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Revision 1569 by tim, Thu Oct 14 23:28:09 2004 UTC vs.
Revision 2069 by tim, Tue Mar 1 20:10:14 2005 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.
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4 + * The University of Notre Dame grants you ("Licensee") a
5 + * non-exclusive, royalty free, license to use, modify and
6 + * redistribute this software in source and binary code form, provided
7 + * that the following conditions are met:
8 + *
9 + * 1. Acknowledgement of the program authors must be made in any
10 + *    publication of scientific results based in part on use of the
11 + *    program.  An acceptable form of acknowledgement is citation of
12 + *    the article in which the program was described (Matthew
13 + *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 + *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 + *    Parallel Simulation Engine for Molecular Dynamics,"
16 + *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 + *
18 + * 2. Redistributions of source code must retain the above copyright
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
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 <
55 > #include <math.h>
56   namespace oopse {
57  
58 <    const double epsilon = 0.000001;
58 >    static const double epsilon = 0.000001;
59  
60      template<typename T>
61      inline bool equal(T e1, T e2) {
# Line 55 | Line 71 | namespace oopse {
71      inline bool equal(double e1, double e2) {
72          return fabs(e1 - e2) < epsilon;
73      }
74 +
75      
76      /**
77       * @class Vector Vector.hpp "math/Vector.hpp"
# Line 64 | Line 81 | namespace oopse {
81      class Vector{
82          public:
83  
84 +            typedef Real ElemType;
85 +            typedef Real* ElemPoinerType;
86 +
87              /** default constructor */
88              inline Vector(){
89                  for (unsigned int i = 0; i < Dim; i++)
90 <                    data_[i] = 0.0;
90 >                    this->data_[i] = 0;
91              }
92  
93              /** Constructs and initializes a Vector from a vector */
# Line 81 | Line 101 | namespace oopse {
101                      return *this;
102                  
103                  for (unsigned int i = 0; i < Dim; i++)            
104 <                    data_[i] = v[i];
104 >                    this->data_[i] = v[i];
105                  
106                  return *this;
107              }
108 +
109 +            template<typename T>
110 +            inline Vector(const T& s){
111 +                for (unsigned int i = 0; i < Dim; i++)
112 +                    this->data_[i] = s;
113 +            }
114              
115              /** Constructs and initializes a Vector from an array */            
116 <            inline Vector( double* v) {
117 <                for (unsigned int i = 0; i < Dim; i++)
118 <                    data_[i] = v[i];
116 >            inline Vector( Real* v) {
117 >                for (unsigned int i = 0; i < Dim; i++)
118 >                    this->data_[i] = v[i];
119              }
120  
121              /**
# Line 97 | Line 123 | namespace oopse {
123               * @return reference of ith element
124               * @param i index
125               */
126 <            inline double& operator[](unsigned int  i) {
126 >            inline Real& operator[](unsigned int  i) {
127                  assert( i < Dim);
128 <                return data_[i];
128 >                return this->data_[i];
129              }
130  
131              /**
# Line 107 | Line 133 | namespace oopse {
133               * @return reference of ith element
134               * @param i index
135               */
136 <            inline double& operator()(unsigned int  i) {
136 >            inline Real& operator()(unsigned int  i) {
137                  assert( i < Dim);
138 <                return data_[i];
138 >                return this->data_[i];
139              }
140  
141              /**
# Line 117 | Line 143 | namespace oopse {
143               * @return reference of ith element
144               * @param i index
145               */
146 <            inline  const double& operator[](unsigned int i) const {
146 >            inline  const Real& operator[](unsigned int i) const {
147                  assert( i < Dim);
148 <                return data_[i];
148 >                return this->data_[i];
149              }
150  
151              /**
# Line 127 | Line 153 | namespace oopse {
153               * @return reference of ith element
154               * @param i index
155               */
156 <            inline  const double& operator()(unsigned int i) const {
156 >            inline  const Real& operator()(unsigned int i) const {
157                  assert( i < Dim);
158 <                return data_[i];
158 >                return this->data_[i];
159              }
160  
161 +            /** Copy the internal data to an array*/
162 +            void getArray(Real* array) {
163 +                for (unsigned int i = 0; i < Dim; i ++) {
164 +                    array[i] = this->data_[i];
165 +                }                
166 +            }
167 +
168 +            /** Returns the pointer of internal array */
169 +            Real* getArrayPointer() {
170 +                return this->data_;
171 +            }
172 +            
173              /**
174               * Tests if this vetor is equal to other vector
175               * @return true if equal, otherwise return false
# Line 140 | Line 178 | namespace oopse {
178               inline bool operator ==(const Vector<Real, Dim>& v) {
179  
180                  for (unsigned int i = 0; i < Dim; i ++) {
181 <                    if (!equal(data_[i], v[i])) {
181 >                    if (!equal(this->data_[i], v[i])) {
182                          return false;
183                      }
184                  }
# Line 159 | Line 197 | namespace oopse {
197              
198              /** Negates the value of this vector in place. */          
199              inline void negate() {
200 <                data_[0] = -data_[0];
201 <                data_[1] = -data_[1];
164 <                data_[2] = -data_[2];
200 >                for (unsigned int i = 0; i < Dim; i++)
201 >                    this->data_[i] = -this->data_[i];
202              }
203  
204              /**
# Line 170 | Line 207 | namespace oopse {
207              */
208              inline void negate(const Vector<Real, Dim>& v1) {
209                  for (unsigned int i = 0; i < Dim; i++)
210 <                    data_[i] = -v1.data_[i];
210 >                    this->data_[i] = -v1.data_[i];
211  
212              }
213              
# Line 179 | Line 216 | namespace oopse {
216              * @param v1 the other vector
217              */
218              inline void add( const Vector<Real, Dim>& v1 ) {
219 <                for (unsigned int i = 0; i < Dim; i++)
220 <                    data_[i] += v1.data_[i];
221 <                }
219 >                for (unsigned int i = 0; i < Dim; i++)
220 >                    this->data_[i] += v1.data_[i];
221 >            }
222  
223              /**
224              * Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2).
