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root/OpenMD/trunk/src/primitives/RigidBody.cpp
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Comparing trunk/src/primitives/RigidBody.cpp (file contents):
Revision 1878 by gezelter, Mon Sep 10 20:58:00 2012 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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 74 | Line 74 | namespace OpenMD {
74    
75    void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
76      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
77 <    
78 <    //((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;    
79 <    
77 >        
78      for (unsigned int i = 0 ; i < atoms_.size(); ++i){
79        if (atoms_[i]->isDirectional()) {
80          atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
# Line 228 | Line 226 | namespace OpenMD {
226      Vector3d apos;
227      Vector3d rpos;
228      Vector3d frc(0.0);
229 <    Vector3d trq(0.0);    
229 >    Vector3d trq(0.0);
230 >    Vector3d ef(0.0);
231      Vector3d pos = this->getPos();
232 +    AtomType* atype;
233 +    int eCount = 0;
234 +    
235 +    int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout();
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 248 | Line 254 | namespace OpenMD {
254        if (atoms_[i]->isDirectional()) {
255          atrq = atoms_[i]->getTrq();
256          trq += atrq;
257 <      }      
257 >      }
258 >
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 /= eCount;
269 +      setElectricField(ef);
270 +    }
271 +
272    }
273  
274    Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() {
# Line 261 | Line 278 | namespace OpenMD {
278      Vector3d rpos;
279      Vector3d dfrc;
280      Vector3d frc(0.0);
281 <    Vector3d trq(0.0);    
281 >    Vector3d trq(0.0);
282 >    Vector3d ef(0.0);
283 >    AtomType* atype;
284 >    int eCount = 0;
285 >
286      Vector3d pos = this->getPos();
287      Mat3x3d tau_(0.0);
288  
289 +    int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout();
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 283 | Line 308 | namespace OpenMD {
308        if (atoms_[i]->isDirectional()) {
309          atrq = atoms_[i]->getTrq();
310          trq += atrq;
311 +      }
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 298 | Line 328 | namespace OpenMD {
328      }
329      addFrc(frc);
330      addTrq(trq);
331 +
332 +    if (sl & DataStorage::dslElectricField) {
333 +      ef /= eCount;
334 +      setElectricField(ef);
335 +    }
336 +
337      return tau_;
338    }
339  
# Line 319 | 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 346 | 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  

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