--- trunk/src/selection/DistanceFinder.cpp	2005/02/07 19:13:18	295
+++ trunk/src/selection/DistanceFinder.cpp	2009/11/25 20:02:06	1390
@@ -6,19 +6,10 @@
  * 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.
@@ -37,13 +28,22 @@
  * 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]  Vardeman & Gezelter, in progress (2009).                        
  */
 
 #include "selection/DistanceFinder.hpp"
 #include "primitives/Molecule.hpp"
-namespace oopse {
+namespace OpenMD {
 
-DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
+  DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
 
     nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
     stuntdoubles_.resize(nStuntDoubles_);
@@ -58,38 +58,38 @@ DistanceFinder::DistanceFinder(SimInfo* info) : info_(
     
     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
         
-        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
-            stuntdoubles_[atom->getGlobalIndex()] = atom;
-        }
+      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)) {
-            stuntdoubles_[rb->getGlobalIndex()] = rb;
-        }
+      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.nextOnBit(-1); i != -1; i = bs.nextOnBit(i)) {
-        center = stuntdoubles_[i];
-        centerPos = center->getPos();
-        for (int j = 0; j < stuntdoubles_.size(); ++j) {
-            Vector3d r =centerPos - stuntdoubles_[j]->getPos();
-            currSnapshot->wrapVector(r);
-            if (r.length() <= distance) {
-                bsResult.setBitOn(j);
-            }
-        }
+    for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
+      center = stuntdoubles_[i];
+      centerPos = center->getPos();
+      for (int j = 0; j < stuntdoubles_.size(); ++j) {
+	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
+	currSnapshot->wrapVector(r);
+	if (r.length() <= distance) {
+	  bsResult.setBitOn(j);
+	}
+      }
     }
 
     return bsResult;
-}
+  }
 
 }