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Comparing trunk/src/brains/DataStorage.cpp (file contents):
Revision 155 by tim, Tue Oct 26 22:19:22 2004 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 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. 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  
42 < /**
43 <  * @file DataStorage.cpp
44 <  * @author tlin
45 <  * @date 10/26/2004
46 <  * @time 11:56am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file DataStorage.cpp
44 > * @author tlin
45 > * @date 10/26/2004
46 > * @time 11:56am
47 > * @version 1.0
48 > */
49  
50   #include "brains/DataStorage.hpp"
51  
52 + namespace oopse {
53  
54 < DataStorage::DataStorage() : size_(0), storageLayout_(0){
54 >  DataStorage::DataStorage() : size_(0), storageLayout_(0){
55  
56 < }
56 >  }
57  
58 < DataStorage::DataStorage(int size, int storageLayout) : size_(size){
58 >  DataStorage::DataStorage(int size, int storageLayout) : size_(size){
59      setStorageLayout(storageLayout);
60      resize(size);
61 < }
61 >  }
62  
63 < int DataStorage::getSize() {
63 >  int DataStorage::getSize() {
64  
65      if (storageLayout_ & dslPosition && position.size() != size_) {
66 <        //error
67 <        std::cerr << "size does not match"<< std::endl;
66 >      //error
67 >      std::cerr << "size does not match"<< std::endl;
68      }
69  
70      if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71 <        //error
72 <        std::cerr << "size does not match"<< std::endl;        
71 >      //error
72 >      std::cerr << "size does not match"<< std::endl;        
73      }
74  
75      if (storageLayout_ & dslAmat && aMat.size() != size_) {
76 <        //error
77 <        std::cerr << "size does not match"<< std::endl;        
76 >      //error
77 >      std::cerr << "size does not match"<< std::endl;        
78      }
79  
80      if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
81 <        //error
82 <        std::cerr << "size does not match"<< std::endl;        
81 >      //error
82 >      std::cerr << "size does not match"<< std::endl;        
83      }
84  
85 <    if (storageLayout_ & dslUnitVector && unitVector.size() != size_) {
86 <        //error
87 <        std::cerr << "size does not match"<< std::endl;        
85 >    if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
86 >      //error
87 >      std::cerr << "size does not match"<< std::endl;        
88      }
89  
90      if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
91 <        //error
92 <        std::cerr << "size does not match"<< std::endl;        
91 >      //error
92 >      std::cerr << "size does not match"<< std::endl;        
93      }
94  
95      if (storageLayout_ & dslForce && force.size() != size_) {
96 <        //error
97 <        std::cerr << "size does not match"<< std::endl;        
96 >      //error
97 >      std::cerr << "size does not match"<< std::endl;        
98      }
99  
100      if (storageLayout_ & dslTorque && torque.size() != size_) {
101 <        //error
102 <        std::cerr << "size does not match"<< std::endl;        
101 >      //error
102 >      std::cerr << "size does not match"<< std::endl;        
103      }
104  
105      return size_;
106  
107 < }
107 >  }
108  
109 < void DataStorage::resize(int newSize) {
109 >  void DataStorage::resize(int newSize) {
110  
111      if (storageLayout_ & dslPosition) {
112 <        internalResize(position, newSize);
112 >      internalResize(position, newSize);
113      }
114  
115      if (storageLayout_ & dslVelocity) {
116 <        internalResize(velocity, newSize);
116 >      internalResize(velocity, newSize);
117      }
118  
119      if (storageLayout_ & dslAmat) {
120 <        internalResize(aMat, newSize);
120 >      internalResize(aMat, newSize);
121      }
122  
123      if (storageLayout_ & dslAngularMomentum) {
124 <        internalResize(angularMomentum, newSize);
124 >      internalResize(angularMomentum, newSize);
125      }
126  
127 <    if (storageLayout_ & dslUnitVector) {
128 <        internalResize(unitVector, newSize);
127 >    if (storageLayout_ & dslElectroFrame) {
128 >      internalResize(electroFrame, newSize);
129      }
130      
131      if (storageLayout_ & dslZAngle) {
132 <        internalResize(zAngle, newSize);
132 >      internalResize(zAngle, newSize);
133      }
134  
135      if (storageLayout_ & dslForce) {
136 <        internalResize(force, newSize);
136 >      internalResize(force, newSize);
137      }
