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Comparing trunk/src/math/Vector.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 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 54 | Line 55
55		#include <iostream>
56		#include <math.h>
57		#include "config.h"
58	<	namespace oopse {
58	>	namespace OpenMD {
59
60		static const RealType epsilon = 0.000001;
61
#	Line 72 | Line 73 | namespace oopse {
73		inline bool equal(RealType e1, RealType e2) {
74		return fabs(e1 - e2) < epsilon;
75		}
75	–
76
77		/**
78		* @class Vector Vector.hpp "math/Vector.hpp"
#	Line 107 | Line 107 | namespace oopse {
107		return *this;
108		}
109
110	<	template<typename T>
111	<	inline Vector(const T& s){
110	>	// template<typename T>
111	>	// inline Vector(const T& s){
112	>	inline Vector(const Real& s) {
113		for (unsigned int i = 0; i < Dim; i++)
114	<	this->data_[i] = s;
114	>	this->data_[i] = s;
115		}
116
117		/** Constructs and initializes a Vector from an array */
#	Line 195 | Line 196 | namespace oopse {
196		inline bool operator !=(const Vector<Real, Dim>& v) {
197		return !(*this == v);
198		}
199	+
200	+	/** Zeros out the values in this vector in place */
201	+	inline void zero() {
202	+	for (unsigned int i = 0; i < Dim; i++)
203	+	this->data_[i] = 0;
204	+	}
205
206		/** Negates the value of this vector in place. */
207		inline void negate() {
#	Line 271 | Line 278 | namespace oopse {
278		}
279
280		/**
281	+	* Sets the elements of this vector to the multiplication of
282	+	* elements of two other vectors.  Not to be confused with scalar
283	+	* multiplication (mul) or dot products.
284	+	*
285	+	* (*this.data_[i] =  v1.data_[i] * v2.data_[i]).
286	+	* @param v1 the first vector
287	+	* @param v2 the second vector
288	+	*/
289	+	inline void Vmul( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
290	+	for (unsigned int i = 0; i < Dim; i++)
291	+	this->data_[i] = v1.data_[i] * v2.data_[i];
292	+	}
293	+
294	+	/* replaces the elements with the absolute values of those elements */
295	+	inline Vector<Real, Dim>& abs() {
296	+	for (unsigned int i = 0; i < Dim; i++) {
297	+	this->data_[i] = std::abs(this->data_[i]);
298	+	}
299	+	return *this;
300	+	}
301	+
302	+	/* returns the maximum value in this vector */
303	+	inline Real max() {
304	+	Real val = this->data_[0];
305	+	for (unsigned int i = 0; i < Dim; i++) {
306	+	if (this->data_[i] > val) val = this->data_[i];
307	+	}
308	+	return val;
309	+	}
310	+
311	+	/**
312		* Sets the value of this vector to the scalar division of itself  (*this /= s ).
313		* @param s the scalar value
314		*/
#	Line 289 | Line 327 | namespace oopse {
327		this->data_[i] = v1.data_[i] / s;
328		}
329
330	+	/**
331	+	* Sets the elements of this vector to the division of
332	+	* elements of two other vectors.  Not to be confused with scalar
333	+	* division (div)
334	+	*
335	+	* (*this.data_[i] =  v1.data_[i] / v2.data_[i]).
336	+	* @param v1 the first vector
337	+	* @param v2 the second vector
338	+	*/
339	+	inline void Vdiv( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
340	+	for (unsigned int i = 0; i < Dim; i++)
341	+	this->data_[i] = v1.data_[i] / v2.data_[i];
342	+	}
343	+
344	+
345		/** @see #add */
346		inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
347		add(v1);
#	Line 314 | Line 367 | namespace oopse {
367		}
368
369		/**
370	+	* Returns the sum of all elements of this vector.
371	+	* @return the sum of all elements of this vector
372	+	*/
373	+	inline Real sum() {
374	+	Real tmp;
375	+	tmp = 0;
376	+	for (unsigned int i = 0; i < Dim; i++)
377	+	tmp += this->data_[i];
378	+	return tmp;
379	+	}
380	+
381	+	/**
382	+	* Returns the product of all elements of this vector.
383	+	* @return the product of all elements of this vector
384	+	*/
385	+	inline Real componentProduct() {
386	+	Real tmp;
387	+	tmp = 1;
388	+	for (unsigned int i = 0; i < Dim; i++)
389	+	tmp *= this->data_[i];
390	+	return tmp;
391	+	}
392	+
393	+	/**
394		* Returns the length of this vector.
395		* @return the length of this vector
396		*/
#	Line 335 | Line 412 | namespace oopse {
412
413		len = length();
414
415	<	//if (len < oopse:epsilon)
415	>	//if (len < OpenMD::NumericConstant::epsilon)
416		//  throw();
417
418		*this /= len;
#	Line 446 | Line 523 | namespace oopse {
523		return tmp;
524		}
525
526	+
527	+
528	+
529		/**
530	+	* Returns the wide dot product of three Vectors.  Compare with
531	+	* Rapaport's VWDot function.
532	+	*
533	+	* @param v1 first vector
534	+	* @param v2 second vector
535	+	* @param v3 third vector
536	+	* @return the wide dot product of v1, v2, and v3.
537	+	*/
538	+	template<typename Real, unsigned int Dim>
539	+	inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2, const Vector<Real, Dim>& v3 ) {
540	+	Real tmp;
541	+	tmp = 0;
542	+
543	+	for (unsigned int i = 0; i < Dim; i++)
544	+	tmp += v1[i] * v2[i] * v3[i];
545	+
546	+	return tmp;
547	+	}
548	+
549	+
550	+	/**
551		* Returns the distance between  two Vectors
552		* @param v1 first vector
553		* @param v2 second vector

Comparing trunk/src/math/Vector.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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