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, 234107 (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);
    }

    /** Zeros out the values in this vector in place */
    inline void zero() {
      for (unsigned int i = 0; i < Dim; i++)
        this->data_[i] = 0;
    }      
             
    /** 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:	1877
Committed:	Thu Jun 6 15:43:35 2013 UTC (11 years, 10 months ago) by gezelter
File size:	16782 byte(s)
Log Message:	New electrostatic method, starting to do some performance tuning.
#	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, 234107 (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	/** Zeros out the values in this vector in place */
201	inline void zero() {
202	for (unsigned int i = 0; i < Dim; i++)
203	this->data_[i] = 0;
204	}
205
206	/** Negates the value of this vector in place. */
207	inline void negate() {
208	for (unsigned int i = 0; i < Dim; i++)
209	this->data_[i] = -this->data_[i];
210	}
211
212	/**
213	* Sets the value of this vector to the negation of vector v1.
214	* @param v1 the source vector
215	*/
216	inline void negate(const Vector<Real, Dim>& v1) {
217	for (unsigned int i = 0; i < Dim; i++)
218	this->data_[i] = -v1.data_[i];
219
220	}
221
222	/**
223	* Sets the value of this vector to the sum of itself and v1 (*this += v1).
224	* @param v1 the other vector
225	*/
226	inline void add( const Vector<Real, Dim>& v1 ) {
227	for (unsigned int i = 0; i < Dim; i++)
228	this->data_[i] += v1.data_[i];
229	}
230
231	/**
232	* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
233	* @param v1 the first vector
234	* @param v2 the second vector
235	*/
236	inline void add( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
237	for (unsigned int i = 0; i < Dim; i++)
238	this->data_[i] = v1.data_[i] + v2.data_[i];
239	}
240
241	/**
242	* Sets the value of this vector to the difference of itself and v1 (*this -= v1).
243	* @param v1 the other vector
244	*/
245	inline void sub( const Vector<Real, Dim>& v1 ) {
246	for (unsigned int i = 0; i < Dim; i++)
247	this->data_[i] -= v1.data_[i];
248	}
249
250	/**
251	* Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2).
252	* @param v1 the first vector
253	* @param v2 the second vector
254	*/
255	inline void sub( const Vector<Real, Dim>& v1, const Vector &v2 ){
256	for (unsigned int i = 0; i < Dim; i++)
257	this->data_[i] = v1.data_[i] - v2.data_[i];
258	}
259
260	/**
261	* Sets the value of this vector to the scalar multiplication of itself (this = s).
262	* @param s the scalar value
263	*/
264	inline void mul( Real s ) {
265	for (unsigned int i = 0; i < Dim; i++)
266	this->data_[i] *= s;
267	}
268
269	/**
270	* Sets the value of this vector to the scalar multiplication of vector v1
271	* (this = s v1).
272	* @param v1 the vector
273	* @param s the scalar value
274	*/
275	inline void mul( const Vector<Real, Dim>& v1, Real s) {
276	for (unsigned int i = 0; i < Dim; i++)
277	this->data_[i] = s * v1.data_[i];
278	}
279
280	/**
281	* Sets the elements of this vector to the multiplication of
282	* elements of two other vectors. Not to be confused with scalar
283	* multiplication (mul) or dot products.
284	*
285	* (this.data_[i] = v1.data_[i] v2.data_[i]).
286	* @param v1 the first vector
287	* @param v2 the second vector
288	*/
289	inline void Vmul( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
290	for (unsigned int i = 0; i < Dim; i++)
291	this->data_[i] = v1.data_[i] * v2.data_[i];
292	}
293
294	/* replaces the elements with the absolute values of those elements */
295	inline Vector<Real, Dim>& abs() {
296	for (unsigned int i = 0; i < Dim; i++) {
297	this->data_[i] = std::abs(this->data_[i]);
298	}
299	return *this;
300	}
301
302	/* returns the maximum value in this vector */
303	inline Real max() {
304	Real val = this->data_[0];
305	for (unsigned int i = 0; i < Dim; i++) {
306	if (this->data_[i] > val) val = this->data_[i];
307	}
308	return val;
309	}
310
311	/**
312	* Sets the value of this vector to the scalar division of itself (*this /= s ).
