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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 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 "openbabel/mol.hpp"
48 > #include "utils/ElementsTable.hpp"
49  
49 – using namespace OpenBabel;
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);
152               integrableObject != NULL;
153               integrableObject = mol->nextIntegrableObject(j)) {
154            Shape* currShape = NULL;
155 <          if (integrableObject->isDirectionalAtom()) {
156 <            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
157 <            AtomType* atomType = dAtom->getAtomType();
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);
150 <              
160 >              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
161                GenericData* data = dAtomType->getPropertyByName("GayBerne");
162                if (data != NULL) {
163                  GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
# 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_l / 2.0,
169 >                                            gayBerneParam.GB_d / 2.0,
170                                              Mat3x3d::identity());
171                  } else {
172                    sprintf( painCave.errMsg,
# Line 171 | Line 181 | namespace oopse {
181                  painCave.isFatal = 1;
182                  simError();    
183                }
184 <            }
185 <          } else {
186 <            Atom* atom = static_cast<Atom*>(integrableObject);
187 <            AtomType* atomType = atom->getAtomType();
188 <            if (atomType->isLennardJones()){
189 <              GenericData* data = atomType->getPropertyByName("LennardJones");
190 <              if (data != NULL) {
191 <                LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
192 <                
193 <                if (ljData != NULL) {
194 <                  LJParam ljParam = ljData->getData();
195 <                  currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
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 <                           "Can not cast GenericData to LJParam\n");
206 >                           "Could not find atom type in default element.txt\n");
207                    painCave.severity = OOPSE_ERROR;
208                    painCave.isFatal = 1;
209                    simError();          
210 <                }      
210 >                }
211                }
194 –            } else {
195 –              int obanum = etab.GetAtomicNum((atom->getType()).c_str());
196 –              if (obanum != 0) {
197 –                currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
198 –              } else {
199 –                sprintf( painCave.errMsg,
200 –                         "Could not find atom type in default element.txt\n");
201 –                painCave.severity = OOPSE_ERROR;
202 –                painCave.isFatal = 1;
203 –                simError();          
204 –              }
212              }
213            }
214 <          HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
215 <          std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
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 <            HydroProp myProp;
220 <            myProp.cor = V3Zero;
221 <            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);
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 <  }
231 <  
232 <  
227 >  }  
228  
229 <
230 <
236 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237 <    std::map<std::string, HydroProp> props;
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 243 | 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;
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 <      }
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 317 | Line 256 | namespace oopse {
256      Mat3x3d Atrans;
257      Vector3d Tb;
258      Vector3d ji;
320 –    RealType 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          RealType molRad = molPos.length();
277 <        
277 >
278          doLangevinForces = false;
335 –        freezeMolecule = false;
279          
280          if (molRad > langevinBufferRadius_) {
281            doLangevinForces = true;
# Line 350 | Line 293 | namespace oopse {
293          if (freezeMolecule)
294            fdf += integrableObject->freeze();
295          
296 <        if (doLangevinForces) {          
296 >        if (doLangevinForces) {  
297            vel =integrableObject->getVel();
298 +          mass = integrableObject->getMass();
299            if (integrableObject->isDirectional()){
356 –            //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_);
# Line 408 | Line 357 | namespace oopse {
357      
358        }
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, RealType variance) {
# Line 418 | Line 372 | void LDForceManager::genRandomForceAndTorque(Vector3d&
372  
373      Vector<RealType, 6> Z;
374      Vector<RealType, 6> generalForce;
421 –
375          
376      Z[0] = randNumGen_.randNorm(0, variance);
377      Z[1] = randNumGen_.randNorm(0, variance);
# Line 427 | Line 380 | void LDForceManager::genRandomForceAndTorque(Vector3d&
380      Z[4] = randNumGen_.randNorm(0, variance);
381      Z[5] = randNumGen_.randNorm(0, variance);
382      
383 <
431 <    generalForce = hydroProps_[index].S*Z;
383 >    generalForce = hydroProps_[index]->getS()*Z;
384      
385      force[0] = generalForce[0];
386      force[1] = generalForce[1];
# Line 437 | 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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