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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 1216 by xsun, Wed Jan 23 21:22:50 2008 UTC

# Line 45 | Line 45
45   #include "utils/OOPSEConstant.hpp"
46   #include "hydrodynamics/Sphere.hpp"
47   #include "hydrodynamics/Ellipsoid.hpp"
48 < #include "openbabel/mol.hpp"
48 > #include "utils/ElementsTable.hpp"
49  
50 – using namespace OpenBabel;
50   namespace oopse {
51  
52    LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
# Line 153 | Line 152 | namespace oopse {
152               integrableObject != NULL;
153               integrableObject = mol->nextIntegrableObject(j)) {
154            Shape* currShape = NULL;
155 <          if (integrableObject->isDirectionalAtom()) {
156 <            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
157 <            AtomType* atomType = dAtom->getAtomType();
155 >
156 >          if (integrableObject->isAtom()){
157 >            Atom* atom = static_cast<Atom*>(integrableObject);
158 >            AtomType* atomType = atom->getAtomType();
159              if (atomType->isGayBerne()) {
160 <              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
161 <              
160 >              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
161                GenericData* data = dAtomType->getPropertyByName("GayBerne");
162                if (data != NULL) {
163                  GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
# Line 166 | Line 165 | namespace oopse {
165                  if (gayBerneData != NULL) {  
166                    GayBerneParam gayBerneParam = gayBerneData->getData();
167                    currShape = new Ellipsoid(V3Zero,
169 –                                            gayBerneParam.GB_d / 2.0,
168                                              gayBerneParam.GB_l / 2.0,
169 +                                            gayBerneParam.GB_d / 2.0,
170                                              Mat3x3d::identity());
171                  } else {
172                    sprintf( painCave.errMsg,
# Line 182 | Line 181 | namespace oopse {
181                  painCave.isFatal = 1;
182                  simError();    
183                }
184 <            }
185 <          } else {
186 <            Atom* atom = static_cast<Atom*>(integrableObject);
187 <            AtomType* atomType = atom->getAtomType();
188 <            if (atomType->isLennardJones()){
189 <              GenericData* data = atomType->getPropertyByName("LennardJones");
190 <              if (data != NULL) {
191 <                LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
192 <                
193 <                if (ljData != NULL) {
194 <                  LJParam ljParam = ljData->getData();
195 <                  currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
184 >            } else {
185 >              if (atomType->isLennardJones()){
186 >                GenericData* data = atomType->getPropertyByName("LennardJones");
187 >                if (data != NULL) {
188 >                  LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
189 >                  if (ljData != NULL) {
190 >                    LJParam ljParam = ljData->getData();
191 >                    currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
192 >                  } else {
193 >                    sprintf( painCave.errMsg,
194 >                             "Can not cast GenericData to LJParam\n");
195 >                    painCave.severity = OOPSE_ERROR;
196 >                    painCave.isFatal = 1;
197 >                    simError();          
198 >                  }      
199 >                }
200 >              } else {
201 >                int obanum = etab.GetAtomicNum((atom->getType()).c_str());
202 >                if (obanum != 0) {
203 >                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
204                  } else {
205                    sprintf( painCave.errMsg,
206 <                           "Can not cast GenericData to LJParam\n");
206 >                           "Could not find atom type in default element.txt\n");
207                    painCave.severity = OOPSE_ERROR;
208                    painCave.isFatal = 1;
209                    simError();          
210 <                }      
210 >                }
211                }
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();          
215 –              }
212              }
213            }
214            HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
# Line 247 | Line 243 | namespace oopse {
243      return props;
244    }
245    
246 <  void LDForceManager::postCalculation() {
246 >  void LDForceManager::postCalculation(bool needStress){
247      SimInfo::MoleculeIterator i;
248      Molecule::IntegrableObjectIterator  j;
249      Molecule* mol;
250      StuntDouble* integrableObject;
251 +    RealType mass;
252      Vector3d vel;
253      Vector3d pos;
254      Vector3d frc;
# Line 259 | Line 256 | namespace oopse {
256      Mat3x3d Atrans;
257      Vector3d Tb;
258      Vector3d ji;
262 –    RealType mass;
259      unsigned int index = 0;
