src/math/DynamicVector.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file DynamicVector.hpp
 * @author Teng Lin
 * @date 09/14/2004
 * @version 1.0
 */
 
#ifndef MATH_DYNAMICVECTOR_HPP
#define MATH_DYNAMICVECTOR_HPP

#include <cassert>
#include <cmath>
#include <iostream>
#include <math.h>
#include <algorithm>
#include <vector>

namespace OpenMD {
    
  /**
   * @class DynamicVector DynamicVector.hpp "math/DynamicVector.hpp"
   * @brief Fix length vector class
   */
  template<typename Real, typename Alloc = std::allocator<Real> >
  class DynamicVector : public std::vector<Real, Alloc> {
  
  public:
      typedef Real value_type;
      typedef std::vector<Real, Alloc> VectorType;
      typedef typename VectorType::pointer pointer;
      typedef typename VectorType::const_pointer const_pointer;
      typedef typename VectorType::reference reference;
      typedef typename VectorType::const_reference const_reference;
      typedef typename VectorType::iterator iterator;
      typedef typename VectorType::const_iterator const_iterator;
      typedef typename VectorType::const_reverse_iterator  const_reverse_iterator;
      typedef typename VectorType::reverse_iterator reverse_iterator;
      typedef typename VectorType::size_type size_type;
      typedef typename VectorType::difference_type difference_type;
      typedef typename VectorType::allocator_type allocator_type;


      // [23.2.4.1] construct/copy/destroy
      // (assign() and get_allocator() are also listed in this section)
      /**
       *  @brief  Default constructor creates no elements.
       */      explicit
      DynamicVector(const allocator_type& alloc = allocator_type())
      : std::vector<Real, Alloc>(alloc) { }
  
      /**
       *  @brief  Create a %DynamicVector with copies of an exemplar element.
       *  @param  n  The number of elements to initially create.
       *  @param  value  An element to copy.
       *
       *  This constructor fills the %DynamicVector with @a n copies of @a value.
       */
      DynamicVector(size_type n, const value_type& value,
             const allocator_type& alloc = allocator_type())
      : std::vector<Real, Alloc>(n, value, alloc){ }

      /**
       *  @brief  Create a %DynamicVector with default elements.
       *  @param  n  The number of elements to initially create.
       *
       *  This constructor fills the %DynamicVector with @a n copies of a
       *  default-constructed element.
       */
      explicit
      DynamicVector(size_type n) : std::vector<Real, Alloc>(n) { }

      /**
       *  @brief  %Vector copy constructor.
       *  @param  x  A %DynamicVector of identical element and allocator types.
       *
       *  The newly-created %DynamicVector uses a copy of the allocation
       *  object used by @a x.  All the elements of @a x are copied,
       *  but any extra memory in
       *  @a x (for fast expansion) will not be copied.
       */
      DynamicVector(const DynamicVector& x)
      : std::vector<Real, Alloc>(x) {}

      template<typename _InputIterator>
        DynamicVector(_InputIterator first, _InputIterator last,
               const allocator_type& alloc = allocator_type())
        : std::vector<Real, Alloc>(first, last, alloc) {}
       
    inline Real operator()(unsigned int i) const{
      return (*this)[i];
    }
    
    inline Real& operator()(unsigned int i){
      return (*this)[i];
    }     
    /**
     * Tests if this vetor is equal to other vector
     * @return true if equal, otherwise return false
     * @param v vector to be compared
     */
    inline bool operator ==(const DynamicVector<Real>& v) {

      for (unsigned int i = 0; i < this->size(); i ++) {
        if (!equal((*this)[i], v[i])) {
          return false;
        }
      }
                
      return true;
    }

    /**
     * Tests if this vetor is not equal to other vector
     * @return true if equal, otherwise return false
     * @param v vector to be compared
     */
    inline bool operator !=(const DynamicVector<Real>& v) {
      return !(*this == v);
    }
             
