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 (12 years, 4 months ago) by gezelter
File size:	16782 byte(s)
Log Message:	New electrostatic method, starting to do some performance tuning.
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	1767	// template<typename T>
111			// inline Vector(const T& s){
112			inline Vector(const Real& s) {
113	gezelter	507	for (unsigned int i = 0; i < Dim; i++)
114	gezelter	1767	this->data_[i] = s;
115	gezelter	507	}
116	tim	70
117	gezelter	507	/** 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	tim	70
123	gezelter	507	/**
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	tim	70
133	gezelter	507	/**
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	tim	70
143	gezelter	507	/**
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	tim	70
153	gezelter	507	/**
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	tim	70
163	gezelter	507	/** 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	tim	151
170	gezelter	507	/** Returns the pointer of internal array */
171			Real* getArrayPointer() {
172			return this->data_;
173			}
174	tim	137
175	gezelter	507	/**
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	tim	76
182	gezelter	507	for (unsigned int i = 0; i < Dim; i ++) {
183			if (!equal(this->data_[i], v[i])) {
184			return false;
185			}
186			}
187	tim	76
188	gezelter	507	return true;
189			}
190	tim	76
191	gezelter	507	/**
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	gezelter	1877
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	tim	76
206	gezelter	507	/** 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	tim	70
212	gezelter	507	/**
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	tim	70
220	gezelter	507	}
221	tim	70
222	gezelter	507	/**
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	tim	70	}
230
231			/**
232	gezelter	507	* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
233	tim	70	* @param v1 the first vector
234			* @param v2 the second vector
235	gezelter	507	*/
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	tim	70	}
240
241			/**
242	gezelter	507	* 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	tim	70	* @param v1 the first vector
253			* @param v2 the second vector
254	gezelter	507	*/
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	tim	70	}
259	gezelter	507
260	tim	70	/**
261	gezelter	507	* Sets the value of this vector to the scalar multiplication of itself (this = s).
262	tim	70	* @param s the scalar value
263	gezelter	507	*/
264			inline void mul( Real s ) {
265			for (unsigned int i = 0; i < Dim; i++)
266			this->data_[i] *= s;
267	tim	70	}
268	gezelter	507
269	tim	70	/**
270	gezelter	507	* Sets the value of this vector to the scalar multiplication of vector v1
271			* (this = s v1).
272			* @param v1 the vector
273	tim	70	* @param s the scalar value
274	gezelter	507	*/
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	tim	70	}
279
280			/**
281	gezelter	1562	* 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	gezelter	1760	/* 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	gezelter	1562	/**
312	gezelter	507	* 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	tim	70	* @param v1 the source vector
323			* @param s the scalar value
324	gezelter	507	*/
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	tim	70	}
329
330	gezelter	1562	/**
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	gezelter	507	/** @see #add */
346			inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
347			add(v1);
348			return *this;
349			}
350	tim	93
351	gezelter	507	/** @see #sub */
352			inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) {
353			sub(v1);
354			return *this;
355	tim	70	}
356
357	gezelter	507	/** @see #mul */
358			inline Vector<Real, Dim>& operator *=( Real s) {
359			mul(s);
360			return *this;
361	tim	70	}
362
363	gezelter	507	/** @see #div */
364			inline Vector<Real, Dim>& operator /=( Real s ) {
365			div(s);
366			return *this;
367			}
368
369	tim	70	/**
370	cli2	1349	* 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	gezelter	1562
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	cli2	1349
393			/**
394	gezelter	507	* Returns the length of this vector.
395			* @return the length of this vector
396	tim	70	*/
397	gezelter	507	inline Real length() {
398			return sqrt(lengthSquare());
399	tim	70	}
400	gezelter	507
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	tim	70
413	gezelter	507	len = length();
414
415	gezelter	1390	//if (len < OpenMD::NumericConstant::epsilon)
416	gezelter	507	// throw();
417
418			*this /= len;
419			}
420
421	tim	70	/**
422	gezelter	507	* Tests if this vector is normalized
423			* @return true if this vector is normalized, otherwise return false
424	tim	70	*/
425	gezelter	507	inline bool isNormalized() {
426	tim	963	return equal(lengthSquare(), (RealType)1);
427	gezelter	507	}
428	tim	886
429			unsigned int size() {return Dim;}
430	gezelter	507	protected:
431			Real data_[Dim];
432
433			};
434	tim	93
435	gezelter	507	/** 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	tim	110
453	gezelter	507	result.add(v1, v2);
454			return result;
455			}
456	tim	110
457	gezelter	507	/**
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	tim	110
496	gezelter	507	/**
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	gezelter	1562
527
528
529	gezelter	507	/**
530	gezelter	1562	* 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	gezelter	507	* 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	tim	70	}
589	gezelter	507
590			o << " ]";
591			return o;
592			}
593	tim	70
594			}
595			#endif