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
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	70	*
4	gezelter	246	* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	70	*/
42	gezelter	246
43	tim	70	/**
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	tim	71	#include <iostream>
56	tim	253	#include <math.h>
57	tim	963	#include "config.h"
58	gezelter	1390	namespace OpenMD {
59	tim	70
60	tim	963	static const RealType epsilon = 0.000001;
61	tim	76
62	gezelter	507	template<typename T>
63			inline bool equal(T e1, T e2) {
64			return e1 == e2;
65			}
66	tim	76
67	tim	963	//template<>
68			//inline bool equal(float e1, float e2) {
69			// return fabs(e1 - e2) < epsilon;
70			//}
71	tim	76
72	gezelter	507	template<>
73	tim	963	inline bool equal(RealType e1, RealType e2) {
74	gezelter	507	return fabs(e1 - e2) < epsilon;
75			}
76	tim	76
77	gezelter	507	/**
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	tim	70
85	gezelter	507	typedef Real ElemType;
86			typedef Real* ElemPoinerType;
87	tim	137
88	gezelter	507	/** default constructor */
89			inline Vector(){
90			for (unsigned int i = 0; i < Dim; i++)
91			this->data_[i] = 0;
92			}
93	tim	70
94	gezelter	507	/** Constructs and initializes a Vector from a vector */
95			inline Vector(const Vector<Real, Dim>& v) {
96			*this = v;
97			}
98	tim	70
99	gezelter	507	/** copy assignment operator */
100			inline Vector<Real, Dim>& operator=(const Vector<Real, Dim>& v) {
101			if (this == &v)
102			return *this;
103	tim	70
104	gezelter	507	for (unsigned int i = 0; i < Dim; i++)
105			this->data_[i] = v[i];
106	tim	70
107	gezelter	507	return *this;
108			}
109	tim	101
110	gezelter	507	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	tim	70
116	gezelter	507	/** 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	tim	70
122	gezelter	507	/**
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	tim	70
132	gezelter	507	/**
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	tim	70
142	gezelter	507	/**
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	tim	70
152	gezelter	507	/**
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	tim	70
162	gezelter	507	/** 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	tim	151
169	gezelter	507	/** Returns the pointer of internal array */
170			Real* getArrayPointer() {
171			return this->data_;
172			}
173	tim	137
174	gezelter	507	/**
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	tim	76
181	gezelter	507	for (unsigned int i = 0; i < Dim; i ++) {
182			if (!equal(this->data_[i], v[i])) {
183			return false;
184			}
185			}
186	tim	76
187	gezelter	507	return true;
188			}
189	tim	76
190	gezelter	507	/**
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	tim	76
199	gezelter	507	/** 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	tim	70
205	gezelter	507	/**
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	tim	70
213	gezelter	507	}
214	tim	70
215	gezelter	507	/**
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	tim	70	}
223
224			/**
225	gezelter	507	* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
226	tim	70	* @param v1 the first vector
227			* @param v2 the second vector
228	gezelter	507	*/
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	tim	70	}
233
234			/**
235	gezelter	507	* 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	tim	70	* @param v1 the first vector
246			* @param v2 the second vector
247	gezelter	507	*/
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	tim	70	}
252	gezelter	507
253	tim	70	/**
254	gezelter	507	* Sets the value of this vector to the scalar multiplication of itself (this = s).
255	tim	70	* @param s the scalar value
256	gezelter	507	*/
257			inline void mul( Real s ) {
258			for (unsigned int i = 0; i < Dim; i++)
259			this->data_[i] *= s;
260	tim	70	}
261	gezelter	507
262	tim	70	/**
263	gezelter	507	* Sets the value of this vector to the scalar multiplication of vector v1
264			* (this = s v1).
265			* @param v1 the vector
266	tim	70	* @param s the scalar value
267	gezelter	507	*/
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	tim	70	}
272
273			/**
274	gezelter	1562	* 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	gezelter	1760	/* 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	gezelter	1562	/**
305	gezelter	507	* 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	tim	70	* @param v1 the source vector
316			* @param s the scalar value
317	gezelter	507	*/
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	tim	70	}
322
323	gezelter	1562	/**
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	gezelter	507	/** @see #add */
339			inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
340			add(v1);
341			return *this;
342			}
343	tim	93
344	gezelter	507	/** @see #sub */
345			inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) {
346			sub(v1);
347			return *this;
348	tim	70	}
349
350	gezelter	507	/** @see #mul */
351			inline Vector<Real, Dim>& operator *=( Real s) {
352			mul(s);
353			return *this;
354	tim	70	}
355
356	gezelter	507	/** @see #div */
357			inline Vector<Real, Dim>& operator /=( Real s ) {
358			div(s);
359			return *this;
360			}
361
362	tim	70	/**
363	cli2	1349	* 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	gezelter	1562
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	cli2	1349
386			/**
387	gezelter	507	* Returns the length of this vector.
388			* @return the length of this vector
389	tim	70	*/
390	gezelter	507	inline Real length() {
391			return sqrt(lengthSquare());
392	tim	70	}
393	gezelter	507
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	tim	70
406	gezelter	507	len = length();
407
408	gezelter	1390	//if (len < OpenMD::NumericConstant::epsilon)
409	gezelter	507	// throw();
410
411			*this /= len;
412			}
413
414	tim	70	/**
415	gezelter	507	* Tests if this vector is normalized
416			* @return true if this vector is normalized, otherwise return false
417	tim	70	*/
418	gezelter	507	inline bool isNormalized() {
419	tim	963	return equal(lengthSquare(), (RealType)1);
420	gezelter	507	}
421	tim	886
422			unsigned int size() {return Dim;}
423	gezelter	507	protected:
424			Real data_[Dim];
425
426			};
427	tim	93
428	gezelter	507	/** 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	tim	110
446	gezelter	507	result.add(v1, v2);
447			return result;
448			}
449	tim	110
450	gezelter	507	/**
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	tim	110
489	gezelter	507	/**
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	gezelter	1562
520
521
522	gezelter	507	/**
523	gezelter	1562	* 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	gezelter	507	* 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	tim	70	}
582	gezelter	507
583			o << " ]";
584			return o;
585			}
586	tim	70
587			}
588			#endif