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Comparing trunk/src/brains/DataStorage.cpp (file contents):
Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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  
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 {
52 > namespace OpenMD {
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_ & dslElectroFrame && electroFrame.size() != size_) {
86 <        //error
87 <        std::cerr << "size does not match"<< std::endl;        
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 <
104 >    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
105 >      //error
106 >      std::cerr << "size does not match"<< std::endl;        
107 >    }
108 >    
109      return size_;
110  
111 < }
111 >  }
112  
113 < void DataStorage::resize(int newSize) {
113 >  void DataStorage::resize(int newSize) {
114  
115      if (storageLayout_ & dslPosition) {
116 <        internalResize(position, newSize);
116 >      internalResize(position, newSize);
117      }
118  
119      if (storageLayout_ & dslVelocity) {
120 <        internalResize(velocity, newSize);
120 >      internalResize(velocity, newSize);
121      }
122  
123      if (storageLayout_ & dslAmat) {
124 <        internalResize(aMat, newSize);
124 >      internalResize(aMat, newSize);
125      }
126  
127      if (storageLayout_ & dslAngularMomentum) {
128 <        internalResize(angularMomentum, newSize);
128 >      internalResize(angularMomentum, newSize);
129      }
130  
131      if (storageLayout_ & dslElectroFrame) {
132 <        internalResize(electroFrame, newSize);
132 >      internalResize(electroFrame, newSize);
133      }
134      
135      if (storageLayout_ & dslZAngle) {
136 <        internalResize(zAngle, newSize);
136 >      internalResize(zAngle, newSize);
137      }
138  
139      if (storageLayout_ & dslForce) {
140 <        internalResize(force, newSize);
140 >      internalResize(force, newSize);
141      }
142  
143      if (storageLayout_ & dslTorque) {
144 <        internalResize(torque, newSize);
144 >      internalResize(torque, newSize);
145      }
146  
147 +    if (storageLayout_ & dslParticlePot) {
148 +      internalResize(particlePot, newSize);
149 +    }
150 +
151      size_ = newSize;
152 < }
152 >  }
153  
154 < void DataStorage::reserve(int size) {
154 >  void DataStorage::reserve(int size) {
155      if (storageLayout_ & dslPosition) {
156 <        position.reserve(size);
156 >      position.reserve(size);
157      }
158  
159      if (storageLayout_ & dslVelocity) {
160 <        velocity.reserve(size);
160 >      velocity.reserve(size);
161      }
162  
163      if (storageLayout_ & dslAmat) {
164 <        aMat.reserve(size);
164 >      aMat.reserve(size);
165      }
166  
167      if (storageLayout_ & dslAngularMomentum) {
168 <        angularMomentum.reserve(size);
168 >      angularMomentum.reserve(size);
169      }
170  
171      if (storageLayout_ & dslElectroFrame) {
172 <        electroFrame.reserve(size);
172 >      electroFrame.reserve(size);
173      }
174      
175      if (storageLayout_ & dslZAngle) {
176 <        zAngle.reserve(size);
176 >      zAngle.reserve(size);
177      }
178  
179      if (storageLayout_ & dslForce) {
180 <        force.reserve(size);
180 >      force.reserve(size);
181      }
182  
183      if (storageLayout_ & dslTorque) {
184 <        torque.reserve(size);
184 >      torque.reserve(size);
185      }
186 +    
187 +    if (storageLayout_ & dslParticlePot) {
188 +      particlePot.reserve(size);
189 +    }
190  
191 < }
191 >  }
192  
193 < void DataStorage::copy(int source, int num, int target) {
193 >  void DataStorage::copy(int source, int num, int target) {
194      if (num + target > size_ ) {
195 <        //error
195 >      //error
196      }
197      
198      if (storageLayout_ & dslPosition) {
199 <        internalCopy(position, source, num, target);
199 >      internalCopy(position, source, num, target);
200      }
201  
202      if (storageLayout_ & dslVelocity) {
