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Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
44   * @file DataStorage.cpp
45   * @author tlin
46   * @date 10/26/2004
46 – * @time 11:56am
47   * @version 1.0
48   */
49  
50   #include "brains/DataStorage.hpp"
51 <
51 > using namespace std;
52   namespace OpenMD {
53  
54    DataStorage::DataStorage() : size_(0), storageLayout_(0){
# Line 64 | Line 64 | namespace OpenMD {
64  
65      if (storageLayout_ & dslPosition && position.size() != size_) {
66        //error
67 <      std::cerr << "size does not match"<< std::endl;
67 >      cerr << "size does not match"<< endl;
68      }
69  
70      if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71        //error
72 <      std::cerr << "size does not match"<< std::endl;        
72 >      cerr << "size does not match"<< endl;        
73      }
74  
75 <    if (storageLayout_ & dslAmat && aMat.size() != size_) {
75 >    if (storageLayout_ & dslForce && force.size() != size_) {
76        //error
77 <      std::cerr << "size does not match"<< std::endl;        
77 >      cerr << "size does not match"<< endl;        
78      }
79  
80 <    if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
80 >    if (storageLayout_ & dslAmat && aMat.size() != size_) {
81        //error
82 <      std::cerr << "size does not match"<< std::endl;        
82 >      cerr << "size does not match"<< endl;        
83      }
84  
85 <    if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
85 >    if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
86        //error
87 <      std::cerr << "size does not match"<< std::endl;        
87 >      cerr << "size does not match"<< endl;        
88      }
89  
90 <    if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
90 >    if (storageLayout_ & dslTorque && torque.size() != size_) {
91        //error
92 <      std::cerr << "size does not match"<< std::endl;        
92 >      cerr << "size does not match"<< endl;        
93      }
94  
95 <    if (storageLayout_ & dslForce && force.size() != size_) {
95 >    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
96        //error
97 <      std::cerr << "size does not match"<< std::endl;        
97 >      cerr << "size does not match"<< endl;        
98      }
99  
100 <    if (storageLayout_ & dslTorque && torque.size() != size_) {
100 >    if (storageLayout_ & dslDensity && density.size() != size_) {
101        //error
102 <      std::cerr << "size does not match"<< std::endl;        
102 >      cerr << "size does not match"<< endl;        
103      }
104  
105 <    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
105 >    if (storageLayout_ & dslFunctional && functional.size() != size_) {
106        //error
107 <      std::cerr << "size does not match"<< std::endl;        
107 >      cerr << "size does not match"<< endl;        
108      }
109  
110 <    if (storageLayout_ & dslDensity && density.size() != size_) {
110 >    if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
111        //error
112 <      std::cerr << "size does not match"<< std::endl;        
112 >      cerr << "size does not match"<< endl;        
113      }
114  
115 <    if (storageLayout_ & dslFunctional && functional.size() != size_) {
115 >    if (storageLayout_ & dslDipole && dipole.size() != size_) {
116        //error
117 <      std::cerr << "size does not match"<< std::endl;        
117 >      cerr << "size does not match"<< endl;        
118      }
119  
120 <    if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
120 >    if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
121        //error
122 <      std::cerr << "size does not match"<< std::endl;        
122 >      cerr << "size does not match"<< endl;        
123      }
124  
125      if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126        //error
127 <      std::cerr << "size does not match"<< std::endl;        
127 >      cerr << "size does not match"<< endl;        
128      }
129  
130      if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
131        //error
132 <      std::cerr << "size does not match"<< std::endl;        
132 >      cerr << "size does not match"<< endl;        
133      }
134 +
135 +    if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
136 +      //error
137 +      cerr << "size does not match"<< endl;        
138 +    }
139 +
140 +    if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
141 +      //error
142 +      cerr << "size does not match"<< endl;        
143 +    }
144 +
145 +    if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
146 +      //error
