--- trunk/src/math/Vector.hpp	2010/05/10 17:28:26	1442
+++ trunk/src/math/Vector.hpp	2013/06/16 15:15:42	1879
@@ -35,8 +35,9 @@
  *                                                                      
  * [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).                        
+ * [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).
  */
  
 /**
@@ -72,7 +73,6 @@ namespace OpenMD {
   inline bool equal(RealType e1, RealType e2) {
     return fabs(e1 - e2) < epsilon;
   }
-
     
   /**
    * @class Vector Vector.hpp "math/Vector.hpp"
@@ -107,10 +107,11 @@ namespace OpenMD {
       return *this;
     }
 
-    template<typename T>
-    inline Vector(const T& s){
+    // template<typename T>
+    // inline Vector(const T& s){
+    inline Vector(const Real& s) {
       for (unsigned int i = 0; i < Dim; i++)
-	this->data_[i] = s;
+        this->data_[i] = s;
     }
             
     /** Constructs and initializes a Vector from an array */            
@@ -195,6 +196,12 @@ namespace OpenMD {
     inline bool operator !=(const Vector<Real, Dim>& v) {
       return !(*this == v);
     }
+
+    /** Zeros out the values in this vector in place */
+    inline void zero() {
+      for (unsigned int i = 0; i < Dim; i++)
+	this->data_[i] = 0;
+    }      
              
     /** Negates the value of this vector in place. */           
     inline void negate() {
@@ -268,8 +275,39 @@ namespace OpenMD {
     inline void mul( const Vector<Real, Dim>& v1, Real s) {
       for (unsigned int i = 0; i < Dim; i++)
 	this->data_[i] = s * v1.data_[i];
+    }
+
+    /**
+     * Sets the elements of this vector to the multiplication of
+     * elements of two other vectors.  Not to be confused with scalar
+     * multiplication (mul) or dot products.
+     *
+     * (*this.data_[i] =  v1.data_[i] * v2.data_[i]).
+     * @param v1 the first vector            
+     * @param v2 the second vector
+     */
+    inline void Vmul( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
+      for (unsigned int i = 0; i < Dim; i++)
+	this->data_[i] = v1.data_[i] * v2.data_[i];
     }
 
+    /* replaces the elements with the absolute values of those elements */
+    inline Vector<Real, Dim>& abs() {
+      for (unsigned int i = 0; i < Dim; i++) {
+        this->data_[i] = std::abs(this->data_[i]);
+      }
+      return *this;
+    }
+    
+    /* returns the maximum value in this vector */
+    inline Real max() {
+      Real val = this->data_[0];
+      for (unsigned int i = 0; i < Dim; i++) {
+        if (this->data_[i] > val) val = this->data_[i];
+      }
+      return val;
+    }
+     
     /**
      * Sets the value of this vector to the scalar division of itself  (*this /= s ).
      * @param s the scalar value
@@ -289,6 +327,21 @@ namespace OpenMD {
 	this->data_[i] = v1.data_[i] / s;
     }
 
+    /**
+     * Sets the elements of this vector to the division of
+     * elements of two other vectors.  Not to be confused with scalar
+     * division (div)
+     *
+     * (*this.data_[i] =  v1.data_[i] / v2.data_[i]).
+     * @param v1 the first vector            
+     * @param v2 the second vector
+     */
+    inline void Vdiv( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
+      for (unsigned int i = 0; i < Dim; i++)
+	this->data_[i] = v1.data_[i] / v2.data_[i];
+    }
+
+
     /** @see #add */
     inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
       add(v1);
@@ -324,6 +377,18 @@ namespace OpenMD {
 	tmp += this->data_[i];
       return tmp;  
     }
+
+    /**
+     * Returns the product of all elements of this vector.
+     * @return the product of all elements of this vector
+     */
+    inline Real componentProduct() {
+      Real tmp;
+      tmp = 1;
+      for (unsigned int i = 0; i < Dim; i++)
+	tmp *= this->data_[i];
+      return tmp;  
+    }
             
     /**
      * Returns the length of this vector.
@@ -458,7 +523,31 @@ namespace OpenMD {
     return tmp;
   }
 
+
+  
+
   /**
+   * Returns the wide dot product of three Vectors.  Compare with
+   * Rapaport's VWDot function.
+   *
+   * @param v1 first vector
+   * @param v2 second vector
+   * @param v3 third vector
+   * @return the wide dot product of v1, v2, and v3.
+   */
+  template<typename Real, unsigned int Dim>    
+  inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2, const Vector<Real, Dim>& v3 ) {
+    Real tmp;
+    tmp = 0;
+
+    for (unsigned int i = 0; i < Dim; i++)
+      tmp += v1[i] * v2[i] * v3[i];
+
+    return tmp;
+  }
+
+
+  /**
    * Returns the distance between  two Vectors
    * @param v1 first vector
    * @param v2 second vector