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Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 56 | Line 57 | namespace OpenMD {
57    /**
58     * @class SquareMatrix SquareMatrix.hpp "math/SquareMatrix.hpp"
59     * @brief A square matrix class
60 <   * @template Real the element type
61 <   * @template Dim the dimension of the square matrix
60 >   * \tparam Real the element type
61 >   * \tparam Dim the dimension of the square matrix
62     */
63    template<typename Real, int Dim>
64    class SquareMatrix : public RectMatrix<Real, Dim, Dim> {
# Line 124 | Line 125 | namespace OpenMD {
125        Real det;
126        return det;
127      }
128 <
128 >    
129      /** Returns the trace of this matrix. */
130      Real trace() const {
131        Real tmp = 0;
# Line 134 | Line 135 | namespace OpenMD {
135  
136        return tmp;
137      }
138 +    
139 +    /**
140 +     * Returns the tensor contraction (double dot product) of two rank 2
141 +     * tensors (or Matrices)
142 +     * @param t1 first tensor
143 +     * @param t2 second tensor
144 +     * @return the tensor contraction (double dot product) of t1 and t2
145 +     */
146 +    Real doubleDot( const SquareMatrix<Real, Dim>& t1, const SquareMatrix<Real, Dim>& t2 ) {
147 +      Real tmp;
148 +      tmp = 0;
149 +      
150 +      for (unsigned int i = 0; i < Dim; i++)
151 +        for (unsigned int j =0; j < Dim; j++)
152 +          tmp += t1[i][j] * t2[i][j];
153 +      
154 +      return tmp;
155 +    }
156  
157 +
158      /** Tests if this matrix is symmetrix. */            
159      bool isSymmetric() const {
160        for (unsigned int i = 0; i < Dim - 1; i++)
# Line 164 | Line 184 | namespace OpenMD {
184        return true;
185      }
186  
187 +    /**
188 +     * Returns a column vector that contains the elements from the
189 +     * diagonal of m in the order R(0) = m(0,0), R(1) = m(1,1), and so
190 +     * on.
191 +     */
192 +    Vector<Real, Dim> diagonals() const {
193 +      Vector<Real, Dim> result;
194 +      for (unsigned int i = 0; i < Dim; i++) {
195 +        result(i) = this->data_[i][i];
196 +      }
197 +      return result;
198 +    }
199 +
200      /** Tests if this matrix is the unit matrix. */
201      bool isUnitMatrix() const {
202        if (!isDiagonal())
# Line 199 | Line 232 | namespace OpenMD {
232       * @return true if success, otherwise return false
233       * @param a symmetric matrix whose eigenvectors are to be computed. On return, the matrix is
234       *     overwritten
235 <     * @param w will contain the eigenvalues of the matrix On return of this function
235 >     * @param d will contain the eigenvalues of the matrix On return of this function
236       * @param v the columns of this matrix will contain the eigenvectors. The eigenvectors are
237       *    normalized and mutually orthogonal.
238       */

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