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Comparing branches/development/src/math/SquareMatrix3.hpp (file contents):
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 47 | Line 48
48   */
49   #ifndef MATH_SQUAREMATRIX3_HPP
50   #define  MATH_SQUAREMATRIX3_HPP
51 + #include "config.h"
52 + #include <cmath>
53   #include <vector>
54   #include "Quaternion.hpp"
55   #include "SquareMatrix.hpp"
# Line 109 | Line 112 | namespace OpenMD {
112        return *this;
113      }
114  
115 +    
116      /**
117       * Sets this matrix to a rotation matrix by three euler angles
118       * @ param euler
# Line 121 | Line 125 | namespace OpenMD {
125       * Sets this matrix to a rotation matrix by three euler angles
126       * @param phi
127       * @param theta
128 <     * @psi theta
128 >     * @param psi
129       */
130      void setupRotMat(Real phi, Real theta, Real psi) {
131        Real sphi, stheta, spsi;
# Line 187 | Line 191 | namespace OpenMD {
191      }
192  
193  
190 –
194      /**
195       * Returns the quaternion from this rotation matrix
196       * @return the quaternion from this rotation matrix
# Line 417 | Line 420 | namespace OpenMD {
420      Vector3<Real> v_maxI, v_k, v_j;
421  
422      // diagonalize using Jacobi
423 <    jacobi(a, w, v);
423 >    SquareMatrix3<Real>::jacobi(a, w, v);
424      // if all the eigenvalues are the same, return identity matrix
425      if (w[0] == w[1] && w[0] == w[2] ) {
426        v = SquareMatrix3<Real>::identity();

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