src/math/Vector.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 Vector.hpp
 * @author Teng Lin
 * @date 09/14/2004
 * @version 1.0
 */
 
#ifndef MATH_VECTOR_HPP
#define MATH_VECTOR_HPP

#include <cassert>
#include <cmath>
#include <iostream>
#include <math.h>
#include "config.h"
namespace OpenMD {

  static const RealType epsilon = 0.000001;

  template<typename T>
  inline bool equal(T e1, T e2) {
    return e1 == e2;
  }

  //template<>
  //inline bool equal(float e1, float e2) {
  //  return fabs(e1 - e2) < epsilon;
  //}

  template<>
  inline bool equal(RealType e1, RealType e2) {
    return fabs(e1 - e2) < epsilon;
  }
    
  /**
   * @class Vector Vector.hpp "math/Vector.hpp"
   * @brief Fix length vector class
   */
  template<typename Real, unsigned int Dim>
  class Vector{
  public:

    typedef Real ElemType;
    typedef Real* ElemPoinerType;

    /** default constructor */
    inline Vector(){
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = 0;
    }

    /** Constructs and initializes a Vector from a vector */
    inline Vector(const Vector<Real, Dim>& v) {
      *this  = v;
    }

    /** copy assignment operator */
    inline Vector<Real, Dim>& operator=(const Vector<Real, Dim>& v) {
      if (this == &v)
        return *this;
                
      for (unsigned int i = 0; i < Dim; i++)            
        this->data_[i] = v[i];
                
      return *this;
    }

    // template<typename T>
    // inline Vector(const T& s){
    inline Vector(const Real& s) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = s;
    }
            
    /** Constructs and initializes a Vector from an array */            
    inline Vector( Real* v) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = v[i];
    }

    /** 
     * Returns reference of ith element.
     * @return reference of ith element
     * @param i index
     */
    inline Real& operator[](unsigned int  i) {
      assert( i < Dim);
      return this->data_[i];
    }

    /** 
     * Returns reference of ith element.
     * @return reference of ith element
     * @param i index
     */
    inline Real& operator()(unsigned int  i) {
      assert( i < Dim);
      return this->data_[i];
    }

    /** 
     * Returns constant reference of ith element.
     * @return reference of ith element
     * @param i index
     */
    inline  const Real& operator[](unsigned int i) const {
      assert( i < Dim);
      return this->data_[i];
    }

    /** 
     * Returns constant reference of ith element.
     * @return reference of ith element
     * @param i index
     */
    inline  const Real& operator()(unsigned int i) const {
      assert( i < Dim);
      return this->data_[i];
    }

    /** Copy the internal data to an array*/
    void getArray(Real* array) {
      for (unsigned int i = 0; i < Dim; i ++) {
        array[i] = this->data_[i];
      }                
    }

    /** Returns the pointer of internal array */
    Real* getArrayPointer() {
      return this->data_;
    }
            
    /**
     * 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 Vector<Real, Dim>& v) {

      for (unsigned int i = 0; i < Dim; i ++) {
        if (!equal(this->data_[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 Vector<Real, Dim>& v) {
      return !(*this == v);
    }
             
    /** Negates the value of this vector in place. */           
    inline void negate() {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = -this->data_[i];
    }

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

    /**
     * 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 Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = v1.data_[i] + v2.data_[i];
    }

    /**
     * Sets the value of this vector to the difference  of itself and v1 (*this -= v1).
     * @param v1 the other vector
     */
    inline void sub( const Vector<Real, Dim>& v1 ) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] -= v1.data_[i];
    }

    /**
     * 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 Vector<Real, Dim>& v1, const Vector  &v2 ){
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = v1.data_[i] - v2.data_[i];
    }

    /**
     * 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 < Dim; i++)
        this->data_[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 Vector<Real, Dim>& v1, Real s) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = s * v1.data_[i];
    }

