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Revision 71 by tim, Wed Oct 13 22:24:59 2004 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3 < *
4 < * Contact: oopse@oopse.org
5 < *
6 < * This program is free software; you can redistribute it and/or
7 < * modify it under the terms of the GNU Lesser General Public License
8 < * as published by the Free Software Foundation; either version 2.1
9 < * of the License, or (at your option) any later version.
10 < * All we ask is that proper credit is given for our work, which includes
11 < * - but is not limited to - adding the above copyright notice to the beginning
12 < * of your source code files, and to any copyright notice that you may distribute
13 < * with programs based on this work.
14 < *
15 < * This program is distributed in the hope that it will be useful,
16 < * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 < * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 < * GNU Lesser General Public License for more details.
19 < *
20 < * You should have received a copy of the GNU Lesser General Public License
21 < * along with this program; if not, write to the Free Software
22 < * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 <
41 >
42   /**
43   * @file Vector.hpp
44   * @author Teng Lin
# Line 36 | Line 52
52   #include <cassert>
53   #include <cmath>
54   #include <iostream>
55 + #include <math.h>
56 + #include "config.h"
57 + namespace OpenMD {
58  
59 < namespace oopse {
59 >  static const RealType epsilon = 0.000001;
60  
61 <    /**
62 <     * @class Vector Vector.hpp "math/Vector.hpp"
63 <     * @brief Fix length vector class
64 <     */
46 <    template<typename Real, unsigned int Dim>
47 <    class Vector{
48 <        public:
61 >  template<typename T>
62 >  inline bool equal(T e1, T e2) {
63 >    return e1 == e2;
64 >  }
65  
66 <            /** default constructor */
67 <            inline Vector(){
68 <                for (unsigned int i = 0; i < Dim; i++)
69 <                    data_[i] = 0.0;
54 <            }
66 >  //template<>
67 >  //inline bool equal(float e1, float e2) {
68 >  //  return fabs(e1 - e2) < epsilon;
69 >  //}
70  
71 <            /** Constructs and initializes a Vector from a vector */
72 <            inline Vector(const Vector<Real, Dim>& v) {
73 <                *this  = v;
74 <            }
71 >  template<>
72 >  inline bool equal(RealType e1, RealType e2) {
73 >    return fabs(e1 - e2) < epsilon;
74 >  }
75  
76 <            /** copy assignment operator */
77 <            inline Vector<Real, Dim>& operator=(const Vector<Real, Dim>& v) {
78 <                if (this == &v)
79 <                    return *this;
80 <                
81 <                for (unsigned int i = 0; i < Dim; i++)            
82 <                    data_[i] = v[i];
83 <                
69 <                return *this;
70 <            }
71 <            
72 <            /** Constructs and initializes a Vector from an array */            
73 <            inline Vector( double* v) {
74 <                for (unsigned int i = 0; i < Dim; i++)
75 <                    data_[i] = v[i];
76 <            }
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 <            /**
86 <             * Returns reference of ith element.
80 <             * @return reference of ith element
81 <             * @param i index
82 <             */
83 <            inline double& operator[](unsigned int  i) {
84 <                assert( i < Dim);
85 <                return data_[i];
86 <            }
85 >    typedef Real ElemType;
86 >    typedef Real* ElemPoinerType;
87  
88 <            /**
89 <             * Returns reference of ith element.
90 <             * @return reference of ith element
91 <             * @param i index
92 <             */
93 <            inline double& operator()(unsigned int  i) {
94 <                assert( i < Dim);
95 <                return data_[i];
96 <            }
88 >    /** default constructor */
89 >    inline Vector(){
90 >      for (unsigned int i = 0; i < Dim; i++)
91 >        this->data_[i] = 0;
92 >    }
93  
94 <            /**
95 <             * Returns constant reference of ith element.
96 <             * @return reference of ith element
97 <             * @param i index
102 <             */
103 <            inline  const double& operator[](unsigned int i) const {
104 <                assert( i < Dim);
105 <                return data_[i];
106 <            }
94 >    /** Constructs and initializes a Vector from a vector */
95 >    inline Vector(const Vector<Real, Dim>& v) {
96 >      *this  = v;
97 >    }
98  
99 <            /**
100 <             * Returns constant reference of ith element.
