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root/OpenMD/trunk/src/brains/DataStorage.cpp
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Comparing trunk/src/brains/DataStorage.cpp (file contents):
Revision 1104 by gezelter, Fri Dec 29 21:43:18 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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 <
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    }
# Line 140 | Line 144 | namespace oopse {
144        internalResize(torque, newSize);
145      }
146  
147 +    if (storageLayout_ & dslParticlePot) {
148 +      internalResize(particlePot, newSize);
149 +    }
150 +
151      size_ = newSize;
152    }
153  
# Line 175 | Line 183 | namespace oopse {
183      if (storageLayout_ & dslTorque) {
184        torque.reserve(size);
185      }
186 +    
187 +    if (storageLayout_ & dslParticlePot) {
188 +      particlePot.reserve(size);
189 +    }
190  
191    }
192  
# Line 213 | Line 225 | namespace oopse {
225  
226      if (storageLayout_ & dslTorque) {
227        internalCopy(torque, source, num, target);
228 +    }
229 +
230 +    if (storageLayout_ & dslParticlePot) {
231 +      internalCopy(particlePot, source, num, target);
232      }
233      
234  
# Line 261 | Line 277 | namespace oopse {
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
# Line 338 | Line 358 | namespace oopse {
358        bytes += sizeof(Vector3d);
359      }
360      if (layout & dslAmat) {
361 <      bytes += sizeof(Mat3x3d);    
361 >      bytes += sizeof(RotMat3x3d);    
362      }
363      if (layout & dslAngularMomentum) {
364        bytes += sizeof(Vector3d);
# Line 347 | Line 367 | namespace oopse {
367        bytes += sizeof(Mat3x3d);
368      }
369      if (layout & dslZAngle) {
370 <      bytes += sizeof(Vector3d);
370 >      bytes += sizeof(RealType);
371      }
372      if (layout & dslForce) {
373        bytes += sizeof(Vector3d);
# Line 355 | Line 375 | namespace oopse {
375      if (layout & dslTorque) {
376        bytes += sizeof(Vector3d);
377      }
378 +    if (layout & dslParticlePot) {
379 +      bytes += sizeof(RealType);
380 +    }
381      return bytes;
382    }
383  

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