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Comparing trunk/src/math/DynamicVector.hpp (file contents):
Revision 1349 by cli2, Wed May 20 19:35:05 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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 56 | Line 57
57   #include <algorithm>
58   #include <vector>
59  
60 < namespace oopse {
60 > namespace OpenMD {
61      
62    /**
63     * @class DynamicVector DynamicVector.hpp "math/DynamicVector.hpp"
# Line 225 | Line 226 | namespace oopse {
226       * @param s the scalar value
227       */
228      inline void mul( const DynamicVector<Real>& v1, Real s) {
229 +      this->resize(v1.size());
230        for (unsigned int i = 0; i < this->size(); i++)
231          (*this)[i] = s * v1[i];
232      }
# Line 272 | Line 274 | namespace oopse {
274        return *this;
275      }
276  
277 +    /** zero out the vector */
278 +    inline void setZero( ) {
279 +      for (unsigned int i = 0; i < this->size(); i++)
280 +        (*this)[i] = 0;
281 +    }
282 +
283      /**
284       * Returns the length of this vector.
285       * @return the length of this vector
# Line 294 | Line 302 | namespace oopse {
302  
303        len = length();
304                  
305 <      //if (len < oopse:epsilon)
305 >      //if (len < OpenMD::NumericConstant::epsilon)
306        //  throw();
307                  
308        *this /= len;
# Line 335 | Line 343 | namespace oopse {
343     */  
344    template<typename Real>    
345    inline DynamicVector<Real> operator +(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
346 <    DynamicVector<Real> result;
347 <        
346 >    assert(v1.size() == v2.size());
347 >    DynamicVector<Real>result(v1.size());
348      result.add(v1, v2);
349      return result;        
350    }
# Line 349 | Line 357 | namespace oopse {
357     */  
358    template<typename Real>    
359    DynamicVector<Real> operator -(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
360 <    DynamicVector<Real> result;
360 >    assert(v1.size() == v2.size());
361 >    DynamicVector<Real> result(v1.size());
362      result.sub(v1, v2);
363      return result;        
364    }
# Line 361 | Line 370 | namespace oopse {
370     * @param s the scalar value
371     */
372    template<typename Real>                
373 <  DynamicVector<Real> operator * ( const DynamicVector<Real>& v1, Real s) {      
374 <    DynamicVector<Real> result;
373 >  DynamicVector<Real> operator *( const DynamicVector<Real>& v1, Real s) {      
374 >    DynamicVector<Real> result(v1.size());
375      result.mul(v1,s);
376      return result;          
377    }
# Line 374 | Line 383 | namespace oopse {
383     * @param v1 the source vector
384     */  
385    template<typename Real>
386 <  DynamicVector<Real> operator * ( Real s, const DynamicVector<Real>& v1 ) {
387 <    DynamicVector<Real> result;
386 >  DynamicVector<Real> operator *( Real s, const DynamicVector<Real>& v1 ) {
387 >    DynamicVector<Real> result(v1.size());
388      result.mul(v1, s);
389      return result;          
390    }
# Line 387 | Line 396 | namespace oopse {
396     * @param s the scalar value
397     */
398    template<typename Real>    
399 <  DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {      
400 <    DynamicVector<Real> result;
399 >  DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {    
400 >    DynamicVector<Real> result(v1.size());
401      result.div( v1,s);
402      return result;          
403    }

Comparing trunk/src/math/DynamicVector.hpp (property svn:keywords):
Revision 1349 by cli2, Wed May 20 19:35:05 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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