260      bool doLangevinForces;
261      bool freezeMolecule;
262      int fdf;
263 <    int nIntegrated;
268 <    int nFrozen;
263 >
264  
265 +
266      fdf = 0;
267  
268      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
# Line 299 | Line 295 | namespace oopse {
295          
296          if (doLangevinForces) {  
297            vel =integrableObject->getVel();
298 +          mass = integrableObject->getMass();
299            if (integrableObject->isDirectional()){
303 –            //calculate angular velocity in lab frame
300              Mat3x3d I = integrableObject->getI();
301              Vector3d angMom = integrableObject->getJ();
302 <            Vector3d omega;
302 >            A = integrableObject->getA();
303 >            Atrans = A.transpose();
304 >
305 >            Vector3d omegaBody;
306              
307              if (integrableObject->isLinear()) {
308                int linearAxis = integrableObject->linearAxis();
309                int l = (linearAxis +1 )%3;
310                int m = (linearAxis +2 )%3;
311 <              omega[l] = angMom[l] /I(l, l);
312 <              omega[m] = angMom[m] /I(m, m);
311 >              omegaBody[l] = angMom[l] /I(l, l);
312 >              omegaBody[m] = angMom[m] /I(m, m);
313                
314              } else {
315 <              omega[0] = angMom[0] /I(0, 0);
316 <              omega[1] = angMom[1] /I(1, 1);
317 <              omega[2] = angMom[2] /I(2, 2);
315 >              omegaBody[0] = angMom[0] /I(0, 0);
316 >              omegaBody[1] = angMom[1] /I(1, 1);
317 >              omegaBody[2] = angMom[2] /I(2, 2);
318              }
319 <            
320 <            //apply friction force and torque at center of resistance
321 <            A = integrableObject->getA();
322 <            Atrans = A.transpose();
323 <            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
324 <            Vector3d vcdLab = vel + cross(omega, rcr);
325 <            Vector3d vcdBody = A* vcdLab;
326 <            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
327 <            Vector3d frictionForceLab = Atrans*frictionForceBody;
319 >
320 >            Vector3d omegaLab = Atrans * omegaBody;
321 >
322 >            // apply friction force and torque at center of resistance
323 >
324 >            Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
325 >            Vector3d vcdLab = vel + cross(omegaLab, rcrLab);
326 >        
327 >            Vector3d vcdBody = A * vcdLab;
328 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
329 >
330 >            Vector3d frictionForceLab = Atrans * frictionForceBody;
331              integrableObject->addFrc(frictionForceLab);
332 <            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
333 <            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
334 <            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
335 <            
332 >            Vector3d frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
333 >            Vector3d frictionTorqueLab = Atrans * frictionTorqueBody;
334 >            integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
335 >
336              //apply random force and torque at center of resistance
337              Vector3d randomForceBody;
338              Vector3d randomTorqueBody;
339              genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
340 <            Vector3d randomForceLab = Atrans*randomForceBody;
341 <            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
340 >            Vector3d randomForceLab = Atrans * randomForceBody;
341 >            Vector3d randomTorqueLab = Atrans * randomTorqueBody;
342              integrableObject->addFrc(randomForceLab);            
343 <            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
343 >            integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));            
344              
345            } else {
346              //spherical atom
# Line 362 | Line 364 | namespace oopse {
364      if(!simParams->getUsePeriodicBoundaryConditions())
365        veloMunge->removeAngularDrift();
366  
367 <    ForceManager::postCalculation();  
367 >    ForceManager::postCalculation(needStress);  
368    }
369  
370   void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
# Line 370 | Line 372 | void LDForceManager::genRandomForceAndTorque(Vector3d&
372  
373      Vector<RealType, 6> Z;
374      Vector<RealType, 6> generalForce;
373 –
375          
376      Z[0] = randNumGen_.randNorm(0, variance);
377      Z[1] = randNumGen_.randNorm(0, variance);
# Line 379 | Line 380 | void LDForceManager::genRandomForceAndTorque(Vector3d&
380      Z[4] = randNumGen_.randNorm(0, variance);
381      Z[5] = randNumGen_.randNorm(0, variance);
382      
382 –
383      generalForce = hydroProps_[index]->getS()*Z;
384      
385      force[0] = generalForce[0];
# Line 389 | Line 389 | void LDForceManager::genRandomForceAndTorque(Vector3d&
389      torque[1] = generalForce[4];
390      torque[2] = generalForce[5];
391      
392 < }
392 > }
393  
394   }

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