    /** Negates the value of this vector in place. */           
    inline void negate() {
      for (unsigned int i = 0; i < this->size(); i++)
        (*this)[i] = -(*this)[i];
    }

    /**
     * Sets the value of this vector to the negation of vector v1.
     * @param v1 the source vector
     */
    inline void negate(const DynamicVector<Real>& v1) {
      for (unsigned int i = 0; i < this->size(); i++)
        (*this)[i] = -v1[i];

    }
            
    /**
     * Sets the value of this vector to the sum of itself and v1 (*this += v1).
     * @param v1 the other vector
     */
    inline void add( const DynamicVector<Real>& v1 ) {
      std::transform(this->begin(), this->end(), v1.begin(),this->begin(),std::plus<Real>());
    }

    /**
     * Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
     * @param v1 the first vector
     * @param v2 the second vector
     */
    inline void add( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
      std::transform(v1.begin(), v1.end(), v2.begin(),this->begin(),std::plus<Real>());
    }

    /**
     * Sets the value of this vector to the difference  of itself and v1 (*this -= v1).
     * @param v1 the other vector
     */
    inline void sub( const DynamicVector<Real>& v1 ) {
        std::transform(this->begin(), this->end(), v1.begin(),this->begin(),std::minus<Real>());
    }

    /**
     * Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2).
     * @param v1 the first vector
     * @param v2 the second vector
     */
    inline void sub( const DynamicVector<Real>& v1, const DynamicVector  &v2 ){
      std::transform(v1.begin(), v1.end(), v2.begin(),this->begin(),std::minus<Real>());    
    }

    /**
     * Sets the value of this vector to the scalar multiplication of itself (*this *= s).
     * @param s the scalar value
     */
    inline void mul( Real s ) {
      for (unsigned int i = 0; i < this->size(); i++)
        (*this)[i] *= s;
    }

    /**
     * Sets the value of this vector to the scalar multiplication of vector v1  
     * (*this = s * v1).
     * @param v1 the vector            
     * @param s the scalar value
     */
    inline void mul( const DynamicVector<Real>& v1, Real s) {
      this->resize(v1.size());
      for (unsigned int i = 0; i < this->size(); i++)
        (*this)[i] = s * v1[i];
    }

    /**
     * Sets the value of this vector to the scalar division of itself  (*this /= s ).
     * @param s the scalar value
     */             
    inline void div( Real s) {
      for (unsigned int i = 0; i < this->size(); i++)            
        (*this)[i] /= s;
    }

    /**
     * Sets the value of this vector to the scalar division of vector v1  (*this = v1 / s ).
     * @param v1 the source vector
     * @param s the scalar value
     */                         
    inline void div( const DynamicVector<Real>& v1, Real s ) {
      for (unsigned int i = 0; i < this->size(); i++)
        (*this)[i] = v1[i] / s;
    }

    /** @see #add */
    inline DynamicVector<Real>& operator +=( const DynamicVector<Real>& v1 ) {
      add(v1);
      return *this;
    }

    /** @see #sub */
    inline DynamicVector<Real>& operator -=( const DynamicVector<Real>& v1 ) {
      sub(v1);
      return *this;
    }

    /** @see #mul */
    inline DynamicVector<Real>& operator *=( Real s) {
      mul(s);
      return *this;
    }

    /** @see #div */
    inline DynamicVector<Real>& operator /=( Real s ) {
      div(s);
      return *this;
    }

    /** zero out the vector */
    inline void setZero( ) {
      for (unsigned int i = 0; i < this->size(); i++)
        (*this)[i] = 0;
    }

    /**
     * Returns the length of this vector.
     * @return the length of this vector
     */
    inline Real length() {
      return sqrt(lengthSquare());  
    }
            
    /**
     * Returns the squared length of this vector.
     * @return the squared length of this vector
     */
    inline Real lengthSquare() {
      return dot(*this, *this);
    }
            
    /** Normalizes this vector in place */
    inline void normalize() {
      Real len;

      len = length();
                
