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Comparing branches/development/src/math/DynamicRectMatrix.hpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).                        
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 108 | Line 109 | namespace OpenMD {
109      ~DynamicRectMatrix() { deallocate();}
110  
111      /** copy assignment operator */
112 <    DynamicRectMatrix<Real> operator =(const DynamicRectMatrix<Real> m) {
112 >    DynamicRectMatrix<Real> operator =(const DynamicRectMatrix<Real> &m) {
113        if (this == &m)
114            return *this;
115        if (nrow_ != m.getNRow() || ncol_ != m.getNCol()) {
# Line 232 | Line 233 | namespace OpenMD {
233      /**
234       * Tests if this matrix is identical to matrix m
235       * @return true if this matrix is equal to the matrix m, return false otherwise
236 <     * @m matrix to be compared
236 >     * @param m matrix to be compared
237       *
238       * @todo replace operator == by template function equal
239       */
240 <    bool operator ==(const DynamicRectMatrix<Real> m) {
240 >    bool operator ==(const DynamicRectMatrix<Real> &m) {
241        assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
242        for (unsigned int i = 0; i < nrow_; i++)
243          for (unsigned int j = 0; j < ncol_; j++)
# Line 249 | Line 250 | namespace OpenMD {
250      /**
251       * Tests if this matrix is not equal to matrix m
252       * @return true if this matrix is not equal to the matrix m, return false otherwise
253 <     * @m matrix to be compared
253 >     * @param m matrix to be compared
254       */
255 <    bool operator !=(const DynamicRectMatrix<Real> m) {
255 >    bool operator !=(const DynamicRectMatrix<Real> &m) {
256        return !(*this == m);
257      }
258  
# Line 266 | Line 267 | namespace OpenMD {
267       * Sets the value of this matrix to the negation of matrix m.
268       * @param m the source matrix
269       */
270 <    inline void negate(const DynamicRectMatrix<Real> m) {
270 >    inline void negate(const DynamicRectMatrix<Real> &m) {
271        for (unsigned int i = 0; i < nrow_; i++)
272          for (unsigned int j = 0; j < ncol_; j++)
273            this->data_[i][j] = -m.data_[i][j];        
# Line 276 | Line 277 | namespace OpenMD {
277       * Sets the value of this matrix to the sum of itself and m (*this += m).
278       * @param m the other matrix
279       */
280 <    inline void add( const DynamicRectMatrix<Real> m ) {
280 >    inline void add( const DynamicRectMatrix<Real> &m ) {
281        assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
282        for (unsigned int i = 0; i < nrow_; i++)
283          for (unsigned int j = 0; j < ncol_; j++)        
# Line 288 | Line 289 | namespace OpenMD {
289       * @param m1 the first matrix
290       * @param m2 the second matrix
291       */
292 <    inline void add( const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2 ) {
292 >    inline void add( const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2 ) {
293        assert(m1.getNRow() == m2.getNRow() && m1.getNCol() == m2.getNCol());
294        for (unsigned int i = 0; i < nrow_; i++)
295          for (unsigned int j = 0; j < ncol_; j++)        
# Line 299 | Line 300 | namespace OpenMD {
300       * Sets the value of this matrix to the difference  of itself and m (*this -= m).
301       * @param m the other matrix
302       */
303 <    inline void sub( const DynamicRectMatrix<Real> m ) {
303 >    inline void sub( const DynamicRectMatrix<Real> &m ) {
304        assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
305        for (unsigned int i = 0; i < nrow_; i++)
306          for (unsigned int j = 0; j < ncol_; j++)        
# Line 311 | Line 312 | namespace OpenMD {
312       * @param m1 the first matrix
313       * @param m2 the second matrix
314       */
315 <    inline void sub( const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2){
315 >    inline void sub( const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2){
316        assert(m1.getNRow() == m2.getNRow() && m1.getNCol() == m2.getNCol());
317        for (unsigned int i = 0; i < nrow_; i++)
318          for (unsigned int j = 0; j < ncol_; j++)        
# Line 333 | Line 334 | namespace OpenMD {
334       * @param s the scalar value
335       * @param m the matrix
336       */
337 <    inline void mul( Real s, const DynamicRectMatrix<Real> m ) {
337 >    inline void mul( Real s, const DynamicRectMatrix<Real> &m ) {
338        assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());    
339        for (unsigned int i = 0; i < nrow_; i++)
340          for (unsigned int j = 0; j < ncol_; j++)  
# Line 355 | Line 356 | namespace OpenMD {
356       * @param s the scalar value
357       * @param m the matrix
