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 (13 years 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
#	User	Rev	Content
1	tim	891	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	891	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	891	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	891	*/
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	gezelter	1390	namespace OpenMD {
61	tim	891
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	gezelter	1808	* @param alloc The allocator_type to use
98	tim	891	*
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	cli2	1349
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	tim	891	/**
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	gezelter	1744	this->resize(v1.size());
231	tim	891	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	gezelter	1744	/** 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	tim	891	/**
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	gezelter	1390	//if (len < OpenMD::NumericConstant::epsilon)
307	tim	891	// 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	cli2	1349
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	tim	891
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	gezelter	1744	assert(v1.size() == v2.size());
348			DynamicVector<Real>result(v1.size());
349	tim	891	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	gezelter	1744	assert(v1.size() == v2.size());
362			DynamicVector<Real> result(v1.size());
363	tim	891	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	gezelter	1744	DynamicVector<Real> operator *( const DynamicVector<Real>& v1, Real s) {
375			DynamicVector<Real> result(v1.size());
376	tim	891	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	gezelter	1744	DynamicVector<Real> operator *( Real s, const DynamicVector<Real>& v1 ) {
388			DynamicVector<Real> result(v1.size());
389	tim	891	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	gezelter	1744	DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {
401			DynamicVector<Real> result(v1.size());
402	tim	891	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