--- trunk/src/selection/DistanceFinder.cpp	2012/11/16 15:12:21	1811
+++ trunk/src/selection/DistanceFinder.cpp	2013/10/31 15:32:17	1938
@@ -35,17 +35,18 @@
  *                                                                      
  * [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).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
  * [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 <mpi.h>
 #endif
 
+#include "selection/DistanceFinder.hpp"
+#include "primitives/Molecule.hpp"
+
 namespace OpenMD {
   
   DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
@@ -137,4 +138,67 @@ namespace OpenMD {
     }
     return bsResult;
   }
+
+
+OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) {
+    StuntDouble * center;
+    Vector3d centerPos;
+    Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
+    OpenMDBitSet bsResult(nStuntDoubles_);   
+    assert(bsResult.size() == bs.size());
+
+#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<RigidBody*>(stuntdoubles_[j]);
+        rb->updateAtoms(frame);
+      }
+    }
+       
+    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(frame);
+        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(frame);
+#endif
+      
+      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
+	Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
+	currSnapshot->wrapVector(r);
+	if (r.length() <= distance) {
+	  bsResult.setBitOn(j);
+	}
+      }
+    }
+    return bsResult;
+  }
 }