--- trunk/src/selection/DistanceFinder.cpp	2010/04/14 14:41:33	1434
+++ trunk/src/selection/DistanceFinder.cpp	2013/10/31 15:32:17	1938
@@ -35,16 +35,22 @@
  *                                                                      
  * [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]  Vardeman & Gezelter, in progress (2009).                        
+ * [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).
  */
 
+#ifdef IS_MPI
+#include <mpi.h>
+#endif
+
 #include "selection/DistanceFinder.hpp"
 #include "primitives/Molecule.hpp"
-namespace OpenMD {
 
+namespace OpenMD {
+  
   DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
-
+    
     nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
     stuntdoubles_.resize(nStuntDoubles_);
     
@@ -54,40 +60,75 @@ namespace OpenMD {
     Atom* atom;
     Molecule::RigidBodyIterator rbIter;
     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;
       }
-        
-    }    
-
+    }
   }
 
   OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
     StuntDouble * center;
     Vector3d centerPos;
     Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
-    OpenMDBitSet bsResult(nStuntDoubles_);
+    OpenMDBitSet bsResult(nStuntDoubles_);   
     assert(bsResult.size() == bs.size());
-   
-    for (int j = 0; j < stuntdoubles_.size(); ++j) {
+
+#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();
       }
     }
-   
-    for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
+       
+    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) {
@@ -95,8 +136,69 @@ 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;
+  }
 }