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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 1216 by xsun, Wed Jan 23 21:22:50 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()){
235 –            //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].cor;  
324 <            Vector3d vcdLab = vel + cross(omega, rcr);
325 <            Vector3d vcdBody = A* vcdLab;
326 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * 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].Xirtr * vcdBody + hydroProps_[index].Xirrr * 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
347 <            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
347 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
348              Vector3d randomForce;
349              Vector3d randomTorque;
350              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
351              
352              integrableObject->addFrc(frictionForce+randomForce);            
353            }
354 +        }
355            
356 <          ++index;
356 >        ++index;
357      
287 –        }
358        }
359 <      if (freezeMolecule)
360 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 <             integrableObject = mol->nextIntegrableObject(j)) {          
292 <          fdf += integrableObject->freeze();
293 <        }
294 <    }
295 <    
359 >    }    
360 >
361      info_->setFdf(fdf);
362 <    
363 <    ForceManager::postCalculation();  
362 >    veloMunge->removeComDrift();
363 >    // Remove angular drift if we are not using periodic boundary conditions.
364 >    if(!simParams->getUsePeriodicBoundaryConditions())
365 >      veloMunge->removeAngularDrift();
366 >
367 >    ForceManager::postCalculation(needStress);  
368    }
369  
370 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
370 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
371  
372  
373 <    Vector<double, 6> Z;
374 <    Vector<double, 6> generalForce;
306 <
373 >    Vector<RealType, 6> Z;
374 >    Vector<RealType, 6> generalForce;
375          
376      Z[0] = randNumGen_.randNorm(0, variance);
377      Z[1] = randNumGen_.randNorm(0, variance);
# Line 312 | Line 380 | void LDForceManager::genRandomForceAndTorque(Vector3d&
380      Z[4] = randNumGen_.randNorm(0, variance);
381      Z[5] = randNumGen_.randNorm(0, variance);
382      
383 <
316 <    generalForce = hydroProps_[index].S*Z;
383 >    generalForce = hydroProps_[index]->getS()*Z;
384      
385      force[0] = generalForce[0];
386      force[1] = generalForce[1];
# Line 322 | 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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