--- trunk/src/selection/DistanceFinder.cpp	2013/12/05 18:19:26	1953
+++ trunk/src/selection/DistanceFinder.cpp	2015/01/09 19:06:35	2052
@@ -55,12 +55,14 @@ namespace OpenMD {
     nObjects_.push_back(info_->getNGlobalBends());
     nObjects_.push_back(info_->getNGlobalTorsions());
     nObjects_.push_back(info_->getNGlobalInversions());
+    nObjects_.push_back(info_->getNGlobalMolecules());
 
     stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
     bonds_.resize(nObjects_[BOND]);
     bends_.resize(nObjects_[BEND]);
     torsions_.resize(nObjects_[TORSION]);
     inversions_.resize(nObjects_[INVERSION]);
+    molecules_.resize(nObjects_[MOLECULE]);
     
     SimInfo::MoleculeIterator mi;
     Molecule::AtomIterator ai;
@@ -80,7 +82,9 @@ namespace OpenMD {
     
     for (mol = info_->beginMolecule(mi); mol != NULL; 
          mol = info_->nextMolecule(mi)) {
-        
+
+      molecules_[mol->getGlobalIndex()] = mol;
+      
       for(atom = mol->beginAtom(ai); atom != NULL; 
           atom = mol->nextAtom(ai)) {
 	stuntdoubles_[atom->getGlobalIndex()] = atom;
@@ -120,7 +124,8 @@ namespace OpenMD {
     int mol;
     int proc;
     RealType data[3];
-    int worldRank = MPI::COMM_WORLD.Get_rank();
+    int worldRank;
+    MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
 #endif
  
     for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
@@ -151,9 +156,9 @@ namespace OpenMD {
         data[0] = centerPos.x();
         data[1] = centerPos.y();
         data[2] = centerPos.z();          
-        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
+        MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
       } else {
-        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
+        MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
         centerPos = Vector3d(data);
       }
 #else
@@ -161,6 +166,13 @@ namespace OpenMD {
       centerPos = center->getPos();
 #endif
       
+      for (unsigned int j = 0; j < molecules_.size(); ++j) {
+	Vector3d r =centerPos - molecules_[j]->getCom();
+	currSnapshot->wrapVector(r);
+	if (r.length() <= distance) {
+	  bsResult.bitsets_[MOLECULE].setBitOn(j);
+	}
+      }
       for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
 	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
 	currSnapshot->wrapVector(r);
@@ -229,7 +241,8 @@ namespace OpenMD {
     int mol;
     int proc;
     RealType data[3];
-    int worldRank = MPI::COMM_WORLD.Get_rank();
+    int worldRank;
+    MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
 #endif
  
     for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
@@ -260,15 +273,23 @@ namespace OpenMD {
         data[0] = centerPos.x();
         data[1] = centerPos.y();
         data[2] = centerPos.z();          
-        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
+        MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
       } else {
-        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
+        MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
         centerPos = Vector3d(data);
       }
 #else
       center = stuntdoubles_[i];
       centerPos = center->getPos(frame);
 #endif
+      for (unsigned int j = 0; j < molecules_.size(); ++j) {
+	Vector3d r =centerPos - molecules_[j]->getCom(frame);
+	currSnapshot->wrapVector(r);
+	if (r.length() <= distance) {
+	  bsResult.bitsets_[MOLECULE].setBitOn(j);
+	}
+      }
+      
       for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
 	Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
 	currSnapshot->wrapVector(r);