203 <        internalCopy(velocity, source, num, target);
204 <  }
203 >      internalCopy(velocity, source, num, target);
204 >    }
205  
206      if (storageLayout_ & dslAmat) {
207 <        internalCopy(aMat, source, num, target);
208 <   }
207 >      internalCopy(aMat, source, num, target);
208 >    }
209  
210      if (storageLayout_ & dslAngularMomentum) {
211 <        internalCopy(angularMomentum, source, num, target);
211 >      internalCopy(angularMomentum, source, num, target);
212      }
213  
214      if (storageLayout_ & dslElectroFrame) {
215 <        internalCopy(electroFrame, source, num, target);
215 >      internalCopy(electroFrame, source, num, target);
216      }
217      
218      if (storageLayout_ & dslZAngle) {
219 <        internalCopy(zAngle, source, num, target);
219 >      internalCopy(zAngle, source, num, target);
220      }
221  
222      if (storageLayout_ & dslForce) {
223 <        internalCopy(force, source, num, target);
223 >      internalCopy(force, source, num, target);
224      }
225  
226      if (storageLayout_ & dslTorque) {
227 <        internalCopy(torque, source, num, target);
227 >      internalCopy(torque, source, num, target);
228      }
229 +
230 +    if (storageLayout_ & dslParticlePot) {
231 +      internalCopy(particlePot, source, num, target);
232 +    }
233      
234  
235 < }
235 >  }
236  
237 < int DataStorage::getStorageLayout() {
237 >  int DataStorage::getStorageLayout() {
238      return storageLayout_;
239 < }
239 >  }
240  
241 < void DataStorage::setStorageLayout(int layout) {
241 >  void DataStorage::setStorageLayout(int layout) {
242      storageLayout_ = layout;
243      resize(size_);
244 < }
244 >  }
245  
246 < double* DataStorage::getArrayPointer(int whichArray) {
246 >  RealType* DataStorage::getArrayPointer(int whichArray) {
247  
248      switch (whichArray) {
249 <        case dslPosition:
250 <            return internalGetArrayPointer(position);
251 <            break;
249 >    case dslPosition:
250 >      return internalGetArrayPointer(position);
251 >      break;
252              
253 <        case dslVelocity:
254 <            return internalGetArrayPointer(velocity);
255 <            break;
240 <            
241 <        case dslAmat:
242 <            return internalGetArrayPointer(aMat);
243 <            break;            
253 >    case dslVelocity:
254 >      return internalGetArrayPointer(velocity);
255 >      break;
256              
257 <        case dslAngularMomentum:
258 <            return internalGetArrayPointer(angularMomentum);
259 <            break;
257 >    case dslAmat:
258 >      return internalGetArrayPointer(aMat);
259 >      break;            
260              
261 <        case dslElectroFrame:
262 <            return internalGetArrayPointer(electroFrame);
263 <            break;
261 >    case dslAngularMomentum:
262 >      return internalGetArrayPointer(angularMomentum);
263 >      break;
264              
265 <        case dslZAngle:
266 <            return internalGetArrayPointer(zAngle);
267 <            break;
265 >    case dslElectroFrame:
266 >      return internalGetArrayPointer(electroFrame);
267 >      break;
268 >            
269 >    case dslZAngle:
270 >      return internalGetArrayPointer(zAngle);
271 >      break;
272  
273 <        case dslForce:
274 <            return internalGetArrayPointer(force);
275 <            break;            
273 >    case dslForce:
274 >      return internalGetArrayPointer(force);
275 >      break;            
276  
277 <        case dslTorque:
278 <            return internalGetArrayPointer(torque);
279 <            break;  
277 >    case dslTorque:
278 >      return internalGetArrayPointer(torque);
279 >      break;
280 >
281 >    case dslParticlePot:
282 >      return internalGetArrayPointer(particlePot);
283 >      break;
284              
285 <        default:
286 <            //error message
287 <            return NULL;
285 >    default:
286 >      //error message
287 >      return NULL;
288  
289      }
290 < }    
290 >  }    
291  
