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Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 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   /**
# Line 48 | Line 49
49   */
50  
51   #include "brains/DataStorage.hpp"
52 <
52 > using namespace std;
53   namespace OpenMD {
54  
55    DataStorage::DataStorage() : size_(0), storageLayout_(0){
# Line 64 | Line 65 | namespace OpenMD {
65  
66      if (storageLayout_ & dslPosition && position.size() != size_) {
67        //error
68 <      std::cerr << "size does not match"<< std::endl;
68 >      cerr << "size does not match"<< endl;
69      }
70  
71      if (storageLayout_ & dslVelocity && velocity.size() != size_) {
72        //error
73 <      std::cerr << "size does not match"<< std::endl;        
73 >      cerr << "size does not match"<< endl;        
74      }
75  
76 <    if (storageLayout_ & dslAmat && aMat.size() != size_) {
76 >    if (storageLayout_ & dslForce && force.size() != size_) {
77        //error
78 <      std::cerr << "size does not match"<< std::endl;        
78 >      cerr << "size does not match"<< endl;        
79      }
80  
81 <    if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
81 >    if (storageLayout_ & dslAmat && aMat.size() != size_) {
82        //error
83 <      std::cerr << "size does not match"<< std::endl;        
83 >      cerr << "size does not match"<< endl;        
84      }
85  
86 <    if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
86 >    if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
87        //error
88 <      std::cerr << "size does not match"<< std::endl;        
88 >      cerr << "size does not match"<< endl;        
89      }
90  
91 <    if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
91 >    if (storageLayout_ & dslTorque && torque.size() != size_) {
92        //error
93 <      std::cerr << "size does not match"<< std::endl;        
93 >      cerr << "size does not match"<< endl;        
94      }
95  
96 <    if (storageLayout_ & dslForce && force.size() != size_) {
96 >    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
97        //error
98 <      std::cerr << "size does not match"<< std::endl;        
98 >      cerr << "size does not match"<< endl;        
99      }
100  
101 <    if (storageLayout_ & dslTorque && torque.size() != size_) {
101 >    if (storageLayout_ & dslDensity && density.size() != size_) {
102        //error
103 <      std::cerr << "size does not match"<< std::endl;        
103 >      cerr << "size does not match"<< endl;        
104      }
105  
106 <    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
106 >    if (storageLayout_ & dslFunctional && functional.size() != size_) {
107        //error
108 <      std::cerr << "size does not match"<< std::endl;        
108 >      cerr << "size does not match"<< endl;        
109      }
110  
111 <    if (storageLayout_ & dslDensity && density.size() != size_) {
111 >    if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
112        //error
113 <      std::cerr << "size does not match"<< std::endl;        
113 >      cerr << "size does not match"<< endl;        
114      }
115  
116 <    if (storageLayout_ & dslFunctional && functional.size() != size_) {
116 >    if (storageLayout_ & dslDipole && dipole.size() != size_) {
117        //error
118 <      std::cerr << "size does not match"<< std::endl;        
118 >      cerr << "size does not match"<< endl;        
119      }
120  
121 <    if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
121 >    if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
122        //error
123 <      std::cerr << "size does not match"<< std::endl;        
123 >      cerr << "size does not match"<< endl;        
124      }
125  
126      if (storageLayout_ & dslElectricField && electricField.size() != size_) {
127        //error
128 <      std::cerr << "size does not match"<< std::endl;        
128 >      cerr << "size does not match"<< endl;        
129      }
130  
131      if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
132        //error
133 <      std::cerr << "size does not match"<< std::endl;        
133 >      cerr << "size does not match"<< endl;        
134      }
135 +
136 +    if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
137 +      //error