# Line 189 | Line 226 | namespace oopse {
226              * @param v2 the second vector
227              */
228              inline void add( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
229 <                for (unsigned int i = 0; i < Dim; i++)
230 <                    data_[i] = v1.data_[i] + v2.data_[i];
229 >                for (unsigned int i = 0; i < Dim; i++)
230 >                    this->data_[i] = v1.data_[i] + v2.data_[i];
231              }
232  
233              /**
# Line 199 | Line 236 | namespace oopse {
236              */
237              inline void sub( const Vector<Real, Dim>& v1 ) {
238                  for (unsigned int i = 0; i < Dim; i++)
239 <                    data_[i] -= v1.data_[i];
239 >                    this->data_[i] -= v1.data_[i];
240              }
241  
242              /**
# Line 209 | Line 246 | namespace oopse {
246              */
247              inline void sub( const Vector<Real, Dim>& v1, const Vector  &v2 ){
248                  for (unsigned int i = 0; i < Dim; i++)
249 <                    data_[i] = v1.data_[i] - v2.data_[i];
249 >                    this->data_[i] = v1.data_[i] - v2.data_[i];
250              }
251  
252              /**
253              * Sets the value of this vector to the scalar multiplication of itself (*this *= s).
254              * @param s the scalar value
255              */
256 <            inline void mul( double s ) {
257 <                for (unsigned int i = 0; i < Dim; i++)
258 <                   data_[i] *= s;
256 >            inline void mul( Real s ) {
257 >                for (unsigned int i = 0; i < Dim; i++)
258 >                   this->data_[i] *= s;
259              }
260  
261              /**
262              * Sets the value of this vector to the scalar multiplication of vector v1  
263              * (*this = s * v1).
264 +            * @param v1 the vector            
265              * @param s the scalar value
228 –            * @param v1 the vector
266              */
267 <            inline void mul( double s, const Vector<Real, Dim>& v1 ) {
268 <                for (unsigned int i = 0; i < Dim; i++)
269 <                    data_[i] = s * v1.data_[i];
267 >            inline void mul( const Vector<Real, Dim>& v1, Real s) {
268 >                for (unsigned int i = 0; i < Dim; i++)
269 >                    this->data_[i] = s * v1.data_[i];
270              }
271  
272              /**
273              * Sets the value of this vector to the scalar division of itself  (*this /= s ).
274              * @param s the scalar value
275              */            
276 <            inline void div( double s) {
277 <                for (unsigned int i = 0; i < Dim; i++)            
278 <                    data_[i] /= s;
276 >            inline void div( Real s) {
277 >                for (unsigned int i = 0; i < Dim; i++)            
278 >                    this->data_[i] /= s;
279              }
280  
281              /**
# Line 246 | Line 283 | namespace oopse {
283              * @param v1 the source vector
284              * @param s the scalar value
285              */                        
286 <            inline void div( const Vector<Real, Dim>& v1, double s ) {
287 <                for (unsigned int i = 0; i < Dim; i++)
288 <                    data_[i] = v1.data_[i] / s;
286 >            inline void div( const Vector<Real, Dim>& v1, Real s ) {
287 >                for (unsigned int i = 0; i < Dim; i++)
288 >                    this->data_[i] = v1.data_[i] / s;
289              }
290  
291              /** @see #add */
# Line 264 | Line 301 | namespace oopse {
301              }
302  
303              /** @see #mul */
304 <            inline Vector<Real, Dim>& operator *=( double s) {
304 >            inline Vector<Real, Dim>& operator *=( Real s) {
305                  mul(s);
306                  return *this;
307              }
308  
309              /** @see #div */
310 <            inline Vector<Real, Dim>& operator /=( double s ) {
310 >            inline Vector<Real, Dim>& operator /=( Real s ) {
311                  div(s);
312                  return *this;
313              }
# Line 279 | Line 316 | namespace oopse {
316               * Returns the length of this vector.
