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){
      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:	1760
Committed:	Thu Jun 21 19:26:46 2012 UTC (12 years, 10 months ago) by gezelter
File size:	16573 byte(s)
Log Message:	Some bugfixes (CholeskyDecomposition), more work on fluctuating charges, migrating stats stuff into frameData
#	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	for (unsigned int i = 0; i < Dim; i++)
113	this->data_[i] = s;
114	}
115
116	/** Constructs and initializes a Vector from an array */
117	inline Vector( Real* v) {
118	for (unsigned int i = 0; i < Dim; i++)
119	this->data_[i] = v[i];
120	}
121
122	/**
123	* Returns reference of ith element.
124	* @return reference of ith element
125	* @param i index
126	*/
127	inline Real& operator[](unsigned int i) {
128	assert( i < Dim);
129	return this->data_[i];
130	}
131
132	/**
133	* Returns reference of ith element.
134	* @return reference of ith element
135	* @param i index
136	*/
137	inline Real& operator()(unsigned int i) {
138	assert( i < Dim);
139	return this->data_[i];
140	}
141
142	/**
143	* Returns constant reference of ith element.
144	* @return reference of ith element
145	* @param i index
146	*/
147	inline const Real& operator[](unsigned int i) const {
148	assert( i < Dim);
149	return this->data_[i];
150	}
151
152	/**
153	* Returns constant reference of ith element.
154	* @return reference of ith element
155	* @param i index
156	*/
157	inline const Real& operator()(unsigned int i) const {
158	assert( i < Dim);
159	return this->data_[i];
160	}
161
162	/** Copy the internal data to an array*/
163	void getArray(Real* array) {
164	for (unsigned int i = 0; i < Dim; i ++) {
165	array[i] = this->data_[i];
166	}
167	}
168
169	/** Returns the pointer of internal array */
170	Real* getArrayPointer() {
171	return this->data_;
172	}
173
174	/**
175	* Tests if this vetor is equal to other vector
176	* @return true if equal, otherwise return false
177	* @param v vector to be compared
178	*/
179	inline bool operator ==(const Vector<Real, Dim>& v) {
180
181	for (unsigned int i = 0; i < Dim; i ++) {
182	if (!equal(this->data_[i], v[i])) {
183	return false;
184	}
185	}
186
187	return true;
188	}
189
190	/**
191	* Tests if this vetor is not equal to other vector
192	* @return true if equal, otherwise return false
193	* @param v vector to be compared
194	*/
195	inline bool operator !=(const Vector<Real, Dim>& v) {
196	return !(*this == v);
197	}
198
199	/** Negates the value of this vector in place. */
200	inline void negate() {
201	for (unsigned int i = 0; i < Dim; i++)
202	this->data_[i] = -this->data_[i];
203	}
204
205	/**
206	* Sets the value of this vector to the negation of vector v1.
207	* @param v1 the source vector
208	*/
209	inline void negate(const Vector<Real, Dim>& v1) {
210	for (unsigned int i = 0; i < Dim; i++)
211	this->data_[i] = -v1.data_[i];
212
213	}
214
215	/**
216	* Sets the value of this vector to the sum of itself and v1 (*this += v1).
217	* @param v1 the other vector
218	*/
219	inline void add( const Vector<Real, Dim>& v1 ) {
220	for (unsigned int i = 0; i < Dim; i++)
221	this->data_[i] += v1.data_[i];
222	}
223
224	/**
225	* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
226	* @param v1 the first vector
227	* @param v2 the second vector
228	*/
229	inline void add( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
230	for (unsigned int i = 0; i < Dim; i++)
231	this->data_[i] = v1.data_[i] + v2.data_[i];
232	}
233
234	/**
235	* Sets the value of this vector to the difference of itself and v1 (*this -= v1).
236	* @param v1 the other vector
237	*/
238	inline void sub( const Vector<Real, Dim>& v1 ) {
239	for (unsigned int i = 0; i < Dim; i++)
240	this->data_[i] -= v1.data_[i];
241	}
242
243	/**
244	* Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2).
245	* @param v1 the first vector
246	* @param v2 the second vector
247	*/
248	inline void sub( const Vector<Real, Dim>& v1, const Vector &v2 ){
249	for (unsigned int i = 0; i < Dim; i++)
250	this->data_[i] = v1.data_[i] - v2.data_[i];
251	}
252
253	/**
254	* Sets the value of this vector to the scalar multiplication of itself (this = s).