292 < double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
292 >  RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
293      if (v.size() == 0) {
294 <        return NULL;
294 >      return NULL;
295      } else {
296 <        return v[0].getArrayPointer();
296 >      return v[0].getArrayPointer();
297      }
298 < }
298 >  }
299  
300 < double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
300 >  RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
301      if (v.size() == 0) {
302 <        return NULL;
302 >      return NULL;
303      } else {
304 <        return v[0].getArrayPointer();
304 >      return v[0].getArrayPointer();
305      }
306  
307 < }
307 >  }
308  
309 < double* DataStorage::internalGetArrayPointer(std::vector<double>& v) {
309 >  RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
310      if (v.size() == 0) {
311 <        return NULL;
311 >      return NULL;
312      } else {
313 <        return &(v[0]);
313 >      return &(v[0]);
314      }
315  
316 < }    
316 >  }    
317  
318 < template<typename T>
319 < void DataStorage::internalResize(std::vector<T>& v, int newSize){
318 >  template<typename T>
319 >  void DataStorage::internalResize(std::vector<T>& v, int newSize){
320      int oldSize = v.size();
321  
322      if (oldSize == newSize) {
323 <        return;
323 >      return;
324      } else if (oldSize < newSize) {
325 <        v.insert(v.end(), newSize-oldSize, T());
325 >      v.insert(v.end(), newSize-oldSize, T());
326      } else {
327 <        typename std::vector<T>::iterator i;
328 <        i = v.begin();
329 <        std::advance(i, newSize);        
330 <        v.erase(i, v.end());
327 >      typename std::vector<T>::iterator i;
328 >      i = v.begin();
329 >      std::advance(i, newSize);        
330 >      v.erase(i, v.end());
331      }
332 < }
332 >  }
333  
334 < template<typename T>
335 < void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
334 >  template<typename T>
335 >  void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
336      typename std::vector<T>::iterator first;
337      typename std::vector<T>::iterator last;
338      typename std::vector<T>::iterator result;
# Line 327 | Line 347 | void DataStorage::internalCopy(std::vector<T>& v, int
347      std::advance(result, target );
348  
349      std::copy(first, last, result);
350 < }
350 >  }
351  
352 < int DataStorage::getBytesPerStuntDouble(int layout) {
352 >  int DataStorage::getBytesPerStuntDouble(int layout) {
353      int bytes = 0;
354      if (layout & dslPosition) {
355 <        bytes += sizeof(Vector3d);
336 <    } else if (layout & dslVelocity) {
337 <        bytes += sizeof(Vector3d);
338 <    } else if (layout & dslAmat) {
339 <        bytes += sizeof(Mat3x3d);    
340 <    } else if (layout & dslAngularMomentum) {
341 <        bytes += sizeof(Vector3d);
342 <    } else if (layout & dslElectroFrame) {
343 <        bytes += sizeof(Mat3x3d);
344 <    } else if (layout & dslZAngle) {
345 <        bytes += sizeof(Vector3d);
346 <    } else if (layout & dslForce) {
347 <        bytes += sizeof(Vector3d);
348 <    } else if (layout & dslTorque) {
349 <        bytes += sizeof(Vector3d);
355 >      bytes += sizeof(Vector3d);
356      }
357 +    if (layout & dslVelocity) {
358 +      bytes += sizeof(Vector3d);
359 +    }
360 +    if (layout & dslAmat) {
361 +      bytes += sizeof(RotMat3x3d);    
362 +    }
363 +    if (layout & dslAngularMomentum) {
364 +      bytes += sizeof(Vector3d);
365 +    }
366 +    if (layout & dslElectroFrame) {
367 +      bytes += sizeof(Mat3x3d);
368 +    }
369 +    if (layout & dslZAngle) {
370 +      bytes += sizeof(RealType);
371 +    }
372 +    if (layout & dslForce) {
373 +      bytes += sizeof(Vector3d);
374 +    }
375 +    if (layout & dslTorque) {
376 +      bytes += sizeof(Vector3d);
377 +    }
378 +    if (layout & dslParticlePot) {
379 +      bytes += sizeof(RealType);
380 +    }
381      return bytes;
382 < }
382 >  }
383  
384   }

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