138  
139      if (storageLayout_ & dslTorque) {
140 <        internalResize(torque, newSize);
140 >      internalResize(torque, newSize);
141      }
142  
143      size_ = newSize;
144 < }
144 >  }
145  
146 < void DataStorage::reserve(int size) {
146 >  void DataStorage::reserve(int size) {
147      if (storageLayout_ & dslPosition) {
148 <        position.reserve(size);
148 >      position.reserve(size);
149      }
150  
151      if (storageLayout_ & dslVelocity) {
152 <        velocity.reserve(size);
152 >      velocity.reserve(size);
153      }
154  
155      if (storageLayout_ & dslAmat) {
156 <        aMat.reserve(size);
156 >      aMat.reserve(size);
157      }
158  
159      if (storageLayout_ & dslAngularMomentum) {
160 <        angularMomentum.reserve(size);
160 >      angularMomentum.reserve(size);
161      }
162  
163 <    if (storageLayout_ & dslUnitVector) {
164 <        unitVector.reserve(size);
163 >    if (storageLayout_ & dslElectroFrame) {
164 >      electroFrame.reserve(size);
165      }
166      
167      if (storageLayout_ & dslZAngle) {
168 <        zAngle.reserve(size);
168 >      zAngle.reserve(size);
169      }
170  
171      if (storageLayout_ & dslForce) {
172 <        force.reserve(size);
172 >      force.reserve(size);
173      }
174  
175      if (storageLayout_ & dslTorque) {
176 <        torque.reserve(size);
176 >      torque.reserve(size);
177      }
178  
179 < }
179 >  }
180  
181 < void DataStorage::copy(int source, int num, int target) {
181 >  void DataStorage::copy(int source, int num, int target) {
182      if (num + target > size_ ) {
183 <        //error
183 >      //error
184      }
185      
186      if (storageLayout_ & dslPosition) {
187 <        interalCopy(position, source, num, target);
187 >      internalCopy(position, source, num, target);
188      }
189  
190      if (storageLayout_ & dslVelocity) {
191 <        interalCopy(velocity, source, num, target);
192 <  }
191 >      internalCopy(velocity, source, num, target);
192 >    }
193  
194      if (storageLayout_ & dslAmat) {
195 <        interalCopy(aMat, source, num, target);
196 <   }
195 >      internalCopy(aMat, source, num, target);
196 >    }
197  
198      if (storageLayout_ & dslAngularMomentum) {
199 <        interalCopy(angularMomentum, source, num, target);
199 >      internalCopy(angularMomentum, source, num, target);
200      }
201  
202 <    if (storageLayout_ & dslUnitVector) {
203 <        interalCopy(unitVector, source, num, target);
202 >    if (storageLayout_ & dslElectroFrame) {
203 >      internalCopy(electroFrame, source, num, target);
204      }
205      
206      if (storageLayout_ & dslZAngle) {
207 <        interalCopy(zAngle, source, num, target);
207 >      internalCopy(zAngle, source, num, target);
208      }
209  
210      if (storageLayout_ & dslForce) {
211 <        interalCopy(force, source, num, target);
211 >      internalCopy(force, source, num, target);
212      }
213  
214      if (storageLayout_ & dslTorque) {
215 <        interalCopy(torque, source, num, target);
215 >      internalCopy(torque, source, num, target);
216      }
217      
218  
219 < }
219 >  }
220  
221 < int DataStorage::getStorageLayout() {
221 >  int DataStorage::getStorageLayout() {
222      return storageLayout_;
223 < }
223 >  }
224  
225 < void DataStorage::setStorageLayout(int layout) {
225 >  void DataStorage::setStorageLayout(int layout) {
226      storageLayout_ = layout;
227      resize(size_);
228 < }
228 >  }
229  
230 < double* DataStorage::getArrayPointer(int whichArray) {
230 >  RealType* DataStorage::getArrayPointer(int whichArray) {
231  
232      switch (whichArray) {
233 <        case dslPosition:
234 <            return internalGetArrayPointer(torque);
235 <            break;
233 >    case dslPosition:
234 >      return internalGetArrayPointer(position);
235 >      break;
236              
237 <        case dslVelocity:
238 <            return internalGetArrayPointer(velocity);
239 <            break;
237 >    case dslVelocity:
238 >      return internalGetArrayPointer(velocity);
239 >      break;
240              
241 <        case dslAmat:
242 <            return internalGetArrayPointer(aMat);
243 <            break;            
241 >    case dslAmat:
242 >      return internalGetArrayPointer(aMat);
243 >      break;            
244              
245 <        case dslAngularMomentum:
246 <            return internalGetArrayPointer(angularMomentum);
247 <            break;