      //if (len < OpenMD::NumericConstant::epsilon)
      //  throw();
                
      *this /= len;
    }

    /**
     * Tests if this vector is normalized
     * @return true if this vector is normalized, otherwise return false
     */
    inline bool isNormalized() {
      return equal(lengthSquare(), 1.0);
    }           

    template<class VectorType>
    void getSubVector(unsigned int beginning, VectorType& v) {
        assert(beginning + v.size() -1 <= this->size());

        for (unsigned int i = 0; i < v.size(); ++i)
             v(i) = (*this)[beginning+i];
    }

    
  };

  /** unary minus*/
  template<typename Real>    
  inline DynamicVector<Real> operator -(const DynamicVector<Real>& v1){
    DynamicVector<Real> tmp(v1);
    tmp.negate();
    return tmp;
  }

  /**
   * Return the sum of two vectors  (v1 - v2). 
   * @return the sum of two vectors
   * @param v1 the first vector
   * @param v2 the second vector
   */   
  template<typename Real>    
  inline DynamicVector<Real> operator +(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
    assert(v1.size() == v2.size());
    DynamicVector<Real>result(v1.size());
    result.add(v1, v2);
    return result;        
  }

  /**
   * Return the difference of two vectors  (v1 - v2). 
   * @return the difference of two vectors
   * @param v1 the first vector
   * @param v2 the second vector
   */  
  template<typename Real>    
  DynamicVector<Real> operator -(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
    assert(v1.size() == v2.size());
    DynamicVector<Real> result(v1.size());
    result.sub(v1, v2);
    return result;        
  }
    
  /**
   * Returns the vaule of scalar multiplication of this vector v1 (v1 * r). 
   * @return  the vaule of scalar multiplication of this vector
   * @param v1 the source vector
   * @param s the scalar value
   */ 
  template<typename Real>                 
  DynamicVector<Real> operator *( const DynamicVector<Real>& v1, Real s) {      
    DynamicVector<Real> result(v1.size());
    result.mul(v1,s);
    return result;           
  }
    
  /**
   * Returns the vaule of scalar multiplication of this vector v1 (v1 * r). 
   * @return  the vaule of scalar multiplication of this vector
   * @param s the scalar value
   * @param v1 the source vector
   */  
  template<typename Real>
  DynamicVector<Real> operator *( Real s, const DynamicVector<Real>& v1 ) {
    DynamicVector<Real> result(v1.size());
    result.mul(v1, s);
    return result;           
  }

  /**
   * Returns the  value of division of a vector by a scalar. 
   * @return  the vaule of scalar division of this vector
   * @param v1 the source vector
   * @param s the scalar value
   */
  template<typename Real>    
  DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {     
    DynamicVector<Real> result(v1.size());
    result.div( v1,s);
    return result;           
  }
    
  /**
   * Returns the dot product of two DynamicVectors
   * @param v1 first vector
   * @param v2 second vector
   * @return the dot product of v1 and v2
   */
  template<typename Real>    
  inline Real dot( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
    Real tmp;
    tmp = 0;
    assert(v1.size() == v2.size());
    for (unsigned int i = 0; i < v1.size(); i++)
      tmp += v1[i] * v2[i];

    return tmp;
  }

  /**
   * Returns the distance between  two DynamicVectors
   * @param v1 first vector
   * @param v2 second vector
   * @return the distance between v1 and v2
   */   
  template<typename Real>    
  inline Real distance( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
    DynamicVector<Real> tempDynamicVector = v1 - v2;
    return tempDynamicVector.length();
  }

  /**
   * Returns the squared distance between  two DynamicVectors
   * @param v1 first vector
   * @param v2 second vector
   * @return the squared distance between v1 and v2
   */
  template<typename Real>
  inline Real distanceSquare( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
    DynamicVector<Real> tempDynamicVector = v1 - v2;
    return tempDynamicVector.lengthSquare();
  }

