--- trunk/src/selection/IndexFinder.cpp	2005/12/02 15:38:03	770
+++ trunk/src/selection/IndexFinder.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.
@@ -37,10 +28,19 @@
  * 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/IndexFinder.hpp"
 #include "primitives/Molecule.hpp"
-namespace oopse {
+namespace OpenMD {
 
 
 
@@ -62,7 +62,7 @@ namespace oopse {
     
     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
            
-      OOPSEBitSet bs(nStuntDoubles_);
+      OpenMDBitSet bs(nStuntDoubles_);
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
 	bs.setBitOn(atom->getGlobalIndex());
       }
@@ -76,12 +76,12 @@ namespace oopse {
 
   }
 
-  OOPSEBitSet IndexFinder::find(int molIndex){
+  OpenMDBitSet IndexFinder::find(int molIndex){
     return bitSets_[molIndex];
   }
 
-  OOPSEBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
-    OOPSEBitSet bs(nStuntDoubles_);
+  OpenMDBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
+    OpenMDBitSet bs(nStuntDoubles_);
         
     for (int i = begMolIndex; i < endMolIndex; ++i) {
       bs |= bitSets_[i];