 +        }
199 +      }
200 +    }
201 +    return bsResult;
202 +  }
203   }

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