  /**
   * Write to an output stream
   */
  template<typename Real>
  std::ostream &operator<< ( std::ostream& o, const DynamicVector<Real>& v) {

    o << "[ ";
        
    for (unsigned int i = 0 ; i< v.size(); i++) {
      o << v[i];

      if (i  != v.size() -1) {
        o<< ", ";
      }
    }

    o << " ]";
    return o;        
  }
    
}
#endif

Revision:	1744
Committed:	Tue Jun 5 18:07:08 2012 UTC (12 years, 10 months ago) by gezelter
File size:	14873 byte(s)
Log Message:	Fixes for minimization
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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	/**
44	* @file DynamicVector.hpp
45	* @author Teng Lin
46	* @date 09/14/2004
47	* @version 1.0
48	*/
49
50	#ifndef MATH_DYNAMICVECTOR_HPP
51	#define MATH_DYNAMICVECTOR_HPP
52
53	#include <cassert>
54	#include <cmath>
55	#include <iostream>
56	#include <math.h>
57	#include <algorithm>
58	#include <vector>
59
60	namespace OpenMD {
61
62	/**
63	* @class DynamicVector DynamicVector.hpp "math/DynamicVector.hpp"
64	* @brief Fix length vector class
65	*/
66	template<typename Real, typename Alloc = std::allocator<Real> >
67	class DynamicVector : public std::vector<Real, Alloc> {
68
69	public:
70	typedef Real value_type;
71	typedef std::vector<Real, Alloc> VectorType;
72	typedef typename VectorType::pointer pointer;
73	typedef typename VectorType::const_pointer const_pointer;
74	typedef typename VectorType::reference reference;
75	typedef typename VectorType::const_reference const_reference;
76	typedef typename VectorType::iterator iterator;
77	typedef typename VectorType::const_iterator const_iterator;
78	typedef typename VectorType::const_reverse_iterator const_reverse_iterator;
79	typedef typename VectorType::reverse_iterator reverse_iterator;
80	typedef typename VectorType::size_type size_type;
81	typedef typename VectorType::difference_type difference_type;
82	typedef typename VectorType::allocator_type allocator_type;
83
84
85	// [23.2.4.1] construct/copy/destroy
86	// (assign() and get_allocator() are also listed in this section)
87	/**
88	* @brief Default constructor creates no elements.
89	*/ explicit
90	DynamicVector(const allocator_type& alloc = allocator_type())
91	: std::vector<Real, Alloc>(alloc) { }
92
93	/**
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	*
98	* This constructor fills the %DynamicVector with @a n copies of @a value.
99	*/
100	DynamicVector(size_type n, const value_type& value,
101	const allocator_type& alloc = allocator_type())
102	: std::vector<Real, Alloc>(n, value, alloc){ }
103
104	/**
105	* @brief Create a %DynamicVector with default elements.
106	* @param n The number of elements to initially create.
107	*
108	* This constructor fills the %DynamicVector with @a n copies of a
109	* default-constructed element.
110	*/
111	explicit
112	DynamicVector(size_type n) : std::vector<Real, Alloc>(n) { }
113
114	/**
115	* @brief %Vector copy constructor.
116	* @param x A %DynamicVector of identical element and allocator types.
117	*
118	* The newly-created %DynamicVector uses a copy of the allocation
119	* object used by @a x. All the elements of @a x are copied,
120	* but any extra memory in
121	* @a x (for fast expansion) will not be copied.
122	*/
123	DynamicVector(const DynamicVector& x)
124	: std::vector<Real, Alloc>(x) {}
125
126	template<typename _InputIterator>
127	DynamicVector(_InputIterator first, _InputIterator last,
128	const allocator_type& alloc = allocator_type())
129	: std::vector<Real, Alloc>(first, last, alloc) {}
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
141	* @param v vector to be compared
142	*/
143	inline bool operator ==(const DynamicVector<Real>& v) {
144
145	for (unsigned int i = 0; i < this->size(); i ++) {
146	if (!equal((*this)[i], v[i])) {
147	return false;
148	}
149	}
