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
#	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			*
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	cli2	1349
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	tim	891	/**
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	gezelter	1744	this->resize(v1.size());
230	tim	891	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	gezelter	1744	/** 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	tim	891	/**
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	gezelter	1390	//if (len < OpenMD::NumericConstant::epsilon)
306	tim	891	// 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	cli2	1349
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	tim	891
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	gezelter	1744	assert(v1.size() == v2.size());
347			DynamicVector<Real>result(v1.size());
348	tim	891	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	gezelter	1744	assert(v1.size() == v2.size());
361			DynamicVector<Real> result(v1.size());
362	tim	891	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	gezelter	1744	DynamicVector<Real> operator *( const DynamicVector<Real>& v1, Real s) {
374			DynamicVector<Real> result(v1.size());
375	tim	891	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	gezelter	1744	DynamicVector<Real> operator *( Real s, const DynamicVector<Real>& v1 ) {
387			DynamicVector<Real> result(v1.size());
388	tim	891	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	gezelter	1744	DynamicVector<Real> operator / ( const DynamicVector<Real>& v1, Real s) {
400			DynamicVector<Real> result(v1.size());
401	tim	891	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