138 +      cerr << "size does not match"<< endl;        
139 +    }
140 +
141 +    if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
142 +      //error
143 +      cerr << "size does not match"<< endl;        
144 +    }
145 +
146 +    if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
147 +      //error
148 +      cerr << "size does not match"<< endl;        
149 +    }
150      
151      return size_;
152  
# Line 146 | Line 162 | namespace OpenMD {
162        internalResize(velocity, newSize);
163      }
164  
165 +    if (storageLayout_ & dslForce) {
166 +      internalResize(force, newSize);
167 +    }
168 +
169      if (storageLayout_ & dslAmat) {
170        internalResize(aMat, newSize);
171      }
# Line 153 | Line 173 | namespace OpenMD {
173      if (storageLayout_ & dslAngularMomentum) {
174        internalResize(angularMomentum, newSize);
175      }
156 –
157 –    if (storageLayout_ & dslElectroFrame) {
158 –      internalResize(electroFrame, newSize);
159 –    }
176      
161 –    if (storageLayout_ & dslZAngle) {
162 –      internalResize(zAngle, newSize);
163 –    }
164 –
165 –    if (storageLayout_ & dslForce) {
166 –      internalResize(force, newSize);
167 –    }
168 –
177      if (storageLayout_ & dslTorque) {
178        internalResize(torque, newSize);
179      }
# Line 186 | Line 194 | namespace OpenMD {
194        internalResize(functionalDerivative, newSize);
195      }
196  
197 +    if (storageLayout_ & dslDipole) {
198 +      internalResize(dipole, newSize);
199 +    }
200 +
201 +    if (storageLayout_ & dslQuadrupole) {
202 +      internalResize(quadrupole, newSize);
203 +    }
204 +
205      if (storageLayout_ & dslElectricField) {
206        internalResize(electricField, newSize);
207      }
# Line 194 | Line 210 | namespace OpenMD {
210        internalResize(skippedCharge, newSize);
211      }
212  
213 +    if (storageLayout_ & dslFlucQPosition) {
214 +      internalResize(flucQPos, newSize);
215 +    }
216 +
217 +    if (storageLayout_ & dslFlucQVelocity) {
218 +      internalResize(flucQVel, newSize);
219 +    }
220 +
221 +    if (storageLayout_ & dslFlucQForce) {
222 +      internalResize(flucQFrc, newSize);
223 +    }
224 +
225      size_ = newSize;
226    }
227  
# Line 206 | Line 234 | namespace OpenMD {
234        velocity.reserve(size);
235      }
236  
237 +    if (storageLayout_ & dslForce) {
238 +      force.reserve(size);
239 +    }
240 +
241      if (storageLayout_ & dslAmat) {
242        aMat.reserve(size);
243      }
# Line 214 | Line 246 | namespace OpenMD {
246        angularMomentum.reserve(size);
247      }
248  
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);
227 –    }
228 –
249      if (storageLayout_ & dslTorque) {
250        torque.reserve(size);
251      }
# Line 246 | Line 266 | namespace OpenMD {
266        functionalDerivative.reserve(size);
267      }
268  
269 +    if (storageLayout_ & dslDipole) {
270 +      dipole.reserve(size);
271 +    }
272 +
273 +    if (storageLayout_ & dslQuadrupole) {
274 +      quadrupole.reserve(size);
275 +    }
276 +
277      if (storageLayout_ & dslElectricField) {
278        electricField.reserve(size);
279      }
# Line 254 | Line 282 | namespace OpenMD {
282        skippedCharge.reserve(size);
283      }
284  
285 +    if (storageLayout_ & dslFlucQPosition) {
286 +      flucQPos.reserve(size);
287 +    }
288 +
289 +    if (storageLayout_ & dslFlucQVelocity) {
290 +      flucQVel.reserve(size);
291 +    }
292 +
293 +    if (storageLayout_ & dslFlucQForce) {
294 +      flucQFrc.reserve(size);
295 +    }
296    }
297  
298    void DataStorage::copy(int source, int num, int target) {
# Line 269 | Line 308 | namespace OpenMD {
308        internalCopy(velocity, source, num, target);
309      }
310  
311 +    if (storageLayout_ & dslForce) {
312 +      internalCopy(force, source, num, target);
313 +    }
314 +
315      if (storageLayout_ & dslAmat) {
316        internalCopy(aMat, source, num, target);
317      }
# Line 277 | Line 320 | namespace OpenMD {
320        internalCopy(angularMomentum, source, num, target);
321      }
322  
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 –
323      if (storageLayout_ & dslTorque) {
324        internalCopy(torque, source, num, target);
325      }
# Line 309 | Line 340 | namespace OpenMD {
340        internalCopy(functionalDerivative, source, num, target);
