--- trunk/src/math/Vector3.hpp	2005/01/12 22:41:40	246
+++ trunk/src/math/Vector3.hpp	2013/06/16 15:15:42	1879
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -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).
  */
  
 /**
@@ -54,7 +55,7 @@
 
 #include "Vector.hpp"
 
-namespace oopse {
+namespace OpenMD {
   
   /**
    * @class Vector3 Vector3.hpp "math/Vector3.hpp"
@@ -66,14 +67,13 @@ namespace oopse {
   public:
     typedef Real ElemType;
     typedef Real* ElemPoinerType;
-    
     Vector3() : Vector<Real, 3>(){}
     
     /** Constructs and initializes a Vector3 from x, y, z coordinates */
     inline Vector3( Real x, Real y, Real z) {
-      data_[0] = x;
-      data_[1] = y;
-      data_[2] = z;
+      this->data_[0] = x;
+      this->data_[1] = y;
+      this->data_[2] = z;
     }
 
     /** Constructs and initializes from an array*/
@@ -88,40 +88,40 @@ namespace oopse {
     }
     
     /**
-     * Retunrs reference of the first element of Vector3.
+     * Returns reference of the first element of Vector3.
      * @return reference of the first element of Vector3
      */
-    inline Real& x() {  return data_[0];}
+    inline Real& x() {  return this->data_[0];}
     
     /**
-     * Retunrs the first element of Vector3.
+     * Returns the first element of Vector3.
      * @return  the first element of Vector3
      */
-    inline Real x() const {  return data_[0];}
+    inline Real x() const {  return this->data_[0];}
     
     /**
-     * Retunrs reference of the second element of Vector3.
+     * Returns reference of the second element of Vector3.
      * @return reference of the second element of Vector3
      */
-    inline Real& y() {  return data_[1];}
+    inline Real& y() {  return this->data_[1];}
     
     /**
-     * Retunrs  the second element of Vector3.
+     * Returns  the second element of Vector3.
      * @return c the second element of Vector3
      */
-    inline Real y() const {  return data_[1];}
+    inline Real y() const {  return this->data_[1];}
     
     /**
-     * Retunrs reference of the third element of Vector3.
+     * Returns reference of the third element of Vector3.
      * @return reference of the third element of Vector3
      */
-    inline Real& z() {  return data_[2];}
+    inline Real& z() {  return this->data_[2];}
     
     /**
-     * Retunrs  the third element of Vector3.
+     * Returns  the third element of Vector3.
      * @return f the third element of Vector3
      */
-    inline Real z() const {  return data_[2];}
+    inline Real z() const {  return this->data_[2];}
     
   };
   
@@ -130,10 +130,9 @@ namespace oopse {
    * @param v1 first vector
    * @param v2 second vector
    * @return the cross product  of v1 and v2
-   * @see #vector::dot
    */
   template<typename Real>
-  Vector3<Real> cross( const Vector3<Real>& v1, const Vector3<Real>& v2 ) {
+  inline Vector3<Real> cross( const Vector3<Real>& v1, const Vector3<Real>& v2 ) {
     Vector3<Real> result;
     
     result.x() = v1.y() * v2.z() - v1.z() * v2.y();
@@ -143,15 +142,28 @@ namespace oopse {
     return result;
   }
 
+
+  /**
+   * Returns the linear indexing for integer vectors. Compare to
+   * Rapaport's VLinear
+   *
+   * @param p first vector
+   * @param s second vector
+   */
+  template<typename Real>
+  inline Real Vlinear( const Vector3<Real>& p, const Vector3<Real>& s ) {
+    return (p.z() * s.y() + p.y()) * s.x() + p.x();
+  }
+
   typedef Vector3<int> Vector3i;
   
-  typedef Vector3<double> Vector3d;    
+  typedef Vector3<RealType> Vector3d;    
 
-    const Vector3d V3Zero(0.0 , 0.0, 0.0);
-    const Vector3d V3X( 1.0, 0.0, 0.0 ) ;
-    const Vector3d V3Y( 0.0, 1.0, 0.0 ) ;
-    const Vector3d V3Z ( 0.0, 0.0, 1.0 ) ;    
-  
+  const Vector3d V3Zero(0.0 , 0.0, 0.0);
+  const Vector3d V3X( 1.0, 0.0, 0.0 ) ;
+  const Vector3d V3Y( 0.0, 1.0, 0.0 ) ;
+  const Vector3d V3Z ( 0.0, 0.0, 1.0 ) ;
+ 
 }
 
 #endif