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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
Revision 1210 by gezelter, Wed Jan 23 03:45:33 2008 UTC

# Line 39 | Line 39
39   * such damages.
40   */
41   #include <fstream>
42 + #include <iostream>
43   #include "integrators/LDForceManager.hpp"
44   #include "math/CholeskyDecomposition.hpp"
45   #include "utils/OOPSEConstant.hpp"
46 + #include "hydrodynamics/Sphere.hpp"
47 + #include "hydrodynamics/Ellipsoid.hpp"
48 + #include "utils/ElementsTable.hpp"
49 +
50   namespace oopse {
51  
52    LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
53 <    Globals* simParams = info->getSimParams();
54 <    
55 <    std::map<std::string, HydroProp> hydroPropMap;
51 <    if (simParams->haveHydroPropFile()) {
52 <      hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
53 <    } else {
54 <      sprintf( painCave.errMsg,
55 <               "HydroPropFile must be set if Langevin Dynamics is specified.\n");
56 <      painCave.severity = OOPSE_ERROR;
57 <      painCave.isFatal = 1;
58 <      simError();  
59 <    }
60 <    
53 >    simParams = info->getSimParams();
54 >    veloMunge = new Velocitizer(info);
55 >
56      sphericalBoundaryConditions_ = false;
57      if (simParams->getUseSphericalBoundaryConditions()) {
58        sphericalBoundaryConditions_ = true;
# Line 92 | Line 87 | namespace oopse {
87          simError();  
88        }
89      }
90 <      
91 <    SimInfo::MoleculeIterator i;
92 <    Molecule::IntegrableObjectIterator  j;
90 >
91 >    // Build the hydroProp map:
92 >    std::map<std::string, HydroProp*> hydroPropMap;
93 >
94      Molecule* mol;
95      StuntDouble* integrableObject;
96 <    for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
97 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
96 >    SimInfo::MoleculeIterator i;
97 >    Molecule::IntegrableObjectIterator  j;              
98 >    bool needHydroPropFile = false;
99 >    
100 >    for (mol = info->beginMolecule(i); mol != NULL;
101 >         mol = info->nextMolecule(i)) {
102 >      for (integrableObject = mol->beginIntegrableObject(j);
103 >           integrableObject != NULL;
104             integrableObject = mol->nextIntegrableObject(j)) {
105 <        std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
106 <        if (iter != hydroPropMap.end()) {
107 <          hydroProps_.push_back(iter->second);
108 <        } else {
107 <          sprintf( painCave.errMsg,
108 <                   "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
109 <          painCave.severity = OOPSE_ERROR;
110 <          painCave.isFatal = 1;
111 <          simError();  
105 >        
106 >        if (integrableObject->isRigidBody()) {
107 >          RigidBody* rb = static_cast<RigidBody*>(integrableObject);
108 >          if (rb->getNumAtoms() > 1) needHydroPropFile = true;
109          }
110          
111        }
112      }
113 +        
114 +
115 +    if (needHydroPropFile) {              
116 +      if (simParams->haveHydroPropFile()) {
117 +        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
118 +      } else {              
119 +        sprintf( painCave.errMsg,
120 +                 "HydroPropFile must be set to a file name if Langevin\n"
121 +                 "\tDynamics is specified for rigidBodies which contain more\n"
122 +                 "\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
123 +        painCave.severity = OOPSE_ERROR;
124 +        painCave.isFatal = 1;
125 +        simError();  
126 +      }      
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;
149 +      for (mol = info->beginMolecule(i); mol != NULL;
150 +           mol = info->nextMolecule(i)) {
151 +        for (integrableObject = mol->beginIntegrableObject(j);
152 +             integrableObject != NULL;
153 +             integrableObject = mol->nextIntegrableObject(j)) {
154 +          Shape* currShape = NULL;
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 +              GenericData* data = dAtomType->getPropertyByName("GayBerne");
162 +              if (data != NULL) {
163 +                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
164 +                
165 +                if (gayBerneData != NULL) {  
166 +                  GayBerneParam gayBerneParam = gayBerneData->getData();
167 +                  currShape = new Ellipsoid(V3Zero,
168 +                                            gayBerneParam.GB_l / 2.0,
169 +                                            gayBerneParam.GB_d / 2.0,
170 +                                            Mat3x3d::identity());
171 +                } else {
172 +                  sprintf( painCave.errMsg,
173 +                           "Can not cast GenericData to GayBerneParam\n");
174 +                  painCave.severity = OOPSE_ERROR;
175 +                  painCave.isFatal = 1;
176 +                  simError();  
177 +                }
178 +              } else {
179 +                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
180 +                painCave.severity = OOPSE_ERROR;
181 +                painCave.isFatal = 1;
182 +                simError();    
183 +              }
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 +                           "Could not find atom type in default element.txt\n");
207 +                  painCave.severity = OOPSE_ERROR;
208 +                  painCave.isFatal = 1;
209 +                  simError();          
210 +                }
211 +              }
212 +            }
213 +          }
214 +          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
215 +          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
216 +          if (iter != hydroPropMap.end())
217 +            hydroProps_.push_back(iter->second);
218 +          else {
219 +            currHydroProp->complete();
220 +            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
