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Comparing:
trunk/src/brains/DataStorage.cpp (file contents), Revision 1245 by chuckv, Tue May 27 16:39:06 2008 UTC vs.
branches/development/src/brains/DataStorage.cpp (file contents), Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

# 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   /**
# Line 49 | Line 49
49  
50   #include "brains/DataStorage.hpp"
51  
52 < namespace oopse {
52 > namespace OpenMD {
53  
54    DataStorage::DataStorage() : size_(0), storageLayout_(0){
55  
# Line 101 | Line 101 | namespace oopse {
101        //error
102        std::cerr << "size does not match"<< std::endl;        
103      }
104 +
105      if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
106        //error
107        std::cerr << "size does not match"<< std::endl;        
108      }
109 +
110 +    if (storageLayout_ & dslDensity && density.size() != size_) {
111 +      //error
112 +      std::cerr << "size does not match"<< std::endl;        
113 +    }
114 +
115 +    if (storageLayout_ & dslFunctional && functional.size() != size_) {
116 +      //error
117 +      std::cerr << "size does not match"<< std::endl;        
118 +    }
119 +
120 +    if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
121 +      //error
122 +      std::cerr << "size does not match"<< std::endl;        
123 +    }
124 +
125 +    if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126 +      //error
127 +      std::cerr << "size does not match"<< std::endl;        
128 +    }
129      
130      return size_;
131  
# Line 148 | Line 169 | namespace oopse {
169        internalResize(particlePot, newSize);
170      }
171  
172 +    if (storageLayout_ & dslDensity) {
173 +      internalResize(density, newSize);
174 +    }
175 +
176 +    if (storageLayout_ & dslFunctional) {
177 +      internalResize(functional, newSize);
178 +    }
179 +
180 +    if (storageLayout_ & dslFunctionalDerivative) {
181 +      internalResize(functionalDerivative, newSize);
182 +    }
183 +
184 +    if (storageLayout_ & dslElectricField) {
185 +      internalResize(electricField, newSize);
186 +    }
187 +
188      size_ = newSize;
189    }
190  
# Line 186 | Line 223 | namespace oopse {
223      
224      if (storageLayout_ & dslParticlePot) {
225        particlePot.reserve(size);
226 +    }
227 +
228 +    if (storageLayout_ & dslDensity) {
229 +      density.reserve(size);
230      }
231  
232 +    if (storageLayout_ & dslFunctional) {
233 +      functional.reserve(size);
234 +    }
235 +
236 +    if (storageLayout_ & dslFunctionalDerivative) {
237 +      functionalDerivative.reserve(size);
238 +    }
239 +
240 +    if (storageLayout_ & dslElectricField) {
241 +      electricField.reserve(size);
242 +    }
243 +
244    }
245  
246    void DataStorage::copy(int source, int num, int target) {
# Line 230 | Line 283 | namespace oopse {
283      if (storageLayout_ & dslParticlePot) {
284        internalCopy(particlePot, source, num, target);
285      }
233 –    
286  
287 +    if (storageLayout_ & dslDensity) {
288 +      internalCopy(density, source, num, target);
289 +    }
290 +
291 +    if (storageLayout_ & dslFunctional) {
292 +      internalCopy(functional, source, num, target);
293 +    }
294 +
295 +    if (storageLayout_ & dslFunctionalDerivative) {
296 +      internalCopy(functionalDerivative, source, num, target);
297 +    }
298 +
299 +    if (storageLayout_ & dslElectricField) {
300 +      internalCopy(electricField, source, num, target);
301 +    }
302    }
303  
304    int DataStorage::getStorageLayout() {
# Line 281 | Line 348 | namespace oopse {
348      case dslParticlePot:
349        return internalGetArrayPointer(particlePot);
350        break;
351 <            
351 >
352 >    case dslDensity:
353 >      return internalGetArrayPointer(density);
354 >      break;
355 >
356 >    case dslFunctional:
357 >      return internalGetArrayPointer(functional);
358 >      break;
359 >
360 >    case dslFunctionalDerivative:
361 >      return internalGetArrayPointer(functionalDerivative);
362 >      break;
363 >
364 >    case dslElectricField:
365 >      return internalGetArrayPointer(electricField);
366 >      break;
367 >          
368      default:
369        //error message
370        return NULL;
# Line 378 | Line 461 | namespace oopse {
461      if (layout & dslParticlePot) {
462        bytes += sizeof(RealType);
463      }
464 +    if (layout & dslDensity) {
465 +      bytes += sizeof(RealType);
466 +    }
467 +    if (layout & dslFunctional) {
468 +      bytes += sizeof(RealType);
469 +    }
470 +    if (layout & dslFunctionalDerivative) {
471 +      bytes += sizeof(RealType);
472 +    }
473 +    if (layout & dslElectricField) {
474 +      bytes += sizeof(Vector3d);
475 +    }
476 +
477      return bytes;
478    }
479  

Comparing:
trunk/src/brains/DataStorage.cpp (property svn:keywords), Revision 1245 by chuckv, Tue May 27 16:39:06 2008 UTC vs.
branches/development/src/brains/DataStorage.cpp (property svn:keywords), Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

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