--- trunk/src/selection/SelectionManager.hpp	2005/02/16 19:36:30	353
+++ trunk/src/selection/SelectionManager.hpp	2012/10/01 18:21:15	1801
@@ -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.
@@ -37,114 +28,120 @@
  * 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).
  */
 
 #ifndef SELECTION_SELECTIONMANAGER_HPP
 #define SELECTION_SELECTIONMANAGER_HPP
 
-#include "utils/BitSet.hpp"
+#include "utils/OpenMDBitSet.hpp"
 #include "primitives/StuntDouble.hpp"
-namespace oopse {
+namespace OpenMD {
 
-class SimInfo;
-/**
- * @class SelectionManager SelectionManager.hpp "selection/SelectionManager.hpp"
- * @brief
- */
-class SelectionManager {
-    public:
-        SelectionManager(SimInfo* info);
+  class SimInfo;
+  class SelectionManager {
+  public:
+    SelectionManager(SimInfo* info);
 
-        void addSelection(StuntDouble* sd) {
-            bsSelection_.setBitOn(sd->getGlobalIndex());
-        }
+    void addSelection(StuntDouble* sd) {
+      bsSelection_.setBitOn(sd->getGlobalIndex());
+    }
         
-        void addSelectionSet(const BitSet& bs) {
-            bsSelection_ |= bs;
-        }
+    void addSelectionSet(const OpenMDBitSet& bs) {
+      bsSelection_ |= bs;
+    }
 
-        void setSelection(StuntDouble* sd) {
-            bsSelection_.clearAll();
-            bsSelection_.setBitOn(sd->getGlobalIndex());
-        }
+    void setSelection(StuntDouble* sd) {
+      bsSelection_.clearAll();
+      bsSelection_.setBitOn(sd->getGlobalIndex());
+    }
         
-        void setSelectionSet(const BitSet& bs) {
-            bsSelection_ = bs;           
-        }
+    void setSelectionSet(const OpenMDBitSet& bs) {
+      bsSelection_ = bs;           
+    }
 
-        void toggleSelection(StuntDouble* sd) {
-            bsSelection_.flip(sd->getGlobalIndex());
-        }
+    void toggleSelection(StuntDouble* sd) {
+      bsSelection_.flip(sd->getGlobalIndex());
+    }
 
-        void toggleSelection() {
-            bsSelection_.flip();
-        }
+    void toggleSelection() {
+      bsSelection_.flip();
+    }
         
-        void selectAll() {
-            bsSelection_.setAll();                
-        }
+    void selectAll() {
+      bsSelection_.setAll();                
+    }
 
-        void clearSelection() {
-           bsSelection_.clearAll();
-        }
+    void clearSelection() {
+      bsSelection_.clearAll();
+    }
 
-        void clearSelection(StuntDouble* sd) {
-            bsSelection_.setBitOff(sd->getGlobalIndex());
-        }
+    void clearSelection(StuntDouble* sd) {
+      bsSelection_.setBitOff(sd->getGlobalIndex());
+    }
 
-        bool isSelected(StuntDouble* sd) {
-            return bsSelection_[sd->getGlobalIndex()];
-        }
+    bool isSelected(StuntDouble* sd) {
+      return bsSelection_[sd->getGlobalIndex()];
+    }
 
-        bool isEmpty() {
-            return bsSelection_.none();
-        }
+    bool isEmpty() {
+      return bsSelection_.none();
+    }
 
-        int getSelectionCount() {
-            return bsSelection_.countBits();
-        }
+    int getSelectionCount() {
+      return bsSelection_.countBits();
+    }
 
-        BitSet getSelectionSet() {
-            return bsSelection_;
-        }
+    OpenMDBitSet getSelectionSet() {
+      return bsSelection_;
+    }
 
 
-        StuntDouble* beginSelected(int& i);
-        StuntDouble* nextSelected(int& i);
+    StuntDouble* beginSelected(int& i);
+    StuntDouble* nextSelected(int& i);
 
-        StuntDouble* beginUnselected(int& i);
-        StuntDouble* nextUnSelected(int& i);
+    StuntDouble* beginUnselected(int& i);
+    StuntDouble* nextUnSelected(int& i);
 
-        SelectionManager& operator&= (const SelectionManager &sman) {
-            bsSelection_ &= sman.bsSelection_;
-            return *this; 
-        }
+    SelectionManager& operator&= (const SelectionManager &sman) {
+      bsSelection_ &= sman.bsSelection_;
+      return *this; 
+    }
         
-        SelectionManager& operator|= (const SelectionManager &sman) {
-            bsSelection_ |= sman.bsSelection_;
-            return *this; 
-        }
+    SelectionManager& operator|= (const SelectionManager &sman) {
+      bsSelection_ |= sman.bsSelection_;
+      return *this; 
+    }
         
-        SelectionManager& operator^= (const SelectionManager &sman) {
-            bsSelection_ ^= sman.bsSelection_;
-            return *this; 
-        }
+    SelectionManager& operator^= (const SelectionManager &sman) {
+      bsSelection_ ^= sman.bsSelection_;
+      return *this; 
+    }
 
-        SelectionManager& operator-= (const SelectionManager &sman) {
-            bsSelection_ -= sman.bsSelection_;
-            return *this; 
-        }
+    SelectionManager& operator-= (const SelectionManager &sman) {
+      bsSelection_ -= sman.bsSelection_;
+      return *this; 
+    }
         
-        friend SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2);
-        friend SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2);
-        friend SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2);
-        friend SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2);
+    friend SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2);
+    friend SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2);
+    friend SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2);
+    friend SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2);
         
-    private:
-        SimInfo* info_;
-        BitSet bsSelection_;
-        std::vector<StuntDouble*> stuntdoubles_;
-};
+  private:
+    SimInfo* info_;
+    OpenMDBitSet bsSelection_;
+    std::vector<StuntDouble*> stuntdoubles_;
+  };
 
 }
 #endif