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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 981 by gezelter, Mon Jun 5 18:24:45 2006 UTC

# Line 88 | Line 88 | namespace oopse {
88      }
89  
90      // Build the hydroProp map:
91 <    std::map<std::string, HydroProp> hydroPropMap;
91 >    std::map<std::string, HydroProp*> hydroPropMap;
92  
93      Molecule* mol;
94      StuntDouble* integrableObject;
# Line 123 | Line 123 | namespace oopse {
123          painCave.isFatal = 1;
124          simError();  
125        }      
126 <      std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
127 <      if (iter != hydroPropMap.end()) {
128 <        hydroProps_.push_back(iter->second);
129 <      } else {
130 <        sprintf( painCave.errMsg,
131 <                 "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
132 <        painCave.severity = OOPSE_ERROR;
133 <        painCave.isFatal = 1;
134 <        simError();  
126 >
127 >      for (mol = info->beginMolecule(i); mol != NULL;
128 >           mol = info->nextMolecule(i)) {
129 >        for (integrableObject = mol->beginIntegrableObject(j);
130 >             integrableObject != NULL;
131 >             integrableObject = mol->nextIntegrableObject(j)) {
132 >
133 >          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
134 >          if (iter != hydroPropMap.end()) {
135 >            hydroProps_.push_back(iter->second);
136 >          } else {
137 >            sprintf( painCave.errMsg,
138 >                     "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
139 >            painCave.severity = OOPSE_ERROR;
140 >            painCave.isFatal = 1;
141 >            simError();  
142 >          }        
143 >        }
144        }
145      } else {
146 <
147 <      std::map<std::string, HydroProp> hydroPropMap;
146 >      
147 >      std::map<std::string, HydroProp*> hydroPropMap;
148        for (mol = info->beginMolecule(i); mol != NULL;
149             mol = info->nextMolecule(i)) {
150          for (integrableObject = mol->beginIntegrableObject(j);
# Line 155 | Line 164 | namespace oopse {
164                  if (gayBerneData != NULL) {  
165                    GayBerneParam gayBerneParam = gayBerneData->getData();
166                    currShape = new Ellipsoid(V3Zero,
167 <                                            gayBerneParam.GB_sigma/2.0,
168 <                                            gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0,
167 >                                            gayBerneParam.GB_d / 2.0,
168 >                                            gayBerneParam.GB_l / 2.0,
169                                              Mat3x3d::identity());
170                  } else {
171                    sprintf( painCave.errMsg,
# Line 204 | Line 213 | namespace oopse {
213                }
214              }
215            }
216 <          HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
217 <          std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
216 >          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
217 >          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
218            if (iter != hydroPropMap.end())
219              hydroProps_.push_back(iter->second);
220            else {
221 <            HydroProp myProp;
222 <            myProp.cor = V3Zero;
223 <            for (int i1 = 0; i1 < 3; i1++) {
215 <              for (int j1 = 0; j1 < 3; j1++) {
216 <                myProp.Xirtt(i1,j1) = currHydroProp.Xi(i1,j1);
217 <                myProp.Xirrt(i1,j1) = currHydroProp.Xi(i1,j1+3);
218 <                myProp.Xirtr(i1,j1) = currHydroProp.Xi(i1+3,j1);
219 <                myProp.Xirrr(i1,j1) = currHydroProp.Xi(i1+3,j1+3);
220 <              }
221 <            }
222 <            CholeskyDecomposition(currHydroProp.Xi, myProp.S);
223 <            hydroPropMap.insert(std::map<std::string, HydroProp>::value_type(integrableObject->getType(), myProp));
224 <            hydroProps_.push_back(myProp);
221 >            currHydroProp->complete();
222 >            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
223 >            hydroProps_.push_back(currHydroProp);
224            }
225          }
226        }
227      }
228      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
229 <  }
231 <  
232 <  
229 >  }  
230  
231 <
232 <
236 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237 <    std::map<std::string, HydroProp> props;
231 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
232 >    std::map<std::string, HydroProp*> props;
233      std::ifstream ifs(filename.c_str());
234      if (ifs.is_open()) {
235        
# Line 243 | Line 238 | namespace oopse {
238      const unsigned int BufferSize = 65535;
239      char buffer[BufferSize];  
240      while (ifs.getline(buffer, BufferSize)) {
241 <      StringTokenizer tokenizer(buffer);
242 <      HydroProp currProp;
248 <      if (tokenizer.countTokens() >= 40) {
249 <        std::string atomName = tokenizer.nextToken();
250 <        currProp.cor[0] = tokenizer.nextTokenAsDouble();
251 <        currProp.cor[1] = tokenizer.nextTokenAsDouble();
252 <        currProp.cor[2] = tokenizer.nextTokenAsDouble();
253 <        
254 <        currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
255 <        currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
256 <        currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
257 <        currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
