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root/OpenMD/trunk/src/integrators/LDForceManager.cpp
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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 1120 by chuckv, Fri Feb 2 18:55:21 2007 UTC vs.
Revision 1185 by xsun, Fri Oct 5 19:02:09 2007 UTC

# Line 153 | Line 153 | namespace oopse {
153               integrableObject != NULL;
154               integrableObject = mol->nextIntegrableObject(j)) {
155            Shape* currShape = NULL;
156 <          if (integrableObject->isDirectionalAtom()) {
157 <            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
158 <            AtomType* atomType = dAtom->getAtomType();
156 >
157 >          if (integrableObject->isAtom()){
158 >            Atom* atom = static_cast<Atom*>(integrableObject);
159 >            AtomType* atomType = atom->getAtomType();
160              if (atomType->isGayBerne()) {
161 <              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
161 <              
161 >              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
162                GenericData* data = dAtomType->getPropertyByName("GayBerne");
163                if (data != NULL) {
164                  GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
# Line 166 | Line 166 | namespace oopse {
166                  if (gayBerneData != NULL) {  
167                    GayBerneParam gayBerneParam = gayBerneData->getData();
168                    currShape = new Ellipsoid(V3Zero,
169 –                                            gayBerneParam.GB_d / 2.0,
169                                              gayBerneParam.GB_l / 2.0,
170 +                                            gayBerneParam.GB_d / 2.0,
171                                              Mat3x3d::identity());
172                  } else {
173                    sprintf( painCave.errMsg,
# Line 182 | Line 182 | namespace oopse {
182                  painCave.isFatal = 1;
183                  simError();    
184                }
185 <            }
186 <          } else {
187 <            Atom* atom = static_cast<Atom*>(integrableObject);
188 <            AtomType* atomType = atom->getAtomType();
189 <            if (atomType->isLennardJones()){
190 <              GenericData* data = atomType->getPropertyByName("LennardJones");
191 <              if (data != NULL) {
192 <                LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
193 <                
194 <                if (ljData != NULL) {
195 <                  LJParam ljParam = ljData->getData();
196 <                  currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
185 >            } else {
186 >              if (atomType->isLennardJones()){
187 >                GenericData* data = atomType->getPropertyByName("LennardJones");
188 >                if (data != NULL) {
189 >                  LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
190 >                  if (ljData != NULL) {
191 >                    LJParam ljParam = ljData->getData();
192 >                    currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
193 >                  } else {
194 >                    sprintf( painCave.errMsg,
195 >                             "Can not cast GenericData to LJParam\n");
196 >                    painCave.severity = OOPSE_ERROR;
197 >                    painCave.isFatal = 1;
198 >                    simError();          
199 >                  }      
200 >                }
201 >              } else {
202 >                int obanum = etab.GetAtomicNum((atom->getType()).c_str());
203 >                if (obanum != 0) {
204 >                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
205                  } else {
206                    sprintf( painCave.errMsg,
207 <                           "Can not cast GenericData to LJParam\n");
207 >                           "Could not find atom type in default element.txt\n");
208                    painCave.severity = OOPSE_ERROR;
209                    painCave.isFatal = 1;
210                    simError();          
211 <                }      
204 <              }
205 <            } else {
206 <              int obanum = etab.GetAtomicNum((atom->getType()).c_str());
207 <              if (obanum != 0) {
208 <                currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
209 <              } else {
210 <                sprintf( painCave.errMsg,
211 <                         "Could not find atom type in default element.txt\n");
212 <                painCave.severity = OOPSE_ERROR;
213 <                painCave.isFatal = 1;
214 <                simError();          
211 >                }
212                }
213              }
214            }
# Line 247 | Line 244 | namespace oopse {
244      return props;
245    }
246    
247 <  void LDForceManager::postCalculation() {
247 >  void LDForceManager::postCalculation(bool needStress){
248      SimInfo::MoleculeIterator i;
249      Molecule::IntegrableObjectIterator  j;
250      Molecule* mol;
251      StuntDouble* integrableObject;
252 +    RealType mass;
253      Vector3d vel;
254      Vector3d pos;
255      Vector3d frc;
# Line 259 | Line 257 | namespace oopse {
257      Mat3x3d Atrans;
258      Vector3d Tb;
259      Vector3d ji;
262 –    RealType mass;
260      unsigned int index = 0;
261      bool doLangevinForces;
262      bool freezeMolecule;
263      int fdf;
267 –    int nIntegrated;
268 –    int nFrozen;
264  
265 +
266 +
267      fdf = 0;
268  
269      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
# Line 299 | Line 296 | namespace oopse {
296          
297          if (doLangevinForces) {  
298            vel =integrableObject->getVel();
299 +          mass = integrableObject->getMass();
300            if (integrableObject->isDirectional()){
301              //calculate angular velocity in lab frame
302              Mat3x3d I = integrableObject->getI();
# Line 317 | Line 315 | namespace oopse {
315                omega[1] = angMom[1] /I(1, 1);
316                omega[2] = angMom[2] /I(2, 2);
317              }
318 <            
318 >
319 >            //std::cerr << "I = " << I(0,0) << "\t" << I(1,1) << "\t" << I(2,2) << "\n\n";
320 >
321              //apply friction force and torque at center of resistance
322              A = integrableObject->getA();
323              Atrans = A.transpose();
324 +            //std::cerr << "A = " << integrableObject->getA() << "\n";
325 +            //std::cerr << "Atrans = " << A.transpose() << "\n\n";
326              Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
327 +            //std::cerr << "cor = " << hydroProps_[index]->getCOR() << "\n\n\n\n";
328 +            //std::cerr << "rcr = " << rcr << "\n\n";
329              Vector3d vcdLab = vel + cross(omega, rcr);
330 +        
331 +            //std::cerr << "velL = " << vel << "\n\n";
332 +            //std::cerr << "vcdL = " << vcdLab << "\n\n";
333              Vector3d vcdBody = A* vcdLab;
334 +            //std::cerr << "vcdB = " << vcdBody << "\n\n";
335              Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
336 +
337 +            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
338 +            //std::cerr << "ffB = " << frictionForceBody << "\n\n";
339              Vector3d frictionForceLab = Atrans*frictionForceBody;
340 +            //std::cerr << "ffL = " << frictionForceLab << "\n\n";
341 +            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
342              integrableObject->addFrc(frictionForceLab);
343 +            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
344 +            //std::cerr << "ome = " << omega << "\n\n";
345              Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
346 +            //std::cerr << "ftB = " << frictionTorqueBody << "\n\n";
347              Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
348 +            //std::cerr << "ftL = " << frictionTorqueLab << "\n\n";
349 +            //std::cerr << "ftL2 = " << frictionTorqueLab+cross(rcr,frictionForceLab) << "\n\n";
350 +            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
351              integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
352 <            
352 >            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
353 >
354              //apply random force and torque at center of resistance
355              Vector3d randomForceBody;
356              Vector3d randomTorqueBody;
357              genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
358 +            //std::cerr << "rfB = " << randomForceBody << "\n\n";
359 +            //std::cerr << "rtB = " << randomTorqueBody << "\n\n";
360              Vector3d randomForceLab = Atrans*randomForceBody;
361              Vector3d randomTorqueLab = Atrans* randomTorqueBody;
362              integrableObject->addFrc(randomForceLab);            
363 +            //std::cerr << "rfL = " << randomForceLab << "\n\n";
364 +            //std::cerr << "rtL = " << randomTorqueLab << "\n\n";
365 +            //std::cerr << "rtL2 = " << randomTorqueLab + cross(rcr, randomForceLab) << "\n\n";
366              integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
367              
368            } else {
369              //spherical atom
370              Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
371 +            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
372              Vector3d randomForce;
373              Vector3d randomTorque;
374              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
# Line 362 | Line 388 | namespace oopse {
388      if(!simParams->getUsePeriodicBoundaryConditions())
389        veloMunge->removeAngularDrift();
390  
391 <    ForceManager::postCalculation();  
391 >    ForceManager::postCalculation(needStress);  
392    }
393  
394   void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
# Line 370 | Line 396 | void LDForceManager::genRandomForceAndTorque(Vector3d&
396  
397      Vector<RealType, 6> Z;
398      Vector<RealType, 6> generalForce;
373 –
399          
400      Z[0] = randNumGen_.randNorm(0, variance);
401      Z[1] = randNumGen_.randNorm(0, variance);
402      Z[2] = randNumGen_.randNorm(0, variance);
403 +    //Z[3] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
404 +    //Z[4] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
405 +    //Z[5] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
406      Z[3] = randNumGen_.randNorm(0, variance);
407      Z[4] = randNumGen_.randNorm(0, variance);
408      Z[5] = randNumGen_.randNorm(0, variance);
# Line 389 | Line 417 | void LDForceManager::genRandomForceAndTorque(Vector3d&
417      torque[1] = generalForce[4];
418      torque[2] = generalForce[5];
419      
420 < }
420 > }
421  
422   }

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