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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 1185 by xsun, Fri Oct 5 19:02:09 2007 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 "openbabel/mol.hpp"
49 +
50 + using namespace OpenBabel;
51   namespace oopse {
52  
53    LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
54 <    Globals* simParams = info->getSimParams();
55 <    
56 <    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 <    
54 >    simParams = info->getSimParams();
55 >    veloMunge = new Velocitizer(info);
56 >
57      sphericalBoundaryConditions_ = false;
58      if (simParams->getUseSphericalBoundaryConditions()) {
59        sphericalBoundaryConditions_ = true;
# Line 92 | Line 88 | namespace oopse {
88          simError();  
89        }
90      }
91 <      
92 <    SimInfo::MoleculeIterator i;
93 <    Molecule::IntegrableObjectIterator  j;
91 >
92 >    // Build the hydroProp map:
93 >    std::map<std::string, HydroProp*> hydroPropMap;
94 >
95      Molecule* mol;
96      StuntDouble* integrableObject;
97 <    for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
98 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
97 >    SimInfo::MoleculeIterator i;
98 >    Molecule::IntegrableObjectIterator  j;              
99 >    bool needHydroPropFile = false;
100 >    
101 >    for (mol = info->beginMolecule(i); mol != NULL;
102 >         mol = info->nextMolecule(i)) {
103 >      for (integrableObject = mol->beginIntegrableObject(j);
104 >           integrableObject != NULL;
105             integrableObject = mol->nextIntegrableObject(j)) {
106 <        std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
107 <        if (iter != hydroPropMap.end()) {
108 <          hydroProps_.push_back(iter->second);
109 <        } 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();  
106 >        
107 >        if (integrableObject->isRigidBody()) {
108 >          RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109 >          if (rb->getNumAtoms() > 1) needHydroPropFile = true;
110          }
111          
112        }
113      }
114 +        
115 +
116 +    if (needHydroPropFile) {              
117 +      if (simParams->haveHydroPropFile()) {
118 +        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
119 +      } else {              
120 +        sprintf( painCave.errMsg,
121 +                 "HydroPropFile must be set to a file name if Langevin\n"
122 +                 "\tDynamics is specified for rigidBodies which contain more\n"
123 +                 "\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
124 +        painCave.severity = OOPSE_ERROR;
125 +        painCave.isFatal = 1;
126 +        simError();  
127 +      }      
128 +
129 +      for (mol = info->beginMolecule(i); mol != NULL;
130 +           mol = info->nextMolecule(i)) {
131 +        for (integrableObject = mol->beginIntegrableObject(j);
132 +             integrableObject != NULL;
133 +             integrableObject = mol->nextIntegrableObject(j)) {
134 +
135 +          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
136 +          if (iter != hydroPropMap.end()) {
137 +            hydroProps_.push_back(iter->second);
138 +          } else {
139 +            sprintf( painCave.errMsg,
140 +                     "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
141 +            painCave.severity = OOPSE_ERROR;
142 +            painCave.isFatal = 1;
143 +            simError();  
144 +          }        
145 +        }
146 +      }
147 +    } else {
148 +      
149 +      std::map<std::string, HydroProp*> hydroPropMap;
150 +      for (mol = info->beginMolecule(i); mol != NULL;
151 +           mol = info->nextMolecule(i)) {
152 +        for (integrableObject = mol->beginIntegrableObject(j);
153 +             integrableObject != NULL;
154 +             integrableObject = mol->nextIntegrableObject(j)) {
155 +          Shape* currShape = NULL;
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);              
162 +              GenericData* data = dAtomType->getPropertyByName("GayBerne");
163 +              if (data != NULL) {
164 +                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
165 +                
166 +                if (gayBerneData != NULL) {  
167 +                  GayBerneParam gayBerneParam = gayBerneData->getData();
168 +                  currShape = new Ellipsoid(V3Zero,
169 +                                            gayBerneParam.GB_l / 2.0,
170 +                                            gayBerneParam.GB_d / 2.0,
171 +                                            Mat3x3d::identity());
172 +                } else {
173 +                  sprintf( painCave.errMsg,
174 +                           "Can not cast GenericData to GayBerneParam\n");
175 +                  painCave.severity = OOPSE_ERROR;
176 +                  painCave.isFatal = 1;
177 +                  simError();  
178 +                }
179 +              } else {
180 +                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
181 +                painCave.severity = OOPSE_ERROR;
