ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/math/SquareMatrix.hpp
(Generate patch)

Comparing trunk/src/math/SquareMatrix.hpp (file contents):
Revision 906 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
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, 234107 (2008).          
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 49 | Line 50
50   #define MATH_SQUAREMATRIX_HPP
51  
52   #include "math/RectMatrix.hpp"
53 + #include "utils/NumericConstant.hpp"
54  
55 < namespace oopse {
55 > namespace OpenMD {
56  
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 123 | Line 125 | namespace oopse {
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 131 | Line 133 | namespace oopse {
133        for (unsigned int i = 0; i < Dim ; i++)
134          tmp += this->data_[i][i];
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++)
161          for (unsigned int j = i; j < Dim; j++)
162 <          if (fabs(this->data_[i][j] - this->data_[j][i]) > oopse::epsilon)
162 >          if (fabs(this->data_[i][j] - this->data_[j][i]) > epsilon)
163              return false;
164                          
165        return true;
# Line 157 | Line 178 | namespace oopse {
178      bool isDiagonal() const {
179        for (unsigned int i = 0; i < Dim ; i++)
180          for (unsigned int j = 0; j < Dim; j++)
181 <          if (i !=j && fabs(this->data_[i][j]) > oopse::epsilon)
181 >          if (i !=j && fabs(this->data_[i][j]) > epsilon)
182              return false;
183                          
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())
203          return false;
204                  
205        for (unsigned int i = 0; i < Dim ; i++)
206 <        if (fabs(this->data_[i][i] - 1) > oopse::epsilon)
206 >        if (fabs(this->data_[i][i] - 1) > epsilon)
207            return false;
208                      
209        return true;
# Line 198 | Line 232 | namespace oopse {
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       */
# Line 337 | Line 371 | namespace oopse {
371      //// this is NEVER called
372      if ( i >= VTK_MAX_ROTATIONS ) {
373        std::cout << "vtkMath::Jacobi: Error extracting eigenfunctions" << std::endl;
374 +      if (n > 4) {
375 +        delete[] b;
376 +        delete[] z;
377 +      }      
378        return 0;
379      }
380  
# Line 371 | Line 409 | namespace oopse {
409            numPos++;
410          }
411        }
412 <      //    if ( numPos < ceil(double(n)/double(2.0)) )
412 >      //    if ( numPos < ceil(RealType(n)/RealType(2.0)) )
413        if ( numPos < ceil_half_n) {
414          for (i=0; i<n; i++) {
415            v(i, j) *= -1.0;
# Line 387 | Line 425 | namespace oopse {
425    }
426  
427  
428 <  typedef SquareMatrix<double, 6> Mat6x6d;
428 >  typedef SquareMatrix<RealType, 6> Mat6x6d;
429   }
430   #endif //MATH_SQUAREMATRIX_HPP
431  

Comparing trunk/src/math/SquareMatrix.hpp (property svn:keywords):
Revision 906 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines