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root/OpenMD/branches/development/src/primitives/RigidBody.cpp
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Comparing branches/development/src/primitives/RigidBody.cpp (file contents):
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
Revision 1844 by gezelter, Wed Jan 30 14:43:08 2013 UTC

# 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 94 | Line 92 | namespace OpenMD {
92      Vector3d force;
93      Vector3d torque;
94      Vector3d myEuler;
95 <    RealType phi, theta, psi;
95 >    RealType phi, theta;
96 >    // RealType psi;
97      RealType cphi, sphi, ctheta, stheta;
98      Vector3d ephi;
99      Vector3d etheta;
# Line 106 | Line 105 | namespace OpenMD {
105      
106      phi = myEuler[0];
107      theta = myEuler[1];
108 <    psi = myEuler[2];
108 >    // psi = myEuler[2];
109      
110      cphi = cos(phi);
111      sphi = sin(phi);
# Line 227 | 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 247 | 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 260 | 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        afrc = atoms_[i]->getFrc();
# Line 282 | Line 306 | namespace OpenMD {
306        if (atoms_[i]->isDirectional()) {
307          atrq = atoms_[i]->getTrq();
308          trq += atrq;
309 +      }
310 +      if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) {
311 +        ef += atoms_[i]->getElectricField();
312 +        eCount++;
313        }
314        
315        tau_(0,0) -= rpos[0]*afrc[0];
# Line 297 | Line 325 | namespace OpenMD {
325      }
326      addFrc(frc);
327      addTrq(trq);
328 +
329 +    if (sl & DataStorage::dslElectricField) {
330 +      ef /= eCount;
331 +      setElectricField(ef);
332 +    }
333 +
334      return tau_;
335    }
336  

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