182 +                painCave.isFatal = 1;
183 +                simError();    
184 +              }
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 +                           "Could not find atom type in default element.txt\n");
208 +                  painCave.severity = OOPSE_ERROR;
209 +                  painCave.isFatal = 1;
210 +                  simError();          
211 +                }
212 +              }
213 +            }
214 +          }
215 +          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
216 +          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
217 +          if (iter != hydroPropMap.end())
218 +            hydroProps_.push_back(iter->second);
219 +          else {
220 +            currHydroProp->complete();
221 +            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
222 +            hydroProps_.push_back(currHydroProp);
223 +          }
224 +        }
225 +      }
226 +    }
227      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
228 <  }
229 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
230 <    std::map<std::string, HydroProp> props;
228 >  }  
229 >
230 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
231 >    std::map<std::string, HydroProp*> props;
232      std::ifstream ifs(filename.c_str());
233      if (ifs.is_open()) {
234        
# Line 125 | Line 237 | namespace oopse {
237      const unsigned int BufferSize = 65535;
238      char buffer[BufferSize];  
239      while (ifs.getline(buffer, BufferSize)) {
240 <      StringTokenizer tokenizer(buffer);
241 <      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 <      }
240 >      HydroProp* currProp = new HydroProp(buffer);
241 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
242      }
243 <    
243 >
244      return props;
245    }
246 <  
247 <  void LDForceManager::postCalculation() {
246 >  
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 199 | Line 257 | namespace oopse {
257      Mat3x3d Atrans;
258      Vector3d Tb;
259      Vector3d ji;
202 –    double mass;
260      unsigned int index = 0;
261      bool doLangevinForces;
262      bool freezeMolecule;
263      int fdf;
264 <    
264 >
265 >
266 >
267      fdf = 0;
268 +
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 <        double molRad = molPos.length();
278 <        
277 >        RealType molRad = molPos.length();
278 >
279          doLangevinForces = false;
217 –        freezeMolecule = false;
280          
281          if (molRad > langevinBufferRadius_) {
282            doLangevinForces = true;
# Line 226 | Line 288 | namespace oopse {
288          }
289        }
290        
291 <      if (doLangevinForces) {
292 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
231 <             integrableObject = mol->nextIntegrableObject(j)) {
291 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292 >           integrableObject = mol->nextIntegrableObject(j)) {
293            
294 +        if (freezeMolecule)
295 +          fdf += integrableObject->freeze();
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 249 | 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 <            Vector3d rcr = Atrans * hydroProps_[index].cor;  
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 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
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 <            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
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].Xirtt *vel);    
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_);
375              
376              integrableObject->addFrc(frictionForce+randomForce);            
377            }
378 +        }
379            
380 <          ++index;
380 >        ++index;
381      
287 –        }
382        }
383 <      if (freezeMolecule)
384 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 <             integrableObject = mol->nextIntegrableObject(j)) {          
292 <          fdf += integrableObject->freeze();
293 <        }
294 <    }
295 <    
383 >    }    
384 >
385      info_->setFdf(fdf);
386 <    
387 <    ForceManager::postCalculation();  
386 >    veloMunge->removeComDrift();
387 >    // Remove angular drift if we are not using periodic boundary conditions.
388 >    if(!simParams->getUsePeriodicBoundaryConditions())
389 >      veloMunge->removeAngularDrift();
390 >
391 >    ForceManager::postCalculation(needStress);  
392    }
393  
394 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
394 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
395  
396  
397 <    Vector<double, 6> Z;
398 <    Vector<double, 6> generalForce;
306 <
397 >    Vector<RealType, 6> Z;
398 >    Vector<RealType, 6> generalForce;
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);
409      
410  
411 <    generalForce = hydroProps_[index].S*Z;
411 >    generalForce = hydroProps_[index]->getS()*Z;
412      
413      force[0] = generalForce[0];
414      force[1] = generalForce[1];
# Line 322 | 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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