ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/primitives/RigidBody.cpp
(Generate patch)

Comparing branches/development/src/primitives/RigidBody.cpp (file contents):
Revision 1842 by gezelter, Tue Jan 29 19:10:04 2013 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 229 | Line 229 | namespace OpenMD {
229      Vector3d trq(0.0);
230      Vector3d ef(0.0);
231      Vector3d pos = this->getPos();
232 <
232 >    AtomType* atype;
233 >    int eCount = 0;
234 >    
235      int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout();
236 <
236 >    
237      for (unsigned int i = 0; i < atoms_.size(); i++) {
238  
239 +      atype = atoms_[i]->getAtomType();
240 +
241        afrc = atoms_[i]->getFrc();
242        apos = atoms_[i]->getPos();
243        rpos = apos - pos;
# Line 252 | Line 256 | namespace OpenMD {
256          trq += atrq;
257        }
258  
259 <      if (sl & DataStorage::dslElectricField) {
259 >      if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) {
260          ef += atoms_[i]->getElectricField();
261 +        eCount++;
262        }
263      }        
264      addFrc(frc);
265      addTrq(trq);    
266  
267 <    if (sl & DataStorage::dslElectricField) {
268 <      ef /= atoms_.size();
267 >    if (sl & DataStorage::dslElectricField)  {
268 >      ef /= eCount;
269        setElectricField(ef);
270      }
271  
# Line 275 | Line 280 | namespace OpenMD {
280      Vector3d frc(0.0);
281      Vector3d trq(0.0);
282      Vector3d ef(0.0);
283 <    
283 >    AtomType* atype;
284 >    int eCount = 0;
285 >
286      Vector3d pos = this->getPos();
287      Mat3x3d tau_(0.0);
288  
# Line 283 | Line 290 | namespace OpenMD {
290  
291      for (unsigned int i = 0; i < atoms_.size(); i++) {
292        
293 +      atype = atoms_[i]->getAtomType();
294 +
295        afrc = atoms_[i]->getFrc();
296        apos = atoms_[i]->getPos();
297        rpos = apos - pos;
# Line 300 | Line 309 | namespace OpenMD {
309          atrq = atoms_[i]->getTrq();
310          trq += atrq;
311        }
312 <      if (sl & DataStorage::dslElectricField) {
312 >
313 >      if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) {
314          ef += atoms_[i]->getElectricField();
315 +        eCount++;
316        }
317        
318        tau_(0,0) -= rpos[0]*afrc[0];
# Line 319 | Line 330 | namespace OpenMD {
330      addTrq(trq);
331  
332      if (sl & DataStorage::dslElectricField) {
333 <      ef /= atoms_.size();
333 >      ef /= eCount;
334        setElectricField(ef);
335      }
336  
# Line 344 | Line 355 | namespace OpenMD {
355  
356        if (atoms_[i]->isDirectional()) {
357            
358 <        dAtom = (DirectionalAtom *) atoms_[i];
358 >        dAtom = dynamic_cast<DirectionalAtom *>(atoms_[i]);
359          dAtom->setA(refOrients_[i].transpose() * a);
360        }
361  
# Line 371 | Line 382 | namespace OpenMD {
382  
383        if (atoms_[i]->isDirectional()) {
384            
385 <        dAtom = (DirectionalAtom *) atoms_[i];
385 >        dAtom = dynamic_cast<DirectionalAtom *>(atoms_[i]);
386          dAtom->setA(refOrients_[i].transpose() * a, frame);
387        }
388  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines