--- trunk/src/math/DynamicVector.hpp	2006/02/22 20:35:16	891
+++ trunk/src/math/DynamicVector.hpp	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.
@@ -37,6 +28,15 @@
  * 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).                        
  */
  
 /**
@@ -56,7 +56,7 @@
 #include <algorithm>
 #include <vector>
 
-namespace oopse {
+namespace OpenMD {
     
   /**
    * @class DynamicVector DynamicVector.hpp "math/DynamicVector.hpp"
@@ -126,7 +126,14 @@ namespace oopse {
         DynamicVector(_InputIterator first, _InputIterator last,
                const allocator_type& alloc = allocator_type())
         : std::vector<Real, Alloc>(first, last, alloc) {}
-            
+       
+    inline Real operator()(unsigned int i) const{
+      return (*this)[i];
+    }
+    
+    inline Real& operator()(unsigned int i){
+      return (*this)[i];
+    }     
     /**
      * Tests if this vetor is equal to other vector
      * @return true if equal, otherwise return false
@@ -287,7 +294,7 @@ namespace oopse {
 
       len = length();
                 
-      //if (len < oopse:epsilon)
+      //if (len < OpenMD::NumericConstant::epsilon)
       //  throw();
                 
       *this /= len;
@@ -300,6 +307,15 @@ namespace oopse {
     inline bool isNormalized() {
       return equal(lengthSquare(), 1.0);
     }           
+
+    template<class VectorType>
+    void getSubVector(unsigned int beginning, VectorType& v) {
+        assert(beginning + v.size() -1 <= this->size());
+
+        for (unsigned int i = 0; i < v.size(); ++i)
+             v(i) = (*this)[beginning+i];
+    }
+
     
   };