    /**
     * Sets the elements of this vector to the multiplication of
     * elements of two other vectors.  Not to be confused with scalar
     * multiplication (mul) or dot products.
     *
     * (*this.data_[i] =  v1.data_[i] * v2.data_[i]).
     * @param v1 the first vector            
     * @param v2 the second vector
     */
    inline void Vmul( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = v1.data_[i] * v2.data_[i];
    }

    /* replaces the elements with the absolute values of those elements */
    inline Vector<Real, Dim>& abs() {
      for (unsigned int i = 0; i < Dim; i++) {
        this->data_[i] = std::abs(this->data_[i]);
      }
      return *this;
    }
    
    /* returns the maximum value in this vector */
    inline Real max() {
      Real val = this->data_[0];
      for (unsigned int i = 0; i < Dim; i++) {
        if (this->data_[i] > val) val = this->data_[i];
      }
      return val;
    }
     
    /**
     * 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 < Dim; i++)            
        this->data_[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 Vector<Real, Dim>& v1, Real s ) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = v1.data_[i] / s;
    }

    /**
     * Sets the elements of this vector to the division of
     * elements of two other vectors.  Not to be confused with scalar
     * division (div)
     *
     * (*this.data_[i] =  v1.data_[i] / v2.data_[i]).
     * @param v1 the first vector            
     * @param v2 the second vector
     */
    inline void Vdiv( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = v1.data_[i] / v2.data_[i];
    }


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

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

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

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

    /**
     * Returns the sum of all elements of this vector.
     * @return the sum of all elements of this vector
     */
    inline Real sum() {
      Real tmp;
      tmp = 0;
      for (unsigned int i = 0; i < Dim; i++)
        tmp += this->data_[i];
      return tmp;  
    }

    /**
     * Returns the product of all elements of this vector.
     * @return the product of all elements of this vector
     */
    inline Real componentProduct() {
      Real tmp;
      tmp = 1;
      for (unsigned int i = 0; i < Dim; i++)
        tmp *= this->data_[i];
      return tmp;  
    }
            
    /**
     * 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(), (RealType)1);
    }           

    unsigned int size() {return Dim;}
  protected:
    Real data_[Dim];
        
  };

  /** unary minus*/
  template<typename Real, unsigned int Dim>    
  inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){
    Vector<Real, Dim> 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, unsigned int Dim>    
  inline Vector<Real, Dim> operator +(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
    Vector<Real, Dim> result;
        
    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, unsigned int Dim>    
  Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
    Vector<Real, Dim> result;
    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, unsigned int Dim>                 
  Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, Real s) {       
    Vector<Real, Dim> result;
    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, unsigned int Dim>
  Vector<Real, Dim> operator * ( Real s, const Vector<Real, Dim>& v1 ) {
    Vector<Real, Dim> result;
    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, unsigned int Dim>    
  Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, Real s) {       
    Vector<Real, Dim> result;
    result.div( v1,s);
    return result;           
  }
    
  /**
   * Returns the dot product of two Vectors
   * @param v1 first vector
   * @param v2 second vector
   * @return the dot product of v1 and v2
   */
  template<typename Real, unsigned int Dim>    
  inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
    Real tmp;
    tmp = 0;

    for (unsigned int i = 0; i < Dim; i++)
      tmp += v1[i] * v2[i];

    return tmp;
  }


  /**
   * Returns the wide dot product of three Vectors.  Compare with
   * Rapaport's VWDot function.
   *
   * @param v1 first vector
   * @param v2 second vector
   * @param v3 third vector
   * @return the wide dot product of v1, v2, and v3.
   */
  template<typename Real, unsigned int Dim>    
  inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2, const Vector<Real, Dim>& v3 ) {
    Real tmp;
    tmp = 0;

    for (unsigned int i = 0; i < Dim; i++)
      tmp += v1[i] * v2[i] * v3[i];

    return tmp;
  }


  /**
   * Returns the distance between  two Vectors
   * @param v1 first vector
   * @param v2 second vector
   * @return the distance between v1 and v2
   */   
  template<typename Real, unsigned int Dim>    
  inline Real distance( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
    Vector<Real, Dim> tempVector = v1 - v2;
    return tempVector.length();
  }