221 +            hydroProps_.push_back(currHydroProp);
222 +          }
223 +        }
224 +      }
225 +    }
226      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
227 <  }
228 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
229 <    std::map<std::string, HydroProp> props;
227 >  }  
228 >
229 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
230 >    std::map<std::string, HydroProp*> props;
231      std::ifstream ifs(filename.c_str());
232      if (ifs.is_open()) {
233        
# Line 125 | Line 236 | namespace oopse {
236      const unsigned int BufferSize = 65535;
237      char buffer[BufferSize];  
238      while (ifs.getline(buffer, BufferSize)) {
239 <      StringTokenizer tokenizer(buffer);
240 <      HydroProp currProp;
130 <      if (tokenizer.countTokens() >= 40) {
131 <        std::string atomName = tokenizer.nextToken();
132 <        currProp.cor[0] = tokenizer.nextTokenAsDouble();
133 <        currProp.cor[1] = tokenizer.nextTokenAsDouble();
134 <        currProp.cor[2] = tokenizer.nextTokenAsDouble();
135 <        
136 <        currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
137 <        currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
138 <        currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
139 <        currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
140 <        currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
141 <        currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
142 <        currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
143 <        currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
144 <        currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
145 <        
146 <        currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
147 <        currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
148 <        currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
149 <        currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
150 <        currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
151 <        currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
152 <        currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
153 <        currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
154 <        currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
155 <        
156 <        currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
157 <        currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
158 <        currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
159 <        currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
160 <        currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
161 <        currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
162 <        currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
163 <        currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
164 <        currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
165 <        
166 <        currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
167 <        currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
168 <        currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
169 <        currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
170 <        currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
171 <        currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
172 <        currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
173 <        currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
174 <        currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
175 <        
176 <        SquareMatrix<double, 6> Xir;
177 <        Xir.setSubMatrix(0, 0, currProp.Xirtt);
178 <        Xir.setSubMatrix(0, 3, currProp.Xirrt);
179 <        Xir.setSubMatrix(3, 0, currProp.Xirtr);
180 <        Xir.setSubMatrix(3, 3, currProp.Xirrr);
181 <        CholeskyDecomposition(Xir, currProp.S);            
182 <        
183 <        props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
184 <      }
239 >      HydroProp* currProp = new HydroProp(buffer);
240 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
241      }
242 <    
242 >
243      return props;
244    }
245 <  
246 <  void LDForceManager::postCalculation() {
245 >  
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 199 | Line 256 | namespace oopse {
256      Mat3x3d Atrans;
257      Vector3d Tb;
258      Vector3d ji;
202 –    double mass;
259      unsigned int index = 0;
260      bool doLangevinForces;
261      bool freezeMolecule;
262      int fdf;
263 <    
263 >
264 >
265 >
266      fdf = 0;
267 +
268      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
269 <      
269 >
270 >      doLangevinForces = true;          
271 >      freezeMolecule = false;
272 >
273        if (sphericalBoundaryConditions_) {
274          
275          Vector3d molPos = mol->getCom();
276 <        double molRad = molPos.length();
277 <        
276 >        RealType molRad = molPos.length();
277 >
278          doLangevinForces = false;
217 –        freezeMolecule = false;
279          
280          if (molRad > langevinBufferRadius_) {
281            doLangevinForces = true;
# Line 226 | Line 287 | namespace oopse {
287          }
288        }
289        
290 <      if (doLangevinForces) {
291 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
231 <             integrableObject = mol->nextIntegrableObject(j)) {
290 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 >           integrableObject = mol->nextIntegrableObject(j)) {
292            
293 +        if (freezeMolecule)
294 +          fdf += integrableObject->freeze();
295 +        
296 +        if (doLangevinForces) {  
297            vel =integrableObject->getVel();
298 +          mass = integrableObject->getMass();
299            if (integrableObject->isDirectional()){
300              //calculate angular velocity in lab frame
