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Comparing branches/development/src/brains/DataStorage.cpp (file contents):
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 44 | Line 44
44   * @file DataStorage.cpp
45   * @author tlin
46   * @date 10/26/2004
47 – * @time 11:56am
47   * @version 1.0
48   */
49  
# Line 73 | Line 72 | namespace OpenMD {
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        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        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        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        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        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        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        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        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        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        cerr << "size does not match"<< endl;        
123      }
# Line 162 | 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 169 | Line 172 | namespace OpenMD {
172      if (storageLayout_ & dslAngularMomentum) {
173        internalResize(angularMomentum, newSize);
174      }
172 –
173 –    if (storageLayout_ & dslElectroFrame) {
174 –      internalResize(electroFrame, newSize);
175 –    }
175      
177 –    if (storageLayout_ & dslZAngle) {
178 –      internalResize(zAngle, newSize);
179 –    }
180 –
181 –    if (storageLayout_ & dslForce) {
182 –      internalResize(force, newSize);
183 –    }
184 –
176      if (storageLayout_ & dslTorque) {
177        internalResize(torque, newSize);
178      }
# Line 202 | 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 234 | 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      }
# Line 242 | Line 245 | namespace OpenMD {
245        angularMomentum.reserve(size);
246      }
247  
245 –    if (storageLayout_ & dslElectroFrame) {
246 –      electroFrame.reserve(size);
247 –    }
248 –    
249 –    if (storageLayout_ & dslZAngle) {
250 –      zAngle.reserve(size);
251 –    }
252 –
253 –    if (storageLayout_ & dslForce) {
254 –      force.reserve(size);
255 –    }
256 –
248      if (storageLayout_ & dslTorque) {
249        torque.reserve(size);
250      }
# Line 274 | 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 308 | 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 316 | Line 319 | namespace OpenMD {
319        internalCopy(angularMomentum, source, num, target);
320      }
321  
319 –    if (storageLayout_ & dslElectroFrame) {
320 –      internalCopy(electroFrame, source, num, target);
321 –    }
322 –    
323 –    if (storageLayout_ & dslZAngle) {
324 –      internalCopy(zAngle, source, num, target);
325 –    }
326 –
327 –    if (storageLayout_ & dslForce) {
328 –      internalCopy(force, source, num, target);
329 –    }
330 –
322      if (storageLayout_ & dslTorque) {
323        internalCopy(torque, source, num, target);
324      }
# Line 348 | 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 382 | Line 381 | namespace OpenMD {
381      switch (whichArray) {
382      case dslPosition:
383        return internalGetArrayPointer(position);
385 –      break;
384              
385      case dslVelocity:
386        return internalGetArrayPointer(velocity);
389 –      break;
387              
388 +    case dslForce:
389 +      return internalGetArrayPointer(force);
390 +
391      case dslAmat:
392        return internalGetArrayPointer(aMat);
393 –      break;            
393              
394      case dslAngularMomentum:
395        return internalGetArrayPointer(angularMomentum);
397 –      break;
396              
399 –    case dslElectroFrame:
400 –      return internalGetArrayPointer(electroFrame);
401 –      break;
402 –            
403 –    case dslZAngle:
404 –      return internalGetArrayPointer(zAngle);
405 –      break;
406 –
407 –    case dslForce:
408 –      return internalGetArrayPointer(force);
409 –      break;            
410 –
397      case dslTorque:
398        return internalGetArrayPointer(torque);
413 –      break;
399  
400      case dslParticlePot:
401        return internalGetArrayPointer(particlePot);
417 –      break;
402  
403      case dslDensity:
404        return internalGetArrayPointer(density);
421 –      break;
405  
406      case dslFunctional:
407        return internalGetArrayPointer(functional);
425 –      break;
408  
409      case dslFunctionalDerivative:
410        return internalGetArrayPointer(functionalDerivative);
429 –      break;
411  
412 +    case dslDipole:
413 +      return internalGetArrayPointer(dipole);
414 +
415 +    case dslQuadrupole:
416 +      return internalGetArrayPointer(quadrupole);
417 +
418      case dslElectricField:
419        return internalGetArrayPointer(electricField);
433 –      break;
420  
421      case dslSkippedCharge:
422        return internalGetArrayPointer(skippedCharge);
437 –      break;
423  
424      case dslFlucQPosition:
425        return internalGetArrayPointer(flucQPos);
441 –      break;
426  
427      case dslFlucQVelocity:
428        return internalGetArrayPointer(flucQVel);
445 –      break;
429            
430      case dslFlucQForce:
431        return internalGetArrayPointer(flucQFrc);
449 –      break;
432            
433      default:
434        //error message
435        return NULL;
454 –
436      }
437    }    
438  
439    RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
440 <    if (v.size() == 0) {
440 >    if (v.empty()) {
441        return NULL;
442      } else {
443        return v[0].getArrayPointer();
444      }
445    }
446  
447 <  RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
448 <    if (v.size() == 0) {
447 >  RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
448 >    if (v.empty()) {
449        return NULL;
450      } else {
451        return v[0].getArrayPointer();
# Line 473 | Line 454 | namespace OpenMD {
454    }
455  
456    RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
457 <    if (v.size() == 0) {
457 >    if (v.empty()) {
458        return NULL;
459      } else {
460        return &(v[0]);
# Line 523 | Line 504 | namespace OpenMD {
504      if (layout & dslVelocity) {
505        bytes += sizeof(Vector3d);
506      }
507 +    if (layout & dslForce) {
508 +      bytes += sizeof(Vector3d);
509 +    }
510      if (layout & dslAmat) {
511        bytes += sizeof(RotMat3x3d);    
512      }
513      if (layout & dslAngularMomentum) {
514        bytes += sizeof(Vector3d);
515      }
532 –    if (layout & dslElectroFrame) {
533 –      bytes += sizeof(Mat3x3d);
534 –    }
535 –    if (layout & dslZAngle) {
536 –      bytes += sizeof(RealType);
537 –    }
538 –    if (layout & dslForce) {
539 –      bytes += sizeof(Vector3d);
540 –    }
516      if (layout & dslTorque) {
517        bytes += sizeof(Vector3d);
518      }
# Line 553 | Line 528 | namespace OpenMD {
528      if (layout & dslFunctionalDerivative) {
529        bytes += sizeof(RealType);
530      }
531 +    if (layout & dslDipole) {
532 +      bytes += sizeof(Vector3d);
533 +    }
534 +    if (layout & dslQuadrupole) {
535 +      bytes += sizeof(Mat3x3d);
536 +    }
537      if (layout & dslElectricField) {
538        bytes += sizeof(Vector3d);
539      }

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