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.
       *  @param  alloc  The allocator_type to use
       *
       *  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:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	14924 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	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	* @param alloc The allocator_type to use
98	*
99	* This constructor fills the %DynamicVector with @a n copies of @a value.
100	*/
101	DynamicVector(size_type n, const value_type& value,
102	const allocator_type& alloc = allocator_type())
103	: std::vector<Real, Alloc>(n, value, alloc){ }
104
105	/**
106	* @brief Create a %DynamicVector with default elements.
107	* @param n The number of elements to initially create.
108	*
109	* This constructor fills the %DynamicVector with @a n copies of a
110	* default-constructed element.
111	*/
112	explicit
113	DynamicVector(size_type n) : std::vector<Real, Alloc>(n) { }
114
115	/**
116	* @brief %Vector copy constructor.
117	* @param x A %DynamicVector of identical element and allocator types.
118	*
119	* The newly-created %DynamicVector uses a copy of the allocation
120	* object used by @a x. All the elements of @a x are copied,
121	* but any extra memory in
122	* @a x (for fast expansion) will not be copied.
123	*/
124	DynamicVector(const DynamicVector& x)
125	: std::vector<Real, Alloc>(x) {}
126
127	template<typename _InputIterator>
128	DynamicVector(_InputIterator first, _InputIterator last,
129	const allocator_type& alloc = allocator_type())
130	: std::vector<Real, Alloc>(first, last, alloc) {}
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
142	* @param v vector to be compared
143	*/
144	inline bool operator ==(const DynamicVector<Real>& v) {
145
146	for (unsigned int i = 0; i < this->size(); i ++) {
147	if (!equal((*this)[i], v[i])) {
148	return false;
149	}
150	}
151
152	return true;
153	}
154
155	/**
156	* Tests if this vetor is not equal to other vector
157	* @return true if equal, otherwise return false
158	* @param v vector to be compared
159	*/
160	inline bool operator !=(const DynamicVector<Real>& v) {
161	return !(*this == v);
162	}
163
164	/** Negates the value of this vector in place. */
165	inline void negate() {
166	for (unsigned int i = 0; i < this->size(); i++)
167	(this)[i] = -(this)[i];
168	}
169
170	/**
171	* Sets the value of this vector to the negation of vector v1.
172	* @param v1 the source vector
173	*/
174	inline void negate(const DynamicVector<Real>& v1) {
175	for (unsigned int i = 0; i < this->size(); i++)
176	(*this)[i] = -v1[i];
177
178	}
179
180	/**
181	* Sets the value of this vector to the sum of itself and v1 (*this += v1).
182	* @param v1 the other vector
183	*/
184	inline void add( const DynamicVector<Real>& v1 ) {
185	std::transform(this->begin(), this->end(), v1.begin(),this->begin(),std::plus<Real>());
186	}
187
188	/**
189	* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
190	* @param v1 the first vector
191	* @param v2 the second vector
192	*/
193	inline void add( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
194	std::transform(v1.begin(), v1.end(), v2.begin(),this->begin(),std::plus<Real>());
195	}
196
197	/**
198	* Sets the value of this vector to the difference of itself and v1 (*this -= v1).
199	* @param v1 the other vector
200	*/
201	inline void sub( const DynamicVector<Real>& v1 ) {
202	std::transform(this->begin(), this->end(), v1.begin(),this->begin(),std::minus<Real>());
203	}
204
205	/**
206	* Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2).
207	* @param v1 the first vector
208	* @param v2 the second vector
209	*/
210	inline void sub( const DynamicVector<Real>& v1, const DynamicVector &v2 ){
211	std::transform(v1.begin(), v1.end(), v2.begin(),this->begin(),std::minus<Real>());
212	}
213
214	/**
215	* Sets the value of this vector to the scalar multiplication of itself (this = s).
216	* @param s the scalar value
217	*/
218	inline void mul( Real s ) {
219	for (unsigned int i = 0; i < this->size(); i++)
220	(this)[i] = s;
221	}
222
223	/**
224	* Sets the value of this vector to the scalar multiplication of vector v1
225	* (this = s v1).
226	* @param v1 the vector
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	}
234
235	/**
236	* Sets the value of this vector to the scalar division of itself (*this /= s ).
237	* @param s the scalar value
238	*/
239	inline void div( Real s) {
240	for (unsigned int i = 0; i < this->size(); i++)
241	(*this)[i] /= s;
242	}
243
244	/**
245	* Sets the value of this vector to the scalar division of vector v1 (*this = v1 / s ).
246	* @param v1 the source vector
247	* @param s the scalar value
248	*/
249	inline void div( const DynamicVector<Real>& v1, Real s ) {
250	for (unsigned int i = 0; i < this->size(); i++)
251	(*this)[i] = v1[i] / s;
252	}
253
254	/** @see #add */
255	inline DynamicVector<Real>& operator +=( const DynamicVector<Real>& v1 ) {
256	add(v1);
257	return *this;
258	}
259
260	/** @see #sub */
261	inline DynamicVector<Real>& operator -=( const DynamicVector<Real>& v1 ) {
262	sub(v1);
263	return *this;
264	}
265
266	/** @see #mul */
267	inline DynamicVector<Real>& operator *=( Real s) {
268	mul(s);
269	return *this;
270	}
271
272	/** @see #div */
273	inline DynamicVector<Real>& operator /=( Real s ) {
274	div(s);
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
287	*/
288	inline Real length() {
289	return sqrt(lengthSquare());
290	}
291
292	/**
293	* Returns the squared length of this vector.
294	* @return the squared length of this vector
295	*/
296	inline Real lengthSquare() {
297	return dot(this, this);
298	}
299
300	/** Normalizes this vector in place */
301	inline void normalize() {
302	Real len;
303
304	len = length();
305
306	//if (len < OpenMD::NumericConstant::epsilon)
307	// throw();
308
309	*this /= len;
310	}
311
312	/**
313	* Tests if this vector is normalized
314	* @return true if this vector is normalized, otherwise return false
315	*/
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
331	/** unary minus*/
332	template<typename Real>
333	inline DynamicVector<Real> operator -(const DynamicVector<Real>& v1){
334	DynamicVector<Real> tmp(v1);
335	tmp.negate();
336	return tmp;
337	}
338
339	/**
340	* Return the sum of two vectors (v1 - v2).
341	* @return the sum of two vectors
342	* @param v1 the first vector
343	* @param v2 the second vector
344	*/
345	template<typename Real>
346	inline DynamicVector<Real> operator +(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
347	assert(v1.size() == v2.size());
348	DynamicVector<Real>result(v1.size());
349	result.add(v1, v2);
350	return result;
351	}
352
353	/**
354	* Return the difference of two vectors (v1 - v2).
355	* @return the difference of two vectors
356	* @param v1 the first vector
357	* @param v2 the second vector
358	*/
359	template<typename Real>
360	DynamicVector<Real> operator -(const DynamicVector<Real>& v1, const DynamicVector<Real>& v2) {
361	assert(v1.size() == v2.size());
362	DynamicVector<Real> result(v1.size());
363	result.sub(v1, v2);
364	return result;
365	}
366
367	/**
368	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
369	* @return the vaule of scalar multiplication of this vector
370	* @param v1 the source vector
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(v1.size());
376	result.mul(v1,s);
377	return result;
378	}
379
380	/**
381	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
382	* @return the vaule of scalar multiplication of this vector
383	* @param s the scalar value
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(v1.size());
389	result.mul(v1, s);
390	return result;
391	}
392
393	/**
394	* Returns the value of division of a vector by a scalar.
395	* @return the vaule of scalar division of this vector
396	* @param v1 the source vector
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(v1.size());
402	result.div( v1,s);
403	return result;
404	}
405
406	/**
407	* Returns the dot product of two DynamicVectors
408	* @param v1 first vector
409	* @param v2 second vector
410	* @return the dot product of v1 and v2
411	*/
412	template<typename Real>
413	inline Real dot( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
414	Real tmp;
415	tmp = 0;
416	assert(v1.size() == v2.size());
417	for (unsigned int i = 0; i < v1.size(); i++)
418	tmp += v1[i] * v2[i];
419
420	return tmp;
421	}
422
423	/**
424	* Returns the distance between two DynamicVectors
425	* @param v1 first vector
426	* @param v2 second vector
427	* @return the distance between v1 and v2
428	*/
429	template<typename Real>
430	inline Real distance( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
431	DynamicVector<Real> tempDynamicVector = v1 - v2;
432	return tempDynamicVector.length();
433	}
434
435	/**
436	* Returns the squared distance between two DynamicVectors
437	* @param v1 first vector
438	* @param v2 second vector
439	* @return the squared distance between v1 and v2
440	*/
441	template<typename Real>
442	inline Real distanceSquare( const DynamicVector<Real>& v1, const DynamicVector<Real>& v2 ) {
443	DynamicVector<Real> tempDynamicVector = v1 - v2;
444	return tempDynamicVector.lengthSquare();
445	}
446
447	/**
448	* Write to an output stream
449	*/
450	template<typename Real>
451	std::ostream &operator<< ( std::ostream& o, const DynamicVector<Real>& v) {
452
453	o << "[ ";
454
455	for (unsigned int i = 0 ; i< v.size(); i++) {
456	o << v[i];
457
458	if (i != v.size() -1) {
459	o<< ", ";
460	}
461	}
462
463	o << " ]";
464	return o;
465	}
466
467	}
468	#endif
469