--- trunk/src/selection/SelectionManager.cpp	2005/04/15 22:04:00	507
+++ branches/development/src/selection/SelectionManager.cpp	2012/10/03 14:20:07	1803
@@ -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.
@@ -37,18 +28,28 @@
  * 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/SelectionManager.hpp"
 #include "primitives/Molecule.hpp"
 #include "brains/SimInfo.hpp"
-namespace oopse {
+namespace OpenMD {
   SelectionManager::SelectionManager(SimInfo* info) : info_(info){
 
     int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
 
     bsSelection_.resize(nStuntDoubles);
-    stuntdoubles_.resize(nStuntDoubles);
+    stuntdoubles_.resize(nStuntDoubles, NULL);
     
     SimInfo::MoleculeIterator mi;
     Molecule* mol;
@@ -56,27 +57,27 @@ namespace oopse {
     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;
-      }
-        
-    }    
-    
+      }   
+    }
   }
 
-
   StuntDouble* SelectionManager::beginSelected(int& i) {
     i = bsSelection_.firstOnBit();
     return i == -1 ? NULL : stuntdoubles_[i];
   }
+
   StuntDouble* SelectionManager::nextSelected(int& i) {
     i = bsSelection_.nextOnBit(i);
     return i == -1 ? NULL : stuntdoubles_[i];
@@ -86,34 +87,38 @@ namespace oopse {
     i = bsSelection_.firstOffBit();
     return i == -1 ? NULL : stuntdoubles_[i];
   }
+
   StuntDouble* SelectionManager::nextUnSelected(int& i) {
     i = bsSelection_.nextOffBit(i);
     return i == -1 ? NULL : stuntdoubles_[i];
   }
 
-
-  SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
+  SelectionManager operator| (const SelectionManager& sman1, 
+                              const SelectionManager& sman2) {
     SelectionManager result(sman1);
     result |= sman2;
     return result;
   }
-  SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
+
+  SelectionManager operator& (const SelectionManager& sman1, 
+                              const SelectionManager& sman2) {
     SelectionManager result(sman1);
     result &= sman2;
     return result;
-
   }
-  SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
+
+  SelectionManager operator^ (const SelectionManager& sman1, 
+                              const SelectionManager& sman2) {
     SelectionManager result(sman1);
     result ^= sman2;
     return result;
-
   }
-  SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
+
+  SelectionManager operator-(const SelectionManager& sman1, 
+                             const SelectionManager& sman2){
     SelectionManager result(sman1);
     result -= sman2;
     return result;
-
   }
 
 }