--- trunk/src/math/SquareMatrix.hpp	2006/05/17 21:51:42	963
+++ trunk/src/math/SquareMatrix.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).
  */
  
 /**
@@ -51,13 +52,13 @@
 #include "math/RectMatrix.hpp"
 #include "utils/NumericConstant.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   /**
    * @class SquareMatrix SquareMatrix.hpp "math/SquareMatrix.hpp"
    * @brief A square matrix class
-   * @template Real the element type
-   * @template Dim the dimension of the square matrix
+   * \tparam Real the element type
+   * \tparam Dim the dimension of the square matrix
    */
   template<typename Real, int Dim>
   class SquareMatrix : public RectMatrix<Real, Dim, Dim> {
@@ -124,7 +125,7 @@ namespace oopse {
       Real det;
       return det;
     }
-
+    
     /** Returns the trace of this matrix. */
     Real trace() const {
       Real tmp = 0;
@@ -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. */
@@ -199,7 +232,7 @@ namespace oopse {
      * @return true if success, otherwise return false
      * @param a symmetric matrix whose eigenvectors are to be computed. On return, the matrix is
      *     overwritten
-     * @param w will contain the eigenvalues of the matrix On return of this function
+     * @param d will contain the eigenvalues of the matrix On return of this function
      * @param v the columns of this matrix will contain the eigenvectors. The eigenvectors are 
      *    normalized and mutually orthogonal. 
      */
@@ -338,6 +371,10 @@ namespace oopse {
     //// this is NEVER called
     if ( i >= VTK_MAX_ROTATIONS ) {
       std::cout << "vtkMath::Jacobi: Error extracting eigenfunctions" << std::endl;
+      if (n > 4) {
+        delete[] b;
+        delete[] z;
+      }      
       return 0;
     }