101 <             * @return reference of ith element
102 <             * @param i index
103 <             */
104 <            inline  const double& operator()(unsigned int i) const {
105 <                assert( i < Dim);
106 <                return data_[i];
107 <            }
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 <            /** Negates the value of this vector in place. */          
111 <            inline void negate() {
112 <                data_[0] = -data_[0];
113 <                data_[1] = -data_[1];
114 <                data_[2] = -data_[2];
123 <            }
124 <
125 <            /**
126 <            * Sets the value of this vector to the negation of vector v1.
127 <            * @param v1 the source vector
128 <            */
129 <            inline void negate(const Vector<Real, Dim>& v1) {
130 <                for (unsigned int i = 0; i < Dim; i++)
131 <                    data_[i] = -v1.data_[i];
132 <
133 <            }
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 <            /**
117 <            * Sets the value of this vector to the sum of itself and v1 (*this += v1).
118 <            * @param v1 the other vector
119 <            */
120 <            inline void add( const Vector<Real, Dim>& v1 ) {
140 <                for (unsigned int i = 0; i < Dim; i++)
141 <                    data_[i] += v1.data_[i];
142 <                }
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 <            * Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
124 <            * @param v1 the first vector
125 <            * @param v2 the second vector
126 <            */
127 <            inline void add( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
128 <                for (unsigned int i = 0; i < Dim; i++)
129 <                    data_[i] = v1.data_[i] + v2.data_[i];
130 <            }
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 <            * Sets the value of this vector to the difference  of itself and v1 (*this -= v1).
134 <            * @param v1 the other vector
135 <            */
136 <            inline void sub( const Vector<Real, Dim>& v1 ) {
137 <                for (unsigned int i = 0; i < Dim; i++)
138 <                    data_[i] -= v1.data_[i];
139 <            }
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 <            * Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2).
144 <            * @param v1 the first vector
145 <            * @param v2 the second vector
146 <            */
147 <            inline void sub( const Vector<Real, Dim>& v1, const Vector  &v2 ){
148 <                for (unsigned int i = 0; i < Dim; i++)
149 <                    data_[i] = v1.data_[i] - v2.data_[i];
150 <            }
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 <            * Sets the value of this vector to the scalar multiplication of itself (*this *= s).
154 <            * @param s the scalar value
155 <            */
156 <            inline void mul( double s ) {
157 <                for (unsigned int i = 0; i < Dim; i++)
158 <                   data_[i] *= s;
159 <            }
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 <            /**
163 <            * Sets the value of this vector to the scalar multiplication of vector v1  
164 <            * (*this = s * v1).
165 <            * @param s the scalar value
166 <            * @param v1 the vector
167 <            */
188 <            inline void mul( double s, const Vector<Real, Dim>& v1 ) {
189 <                for (unsigned int i = 0; i < Dim; i++)
190 <                    data_[i] = s * v1.data_[i];
191 <            }
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 <            /**
170 <            * Sets the value of this vector to the scalar division of itself  (*this /= s ).
171 <            * @param s the scalar value
172 <            */            
173 <            inline void div( double s) {
174 <                for (unsigned int i = 0; i < Dim; i++)            
175 <                    data_[i] /= s;
176 <            }
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 <            /**
182 <            * Sets the value of this vector to the scalar division of vector v1  (*this = v1 / s ).
183 <            * @param v1 the source vector
184 <            * @param s the scalar value
185 <            */                        
186 <            inline void div( const Vector<Real, Dim>& v1, double s ) {
187 <                for (unsigned int i = 0; i < Dim; i++)
188 <                    data_[i] = v1.data_[i] / s;
210 <            }
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 <            /** @see #add */
191 <            inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
192 <                add(v1);
193 <                return *this;
194 <            }
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 <            /** @see #sub */
206 <            inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) {
207 <                sub(v1);
208 <                return *this;
209 <            }
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 <            /** @see #mul */
225 <            inline Vector<Real, Dim>& operator *=( double s) {
226 <                mul(s);
227 <                return *this;
228 <            }
229 <
230 <            /** @see #div */
231 <            inline Vector<Real, Dim>& operator /=( double s ) {
232 <                div(s);
233 <                return *this;
234 <            }
235 <
236 <            /**
237 <             * Returns the length of this vector.
