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root/OpenMD/branches/development/src/integrators/LDForceManager.cpp
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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 983 by gezelter, Tue Jun 6 17:43:28 2006 UTC

# Line 50 | Line 50 | namespace oopse {
50   namespace oopse {
51  
52    LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
53 <    Globals* simParams = info->getSimParams();
54 <        
53 >    simParams = info->getSimParams();
54 >    veloMunge = new Velocitizer(info);
55 >
56      sphericalBoundaryConditions_ = false;
57      if (simParams->getUseSphericalBoundaryConditions()) {
58        sphericalBoundaryConditions_ = true;
# Line 88 | Line 89 | namespace oopse {
89      }
90  
91      // Build the hydroProp map:
92 <    std::map<std::string, HydroProp> hydroPropMap;
92 >    std::map<std::string, HydroProp*> hydroPropMap;
93  
94      Molecule* mol;
95      StuntDouble* integrableObject;
# Line 123 | Line 124 | namespace oopse {
124          painCave.isFatal = 1;
125          simError();  
126        }      
127 <      std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
128 <      if (iter != hydroPropMap.end()) {
129 <        hydroProps_.push_back(iter->second);
130 <      } else {
131 <        sprintf( painCave.errMsg,
132 <                 "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
133 <        painCave.severity = OOPSE_ERROR;
134 <        painCave.isFatal = 1;
135 <        simError();  
127 >
128 >      for (mol = info->beginMolecule(i); mol != NULL;
129 >           mol = info->nextMolecule(i)) {
130 >        for (integrableObject = mol->beginIntegrableObject(j);
131 >             integrableObject != NULL;
132 >             integrableObject = mol->nextIntegrableObject(j)) {
133 >
134 >          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
135 >          if (iter != hydroPropMap.end()) {
136 >            hydroProps_.push_back(iter->second);
137 >          } else {
138 >            sprintf( painCave.errMsg,
139 >                     "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
140 >            painCave.severity = OOPSE_ERROR;
141 >            painCave.isFatal = 1;
142 >            simError();  
143 >          }        
144 >        }
145        }
146      } else {
147 <
148 <      std::map<std::string, HydroProp> hydroPropMap;
147 >      
148 >      std::map<std::string, HydroProp*> hydroPropMap;
149        for (mol = info->beginMolecule(i); mol != NULL;
150             mol = info->nextMolecule(i)) {
151          for (integrableObject = mol->beginIntegrableObject(j);
# Line 155 | Line 165 | namespace oopse {
165                  if (gayBerneData != NULL) {  
166                    GayBerneParam gayBerneParam = gayBerneData->getData();
167                    currShape = new Ellipsoid(V3Zero,
168 <                                            gayBerneParam.GB_sigma/2.0,
169 <                                            gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0,
168 >                                            gayBerneParam.GB_d / 2.0,
169 >                                            gayBerneParam.GB_l / 2.0,
170                                              Mat3x3d::identity());
171                  } else {
172                    sprintf( painCave.errMsg,
# Line 204 | Line 214 | namespace oopse {
214                }
215              }
216            }
217 <          HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
218 <          std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
217 >          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
218 >          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
219            if (iter != hydroPropMap.end())
220              hydroProps_.push_back(iter->second);
221            else {
222 <            HydroProp myProp;
223 <            myProp.cor = V3Zero;
224 <            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);
222 >            currHydroProp->complete();
223 >            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
224 >            hydroProps_.push_back(currHydroProp);
225            }
226          }
227        }
228      }
229      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
230 <  }
231 <  
232 <  
230 >  }  
231  
232 <
233 <
236 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237 <    std::map<std::string, HydroProp> props;
232 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
233 >    std::map<std::string, HydroProp*> props;
234      std::ifstream ifs(filename.c_str());
235      if (ifs.is_open()) {
236        
# Line 243 | Line 239 | namespace oopse {
239      const unsigned int BufferSize = 65535;
240      char buffer[BufferSize];  
241      while (ifs.getline(buffer, BufferSize)) {
242 <      StringTokenizer tokenizer(buffer);
243 <      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 <      }
242 >      HydroProp* currProp = new HydroProp(buffer);
243 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
244      }
245 <    
245 >
246      return props;
247    }
248 <  
248 >  
249    void LDForceManager::postCalculation() {
250      SimInfo::MoleculeIterator i;
251      Molecule::IntegrableObjectIterator  j;
# Line 322 | Line 263 | namespace oopse {
263      bool doLangevinForces;
264      bool freezeMolecule;
265      int fdf;
266 <    
266 >
267 >
268      fdf = 0;
269      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
270 <      
270 >
271 >      doLangevinForces = true;          
272 >      freezeMolecule = false;
273 >
274        if (sphericalBoundaryConditions_) {
275          
276          Vector3d molPos = mol->getCom();
277          RealType molRad = molPos.length();
278          
279          doLangevinForces = false;
335 –        freezeMolecule = false;
280          
281          if (molRad > langevinBufferRadius_) {
282            doLangevinForces = true;
# Line 374 | Line 318 | namespace oopse {
318              //apply friction force and torque at center of resistance
319              A = integrableObject->getA();
320              Atrans = A.transpose();
321 <            Vector3d rcr = Atrans * hydroProps_[index].cor;  
321 >            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
322              Vector3d vcdLab = vel + cross(omega, rcr);
323              Vector3d vcdBody = A* vcdLab;
324 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
324 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
325              Vector3d frictionForceLab = Atrans*frictionForceBody;
326              integrableObject->addFrc(frictionForceLab);
327 <            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
327 >            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
328              Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
329              integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
330              
# Line 395 | Line 339 | namespace oopse {
339              
340            } else {
341              //spherical atom
342 <            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
342 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
343              Vector3d randomForce;
344              Vector3d randomTorque;
345              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
# Line 409 | Line 353 | namespace oopse {
353        }
354      }    
355      info_->setFdf(fdf);
356 <    
356 >
357 >    veloMunge->removeComDrift();
358 >    // Remove angular drift if we are not using periodic boundary conditions.
359 >    if(!simParams->getUsePeriodicBoundaryConditions())
360 >      veloMunge->removeAngularDrift();
361 >
362      ForceManager::postCalculation();  
363    }
364  
# Line 428 | Line 377 | void LDForceManager::genRandomForceAndTorque(Vector3d&
377      Z[5] = randNumGen_.randNorm(0, variance);
378      
379  
380 <    generalForce = hydroProps_[index].S*Z;
380 >    generalForce = hydroProps_[index]->getS()*Z;
381      
382      force[0] = generalForce[0];
383      force[1] = generalForce[1];

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