358       */
359 <    inline void div( Real s, const DynamicRectMatrix<Real> m ) {
359 >    inline void div( Real s, const DynamicRectMatrix<Real> &m ) {
360        assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
361        for (unsigned int i = 0; i < nrow_; i++)
362          for (unsigned int j = 0; j < ncol_; j++)  
# Line 439 | Line 440 | namespace OpenMD {
440      unsigned int nrow_;
441      unsigned int ncol_;
442    private:
443 <    void allocate(int nrow, int ncol) {
444 <        nrow_ = nrow;
445 <        ncol_ = ncol;
446 <        data_ = new Real*[nrow_];
447 <        for (int i = 0; i < nrow_; ++i)
448 <            data_[i] = new Real[ncol_];
443 >    void allocate( int nrow,  int ncol ) {
444 >      nrow_ = (unsigned int) nrow;
445 >      ncol_ = (unsigned int) ncol;
446 >      data_ = new Real*[nrow_];
447 >      for (unsigned int i = 0; i < nrow_; ++i)
448 >        data_[i] = new Real[ncol_];
449      }
450 <
450 >    
451      void deallocate() {
452 <      for (int i = 0; i < nrow_; ++i)
452 >      for (unsigned int i = 0; i < nrow_; ++i)
453          delete data_[i];
454        delete []data_;
455 <
455 >      
456        nrow_ = 0;
457        ncol_ = 0;
458        data_ = NULL;
# Line 461 | Line 462 | namespace OpenMD {
462  
463    /** Negate the value of every element of this matrix. */
464    template<typename Real>
465 <  inline DynamicRectMatrix<Real> operator -(const DynamicRectMatrix<Real> m) {
465 >  inline DynamicRectMatrix<Real> operator -(const DynamicRectMatrix<Real> &m) {
466      DynamicRectMatrix<Real> result(m);
467  
468      result.negate();
# Line 476 | Line 477 | namespace OpenMD {
477     * @param m2 the second matrix
478     */
479    template<typename Real>
480 <  inline DynamicRectMatrix<Real> operator + (const DynamicRectMatrix<Real> m1,const DynamicRectMatrix<Real> m2) {
480 >  inline DynamicRectMatrix<Real> operator + (const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2) {
481      
482      DynamicRectMatrix<Real> result(m1.getNRow(), m1.getNCol());
483  
# Line 492 | Line 493 | namespace OpenMD {
493     * @param m2 the second matrix
494     */
495    template<typename Real>
496 <  inline DynamicRectMatrix<Real> operator - (const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2) {
496 >  inline DynamicRectMatrix<Real> operator - (const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2) {
497      DynamicRectMatrix<Real> result(m1.getNRow(), m1.getNCol());
498  
499      result.sub(m1, m2);
# Line 507 | Line 508 | namespace OpenMD {
508     * @param s the scalar
509     */
510    template<typename Real>
511 <  inline DynamicRectMatrix<Real> operator *(const DynamicRectMatrix<Real> m, Real s) {
511 >  inline DynamicRectMatrix<Real> operator *(const DynamicRectMatrix<Real> &m, Real s) {
512      DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol());
513  
514      result.mul(s, m);
# Line 522 | Line 523 | namespace OpenMD {
523     * @param m the matrix
524     */
525    template<typename Real>
526 <  inline DynamicRectMatrix<Real> operator *(Real s, const DynamicRectMatrix<Real> m) {
526 >  inline DynamicRectMatrix<Real> operator *(Real s, const DynamicRectMatrix<Real> &m) {
527      DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol());
528  
529      result.mul(s, m);
# Line 558 | Line 559 | namespace OpenMD {
559     * @param v the vector
560     */
561    template<typename Real>
562 <  inline DynamicVector<Real> operator *(const DynamicRectMatrix<Real> m, const DynamicVector<Real>& v) {
562 >  inline DynamicVector<Real> operator *(const DynamicRectMatrix<Real> &m, const DynamicVector<Real> &v) {
563      int nrow = m.getNRow();
564      int ncol = m.getNCol();
565 <    assert(ncol = v.size());
565 >    assert(ncol == v.size());
566      DynamicVector<Real> result(nrow);
567      
568      for (unsigned int i = 0; i < nrow ; i++)
# Line 578 | Line 579 | namespace OpenMD {
579     * @param s the scalar
580     */
581    template<typename Real>
582 <  inline DynamicRectMatrix<Real> operator /(const DynamicRectMatrix<Real> m, Real s) {
582 >  inline DynamicRectMatrix<Real> operator /(const DynamicRectMatrix<Real> &m, Real s) {
583      DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol());
584  
585      result.div(s, m);
# Line 590 | Line 591 | namespace OpenMD {
591     * Write to an output stream
592     */
593    template<typename Real>
594 <  std::ostream &operator<< ( std::ostream& o, const DynamicRectMatrix<Real> m) {
594 >  std::ostream &operator<< ( std::ostream& o, const DynamicRectMatrix<Real> &m) {
595      for (unsigned int i = 0; i < m.getNRow() ; i++) {
596        o << "(";
597        for (unsigned int j = 0; j < m.getNCol() ; j++) {

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