245 >    case dslAngularMomentum:
246 >      return internalGetArrayPointer(angularMomentum);
247 >      break;
248              
249 <        case dslUnitVector:
250 <            return internalGetArrayPointer(unitVector);
251 <            break;
249 >    case dslElectroFrame:
250 >      return internalGetArrayPointer(electroFrame);
251 >      break;
252              
253 <        case dslZAngle:
254 <            return internalGetArrayPointer(zAngle);
255 <            break;
253 >    case dslZAngle:
254 >      return internalGetArrayPointer(zAngle);
255 >      break;
256  
257 <        case dslForce:
258 <            return internalGetArrayPointer(force);
259 <            break;            
257 >    case dslForce:
258 >      return internalGetArrayPointer(force);
259 >      break;            
260  
261 <        case dslTorque:
262 <            return internalGetArrayPointer(torque);
263 <            break;  
261 >    case dslTorque:
262 >      return internalGetArrayPointer(torque);
263 >      break;  
264              
265 <        default:
266 <            //error message
267 <            return NULL;
265 >    default:
266 >      //error message
267 >      return NULL;
268  
269      }
270 < }    
270 >  }    
271  
272 < double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
272 >  RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
273      if (v.size() == 0) {
274 <        return NULL;
274 >      return NULL;
275      } else {
276 <        return v[0].getArrayPointer();
276 >      return v[0].getArrayPointer();
277      }
278 < }
278 >  }
279  
280 < double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
280 >  RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
281      if (v.size() == 0) {
282 <        return NULL;
282 >      return NULL;
283      } else {
284 <        return v[0].getArrayPointer();
284 >      return v[0].getArrayPointer();
285      }
286  
287 < }
287 >  }
288  
289 < double* DataStorage::internalGetArrayPointer(std::vector<double>& v) {
289 >  RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
290      if (v.size() == 0) {
291 <        return NULL;
291 >      return NULL;
292      } else {
293 <        return &(v[0]);
293 >      return &(v[0]);
294      }
295  
296 < }    
296 >  }    
297  
298 < template<typename T>
299 < void DataStorage::internalResize(std::vector<T>& v, int newSize){
298 >  template<typename T>
299 >  void DataStorage::internalResize(std::vector<T>& v, int newSize){
300      int oldSize = v.size();
301  
302      if (oldSize == newSize) {
303 <        return;
303 >      return;
304      } else if (oldSize < newSize) {
305 <        v.insert(v.end(), newSize-oldSize, T());
305 >      v.insert(v.end(), newSize-oldSize, T());
306      } else {
307 <        typename std::vector<T>::iterator i;
308 <        i = v.begin();
309 <        std::advance(i, newSize);        
310 <        v.erase(i, v.end());
307 >      typename std::vector<T>::iterator i;
308 >      i = v.begin();
309 >      std::advance(i, newSize);        
310 >      v.erase(i, v.end());
311      }
312 < }
312 >  }
313  
314 < template<typename T>
315 < void DataStorage::interalCopy(std::vector<T>& v, int source,  int num, int target) {
314 >  template<typename T>
315 >  void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
316      typename std::vector<T>::iterator first;
317      typename std::vector<T>::iterator last;
318      typename std::vector<T>::iterator result;
# Line 310 | Line 327 | void DataStorage::interalCopy(std::vector<T>& v, int s
327      std::advance(result, target );
328  
329      std::copy(first, last, result);
330 +  }
331 +
332 +  int DataStorage::getBytesPerStuntDouble(int layout) {
333 +    int bytes = 0;
334 +    if (layout & dslPosition) {
335 +      bytes += sizeof(Vector3d);
336 +    }
337 +    if (layout & dslVelocity) {
338 +      bytes += sizeof(Vector3d);
339 +    }
340 +    if (layout & dslAmat) {
341 +      bytes += sizeof(Mat3x3d);    
342 +    }
343 +    if (layout & dslAngularMomentum) {
344 +      bytes += sizeof(Vector3d);
345 +    }
346 +    if (layout & dslElectroFrame) {
347 +      bytes += sizeof(Mat3x3d);
348 +    }
349 +    if (layout & dslZAngle) {
350 +      bytes += sizeof(Vector3d);
351 +    }
352 +    if (layout & dslForce) {
353 +      bytes += sizeof(Vector3d);
354 +    }
355 +    if (layout & dslTorque) {
356 +      bytes += sizeof(Vector3d);
357 +    }
358 +    return bytes;
359 +  }
360 +
361   }

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