301              Mat3x3d I = integrableObject->getI();
# Line 249 | Line 314 | namespace oopse {
314                omega[1] = angMom[1] /I(1, 1);
315                omega[2] = angMom[2] /I(2, 2);
316              }
317 <            
317 >
318 >            //std::cerr << "I = " << I(0,0) << "\t" << I(1,1) << "\t" << I(2,2) << "\n\n";
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].cor;  
323 >            //std::cerr << "A = " << integrableObject->getA() << "\n";
324 >            //std::cerr << "Atrans = " << A.transpose() << "\n\n";
325 >            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
326 >            //std::cerr << "cor = " << hydroProps_[index]->getCOR() << "\n\n\n\n";
327 >            //std::cerr << "rcr = " << rcr << "\n\n";
328              Vector3d vcdLab = vel + cross(omega, rcr);
329 +        
330 +            //std::cerr << "velL = " << vel << "\n\n";
331 +            //std::cerr << "vcdL = " << vcdLab << "\n\n";
332              Vector3d vcdBody = A* vcdLab;
333 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
333 >            //std::cerr << "vcdB = " << vcdBody << "\n\n";
334 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
335 >
336 >            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
337 >            //std::cerr << "ffB = " << frictionForceBody << "\n\n";
338              Vector3d frictionForceLab = Atrans*frictionForceBody;
339 +            //std::cerr << "ffL = " << frictionForceLab << "\n\n";
340 +            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
341              integrableObject->addFrc(frictionForceLab);
342 <            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
342 >            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
343 >            //std::cerr << "ome = " << omega << "\n\n";
344 >            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
345 >            //std::cerr << "ftB = " << frictionTorqueBody << "\n\n";
346              Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
347 +            //std::cerr << "ftL = " << frictionTorqueLab << "\n\n";
348 +            //std::cerr << "ftL2 = " << frictionTorqueLab+cross(rcr,frictionForceLab) << "\n\n";
349 +            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
350              integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
351 <            
351 >            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
352 >
353              //apply random force and torque at center of resistance
354              Vector3d randomForceBody;
355              Vector3d randomTorqueBody;
356              genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
357 +            //std::cerr << "rfB = " << randomForceBody << "\n\n";
358 +            //std::cerr << "rtB = " << randomTorqueBody << "\n\n";
359              Vector3d randomForceLab = Atrans*randomForceBody;
360              Vector3d randomTorqueLab = Atrans* randomTorqueBody;
361              integrableObject->addFrc(randomForceLab);            
362 +            //std::cerr << "rfL = " << randomForceLab << "\n\n";
363 +            //std::cerr << "rtL = " << randomTorqueLab << "\n\n";
364 +            //std::cerr << "rtL2 = " << randomTorqueLab + cross(rcr, randomForceLab) << "\n\n";
365              integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
366              
367            } else {
368              //spherical atom
369 <            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
369 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
370 >            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
371              Vector3d randomForce;
372              Vector3d randomTorque;
373              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
374              
375              integrableObject->addFrc(frictionForce+randomForce);            
376            }
377 +        }
378            
379 <          ++index;
379 >        ++index;
380      
287 –        }
381        }
382 <      if (freezeMolecule)
383 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 <             integrableObject = mol->nextIntegrableObject(j)) {          
292 <          fdf += integrableObject->freeze();
293 <        }
294 <    }
295 <    
382 >    }    
383 >
384      info_->setFdf(fdf);
385 <    
386 <    ForceManager::postCalculation();  
385 >    veloMunge->removeComDrift();
386 >    // Remove angular drift if we are not using periodic boundary conditions.
387 >    if(!simParams->getUsePeriodicBoundaryConditions())
388 >      veloMunge->removeAngularDrift();
389 >
390 >    ForceManager::postCalculation(needStress);  
391    }
392  
393 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
393 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
394  
395  
396 <    Vector<double, 6> Z;
397 <    Vector<double, 6> generalForce;
306 <
396 >    Vector<RealType, 6> Z;
397 >    Vector<RealType, 6> generalForce;
398          
399      Z[0] = randNumGen_.randNorm(0, variance);
400      Z[1] = randNumGen_.randNorm(0, variance);
401      Z[2] = randNumGen_.randNorm(0, variance);
402 +    //Z[3] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
403 +    //Z[4] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
404 +    //Z[5] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
405      Z[3] = randNumGen_.randNorm(0, variance);
406      Z[4] = randNumGen_.randNorm(0, variance);
407      Z[5] = randNumGen_.randNorm(0, variance);
408      
409  
410 <    generalForce = hydroProps_[index].S*Z;
410 >    generalForce = hydroProps_[index]->getS()*Z;
411      
412      force[0] = generalForce[0];
413      force[1] = generalForce[1];
# Line 322 | Line 416 | void LDForceManager::genRandomForceAndTorque(Vector3d&
416      torque[1] = generalForce[4];
417      torque[2] = generalForce[5];
418      
419 < }
419 > }
420  
421   }

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