147 +      cerr << "size does not match"<< endl;        
148 +    }
149      
150      return size_;
151  
# Line 146 | Line 161 | namespace OpenMD {
161        internalResize(velocity, newSize);
162      }
163  
164 +    if (storageLayout_ & dslForce) {
165 +      internalResize(force, newSize);
166 +    }
167 +
168      if (storageLayout_ & dslAmat) {
169        internalResize(aMat, newSize);
170      }
# Line 153 | Line 172 | namespace OpenMD {
172      if (storageLayout_ & dslAngularMomentum) {
173        internalResize(angularMomentum, newSize);
174      }
156 –
157 –    if (storageLayout_ & dslElectroFrame) {
158 –      internalResize(electroFrame, newSize);
159 –    }
175      
161 –    if (storageLayout_ & dslZAngle) {
162 –      internalResize(zAngle, newSize);
163 –    }
164 –
165 –    if (storageLayout_ & dslForce) {
166 –      internalResize(force, newSize);
167 –    }
168 –
176      if (storageLayout_ & dslTorque) {
177        internalResize(torque, newSize);
178      }
# Line 186 | Line 193 | namespace OpenMD {
193        internalResize(functionalDerivative, newSize);
194      }
195  
196 +    if (storageLayout_ & dslDipole) {
197 +      internalResize(dipole, newSize);
198 +    }
199 +
200 +    if (storageLayout_ & dslQuadrupole) {
201 +      internalResize(quadrupole, newSize);
202 +    }
203 +
204      if (storageLayout_ & dslElectricField) {
205        internalResize(electricField, newSize);
206      }
# Line 194 | Line 209 | namespace OpenMD {
209        internalResize(skippedCharge, newSize);
210      }
211  
212 +    if (storageLayout_ & dslFlucQPosition) {
213 +      internalResize(flucQPos, newSize);
214 +    }
215 +
216 +    if (storageLayout_ & dslFlucQVelocity) {
217 +      internalResize(flucQVel, newSize);
218 +    }
219 +
220 +    if (storageLayout_ & dslFlucQForce) {
221 +      internalResize(flucQFrc, newSize);
222 +    }
223 +
224      size_ = newSize;
225    }
226  
# Line 206 | Line 233 | namespace OpenMD {
233        velocity.reserve(size);
234      }
235  
236 +    if (storageLayout_ & dslForce) {
237 +      force.reserve(size);
238 +    }
239 +
240      if (storageLayout_ & dslAmat) {
241        aMat.reserve(size);
242      }
243  
244      if (storageLayout_ & dslAngularMomentum) {
245        angularMomentum.reserve(size);
215 –    }
216 –
217 –    if (storageLayout_ & dslElectroFrame) {
218 –      electroFrame.reserve(size);
219 –    }
220 –    
221 –    if (storageLayout_ & dslZAngle) {
222 –      zAngle.reserve(size);
223 –    }
224 –
225 –    if (storageLayout_ & dslForce) {
226 –      force.reserve(size);
246      }
247  
248      if (storageLayout_ & dslTorque) {
# Line 246 | Line 265 | namespace OpenMD {
265        functionalDerivative.reserve(size);
266      }
267  
268 +    if (storageLayout_ & dslDipole) {
269 +      dipole.reserve(size);
270 +    }
271 +
272 +    if (storageLayout_ & dslQuadrupole) {
273 +      quadrupole.reserve(size);
274 +    }
275 +
276      if (storageLayout_ & dslElectricField) {
277        electricField.reserve(size);
278      }
# Line 254 | Line 281 | namespace OpenMD {
281        skippedCharge.reserve(size);
282      }
283  
284 +    if (storageLayout_ & dslFlucQPosition) {
285 +      flucQPos.reserve(size);
286 +    }
287 +
288 +    if (storageLayout_ & dslFlucQVelocity) {
289 +      flucQVel.reserve(size);
290 +    }
291 +
292 +    if (storageLayout_ & dslFlucQForce) {
293 +      flucQFrc.reserve(size);
294 +    }
295    }
296  
297    void DataStorage::copy(int source, int num, int target) {
# Line 269 | Line 307 | namespace OpenMD {
307        internalCopy(velocity, source, num, target);
308      }
309  
310 +    if (storageLayout_ & dslForce) {
311 +      internalCopy(force, source, num, target);
312 +    }
313 +
314      if (storageLayout_ & dslAmat) {
315        internalCopy(aMat, source, num, target);
316      }
# Line 277 | Line 319 | namespace OpenMD {
319        internalCopy(angularMomentum, source, num, target);
320      }
321  
280 –    if (storageLayout_ & dslElectroFrame) {
281 –      internalCopy(electroFrame, source, num, target);
282 –    }
283 –    
284 –    if (storageLayout_ & dslZAngle) {
285 –      internalCopy(zAngle, source, num, target);
286 –    }
287 –
288 –    if (storageLayout_ & dslForce) {
289 –      internalCopy(force, source, num, target);
290 –    }
291 –
322      if (storageLayout_ & dslTorque) {
323        internalCopy(torque, source, num, target);
324      }
# Line 309 | Line 339 | namespace OpenMD {
339        internalCopy(functionalDerivative, source, num, target);
340      }
341  
342 +    if (storageLayout_ & dslDipole) {
343 +      internalCopy(dipole, source, num, target);