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

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

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

      if (i  != Dim -1) {
        o<< ", ";
      }
    }

    o << " ]";
    return o;        
  }
    
}
#endif
Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (13 years, 2 months ago) by gezelter
File size:	16621 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	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 Vector.hpp
45	* @author Teng Lin
46	* @date 09/14/2004
47	* @version 1.0
48	*/
49
50	#ifndef MATH_VECTOR_HPP
51	#define MATH_VECTOR_HPP
52
53	#include <cassert>
54	#include <cmath>
55	#include <iostream>
56	#include <math.h>
57	#include "config.h"
58	namespace OpenMD {
59
60	static const RealType epsilon = 0.000001;
61
62	template<typename T>
63	inline bool equal(T e1, T e2) {
64	return e1 == e2;
65	}
66
67	//template<>
68	//inline bool equal(float e1, float e2) {
69	// return fabs(e1 - e2) < epsilon;
70	//}
71
72	template<>
73	inline bool equal(RealType e1, RealType e2) {
74	return fabs(e1 - e2) < epsilon;
75	}
76
77	/**
78	* @class Vector Vector.hpp "math/Vector.hpp"
79	* @brief Fix length vector class
80	*/
81	template<typename Real, unsigned int Dim>
82	class Vector{
83	public:
84
85	typedef Real ElemType;
86	typedef Real* ElemPoinerType;
87
88	/** default constructor */
89	inline Vector(){
90	for (unsigned int i = 0; i < Dim; i++)
91	this->data_[i] = 0;
92	}
93
94	/** Constructs and initializes a Vector from a vector */
95	inline Vector(const Vector<Real, Dim>& v) {
96	*this = v;
97	}
98
99	/** copy assignment operator */
100	inline Vector<Real, Dim>& operator=(const Vector<Real, Dim>& v) {
101	if (this == &v)
102	return *this;
103
104	for (unsigned int i = 0; i < Dim; i++)
105	this->data_[i] = v[i];
106
107	return *this;
108	}
109
110	// template<typename T>
111	// inline Vector(const T& s){
112	inline Vector(const Real& s) {
113	for (unsigned int i = 0; i < Dim; i++)
114	this->data_[i] = s;
115	}
116
117	/** Constructs and initializes a Vector from an array */
118	inline Vector( Real* v) {
119	for (unsigned int i = 0; i < Dim; i++)
120	this->data_[i] = v[i];
121	}
122
123	/**
124	* Returns reference of ith element.
125	* @return reference of ith element
126	* @param i index
127	*/
128	inline Real& operator[](unsigned int i) {
129	assert( i < Dim);
130	return this->data_[i];
131	}
132
133	/**
134	* Returns reference of ith element.
135	* @return reference of ith element
136	* @param i index
137	*/
138	inline Real& operator()(unsigned int i) {
139	assert( i < Dim);
140	return this->data_[i];
141	}
142
143	/**
144	* Returns constant reference of ith element.
145	* @return reference of ith element
146	* @param i index
147	*/
148	inline const Real& operator[](unsigned int i) const {
149	assert( i < Dim);
150	return this->data_[i];
151	}
152
153	/**
154	* Returns constant reference of ith element.
155	* @return reference of ith element
156	* @param i index
157	*/
158	inline const Real& operator()(unsigned int i) const {
159	assert( i < Dim);
160	return this->data_[i];
161	}
162
163	/** Copy the internal data to an array*/
164	void getArray(Real* array) {
165	for (unsigned int i = 0; i < Dim; i ++) {
166	array[i] = this->data_[i];
167	}
168	}
169
170	/** Returns the pointer of internal array */
171	Real* getArrayPointer() {
172	return this->data_;
173	}
174
175	/**
176	* Tests if this vetor is equal to other vector
177	* @return true if equal, otherwise return false
178	* @param v vector to be compared
179	*/