341      }
342  
343 +    if (storageLayout_ & dslDipole) {
344 +      internalCopy(dipole, source, num, target);
345 +    }
346 +
347 +    if (storageLayout_ & dslQuadrupole) {
348 +      internalCopy(quadrupole, source, num, target);
349 +    }
350 +
351      if (storageLayout_ & dslElectricField) {
352        internalCopy(electricField, source, num, target);
353      }
# Line 316 | Line 355 | namespace OpenMD {
355      if (storageLayout_ & dslSkippedCharge) {
356        internalCopy(skippedCharge, source, num, target);
357      }
358 +
359 +    if (storageLayout_ & dslFlucQPosition) {
360 +      internalCopy(flucQPos, source, num, target);
361 +    }
362 +
363 +    if (storageLayout_ & dslFlucQVelocity) {
364 +      internalCopy(flucQVel, source, num, target);
365 +    }
366 +    if (storageLayout_ & dslFlucQForce) {
367 +      internalCopy(flucQFrc, source, num, target);
368 +    }
369    }
370  
371    int DataStorage::getStorageLayout() {
# Line 338 | Line 388 | namespace OpenMD {
388        return internalGetArrayPointer(velocity);
389        break;
390              
391 +    case dslForce:
392 +      return internalGetArrayPointer(force);
393 +      break;            
394 +
395      case dslAmat:
396        return internalGetArrayPointer(aMat);
397        break;            
# Line 346 | Line 400 | namespace OpenMD {
400        return internalGetArrayPointer(angularMomentum);
401        break;
402              
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 –
403      case dslTorque:
404        return internalGetArrayPointer(torque);
405        break;
# Line 378 | Line 420 | namespace OpenMD {
420        return internalGetArrayPointer(functionalDerivative);
421        break;
422  
423 +    case dslDipole:
424 +      return internalGetArrayPointer(dipole);
425 +      break;
426 +
427 +    case dslQuadrupole:
428 +      return internalGetArrayPointer(quadrupole);
429 +      break;
430 +
431      case dslElectricField:
432        return internalGetArrayPointer(electricField);
433        break;
# Line 385 | Line 435 | namespace OpenMD {
435      case dslSkippedCharge:
436        return internalGetArrayPointer(skippedCharge);
437        break;
438 +
439 +    case dslFlucQPosition:
440 +      return internalGetArrayPointer(flucQPos);
441 +      break;
442 +
443 +    case dslFlucQVelocity:
444 +      return internalGetArrayPointer(flucQVel);
445 +      break;
446            
447 +    case dslFlucQForce:
448 +      return internalGetArrayPointer(flucQFrc);
449 +      break;
450 +          
451      default:
452        //error message
453        return NULL;
# Line 401 | Line 463 | namespace OpenMD {
463      }
464    }
465  
466 <  RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
466 >  RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
467      if (v.size() == 0) {
468        return NULL;
469      } else {
# Line 461 | Line 523 | namespace OpenMD {
523      if (layout & dslVelocity) {
524        bytes += sizeof(Vector3d);
525      }
526 +    if (layout & dslForce) {
527 +      bytes += sizeof(Vector3d);
528 +    }
529      if (layout & dslAmat) {
530        bytes += sizeof(RotMat3x3d);    
531      }
532      if (layout & dslAngularMomentum) {
533        bytes += sizeof(Vector3d);
534      }
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 –    }
535      if (layout & dslTorque) {
536        bytes += sizeof(Vector3d);
537      }
# Line 491 | Line 547 | namespace OpenMD {
547      if (layout & dslFunctionalDerivative) {
548        bytes += sizeof(RealType);
549      }
550 +    if (layout & dslDipole) {
551 +      bytes += sizeof(Vector3d);
552 +    }
553 +    if (layout & dslQuadrupole) {
554 +      bytes += sizeof(Mat3x3d);
555 +    }
556      if (layout & dslElectricField) {
557        bytes += sizeof(Vector3d);
558      }
559      if (layout & dslSkippedCharge) {
560        bytes += sizeof(RealType);
561      }
562 +    if (layout & dslFlucQPosition) {
563 +      bytes += sizeof(RealType);
564 +    }
565 +    if (layout & dslFlucQVelocity) {
566 +      bytes += sizeof(RealType);
567 +    }
568 +    if (layout & dslFlucQForce) {
569 +      bytes += sizeof(RealType);
570 +    }
571  
572      return bytes;
573    }

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