313	* @param s the scalar value
314	*/
315	inline void div( Real s) {
316	for (unsigned int i = 0; i < Dim; i++)
317	this->data_[i] /= s;
318	}
319
320	/**
321	* Sets the value of this vector to the scalar division of vector v1 (*this = v1 / s ).
322	* @param v1 the source vector
323	* @param s the scalar value
324	*/
325	inline void div( const Vector<Real, Dim>& v1, Real s ) {
326	for (unsigned int i = 0; i < Dim; i++)
327	this->data_[i] = v1.data_[i] / s;
328	}
329
330	/**
331	* Sets the elements of this vector to the division of
332	* elements of two other vectors. Not to be confused with scalar
333	* division (div)
334	*
335	* (*this.data_[i] = v1.data_[i] / v2.data_[i]).
336	* @param v1 the first vector
337	* @param v2 the second vector
338	*/
339	inline void Vdiv( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
340	for (unsigned int i = 0; i < Dim; i++)
341	this->data_[i] = v1.data_[i] / v2.data_[i];
342	}
343
344
345	/** @see #add */
346	inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
347	add(v1);
348	return *this;
349	}
350
351	/** @see #sub */
352	inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) {
353	sub(v1);
354	return *this;
355	}
356
357	/** @see #mul */
358	inline Vector<Real, Dim>& operator *=( Real s) {
359	mul(s);
360	return *this;
361	}
362
363	/** @see #div */
364	inline Vector<Real, Dim>& operator /=( Real s ) {
365	div(s);
366	return *this;
367	}
368
369	/**
370	* Returns the sum of all elements of this vector.
371	* @return the sum of all elements of this vector
372	*/
373	inline Real sum() {
374	Real tmp;
375	tmp = 0;
376	for (unsigned int i = 0; i < Dim; i++)
377	tmp += this->data_[i];
378	return tmp;
379	}
380
381	/**
382	* Returns the product of all elements of this vector.
383	* @return the product of all elements of this vector
384	*/
385	inline Real componentProduct() {
386	Real tmp;
387	tmp = 1;
388	for (unsigned int i = 0; i < Dim; i++)
389	tmp *= this->data_[i];
390	return tmp;
391	}
392
393	/**
394	* Returns the length of this vector.
395	* @return the length of this vector
396	*/
397	inline Real length() {
398	return sqrt(lengthSquare());
399	}
400
401	/**
402	* Returns the squared length of this vector.
403	* @return the squared length of this vector
404	*/
405	inline Real lengthSquare() {
406	return dot(this, this);
407	}
408
409	/** Normalizes this vector in place */
410	inline void normalize() {
411	Real len;
412
413	len = length();
414
415	//if (len < OpenMD::NumericConstant::epsilon)
416	// throw();
417
418	*this /= len;
419	}
420
421	/**
422	* Tests if this vector is normalized
423	* @return true if this vector is normalized, otherwise return false
424	*/
425	inline bool isNormalized() {
426	return equal(lengthSquare(), (RealType)1);
427	}
428
429	unsigned int size() {return Dim;}
430	protected:
431	Real data_[Dim];
432
433	};
434
435	/** unary minus*/
436	template<typename Real, unsigned int Dim>
437	inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){
438	Vector<Real, Dim> tmp(v1);
439	tmp.negate();
440	return tmp;
441	}
442
443	/**
444	* Return the sum of two vectors (v1 - v2).