238 <             * @return the length of this vector
239 <             */
240 <             inline double length() {
241 <                return sqrt(lengthSquared());  
242 <            }
213 >    }
214              
215 <            /**
216 <             * Returns the squared length of this vector.
217 <             * @return the squared length of this vector
218 <             */
219 <             inline double lengthSquared() {
220 <                return dot(*this, *this);
221 <            }
251 <            
252 <            /** Normalizes this vector in place */
253 <            inline void normalize() {
254 <                double len;
255 <
256 <                len = length();
257 <                *this /= len;
258 <            }
259 <            
260 <        protected:
261 <            double data_[3];
262 <        
263 <    };
264 <
265 <    /** unary minus*/
266 <    template<typename Real, unsigned int Dim>    
267 <    inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){
268 <        Vector tmp(v1);
269 <        return tmp.negate();
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 <     * Return the sum of two vectors  (v1 - v2).
274 <     * @return the sum of two vectors
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 <    template<typename Real, unsigned int Dim>    
230 <    inline Vector<Real, Dim> operator +(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
231 <        Vector<Real, Dim> result;
281 <        
282 <        result.add(v1, v2);
283 <        return result;        
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 <     * Return the difference of two vectors  (v1 - v2).
236 <     * @return the difference of two vectors
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 <    template<typename Real, unsigned int Dim>    
249 <    Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
250 <        Vector<Real, Dim> result;
295 <        result.sub(v1, v2);
296 <        return result;        
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 <    
252 >
253      /**
254 <     * Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
301 <     * @return  the vaule of scalar multiplication of this vector
302 <     * @param v1 the source vector
254 >     * Sets the value of this vector to the scalar multiplication of itself (*this *= s).
255       * @param s the scalar value
256 <     */
257 <    template<typename Real, unsigned int Dim>                
258 <    Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, double s) {      
259 <        Vector<Real, Dim> result;
308 <        result.mul(s, v1);
309 <        return result;          
256 >     */
257 >    inline void mul( Real s ) {
258 >      for (unsigned int i = 0; i < Dim; i++)
259 >        this->data_[i] *= s;
260      }
261 <    
261 >
262      /**
263 <     * Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
264 <     * @return  the vaule of scalar multiplication of this vector
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 <     * @param v1 the source vector
268 <     */  
269 <    template<typename Real, unsigned int Dim>
270 <    Vector<Real, Dim> operator * ( double s, const Vector<Real, Dim>& v1 ) {
320 <        Vector<Real, Dim> result;
321 <        result.mul(s, v1);
322 <        return result;          
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 <     * Returns the  value of division of a vector by a scalar.
327 <     * @return  the vaule of scalar division of this vector
328 <     * @param v1 the source vector
274 >     * Sets the value of this vector to the scalar division of itself  (*this /= s ).
275       * @param s the scalar value
276 <     */
277 <    template<typename Real, unsigned int Dim>    
278 <    Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, double s) {      
279 <        Vector<Real, Dim> result;
334 <        result.div( v1,s);
335 <        return result;          
276 >     */            
277 >    inline void div( Real s) {
278 >      for (unsigned int i = 0; i < Dim; i++)            
279 >        this->data_[i] /= s;
280      }
281 <    
281 >
282      /**
283 <     * Returns the  value of division of a vector by a scalar.
340 <     * @return  the vaule of scalar division of this vector
341 <     * @param s the scalar value
283 >     * Sets the value of this vector to the scalar division of vector v1  (*this = v1 / s ).
