--- trunk/src/selection/DistanceFinder.cpp	2005/04/15 22:04:00	507
+++ branches/development/src/selection/DistanceFinder.cpp	2012/10/03 14:20:07	1803
@@ -1,24 +1,15 @@
 /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,12 +28,26 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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).          
+ * [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"
-namespace oopse {
+#ifdef IS_MPI
+#include <mpi.h>
+#endif
 
+namespace OpenMD {
+
   DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
 
     nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
@@ -56,31 +61,73 @@ namespace oopse {
     RigidBody* rb;
 
     
-    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+    for (mol = info_->beginMolecule(mi); mol != NULL; 
+         mol = info_->nextMolecule(mi)) {
         
-      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
+      for(atom = mol->beginAtom(ai); atom != NULL; 
+          atom = mol->nextAtom(ai)) {
 	stuntdoubles_[atom->getGlobalIndex()] = atom;
       }
 
-      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+           rb = mol->nextRigidBody(rbIter)) {
 	stuntdoubles_[rb->getGlobalIndex()] = rb;
       }
-        
-    }    
-
+    }
   }
 
-  BitSet DistanceFinder::find(const BitSet& bs, double distance) {
+  OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
     StuntDouble * center;
     Vector3d centerPos;
     Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
-    BitSet bsResult(nStuntDoubles_);
+    OpenMDBitSet bsResult(nStuntDoubles_);   
     assert(bsResult.size() == bs.size());
-    
-    for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
+
+#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();
+      }
+    }
+       
+    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();
+        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();
-      for (int j = 0; j < stuntdoubles_.size(); ++j) {
+#endif
+      
+      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
 	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
 	currSnapshot->wrapVector(r);
 	if (r.length() <= distance) {