150
151	return true;
152	}
153
154	/**
155	* Tests if this vetor is not equal to other vector
156	* @return true if equal, otherwise return false
157	* @param v vector to be compared
158	*/
159	inline bool operator !=(const DynamicVector<Real>& v) {
160	return !(*this == v);
161	}
162
163	/** Negates the value of this vector in place. */
164	inline void negate() {
165	for (unsigned int i = 0; i < this->size(); i++)
166	(this)[i] = -(this)[i];
167	}
168
169	/**
170	* Sets the value of this vector to the negation of vector v1.
171	* @param v1 the source vector
172	*/
173	inline void negate(const DynamicVector<Real>& v1) {
174	for (unsigned int i = 0; i < this->size(); i++)
175	(*this)[i] = -v1[i];
176
177	}
178
179	/**
180	* Sets the value of this vector to the sum of itself and v1 (*this += v1).
181	* @param v1 the other vector
182	*/
183	inline void add( const DynamicVector<Real>& v1 ) {
184	std::transform(this->begin(), this->end(), v1.begin(),this->begin(),std::plus<Real>());
185	}
186
187	/**
188	* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
189	* @param v1 the first vector
190	* @param v2 the second vector
191	*/
192	inline void add( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
193	std::transform(v1.begin(), v1.end(), v2.begin(),this->begin(),std::plus<Real>());
194	}
195
196	/**
197	* Sets the value of this vector to the difference of itself and v1 (*this -= v1).
198	* @param v1 the other vector
199	*/
200	inline void sub( const DynamicVector<Real>& v1 ) {
201	std::transform(this->begin(), this->end(), v1.begin(),this->begin(),std::minus<Real>());
202	}
203
204	/**
205	* Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2).
206	* @param v1 the first vector
207	* @param v2 the second vector
208	*/
209	inline void sub( const DynamicVector<Real>& v1, const DynamicVector &v2 ){
210	std::transform(v1.begin(), v1.end(), v2.begin(),this->begin(),std::minus<Real>());
211	}
212
213	/**
214	* Sets the value of this vector to the scalar multiplication of itself (this = s).
215	* @param s the scalar value
216	*/
217	inline void mul( Real s ) {
218	for (unsigned int i = 0; i < this->size(); i++)
219	(this)[i] = s;
220	}
221
222	/**
223	* Sets the value of this vector to the scalar multiplication of vector v1
224	* (this = s v1).
225	* @param v1 the vector
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	}
233
234	/**
235	* Sets the value of this vector to the scalar division of itself (*this /= s ).
236	* @param s the scalar value
237	*/
238	inline void div( Real s) {
239	for (unsigned int i = 0; i < this->size(); i++)
240	(*this)[i] /= s;
241	}
242
243	/**
244	* Sets the value of this vector to the scalar division of vector v1 (*this = v1 / s ).
245	* @param v1 the source vector
246	* @param s the scalar value
247	*/
248	inline void div( const DynamicVector<Real>& v1, Real s ) {
249	for (unsigned int i = 0; i < this->size(); i++)
250	(*this)[i] = v1[i] / s;
251	}
252
253	/** @see #add */
254	inline DynamicVector<Real>& operator +=( const DynamicVector<Real>& v1 ) {
255	add(v1);
256	return *this;
257	}
258
259	/** @see #sub */
260	inline DynamicVector<Real>& operator -=( const DynamicVector<Real>& v1 ) {
261	sub(v1);
262	return *this;
263	}
264
265	/** @see #mul */
266	inline DynamicVector<Real>& operator *=( Real s) {
267	mul(s);
268	return *this;
269	}
270
271	/** @see #div */
272	inline DynamicVector<Real>& operator /=( Real s ) {
273	div(s);
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
286	*/
287	inline Real length() {
288	return sqrt(lengthSquare());
289	}
290
291	/**
292	* Returns the squared length of this vector.
293	* @return the squared length of this vector
294	*/
295	inline Real lengthSquare() {
296	return dot(this, this);
297	}
298
299	/** Normalizes this vector in place */
300	inline void normalize() {
