--- trunk/src/math/DynamicVector.hpp	2006/02/22 20:35:16	891
+++ trunk/src/math/DynamicVector.hpp	2013/06/16 15:15:42	1879
@@ -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 +28,16 @@
  * 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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -56,7 +57,7 @@
 #include <algorithm>
 #include <vector>
 
-namespace oopse {
+namespace OpenMD {
     
   /**
    * @class DynamicVector DynamicVector.hpp "math/DynamicVector.hpp"
@@ -93,6 +94,7 @@ namespace oopse {
        *  @brief  Create a %DynamicVector with copies of an exemplar element.
        *  @param  n  The number of elements to initially create.
        *  @param  value  An element to copy.
+       *  @param  alloc  The allocator_type to use
        *
        *  This constructor fills the %DynamicVector with @a n copies of @a value.
        */
@@ -126,7 +128,14 @@ 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
@@ -218,6 +227,7 @@ namespace oopse {
      * @param s the scalar value
      */
     inline void mul( const DynamicVector<Real>& v1, Real s) {
+      this->resize(v1.size());
       for (unsigned int i = 0; i < this->size(); i++)
 	(*this)[i] = s * v1[i];
     }
@@ -265,6 +275,12 @@ namespace oopse {
       return *this;
     }
 
+    /** zero out the vector */
+    inline void setZero( ) {
+      for (unsigned int i = 0; i < this->size(); i++)
+	(*this)[i] = 0;
+    }
+
     /**
      * Returns the length of this vector.
      * @return the length of this vector
@@ -287,7 +303,7 @@ namespace oopse {
 
       len = length();
                 
-      //if (len < oopse:epsilon)
+      //if (len < OpenMD::NumericConstant::epsilon)
       //  throw();
                 
       *this /= len;
@@ -300,6 +316,15 @@ 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];
+    }
+
     
   };
 
@@ -319,8 +344,8 @@ namespace oopse {
    */   
   template<typename Real>    
   inline DynamicVector<Real> operator +(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
-    DynamicVector<Real> result;
-        
+    assert(v1.size() == v2.size());
+    DynamicVector<Real>result(v1.size());
     result.add(v1, v2);
     return result;        
   }
@@ -333,7 +358,8 @@ namespace oopse {
    */  
   template<typename Real>    
   DynamicVector<Real> operator -(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
-    DynamicVector<Real> result;
+    assert(v1.size() == v2.size());
+    DynamicVector<Real> result(v1.size());
     result.sub(v1, v2);
     return result;        
   }
@@ -345,8 +371,8 @@ namespace oopse {
    * @param s the scalar value
    */ 
   template<typename Real>                 
-  DynamicVector<Real> operator * ( const DynamicVector<Real>& v1, Real s) {       
-    DynamicVector<Real> result;
+  DynamicVector<Real> operator *( const DynamicVector<Real>& v1, Real s) {      
+    DynamicVector<Real> result(v1.size());
     result.mul(v1,s);
     return result;           
   }
@@ -358,8 +384,8 @@ namespace oopse {
    * @param v1 the source vector
    */  
   template<typename Real>
-  DynamicVector<Real> operator * ( Real s, const DynamicVector<Real>& v1 ) {
-    DynamicVector<Real> result;
+  DynamicVector<Real> operator *( Real s, const DynamicVector<Real>& v1 ) {
+    DynamicVector<Real> result(v1.size());
     result.mul(v1, s);
     return result;           
   }
@@ -371,8 +397,8 @@ namespace oopse {
    * @param s the scalar value
    */
   template<typename Real>    
-  DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {       
-    DynamicVector<Real> result;
+  DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {     
+    DynamicVector<Real> result(v1.size());
     result.div( v1,s);
     return result;           
   }