255	* @param s the scalar value
256	*/
257	inline void mul( Real s ) {
258	for (unsigned int i = 0; i < Dim; i++)
259	this->data_[i] *= s;
260	}
261
262	/**
263	* Sets the value of this vector to the scalar multiplication of vector v1
264	* (this = s v1).
265	* @param v1 the vector
266	* @param s the scalar value
267	*/
268	inline void mul( const Vector<Real, Dim>& v1, Real s) {
269	for (unsigned int i = 0; i < Dim; i++)
270	this->data_[i] = s * v1.data_[i];
271	}
272
273	/**
274	* Sets the elements of this vector to the multiplication of
275	* elements of two other vectors. Not to be confused with scalar
276	* multiplication (mul) or dot products.
277	*
278	* (this.data_[i] = v1.data_[i] v2.data_[i]).
279	* @param v1 the first vector
280	* @param v2 the second vector
281	*/
282	inline void Vmul( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
283	for (unsigned int i = 0; i < Dim; i++)
284	this->data_[i] = v1.data_[i] * v2.data_[i];
285	}
286
287	/* replaces the elements with the absolute values of those elements */
288	inline Vector<Real, Dim>& abs() {
289	for (unsigned int i = 0; i < Dim; i++) {
290	this->data_[i] = std::abs(this->data_[i]);
291	}
292	return *this;
293	}
294
295	/* returns the maximum value in this vector */
296	inline Real max() {
297	Real val = this->data_[0];
298	for (unsigned int i = 0; i < Dim; i++) {
299	if (this->data_[i] > val) val = this->data_[i];
300	}
301	return val;
302	}
303
304	/**
305	* Sets the value of this vector to the scalar division of itself (*this /= s ).
306	* @param s the scalar value
307	*/
308	inline void div( Real s) {
309	for (unsigned int i = 0; i < Dim; i++)
310	this->data_[i] /= s;
311	}
312
313	/**
314	* Sets the value of this vector to the scalar division of vector v1 (*this = v1 / s ).
315	* @param v1 the source vector
316	* @param s the scalar value
317	*/
318	inline void div( const Vector<Real, Dim>& v1, Real s ) {
319	for (unsigned int i = 0; i < Dim; i++)
320	this->data_[i] = v1.data_[i] / s;
321	}
322
323	/**
324	* Sets the elements of this vector to the division of
325	* elements of two other vectors. Not to be confused with scalar
326	* division (div)
327	*
328	* (*this.data_[i] = v1.data_[i] / v2.data_[i]).
329	* @param v1 the first vector
330	* @param v2 the second vector
331	*/
332	inline void Vdiv( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
333	for (unsigned int i = 0; i < Dim; i++)
334	this->data_[i] = v1.data_[i] / v2.data_[i];
335	}
336
337
338	/** @see #add */
339	inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
340	add(v1);
341	return *this;
342	}
343
344	/** @see #sub */
345	inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) {
346	sub(v1);
347	return *this;
348	}
349
350	/** @see #mul */
351	inline Vector<Real, Dim>& operator *=( Real s) {
352	mul(s);
353	return *this;
354	}
355
356	/** @see #div */
357	inline Vector<Real, Dim>& operator /=( Real s ) {
358	div(s);
359	return *this;
360	}
361
362	/**
363	* Returns the sum of all elements of this vector.
364	* @return the sum of all elements of this vector
365	*/
366	inline Real sum() {
367	Real tmp;
368	tmp = 0;
369	for (unsigned int i = 0; i < Dim; i++)
370	tmp += this->data_[i];
371	return tmp;
372	}
373
374	/**
375	* Returns the product of all elements of this vector.
376	* @return the product of all elements of this vector
377	*/
378	inline Real componentProduct() {
379	Real tmp;
380	tmp = 1;
381	for (unsigned int i = 0; i < Dim; i++)
382	tmp *= this->data_[i];
383	return tmp;
384	}
385
386	/**
387	* Returns the length of this vector.
388	* @return the length of this vector
389	*/
390	inline Real length() {
391	return sqrt(lengthSquare());
392	}
393
394	/**
395	* Returns the squared length of this vector.
