# | 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 71 | Line 87 | namespace oopse { | |
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 85 | 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 | } | |
# | Line 93 | Line 109 | namespace oopse { | |
109 | template<typename T> | |
110 | inline Vector(const T& s){ | |
111 | for (unsigned int i = 0; i < Dim; i++) | |
112 | < | data_[i] = s; |
112 | > | this->data_[i] = s; |
113 | } | |
114 | ||
115 | /** Constructs and initializes a Vector from an array */ | |
116 | inline Vector( Real* v) { | |
117 | for (unsigned int i = 0; i < Dim; i++) | |
118 | < | data_[i] = v[i]; |
118 | > | this->data_[i] = v[i]; |
119 | } | |
120 | ||
121 | /** | |
# | Line 109 | Line 125 | namespace oopse { | |
125 | */ | |
126 | inline Real& operator[](unsigned int i) { | |
127 | assert( i < Dim); | |
128 | < | return data_[i]; |
128 | > | return this->data_[i]; |
129 | } | |
130 | ||
131 | /** | |
# | Line 119 | Line 135 | namespace oopse { | |
135 | */ | |
136 | inline Real& operator()(unsigned int i) { | |
137 | assert( i < Dim); | |
138 | < | return data_[i]; |
138 | > | return this->data_[i]; |
139 | } | |
140 | ||
141 | /** | |
# | Line 129 | Line 145 | namespace oopse { | |
145 | */ | |
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 139 | Line 155 | namespace oopse { | |
155 | */ | |
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] = data_[i]; |
164 | > | array[i] = this->data_[i]; |
165 | } | |
166 | } | |
167 | ||
168 | /** Returns the pointer of internal array */ | |
169 | Real* getArrayPointer() { | |
170 | < | return data_; |
170 | > | return this->data_; |
171 | } | |
172 | ||
173 | /** | |
# | Line 162 | 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 182 | Line 198 | namespace oopse { | |
198 | /** Negates the value of this vector in place. */ | |
199 | inline void negate() { | |
200 | for (unsigned int i = 0; i < Dim; i++) | |
201 | < | data_[i] = -data_[i]; |
201 | > | this->data_[i] = -this->data_[i]; |
202 | } | |
203 | ||
204 | /** | |
# | Line 191 | 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 201 | Line 217 | namespace oopse { | |
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]; |
220 | > | this->data_[i] += v1.data_[i]; |
221 | } | |
222 | ||
223 | /** | |
# | Line 211 | Line 227 | namespace oopse { | |
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]; |
230 | > | this->data_[i] = v1.data_[i] + v2.data_[i]; |
231 | } | |
232 | ||
233 | /** | |
# | Line 220 | 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 230 | 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 | /** | |
# | Line 239 | Line 255 | namespace oopse { | |
255 | */ | |
256 | inline void mul( Real s ) { | |
257 | for (unsigned int i = 0; i < Dim; i++) | |
258 | < | data_[i] *= s; |
258 | > | this->data_[i] *= s; |
259 | } | |
260 | ||
261 | /** | |
# | Line 250 | Line 266 | namespace oopse { | |
266 | */ | |
267 | inline void mul( const Vector<Real, Dim>& v1, Real s) { | |
268 | for (unsigned int i = 0; i < Dim; i++) | |
269 | < | data_[i] = s * v1.data_[i]; |
269 | > | this->data_[i] = s * v1.data_[i]; |
270 | } | |
271 | ||
272 | /** | |
# | Line 259 | Line 275 | namespace oopse { | |
275 | */ | |
276 | inline void div( Real s) { | |
277 | for (unsigned int i = 0; i < Dim; i++) | |
278 | < | data_[i] /= s; |
278 | > | this->data_[i] /= s; |
279 | } | |
280 | ||
281 | /** | |
# | Line 269 | Line 285 | namespace oopse { | |
285 | */ | |
286 | inline void div( const Vector<Real, Dim>& v1, Real s ) { | |
287 | for (unsigned int i = 0; i < Dim; i++) | |
288 | < | data_[i] = v1.data_[i] / s; |
288 | > | this->data_[i] = v1.data_[i] / s; |
289 | } | |
290 | ||
291 | /** @see #add */ |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |