--- trunk/src/math/SquareMatrix.hpp	2006/05/16 02:06:37	956
+++ trunk/src/math/SquareMatrix.hpp	2012/08/22 02:28:28	1782
@@ -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, 24107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -51,7 +52,7 @@
 #include "math/RectMatrix.hpp"
 #include "utils/NumericConstant.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   /**
    * @class SquareMatrix SquareMatrix.hpp "math/SquareMatrix.hpp"
@@ -134,7 +135,26 @@ namespace oopse {
 
       return tmp;
     }
+    
+    /**
+     * Returns the tensor contraction (double dot product) of two rank 2
+     * tensors (or Matrices)
+     * @param t1 first tensor
+     * @param t2 second tensor
+     * @return the tensor contraction (double dot product) of t1 and t2
+     */
+    Real doubleDot( const SquareMatrix<Real, Dim>& t1, const SquareMatrix<Real, Dim>& t2 ) {
+      Real tmp;
+      tmp = 0;
+      
+      for (unsigned int i = 0; i < Dim; i++)
+        for (unsigned int j =0; j < Dim; j++)
+          tmp += t1[i][j] * t2[i][j];
+      
+      return tmp;
+    }
 
+
     /** Tests if this matrix is symmetrix. */            
     bool isSymmetric() const {
       for (unsigned int i = 0; i < Dim - 1; i++)
@@ -162,6 +182,19 @@ namespace oopse {
 	    return false;
                         
       return true;
+    }
+
+    /** 
+     * Returns a column vector that contains the elements from the
+     * diagonal of m in the order R(0) = m(0,0), R(1) = m(1,1), and so
+     * on.
+     */
+    Vector<Real, Dim> diagonals() const {
+      Vector<Real, Dim> result;
+      for (unsigned int i = 0; i < Dim; i++) {
+        result(i) = this->data_[i][i];
+      }
+      return result;
     }
 
     /** Tests if this matrix is the unit matrix. */
@@ -372,7 +405,7 @@ namespace oopse {
 	  numPos++;
 	}
       }
-      //    if ( numPos < ceil(double(n)/double(2.0)) )
+      //    if ( numPos < ceil(RealType(n)/RealType(2.0)) )
       if ( numPos < ceil_half_n) {
 	for (i=0; i<n; i++) {
 	  v(i, j) *= -1.0;
@@ -388,7 +421,7 @@ namespace oopse {
   }
 
 
-  typedef SquareMatrix<double, 6> Mat6x6d;
+  typedef SquareMatrix<RealType, 6> Mat6x6d;
 }
 #endif //MATH_SQUAREMATRIX_HPP