396	* @return the squared length of this vector
397	*/
398	inline Real lengthSquare() {
399	return dot(this, this);
400	}
401
402	/** Normalizes this vector in place */
403	inline void normalize() {
404	Real len;
405
406	len = length();
407
408	//if (len < OpenMD::NumericConstant::epsilon)
409	// throw();
410
411	*this /= len;
412	}
413
414	/**
415	* Tests if this vector is normalized
416	* @return true if this vector is normalized, otherwise return false
417	*/
418	inline bool isNormalized() {
419	return equal(lengthSquare(), (RealType)1);
420	}
421
422	unsigned int size() {return Dim;}
423	protected:
424	Real data_[Dim];
425
426	};
427
428	/** unary minus*/
429	template<typename Real, unsigned int Dim>
430	inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){
431	Vector<Real, Dim> tmp(v1);
432	tmp.negate();
433	return tmp;
434	}
435
436	/**
437	* Return the sum of two vectors (v1 - v2).
438	* @return the sum of two vectors
439	* @param v1 the first vector
440	* @param v2 the second vector
441	*/
442	template<typename Real, unsigned int Dim>
443	inline Vector<Real, Dim> operator +(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
444	Vector<Real, Dim> result;
445
446	result.add(v1, v2);
447	return result;
448	}
449
450	/**
451	* Return the difference of two vectors (v1 - v2).
452	* @return the difference of two vectors
453	* @param v1 the first vector
454	* @param v2 the second vector
455	*/
456	template<typename Real, unsigned int Dim>
457	Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
458	Vector<Real, Dim> result;
459	result.sub(v1, v2);
460	return result;
461	}
462
463	/**
464	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
465	* @return the vaule of scalar multiplication of this vector
466	* @param v1 the source vector
467	* @param s the scalar value
468	*/
469	template<typename Real, unsigned int Dim>
470	Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, Real s) {
471	Vector<Real, Dim> result;
472	result.mul(v1,s);
473	return result;
474	}
475
476	/**
477	* Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
478	* @return the vaule of scalar multiplication of this vector
479	* @param s the scalar value
480	* @param v1 the source vector
481	*/
482	template<typename Real, unsigned int Dim>
483	Vector<Real, Dim> operator * ( Real s, const Vector<Real, Dim>& v1 ) {
484	Vector<Real, Dim> result;
485	result.mul(v1, s);
486	return result;
487	}
488
489	/**
490	* Returns the value of division of a vector by a scalar.
491	* @return the vaule of scalar division of this vector
492	* @param v1 the source vector
493	* @param s the scalar value
494	*/
495	template<typename Real, unsigned int Dim>
496	Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, Real s) {
497	Vector<Real, Dim> result;
498	result.div( v1,s);
499	return result;
500	}
501
502	/**
503	* Returns the dot product of two Vectors
504	* @param v1 first vector
505	* @param v2 second vector
506	* @return the dot product of v1 and v2
507	*/
508	template<typename Real, unsigned int Dim>
509	inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
510	Real tmp;
511	tmp = 0;
512
513	for (unsigned int i = 0; i < Dim; i++)
514	tmp += v1[i] * v2[i];
515
516	return tmp;
517	}
518
519
520
521
522	/**
523	* Returns the wide dot product of three Vectors. Compare with
524	* Rapaport's VWDot function.
525	*
526	* @param v1 first vector
527	* @param v2 second vector
528	* @param v3 third vector
529	* @return the wide dot product of v1, v2, and v3.
530	*/
531	template<typename Real, unsigned int Dim>
532	inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2, const Vector<Real, Dim>& v3 ) {
533	Real tmp;
534	tmp = 0;
535
536	for (unsigned int i = 0; i < Dim; i++)
537	tmp += v1[i] * v2[i] * v3[i];
538
539	return tmp;
540	}
541
542
543	/**
544	* Returns the distance between two Vectors
545	* @param v1 first vector
546	* @param v2 second vector
547	* @return the distance between v1 and v2
548	*/
549	template<typename Real, unsigned int Dim>
550	inline Real distance( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
551	Vector<Real, Dim> tempVector = v1 - v2;
552	return tempVector.length();
553	}
554
555	/**
556	* Returns the squared distance between two Vectors
557	* @param v1 first vector
558	* @param v2 second vector
559	* @return the squared distance between v1 and v2
560	*/
561	template<typename Real, unsigned int Dim>
562	inline Real distanceSquare( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
563	Vector<Real, Dim> tempVector = v1 - v2;
564	return tempVector.lengthSquare();
565	}
566
567	/**
568	* Write to an output stream
569	*/
570	template<typename Real, unsigned int Dim>
571	std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v) {
572
573	o << "[ ";
574
575	for (unsigned int i = 0 ; i< Dim; i++) {
576	o << v[i];
577
578	if (i != Dim -1) {
579	o<< ", ";
580	}
581	}
582
583	o << " ]";
584	return o;
585	}
586
587	}
588	#endif