--- trunk/src/math/SquareMatrix.hpp	2009/11/25 20:02:06	1390
+++ trunk/src/math/SquareMatrix.hpp	2013/08/05 21:46:11	1924
@@ -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).
  */
  
 /**
@@ -56,8 +57,8 @@ 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 OpenMD {
       Real det;
       return det;
     }
-
+    
     /** Returns the trace of this matrix. */
     Real trace() const {
       Real tmp = 0;
@@ -162,6 +163,19 @@ namespace OpenMD {
 	    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 +213,7 @@ namespace OpenMD {
      * @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 +352,10 @@ namespace OpenMD {
     //// 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;
     }