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Comparing:
trunk/src/math/SquareMatrix.hpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/math/SquareMatrix.hpp (file contents), Revision 1753 by gezelter, Tue Jun 12 13:20:28 2012 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, 24107 (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"
# 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;
# Line 169 | Line 190 | namespace oopse {
190          return false;
191                  
192        for (unsigned int i = 0; i < Dim ; i++)
193 <        if (fabs(this->data_[i][i] - 1) > oopse::epsilon)
193 >        if (fabs(this->data_[i][i] - 1) > epsilon)
194            return false;
195                      
196        return true;
# Line 371 | Line 392 | namespace oopse {
392            numPos++;
393          }
394        }
395 <      //    if ( numPos < ceil(double(n)/double(2.0)) )
395 >      //    if ( numPos < ceil(RealType(n)/RealType(2.0)) )
396        if ( numPos < ceil_half_n) {
397          for (i=0; i<n; i++) {
398            v(i, j) *= -1.0;
# Line 387 | Line 408 | namespace oopse {
408    }
409  
410  
411 +  typedef SquareMatrix<RealType, 6> Mat6x6d;
412   }
413   #endif //MATH_SQUAREMATRIX_HPP
414  

Comparing:
trunk/src/math/SquareMatrix.hpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/math/SquareMatrix.hpp (property svn:keywords), Revision 1753 by gezelter, Tue Jun 12 13:20:28 2012 UTC

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