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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 1879 by gezelter, Sun Jun 16 15:15:42 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 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 93 | Line 94 | namespace oopse {
94		*  @brief  Create a %DynamicVector with copies of an exemplar element.
95		*  @param  n  The number of elements to initially create.
96		*  @param  value  An element to copy.
97	+	*  @param  alloc  The allocator_type to use
98		*
99		*  This constructor fills the %DynamicVector with @a n copies of @a value.
100		*/
#	Line 126 | Line 128 | namespace oopse {
128		DynamicVector(_InputIterator first, _InputIterator last,
129		const allocator_type& alloc = allocator_type())
130		: std::vector<Real, Alloc>(first, last, alloc) {}
131	<
131	>
132	>	inline Real operator()(unsigned int i) const{
133	>	return (*this)[i];
134	>	}
135	>
136	>	inline Real& operator()(unsigned int i){
137	>	return (*this)[i];
138	>	}
139		/**
140		* Tests if this vetor is equal to other vector
141		* @return true if equal, otherwise return false
#	Line 218 | Line 227 | namespace oopse {
227		* @param s the scalar value
228		*/
229		inline void mul( const DynamicVector<Real>& v1, Real s) {
230	+	this->resize(v1.size());
231		for (unsigned int i = 0; i < this->size(); i++)
232		(*this)[i] = s * v1[i];
233		}
#	Line 265 | Line 275 | namespace oopse {
275		return *this;
276		}
277
278	+	/** zero out the vector */
279	+	inline void setZero( ) {
280	+	for (unsigned int i = 0; i < this->size(); i++)
281	+	(*this)[i] = 0;
282	+	}
283	+
284		/**
285		* Returns the length of this vector.
286		* @return the length of this vector
#	Line 287 | Line 303 | namespace oopse {
303
304		len = length();
305
306	<	//if (len < oopse:epsilon)
306	>	//if (len < OpenMD::NumericConstant::epsilon)
307		//  throw();
308
309		*this /= len;
#	Line 300 | Line 316 | namespace oopse {
316		inline bool isNormalized() {
317		return equal(lengthSquare(), 1.0);
318		}
319	+
320	+	template<class VectorType>
321	+	void getSubVector(unsigned int beginning, VectorType& v) {
322	+	assert(beginning + v.size() -1 <= this->size());
323	+
324	+	for (unsigned int i = 0; i < v.size(); ++i)
325	+	v(i) = (*this)[beginning+i];
326	+	}
327	+
328
329		};
330
#	Line 319 | Line 344 | namespace oopse {
344		*/
345		template<typename Real>
346		inline DynamicVector<Real> operator +(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
347	<	DynamicVector<Real> result;
348	<
347	>	assert(v1.size() == v2.size());
348	>	DynamicVector<Real>result(v1.size());
349		result.add(v1, v2);
350		return result;
351		}
#	Line 333 | Line 358 | namespace oopse {
358		*/
359		template<typename Real>
360		DynamicVector<Real> operator -(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
361	<	DynamicVector<Real> result;
361	>	assert(v1.size() == v2.size());
362	>	DynamicVector<Real> result(v1.size());
363		result.sub(v1, v2);
364		return result;
365		}
#	Line 345 | Line 371 | namespace oopse {
371		* @param s the scalar value
372		*/
373		template<typename Real>
374	<	DynamicVector<Real> operator * ( const DynamicVector<Real>& v1, Real s) {
375	<	DynamicVector<Real> result;
374	>	DynamicVector<Real> operator *( const DynamicVector<Real>& v1, Real s) {
375	>	DynamicVector<Real> result(v1.size());
376		result.mul(v1,s);
377		return result;
378		}
#	Line 358 | Line 384 | namespace oopse {
384		* @param v1 the source vector
385		*/
386		template<typename Real>
387	<	DynamicVector<Real> operator * ( Real s, const DynamicVector<Real>& v1 ) {
388	<	DynamicVector<Real> result;
387	>	DynamicVector<Real> operator *( Real s, const DynamicVector<Real>& v1 ) {
388	>	DynamicVector<Real> result(v1.size());
389		result.mul(v1, s);
390		return result;
391		}
#	Line 371 | Line 397 | namespace oopse {
397		* @param s the scalar value
398		*/
399		template<typename Real>
400	<	DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {
401	<	DynamicVector<Real> result;
400	>	DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {
401	>	DynamicVector<Real> result(v1.size());
402		result.div( v1,s);
403		return result;
404		}

Comparing trunk/src/math/DynamicVector.hpp (property svn:keywords):
Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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