284       * @param v1 the source vector
285 <     */
286 <    template<typename Real, unsigned int Dim>        
287 <    inline Vector<Real, Dim> operator /( double s, const Vector<Real, Dim>& v1 ) {
288 <        Vector<Real, Dim> result;
289 <        result.div( v1,s);
348 <        return result;          
285 >     * @param s the scalar value
286 >     */                        
287 >    inline void div( const Vector<Real, Dim>& v1, Real s ) {
288 >      for (unsigned int i = 0; i < Dim; i++)
289 >        this->data_[i] = v1.data_[i] / s;
290      }
291  
292 <    /** fuzzy comparson */
293 <    template<typename Real, unsigned int Dim>        
294 <    inline bool epsilonEqual( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
292 >    /** @see #add */
293 >    inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) {
294 >      add(v1);
295 >      return *this;
296 >    }
297  
298 +    /** @see #sub */
299 +    inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) {
300 +      sub(v1);
301 +      return *this;
302      }
303  
304 <    
305 <    /**
306 <     * Returns the dot product of two Vectors
307 <     * @param v1 first vector
308 <     * @param v2 second vector
362 <     * @return the dot product of v1 and v2
363 <     */
364 <    template<typename Real, unsigned int Dim>    
365 <    inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
366 <                Real tmp;
367 <                tmp = 0;
304 >    /** @see #mul */
305 >    inline Vector<Real, Dim>& operator *=( Real s) {
306 >      mul(s);
307 >      return *this;
308 >    }
309  
310 <                for (unsigned int i = 0; i < Dim; i++)
311 <                        tmp += v1[i] + v2[i];
312 <                
313 <                return tmp;
310 >    /** @see #div */
311 >    inline Vector<Real, Dim>& operator /=( Real s ) {
312 >      div(s);
313 >      return *this;
314      }
315  
316      /**
317 <     * Returns the distance between  two Vectors
318 <     * @param v1 first vector
319 <     * @param v2 second vector
320 <     * @return the distance between v1 and v2
321 <     */
322 <    template<typename Real, unsigned int Dim>    
323 <    inline Real distance( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
324 <        Vector<Real, Dim> tempVector = v1 - v2;
325 <        return tempVector.length();
317 >     * Returns the sum of all elements of this vector.
318 >     * @return the sum of all elements of this vector
319 >     */
320 >    inline Real sum() {
321 >      Real tmp;
322 >      tmp = 0;
323 >      for (unsigned int i = 0; i < Dim; i++)
324 >        tmp += this->data_[i];
325 >      return tmp;  
326      }
327 <
327 >            
328      /**
329 <     * Returns the squared distance between  two Vectors
330 <     * @param v1 first vector
390 <     * @param v2 second vector
391 <     * @return the squared distance between v1 and v2
329 >     * Returns the length of this vector.
330 >     * @return the length of this vector
331       */
332 <    template<typename Real, unsigned int Dim>
333 <    inline Real distanceSquare( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
395 <        Vector<Real, Dim> tempVector = v1 - v2;
396 <        return tempVector.lengthSquare();
332 >    inline Real length() {
333 >      return sqrt(lengthSquare());  
334      }
335 +            
336 +    /**
337 +     * Returns the squared length of this vector.
338 +     * @return the squared length of this vector
339 +     */
340 +    inline Real lengthSquare() {
341 +      return dot(*this, *this);
342 +    }
343 +            
344 +    /** Normalizes this vector in place */
345 +    inline void normalize() {
346 +      Real len;
347  
348 +      len = length();
349 +                
350 +      //if (len < OpenMD::NumericConstant::epsilon)
351 +      //  throw();
352 +                
353 +      *this /= len;
354 +    }
355 +
356      /**
357 <     * Write to an output stream
357 >     * Tests if this vector is normalized
358 >     * @return true if this vector is normalized, otherwise return false
359       */
360 <    template<typename Real, unsigned int Dim>
361 <    std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v1 ) {
360 >    inline bool isNormalized() {
361 >      return equal(lengthSquare(), (RealType)1);
362 >    }          
363 >
364 >    unsigned int size() {return Dim;}
365 >  protected:
366 >    Real data_[Dim];
367          
368 <        return o;        
368 >  };
369 >
370 >  /** unary minus*/
371 >  template<typename Real, unsigned int Dim>    
372 >  inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){
373 >    Vector<Real, Dim> tmp(v1);
374 >    tmp.negate();
375 >    return tmp;
376 >  }
377 >
378 >  /**
379 >   * Return the sum of two vectors  (v1 - v2).