317               * @return the length of this vector
318               */
319 <             inline double length() {
320 <                return sqrt(lengthSquared());  
319 >             inline Real length() {
320 >                return sqrt(lengthSquare());  
321              }
322              
323              /**
324               * Returns the squared length of this vector.
325               * @return the squared length of this vector
326               */
327 <             inline double lengthSquared() {
327 >             inline Real lengthSquare() {
328                  return dot(*this, *this);
329              }
330              
331              /** Normalizes this vector in place */
332              inline void normalize() {
333 <                double len;
333 >                Real len;
334  
335                  len = length();
336 +                
337 +                //if (len < oopse:epsilon)
338 +                //  throw();
339 +                
340                  *this /= len;
341              }
342 +
343 +            /**
344 +             * Tests if this vector is normalized
345 +             * @return true if this vector is normalized, otherwise return false
346 +             */
347 +            inline bool isNormalized() {
348 +                return equal(lengthSquare(), 1.0);
349 +            }          
350              
351          protected:
352 <            double data_[3];
352 >            Real data_[Dim];
353          
354      };
355  
356      /** unary minus*/
357      template<typename Real, unsigned int Dim>    
358      inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){
359 <        Vector tmp(v1);
360 <        return tmp.negate();
359 >        Vector<Real, Dim> tmp(v1);
360 >        tmp.negate();
361 >        return tmp;
362      }
363  
364      /**
# Line 345 | Line 395 | namespace oopse {
395       * @param s the scalar value
396       */
397      template<typename Real, unsigned int Dim>                
398 <    Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, double s) {      
398 >    Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, Real s) {      
399          Vector<Real, Dim> result;
400 <        result.mul(s, v1);
400 >        result.mul(v1,s);
401          return result;          
402      }
403      
# Line 358 | Line 408 | namespace oopse {
408       * @param v1 the source vector
409       */  
410      template<typename Real, unsigned int Dim>
411 <    Vector<Real, Dim> operator * ( double s, const Vector<Real, Dim>& v1 ) {
411 >    Vector<Real, Dim> operator * ( Real s, const Vector<Real, Dim>& v1 ) {
412          Vector<Real, Dim> result;
413 <        result.mul(s, v1);
413 >        result.mul(v1, s);
414          return result;          
415      }
416  
# Line 371 | Line 421 | namespace oopse {
421       * @param s the scalar value
422       */
423      template<typename Real, unsigned int Dim>    
424 <    Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, double s) {      
424 >    Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, Real s) {      
425          Vector<Real, Dim> result;
426          result.div( v1,s);
427          return result;          
428      }
429      
430      /**
381 –     * Returns the  value of division of a vector by a scalar.
382 –     * @return  the vaule of scalar division of this vector
383 –     * @param s the scalar value
384 –     * @param v1 the source vector
385 –     */
386 –    template<typename Real, unsigned int Dim>        
387 –    inline Vector<Real, Dim> operator /( double s, const Vector<Real, Dim>& v1 ) {
388 –        Vector<Real, Dim> result;
389 –        result.div( v1,s);
390 –        return result;          
391 –    }
392 –
393 –    /** fuzzy comparson */
394 –    template<typename Real, unsigned int Dim>        
395 –    inline bool epsilonEqual( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
396 –
397 –    }
398 –
399 –    
400 –    /**
431       * Returns the dot product of two Vectors
432       * @param v1 first vector
433       * @param v2 second vector
# Line 405 | Line 435 | namespace oopse {
435       */
436      template<typename Real, unsigned int Dim>    
437      inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) {
438 <                Real tmp;
439 <                tmp = 0;
438 >        Real tmp;
439 >        tmp = 0;
440  
441 <                for (unsigned int i = 0; i < Dim; i++)
442 <                        tmp += v1[i] + v2[i];
443 <                
444 <                return tmp;
441 >        for (unsigned int i = 0; i < Dim; i++)
442 >            tmp += v1[i] * v2[i];
443 >
444 >        return tmp;
445      }
446  
447      /**
# Line 442 | Line 472 | namespace oopse {
472       * Write to an output stream
473       */
474      template<typename Real, unsigned int Dim>
475 <    std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v1 ) {
475 >    std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v) {
476 >
477 >        o << "[ ";
478          
479 +        for (unsigned int i = 0 ; i< Dim; i++) {
480 +            o << v[i];
481 +
482 +            if (i  != Dim -1) {
483 +                o<< ", ";
484 +            }
485 +        }
486 +
487 +        o << " ]";
488          return o;        
489      }
490      

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