180	inline bool operator ==(const Vector<Real, Dim>& v) {
181
182	for (unsigned int i = 0; i < Dim; i ++) {
183	if (!equal(this->data_[i], v[i])) {
184	return false;
185	}
186	}
187
188	return true;
189	}
190
191	/**
192	* Tests if this vetor is not equal to other vector
193	* @return true if equal, otherwise return false
194	* @param v vector to be compared
195	*/
196	inline bool operator !=(const Vector<Real, Dim>& v) {
197	return !(*this == v);
198	}
199
200	/** Negates the value of this vector in place. */
201	inline void negate() {
202	for (unsigned int i = 0; i < Dim; i++)
203	this->data_[i] = -this->data_[i];
204	}
205
206	/**
207	* Sets the value of this vector to the negation of vector v1.
208	* @param v1 the source vector
209	*/
210	inline void negate(const Vector<Real, Dim>& v1) {
211	for (unsigned int i = 0; i < Dim; i++)
212	this->data_[i] = -v1.data_[i];
213
214	}
215
216	/**
217	* Sets the value of this vector to the sum of itself and v1 (*this += v1).
218	* @param v1 the other vector
219	*/
220	inline void add( const Vector<Real, Dim>& v1 ) {
221	for (unsigned int i = 0; i < Dim; i++)
222	this->data_[i] += v1.data_[i];
223	}
224
225	/**
226	* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
227	* @param v1 the first vector
228	* @param v2 the second vector
229	*/
230	inline void add( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
231	for (unsigned int i = 0; i < Dim; i++)
232	this->data_[i] = v1.data_[i] + v2.data_[i];
233	}
234
235	/**
236	* Sets the value of this vector to the difference of itself and v1 (*this -= v1).
237	* @param v1 the other vector
238	*/
239	inline void sub( const Vector<Real, Dim>& v1 ) {
240	for (unsigned int i = 0; i < Dim; i++)
241	this->data_[i] -= v1.data_[i];
242	}
243
244	/**
245	* Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2).
246	* @param v1 the first vector
247	* @param v2 the second vector
248	*/
249	inline void sub( const Vector<Real, Dim>& v1, const Vector &v2 ){
250	for (unsigned int i = 0; i < Dim; i++)
251	this->data_[i] = v1.data_[i] - v2.data_[i];
252	}
253
254	/**
255	* Sets the value of this vector to the scalar multiplication of itself (this = s).
256	* @param s the scalar value
257	*/
258	inline void mul( Real s ) {
259	for (unsigned int i = 0; i < Dim; i++)
260	this->data_[i] *= s;
261	}
262
263	/**
264	* Sets the value of this vector to the scalar multiplication of vector v1
265	* (this = s v1).
266	* @param v1 the vector
267	* @param s the scalar value
268	*/
269	inline void mul( const Vector<Real, Dim>& v1, Real s) {
270	for (unsigned int i = 0; i < Dim; i++)
271	this->data_[i] = s * v1.data_[i];
272	}
273
274	/**
275	* Sets the elements of this vector to the multiplication of
276	* elements of two other vectors. Not to be confused with scalar
277	* multiplication (mul) or dot products.
278	*
279	* (this.data_[i] = v1.data_[i] v2.data_[i]).
280	* @param v1 the first vector
281	* @param v2 the second vector
282	*/
283	inline void Vmul( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
284	for (unsigned int i = 0; i < Dim; i++)
285	this->data_[i] = v1.data_[i] * v2.data_[i];
286	}
287
288	/* replaces the elements with the absolute values of those elements */
289	inline Vector<Real, Dim>& abs() {
290	for (unsigned int i = 0; i < Dim; i++) {
291	this->data_[i] = std::abs(this->data_[i]);
292	}
293	return *this;
294	}
295
296	/* returns the maximum value in this vector */
297	inline Real max() {
298	Real val = this->data_[0];
299	for (unsigned int i = 0; i < Dim; i++) {
300	if (this->data_[i] > val) val = this->data_[i];
301	}
302	return val;
303	}
304
305	/**