380 >   * @return the sum of two vectors
381 >   * @param v1 the first vector
382 >   * @param v2 the second vector
383 >   */  
384 >  template<typename Real, unsigned int Dim>    
385 >  inline Vector<Real, Dim> operator +(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
386 >    Vector<Real, Dim> result;
387 >        
388 >    result.add(v1, v2);
389 >    return result;        
390 >  }
391 >
392 >  /**
393 >   * Return the difference of two vectors  (v1 - v2).
394 >   * @return the difference of two vectors
395 >   * @param v1 the first vector
396 >   * @param v2 the second vector
397 >   */  
398 >  template<typename Real, unsigned int Dim>    
399 >  Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) {
400 >    Vector<Real, Dim> result;
401 >    result.sub(v1, v2);
402 >    return result;        
403 >  }
404 >    
405 >  /**
406 >   * Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
407 >   * @return  the vaule of scalar multiplication of this vector
408 >   * @param v1 the source vector
409 >   * @param s the scalar value
410 >   */
411 >  template<typename Real, unsigned int Dim>                
412 >  Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, Real s) {      
413 >    Vector<Real, Dim> result;
414 >    result.mul(v1,s);
415 >    return result;          
416 >  }
417 >    
418 >  /**
419 >   * Returns the vaule of scalar multiplication of this vector v1 (v1 * r).
420 >   * @return  the vaule of scalar multiplication of this vector
421 >   * @param s the scalar value
422 >   * @param v1 the source vector
423 >   */  
424 >  template<typename Real, unsigned int Dim>
425 >  Vector<Real, Dim> operator * ( Real s, const Vector<Real, Dim>& v1 ) {
426 >    Vector<Real, Dim> result;
427 >    result.mul(v1, s);
428 >    return result;          
429 >  }
430 >
431 >  /**
432 >   * Returns the  value of division of a vector by a scalar.
433 >   * @return  the vaule of scalar division of this vector
434 >   * @param v1 the source vector
435 >   * @param s the scalar value
436 >   */
437 >  template<typename Real, unsigned int Dim>    
438 >  Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, Real s) {      
439 >    Vector<Real, Dim> result;
440 >    result.div( v1,s);
441 >    return result;          
442 >  }
443 >    
444 >  /**
445 >   * Returns the dot product of two Vectors
446 >   * @param v1 first vector
447 >   * @param v2 second vector
448 >   * @return the dot product of v1 and v2
449 >   */
450 >  template<typename Real, unsigned int Dim>    
451 >  inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
452 >    Real tmp;
453 >    tmp = 0;
454 >
455 >    for (unsigned int i = 0; i < Dim; i++)
456 >      tmp += v1[i] * v2[i];
457 >
458 >    return tmp;
459 >  }
460 >
461 >  /**
462 >   * Returns the distance between  two Vectors
463 >   * @param v1 first vector
464 >   * @param v2 second vector
465 >   * @return the distance between v1 and v2
466 >   */  
467 >  template<typename Real, unsigned int Dim>    
468 >  inline Real distance( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
469 >    Vector<Real, Dim> tempVector = v1 - v2;
470 >    return tempVector.length();
471 >  }
472 >
473 >  /**
474 >   * Returns the squared distance between  two Vectors
475 >   * @param v1 first vector
476 >   * @param v2 second vector
477 >   * @return the squared distance between v1 and v2
478 >   */
479 >  template<typename Real, unsigned int Dim>
480 >  inline Real distanceSquare( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
481 >    Vector<Real, Dim> tempVector = v1 - v2;
482 >    return tempVector.lengthSquare();
483 >  }
484 >
485 >  /**
486 >   * Write to an output stream
487 >   */
488 >  template<typename Real, unsigned int Dim>
489 >  std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v) {
490 >
491 >    o << "[ ";
492 >        
493 >    for (unsigned int i = 0 ; i< Dim; i++) {
494 >      o << v[i];
495 >
496 >      if (i  != Dim -1) {
497 >        o<< ", ";
498 >      }
499      }
500 +
501 +    o << " ]";
502 +    return o;        
503 +  }
504      
505   }
506   #endif

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