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Comparing trunk/src/math/RectMatrix.hpp (file contents):
Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 1924 by gezelter, Mon Aug 5 21:46:11 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 52 | Line 53
53   #include <cmath>
54   #include "Vector.hpp"
55  
56 < namespace oopse {
56 > namespace OpenMD {
57  
58    /**
59     * @class RectMatrix RectMatrix.hpp "math/RectMatrix.hpp"
# Line 220 | Line 221 | namespace oopse {
221      /**
222       * Tests if this matrix is identical to matrix m
223       * @return true if this matrix is equal to the matrix m, return false otherwise
224 <     * @m matrix to be compared
224 >     * @param m matrix to be compared
225       *
226       * @todo replace operator == by template function equal
227       */
# Line 236 | Line 237 | namespace oopse {
237      /**
238       * Tests if this matrix is not equal to matrix m
239       * @return true if this matrix is not equal to the matrix m, return false otherwise
240 <     * @m matrix to be compared
240 >     * @param m matrix to be compared
241       */
242      bool operator !=(const RectMatrix<Real, Row, Col>& m) {
243        return !(*this == m);
# Line 506 | Line 507 | namespace oopse {
507    }
508      
509    /**
510 <   * Return the multiplication of  a matrix and a vector  (m * v).
510 >   * Returns the multiplication of  a matrix and a vector  (m * v).
511     * @return the multiplication of a matrix and a vector
512     * @param m the matrix
513     * @param v the vector
# Line 523 | Line 524 | namespace oopse {
524    }
525  
526    /**
527 +   * Returns the multiplication of a vector transpose and a matrix  (v^T * m).
528 +   * @return the multiplication of a vector transpose and a matrix
529 +   * @param v the vector
530 +   * @param m the matrix
531 +   */
532 +  template<typename Real, unsigned int Row, unsigned int Col>
533 +  inline Vector<Real, Col> operator *(const Vector<Real, Row>& v, const RectMatrix<Real, Row, Col>& m) {
534 +    Vector<Real, Row> result;
535 +    
536 +    for (unsigned int i = 0; i < Col ; i++)
537 +      for (unsigned int j = 0; j < Row ; j++)            
538 +        result[i] += v[j] * m(j, i);
539 +            
540 +    return result;                                                                
541 +  }
542 +
543 +  /**
544     * Return the scalar division of matrix   (m / s).
545     * @return the scalar division of matrix  
546     * @param m the matrix
# Line 537 | Line 555 | namespace oopse {
555      return result;
556    }    
557  
558 +    
559 +    /**
560 +     * Returns the tensor contraction (double dot product) of two rank 2
561 +     * tensors (or Matrices)
562 +     *
563 +     * \f[ \mathbf{A} \colon \! \mathbf{B} = \sum_\alpha \sum_\beta \mathbf{A}_{\alpha \beta} B_{\alpha \beta} \f]
564 +     *
565 +     * @param t1 first tensor
566 +     * @param t2 second tensor
567 +     * @return the tensor contraction (double dot product) of t1 and t2
568 +     */
569 +  template<typename Real, unsigned int Row, unsigned int Col>
570 +  inline Real doubleDot( const RectMatrix<Real, Row, Col>& t1,
571 +                         const RectMatrix<Real, Row, Col>& t2 ) {
572 +    Real tmp;
573 +    tmp = 0;
574 +    
575 +    for (unsigned int i = 0; i < Row; i++)
576 +      for (unsigned int j =0; j < Col; j++)
577 +        tmp += t1(i,j) * t2(i,j);
578 +    
579 +    return tmp;
580 +  }
581 +  
582 +
583 +  
584    /**
585 +   * Returns the vector (cross) product of two matrices.  This
586 +   * operation is defined in:
587 +   *
588 +   * W. Smith, "Point Multipoles in the Ewald Summation (Revisited),"
589 +   * CCP5 Newsletter No 46., pp. 18-30.
590 +   *
591 +   * Equation 21 defines:
592 +   * \f[
593 +   * V_alpha = \sum_\beta \left[ A_{\alpha+1,\beta} * B_{\alpha+2,\beta}
594 +                           -A_{\alpha+2,\beta} * B_{\alpha+2,\beta} \right]
595 +   * \f]
596 +
597 +   * where \f[\alpha+1\f] and \f[\alpha+2\f] are regarded as cyclic
598 +   * permuations of the matrix indices (i.e. for a 3x3 matrix, when
599 +   * \f[\alpha = 2\f], \f[\alpha + 1 = 3 \f], and \f[\alpha + 2 = 1 \f] ).
600 +   *
601 +   * @param t1 first matrix
602 +   * @param t2 second matrix
603 +   * @return the cross product (vector product) of t1 and t2
604 +   */
605 +  template<typename Real, unsigned int Row, unsigned int Col>
606 +  inline Vector<Real, Row> cross( const RectMatrix<Real, Row, Col>& t1,
607 +                                  const RectMatrix<Real, Row, Col>& t2 ) {
608 +    Vector<Real, Row> result;
609 +    unsigned int i1;
610 +    unsigned int i2;
611 +    
612 +    for (unsigned int i = 0; i < Row; i++) {
613 +      i1 = (i+1)%Row;
614 +      i2 = (i+2)%Row;
615 +      for (unsigned int j = 0; j < Col; j++) {
616 +        result[i] += t1(i1,j) * t2(i2,j) - t1(i2,j) * t2(i1,j);
617 +      }
618 +    }    
619 +    return result;
620 +  }
621 +  
622 +  
623 +  /**
624     * Write to an output stream
625     */
626    template<typename Real,  unsigned int Row, unsigned int Col>

Comparing trunk/src/math/RectMatrix.hpp (property svn:keywords):
Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 1924 by gezelter, Mon Aug 5 21:46:11 2013 UTC

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