445	* @return the sum of two vectors
446	* @param v1 the first vector
447	* @param v2 the second vector
448	*/
449	template<typename Real, unsigned int Dim>
450	inline Vector<Real, Dim> operator +(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
451	Vector<Real, Dim> result;
452
453	result.add(v1, v2);
454	return result;
455	}
456
457	/**
458	* Return the difference of two vectors (v1 - v2).
459	* @return the difference of two vectors
460	* @param v1 the first vector
461	* @param v2 the second vector
462	*/
463	template<typename Real, unsigned int Dim>
464	Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
465	Vector<Real, Dim> result;
466	result.sub(v1, v2);
467	return result;
468	}
469
470	/**
471	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
472	* @return the vaule of scalar multiplication of this vector
473	* @param v1 the source vector
474	* @param s the scalar value
475	*/
476	template<typename Real, unsigned int Dim>
477	Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, Real s) {
478	Vector<Real, Dim> result;
479	result.mul(v1,s);
480	return result;
481	}
482
483	/**
484	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
485	* @return the vaule of scalar multiplication of this vector
486	* @param s the scalar value
487	* @param v1 the source vector
488	*/
489	template<typename Real, unsigned int Dim>
490	Vector<Real, Dim> operator * ( Real s, const Vector<Real, Dim>& v1 ) {
491	Vector<Real, Dim> result;
492	result.mul(v1, s);
493	return result;
494	}
495
496	/**
497	* Returns the value of division of a vector by a scalar.
498	* @return the vaule of scalar division of this vector
499	* @param v1 the source vector
500	* @param s the scalar value
501	*/
502	template<typename Real, unsigned int Dim>
503	Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, Real s) {
504	Vector<Real, Dim> result;
505	result.div( v1,s);
506	return result;
507	}
508
509	/**
510	* Returns the dot product of two Vectors
511	* @param v1 first vector
512	* @param v2 second vector
513	* @return the dot product of v1 and v2
514	*/
515	template<typename Real, unsigned int Dim>
516	inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
517	Real tmp;
518	tmp = 0;
519
520	for (unsigned int i = 0; i < Dim; i++)
521	tmp += v1[i] * v2[i];
522
523	return tmp;
524	}
525
526
527
528
529	/**
530	* Returns the wide dot product of three Vectors. Compare with
531	* Rapaport's VWDot function.
532	*
533	* @param v1 first vector
534	* @param v2 second vector
535	* @param v3 third vector
536	* @return the wide dot product of v1, v2, and v3.
537	*/
538	template<typename Real, unsigned int Dim>
539	inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2, const Vector<Real, Dim>& v3 ) {
540	Real tmp;
541	tmp = 0;
542
543	for (unsigned int i = 0; i < Dim; i++)
544	tmp += v1[i] * v2[i] * v3[i];
545
546	return tmp;
547	}
548
549
550	/**
551	* Returns the distance between two Vectors
552	* @param v1 first vector
553	* @param v2 second vector
554	* @return the distance between v1 and v2
555	*/
556	template<typename Real, unsigned int Dim>
557	inline Real distance( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
558	Vector<Real, Dim> tempVector = v1 - v2;
559	return tempVector.length();
560	}
561
562	/**
563	* Returns the squared distance between two Vectors
564	* @param v1 first vector
565	* @param v2 second vector
566	* @return the squared distance between v1 and v2
567	*/
568	template<typename Real, unsigned int Dim>
569	inline Real distanceSquare( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
570	Vector<Real, Dim> tempVector = v1 - v2;
571	return tempVector.lengthSquare();
572	}
573
574	/**
575	* Write to an output stream
576	*/
577	template<typename Real, unsigned int Dim>
578	std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v) {
579
580	o << "[ ";
581
582	for (unsigned int i = 0 ; i< Dim; i++) {
583	o << v[i];
584
585	if (i != Dim -1) {
586	o<< ", ";
587	}
588	}
589
590	o << " ]";
591	return o;
592	}
593
594	}
595	#endif