301	Real len;
302
303	len = length();
304
305	//if (len < OpenMD::NumericConstant::epsilon)
306	// throw();
307
308	*this /= len;
309	}
310
311	/**
312	* Tests if this vector is normalized
313	* @return true if this vector is normalized, otherwise return false
314	*/
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
330	/** unary minus*/
331	template<typename Real>
332	inline DynamicVector<Real> operator -(const DynamicVector<Real>& v1){
333	DynamicVector<Real> tmp(v1);
334	tmp.negate();
335	return tmp;
336	}
337
338	/**
339	* Return the sum of two vectors (v1 - v2).
340	* @return the sum of two vectors
341	* @param v1 the first vector
342	* @param v2 the second vector
343	*/
344	template<typename Real>
345	inline DynamicVector<Real> operator +(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
346	assert(v1.size() == v2.size());
347	DynamicVector<Real>result(v1.size());
348	result.add(v1, v2);
349	return result;
350	}
351
352	/**
353	* Return the difference of two vectors (v1 - v2).
354	* @return the difference of two vectors
355	* @param v1 the first vector
356	* @param v2 the second vector
357	*/
358	template<typename Real>
359	DynamicVector<Real> operator -(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
360	assert(v1.size() == v2.size());
361	DynamicVector<Real> result(v1.size());
362	result.sub(v1, v2);
363	return result;
364	}
365
366	/**
367	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
368	* @return the vaule of scalar multiplication of this vector
369	* @param v1 the source vector
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(v1.size());
375	result.mul(v1,s);
376	return result;
377	}
378
379	/**
380	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
381	* @return the vaule of scalar multiplication of this vector
382	* @param s the scalar value
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(v1.size());
388	result.mul(v1, s);
389	return result;
390	}
391
392	/**
393	* Returns the value of division of a vector by a scalar.
394	* @return the vaule of scalar division of this vector
395	* @param v1 the source vector
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(v1.size());
401	result.div( v1,s);
402	return result;
403	}
404
405	/**
406	* Returns the dot product of two DynamicVectors
407	* @param v1 first vector
408	* @param v2 second vector
409	* @return the dot product of v1 and v2
410	*/
411	template<typename Real>
412	inline Real dot( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
413	Real tmp;
414	tmp = 0;
415	assert(v1.size() == v2.size());
416	for (unsigned int i = 0; i < v1.size(); i++)
417	tmp += v1[i] * v2[i];
418
419	return tmp;
420	}
421
422	/**
423	* Returns the distance between two DynamicVectors
424	* @param v1 first vector
425	* @param v2 second vector
426	* @return the distance between v1 and v2
427	*/
428	template<typename Real>
429	inline Real distance( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
430	DynamicVector<Real> tempDynamicVector = v1 - v2;
431	return tempDynamicVector.length();
432	}
433
434	/**
435	* Returns the squared distance between two DynamicVectors
436	* @param v1 first vector
437	* @param v2 second vector
438	* @return the squared distance between v1 and v2
439	*/
440	template<typename Real>
441	inline Real distanceSquare( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
442	DynamicVector<Real> tempDynamicVector = v1 - v2;
443	return tempDynamicVector.lengthSquare();
444	}
445
446	/**
447	* Write to an output stream
448	*/
449	template<typename Real>
450	std::ostream &operator<< ( std::ostream& o, const DynamicVector<Real>& v) {
451
452	o << "[ ";
453
454	for (unsigned int i = 0 ; i< v.size(); i++) {
455	o << v[i];
456
457	if (i != v.size() -1) {
458	o<< ", ";
459	}
460	}
461
462	o << " ]";
463	return o;
464	}
465
466	}
467	#endif
468