306	* Sets the value of this vector to the scalar division of itself (*this /= s ).
307	* @param s the scalar value
308	*/
309	inline void div( Real s) {
310	for (unsigned int i = 0; i < Dim; i++)
311	this->data_[i] /= s;
312	}
313
314	/**
315	* Sets the value of this vector to the scalar division of vector v1 (*this = v1 / s ).
316	* @param v1 the source vector
317	* @param s the scalar value
318	*/
319	inline void div( const Vector<Real, Dim>& v1, Real s ) {
320	for (unsigned int i = 0; i < Dim; i++)
321	this->data_[i] = v1.data_[i] / s;
322	}
323
324	/**
325	* Sets the elements of this vector to the division of
326	* elements of two other vectors. Not to be confused with scalar
327	* division (div)
328	*
329	* (*this.data_[i] = v1.data_[i] / v2.data_[i]).
330	* @param v1 the first vector
331	* @param v2 the second vector
332	*/
333	inline void Vdiv( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
334	for (unsigned int i = 0; i < Dim; i++)
335	this->data_[i] = v1.data_[i] / v2.data_[i];
336	}
337
338
339	/** @see #add */
340	inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
341	add(v1);
342	return *this;
343	}
344
345	/** @see #sub */
346	inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) {
347	sub(v1);
348	return *this;
349	}
350
351	/** @see #mul */
352	inline Vector<Real, Dim>& operator *=( Real s) {
353	mul(s);
354	return *this;
355	}
356
357	/** @see #div */
358	inline Vector<Real, Dim>& operator /=( Real s ) {
359	div(s);
360	return *this;
361	}
362
363	/**
364	* Returns the sum of all elements of this vector.
365	* @return the sum of all elements of this vector
366	*/
367	inline Real sum() {
368	Real tmp;
369	tmp = 0;
370	for (unsigned int i = 0; i < Dim; i++)
371	tmp += this->data_[i];
372	return tmp;
373	}
374
375	/**
376	* Returns the product of all elements of this vector.
377	* @return the product of all elements of this vector
378	*/
379	inline Real componentProduct() {
380	Real tmp;
381	tmp = 1;
382	for (unsigned int i = 0; i < Dim; i++)
383	tmp *= this->data_[i];
384	return tmp;
385	}
386
387	/**
388	* Returns the length of this vector.
389	* @return the length of this vector
390	*/
391	inline Real length() {
392	return sqrt(lengthSquare());
393	}
394
395	/**
396	* Returns the squared length of this vector.
397	* @return the squared length of this vector
398	*/
399	inline Real lengthSquare() {
400	return dot(this, this);
401	}
402
403	/** Normalizes this vector in place */
404	inline void normalize() {
405	Real len;
406
407	len = length();
408
409	//if (len < OpenMD::NumericConstant::epsilon)
410	// throw();
411
412	*this /= len;
413	}
414
415	/**
416	* Tests if this vector is normalized
417	* @return true if this vector is normalized, otherwise return false
418	*/
419	inline bool isNormalized() {
420	return equal(lengthSquare(), (RealType)1);
421	}
422
423	unsigned int size() {return Dim;}
424	protected:
425	Real data_[Dim];
426
427	};
428
429	/** unary minus*/
430	template<typename Real, unsigned int Dim>
431	inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){
432	Vector<Real, Dim> tmp(v1);
433	tmp.negate();
434	return tmp;
435	}
436
437	/**
438	* Return the sum of two vectors (v1 - v2).
439	* @return the sum of two vectors
440	* @param v1 the first vector
441	* @param v2 the second vector
442	*/
443	template<typename Real, unsigned int Dim>
444	inline Vector<Real, Dim> operator +(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
445	Vector<Real, Dim> result;
446
447	result.add(v1, v2);
448	return result;
449	}
450
451	/**
452	* Return the difference of two vectors (v1 - v2).