344 +    }
345 +
346 +    if (storageLayout_ & dslQuadrupole) {
347 +      internalCopy(quadrupole, source, num, target);
348 +    }
349 +
350      if (storageLayout_ & dslElectricField) {
351        internalCopy(electricField, source, num, target);
352      }
# Line 316 | Line 354 | namespace OpenMD {
354      if (storageLayout_ & dslSkippedCharge) {
355        internalCopy(skippedCharge, source, num, target);
356      }
357 +
358 +    if (storageLayout_ & dslFlucQPosition) {
359 +      internalCopy(flucQPos, source, num, target);
360 +    }
361 +
362 +    if (storageLayout_ & dslFlucQVelocity) {
363 +      internalCopy(flucQVel, source, num, target);
364 +    }
365 +    if (storageLayout_ & dslFlucQForce) {
366 +      internalCopy(flucQFrc, source, num, target);
367 +    }
368    }
369  
370    int DataStorage::getStorageLayout() {
# Line 338 | Line 387 | namespace OpenMD {
387        return internalGetArrayPointer(velocity);
388        break;
389              
390 +    case dslForce:
391 +      return internalGetArrayPointer(force);
392 +      break;            
393 +
394      case dslAmat:
395        return internalGetArrayPointer(aMat);
396        break;            
# Line 346 | Line 399 | namespace OpenMD {
399        return internalGetArrayPointer(angularMomentum);
400        break;
401              
349 –    case dslElectroFrame:
350 –      return internalGetArrayPointer(electroFrame);
351 –      break;
352 –            
353 –    case dslZAngle:
354 –      return internalGetArrayPointer(zAngle);
355 –      break;
356 –
357 –    case dslForce:
358 –      return internalGetArrayPointer(force);
359 –      break;            
360 –
402      case dslTorque:
403        return internalGetArrayPointer(torque);
404        break;
# Line 378 | Line 419 | namespace OpenMD {
419        return internalGetArrayPointer(functionalDerivative);
420        break;
421  
422 +    case dslDipole:
423 +      return internalGetArrayPointer(dipole);
424 +      break;
425 +
426 +    case dslQuadrupole:
427 +      return internalGetArrayPointer(quadrupole);
428 +      break;
429 +
430      case dslElectricField:
431        return internalGetArrayPointer(electricField);
432        break;
# Line 385 | Line 434 | namespace OpenMD {
434      case dslSkippedCharge:
435        return internalGetArrayPointer(skippedCharge);
436        break;
437 +
438 +    case dslFlucQPosition:
439 +      return internalGetArrayPointer(flucQPos);
440 +      break;
441 +
442 +    case dslFlucQVelocity:
443 +      return internalGetArrayPointer(flucQVel);
444 +      break;
445            
446 +    case dslFlucQForce:
447 +      return internalGetArrayPointer(flucQFrc);
448 +      break;
449 +          
450      default:
451        //error message
452        return NULL;
# Line 401 | Line 462 | namespace OpenMD {
462      }
463    }
464  
465 <  RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
465 >  RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
466      if (v.size() == 0) {
467        return NULL;
468      } else {
# Line 461 | Line 522 | namespace OpenMD {
522      if (layout & dslVelocity) {
523        bytes += sizeof(Vector3d);
524      }
525 +    if (layout & dslForce) {
526 +      bytes += sizeof(Vector3d);
527 +    }
528      if (layout & dslAmat) {
529        bytes += sizeof(RotMat3x3d);    
530      }
531      if (layout & dslAngularMomentum) {
532        bytes += sizeof(Vector3d);
533      }
470 –    if (layout & dslElectroFrame) {
471 –      bytes += sizeof(Mat3x3d);
472 –    }
473 –    if (layout & dslZAngle) {
474 –      bytes += sizeof(RealType);
475 –    }
476 –    if (layout & dslForce) {
477 –      bytes += sizeof(Vector3d);
478 –    }
534      if (layout & dslTorque) {
535        bytes += sizeof(Vector3d);
536      }
# Line 491 | Line 546 | namespace OpenMD {
546      if (layout & dslFunctionalDerivative) {
547        bytes += sizeof(RealType);
548      }
549 +    if (layout & dslDipole) {
550 +      bytes += sizeof(Vector3d);
551 +    }
552 +    if (layout & dslQuadrupole) {
553 +      bytes += sizeof(Mat3x3d);
554 +    }
555      if (layout & dslElectricField) {
556        bytes += sizeof(Vector3d);
557      }
558      if (layout & dslSkippedCharge) {
559        bytes += sizeof(RealType);
560      }
561 +    if (layout & dslFlucQPosition) {
562 +      bytes += sizeof(RealType);
563 +    }
564 +    if (layout & dslFlucQVelocity) {
565 +      bytes += sizeof(RealType);
566 +    }
567 +    if (layout & dslFlucQForce) {
568 +      bytes += sizeof(RealType);
569 +    }
570  
571      return bytes;
572    }

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