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root/OpenMD/trunk/src/math/DynamicVector.hpp

Comparing trunk/src/math/DynamicVector.hpp (file contents):
Revision 891 by tim, Wed Feb 22 20:35:16 2006 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 126 | Line 127 | namespace oopse {
127		DynamicVector(_InputIterator first, _InputIterator last,
128		const allocator_type& alloc = allocator_type())
129		: std::vector<Real, Alloc>(first, last, alloc) {}
130	<
130	>
131	>	inline Real operator()(unsigned int i) const{
132	>	return (*this)[i];
133	>	}
134	>
135	>	inline Real& operator()(unsigned int i){
136	>	return (*this)[i];
137	>	}
138		/**
139		* Tests if this vetor is equal to other vector
140		* @return true if equal, otherwise return false
#	Line 218 | 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 265 | 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 287 | 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 300 | Line 315 | namespace oopse {
315		inline bool isNormalized() {
316		return equal(lengthSquare(), 1.0);
317		}
318	+
319	+	template<class VectorType>
320	+	void getSubVector(unsigned int beginning, VectorType& v) {
321	+	assert(beginning + v.size() -1 <= this->size());
322	+
323	+	for (unsigned int i = 0; i < v.size(); ++i)
324	+	v(i) = (*this)[beginning+i];
325	+	}
326	+
327
328		};
329
#	Line 319 | 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 333 | 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 345 | 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 358 | 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 371 | 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 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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