453	* @return the difference of two vectors
454	* @param v1 the first vector
455	* @param v2 the second vector
456	*/
457	template<typename Real, unsigned int Dim>
458	Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
459	Vector<Real, Dim> result;
460	result.sub(v1, v2);
461	return result;
462	}
463
464	/**
465	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
466	* @return the vaule of scalar multiplication of this vector
467	* @param v1 the source vector
468	* @param s the scalar value
469	*/
470	template<typename Real, unsigned int Dim>
471	Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, Real s) {
472	Vector<Real, Dim> result;
473	result.mul(v1,s);
474	return result;
475	}
476
477	/**
478	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
479	* @return the vaule of scalar multiplication of this vector
480	* @param s the scalar value
481	* @param v1 the source vector
482	*/
483	template<typename Real, unsigned int Dim>
484	Vector<Real, Dim> operator * ( Real s, const Vector<Real, Dim>& v1 ) {
485	Vector<Real, Dim> result;
486	result.mul(v1, s);
487	return result;
488	}
489
490	/**
491	* Returns the value of division of a vector by a scalar.
492	* @return the vaule of scalar division of this vector
493	* @param v1 the source vector
494	* @param s the scalar value
495	*/
496	template<typename Real, unsigned int Dim>
497	Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, Real s) {
498	Vector<Real, Dim> result;
499	result.div( v1,s);
500	return result;
501	}
502
503	/**
504	* Returns the dot product of two Vectors
505	* @param v1 first vector
506	* @param v2 second vector
507	* @return the dot product of v1 and v2
508	*/
509	template<typename Real, unsigned int Dim>
510	inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
511	Real tmp;
512	tmp = 0;
513
514	for (unsigned int i = 0; i < Dim; i++)
515	tmp += v1[i] * v2[i];
516
517	return tmp;
518	}
519
520
521
522
523	/**
524	* Returns the wide dot product of three Vectors. Compare with
525	* Rapaport's VWDot function.
526	*
527	* @param v1 first vector
528	* @param v2 second vector
529	* @param v3 third vector
530	* @return the wide dot product of v1, v2, and v3.
531	*/
532	template<typename Real, unsigned int Dim>
533	inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2, const Vector<Real, Dim>& v3 ) {
534	Real tmp;
535	tmp = 0;
536
537	for (unsigned int i = 0; i < Dim; i++)
538	tmp += v1[i] * v2[i] * v3[i];
539
540	return tmp;
541	}
542
543
544	/**
545	* Returns the distance between two Vectors
546	* @param v1 first vector
547	* @param v2 second vector
548	* @return the distance between v1 and v2
549	*/
550	template<typename Real, unsigned int Dim>
551	inline Real distance( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
552	Vector<Real, Dim> tempVector = v1 - v2;
553	return tempVector.length();
554	}
555
556	/**
557	* Returns the squared distance between two Vectors
558	* @param v1 first vector
559	* @param v2 second vector
560	* @return the squared distance between v1 and v2
561	*/
562	template<typename Real, unsigned int Dim>
563	inline Real distanceSquare( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
564	Vector<Real, Dim> tempVector = v1 - v2;
565	return tempVector.lengthSquare();
566	}
567
568	/**
569	* Write to an output stream
570	*/
571	template<typename Real, unsigned int Dim>
572	std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v) {
573
574	o << "[ ";
575
576	for (unsigned int i = 0 ; i< Dim; i++) {
577	o << v[i];
578
579	if (i != Dim -1) {
580	o<< ", ";
581	}
582	}
583
584	o << " ]";
585	return o;
586	}
587
588	}
589	#endif