258 <        currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
259 <        currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
260 <        currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
261 <        currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
262 <        currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
263 <        
264 <        currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
265 <        currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
266 <        currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
267 <        currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
268 <        currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
269 <        currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
270 <        currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
271 <        currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
272 <        currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
273 <        
274 <        currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
275 <        currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
276 <        currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
277 <        currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
278 <        currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
279 <        currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
280 <        currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
281 <        currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
282 <        currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
283 <        
284 <        currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
285 <        currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
286 <        currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
287 <        currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
288 <        currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
289 <        currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
290 <        currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
291 <        currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
292 <        currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
293 <        
294 <        SquareMatrix<RealType, 6> Xir;
295 <        Xir.setSubMatrix(0, 0, currProp.Xirtt);
296 <        Xir.setSubMatrix(0, 3, currProp.Xirrt);
297 <        Xir.setSubMatrix(3, 0, currProp.Xirtr);
298 <        Xir.setSubMatrix(3, 3, currProp.Xirrr);
299 <        CholeskyDecomposition(Xir, currProp.S);            
300 <        
301 <        props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
302 <      }
241 >      HydroProp* currProp = new HydroProp(buffer);
242 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
243      }
244 <    
244 >
245      return props;
246    }
247 <  
247 >  
248    void LDForceManager::postCalculation() {
249      SimInfo::MoleculeIterator i;
250      Molecule::IntegrableObjectIterator  j;
# Line 325 | Line 265 | namespace oopse {
265      
266      fdf = 0;
267      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
268 <      
268 >
269 >      doLangevinForces = true;          
270 >      freezeMolecule = false;
271 >
272        if (sphericalBoundaryConditions_) {
273          
274          Vector3d molPos = mol->getCom();
275          RealType molRad = molPos.length();
276          
277          doLangevinForces = false;
335 –        freezeMolecule = false;
278          
279          if (molRad > langevinBufferRadius_) {
280            doLangevinForces = true;
# Line 374 | Line 316 | namespace oopse {
316              //apply friction force and torque at center of resistance
317              A = integrableObject->getA();
318              Atrans = A.transpose();
319 <            Vector3d rcr = Atrans * hydroProps_[index].cor;  
319 >            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
320              Vector3d vcdLab = vel + cross(omega, rcr);
321              Vector3d vcdBody = A* vcdLab;
322 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
322 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
323              Vector3d frictionForceLab = Atrans*frictionForceBody;
324              integrableObject->addFrc(frictionForceLab);
325 <            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
325 >            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
326              Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
327              integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
328              
# Line 395 | Line 337 | namespace oopse {
337              
338            } else {
339              //spherical atom
340 <            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
340 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
341              Vector3d randomForce;
342              Vector3d randomTorque;
343              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
# Line 428 | Line 370 | void LDForceManager::genRandomForceAndTorque(Vector3d&
370      Z[5] = randNumGen_.randNorm(0, variance);
371      
372  
373 <    generalForce = hydroProps_[index].S*Z;
373 >    generalForce = hydroProps_[index]->getS()*Z;
374      
375      force[0] = generalForce[0];
376      force[1] = generalForce[1];

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