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root/OpenMD/trunk/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 1120 by chuckv, Fri Feb 2 18:55:21 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"
# Line 50 | Line 51 | namespace oopse {
51   namespace oopse {
52  
53    LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
54 <    Globals* simParams = info->getSimParams();
55 <        
54 >    simParams = info->getSimParams();
55 >    veloMunge = new Velocitizer(info);
56 >
57      sphericalBoundaryConditions_ = false;
58      if (simParams->getUseSphericalBoundaryConditions()) {
59        sphericalBoundaryConditions_ = true;
# Line 88 | Line 90 | namespace oopse {
90      }
91  
92      // Build the hydroProp map:
93 <    std::map<std::string, HydroProp> hydroPropMap;
93 >    std::map<std::string, HydroProp*> hydroPropMap;
94  
95      Molecule* mol;
96      StuntDouble* integrableObject;
# Line 123 | Line 125 | namespace oopse {
125          painCave.isFatal = 1;
126          simError();  
127        }      
128 <      std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
129 <      if (iter != hydroPropMap.end()) {
130 <        hydroProps_.push_back(iter->second);
131 <      } else {
132 <        sprintf( painCave.errMsg,
133 <                 "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
134 <        painCave.severity = OOPSE_ERROR;
135 <        painCave.isFatal = 1;
136 <        simError();  
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;
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);
# Line 155 | Line 166 | namespace oopse {
166                  if (gayBerneData != NULL) {  
167                    GayBerneParam gayBerneParam = gayBerneData->getData();
168                    currShape = new Ellipsoid(V3Zero,
169 <                                            gayBerneParam.GB_sigma/2.0,
170 <                                            gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0,
169 >                                            gayBerneParam.GB_d / 2.0,
170 >                                            gayBerneParam.GB_l / 2.0,
171                                              Mat3x3d::identity());
172                  } else {
173                    sprintf( painCave.errMsg,
# Line 204 | Line 215 | namespace oopse {
215                }
216              }
217            }
218 <          HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
219 <          std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
218 >          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
219 >          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
220            if (iter != hydroPropMap.end())
221              hydroProps_.push_back(iter->second);
222            else {
223 <            HydroProp myProp;
224 <            myProp.cor = V3Zero;
225 <            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);
223 >            currHydroProp->complete();
224 >            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
225 >            hydroProps_.push_back(currHydroProp);
226            }
227          }
228        }
229      }
230      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
231 <  }
231 <  
232 <  
231 >  }  
232  
233 <
234 <
236 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237 <    std::map<std::string, HydroProp> props;
233 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
234 >    std::map<std::string, HydroProp*> props;
235      std::ifstream ifs(filename.c_str());
236      if (ifs.is_open()) {
237        
# Line 243 | Line 240 | namespace oopse {
240      const unsigned int BufferSize = 65535;
241      char buffer[BufferSize];  
242      while (ifs.getline(buffer, BufferSize)) {
243 <      StringTokenizer tokenizer(buffer);
244 <      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 <      }
243 >      HydroProp* currProp = new HydroProp(buffer);
244 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
245      }
246 <    
246 >
247      return props;
248    }
249 <  
249 >  
250    void LDForceManager::postCalculation() {
251      SimInfo::MoleculeIterator i;
252      Molecule::IntegrableObjectIterator  j;
# Line 322 | Line 264 | namespace oopse {
264      bool doLangevinForces;
265      bool freezeMolecule;
266      int fdf;
267 <    
267 >    int nIntegrated;
268 >    int nFrozen;
269 >
270      fdf = 0;
271 +
272      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
273 <      
273 >
274 >      doLangevinForces = true;          
275 >      freezeMolecule = false;
276 >
277        if (sphericalBoundaryConditions_) {
278          
279          Vector3d molPos = mol->getCom();
280          RealType molRad = molPos.length();
281 <        
281 >
282          doLangevinForces = false;
335 –        freezeMolecule = false;
283          
284          if (molRad > langevinBufferRadius_) {
285            doLangevinForces = true;
# Line 350 | Line 297 | namespace oopse {
297          if (freezeMolecule)
298            fdf += integrableObject->freeze();
299          
300 <        if (doLangevinForces) {          
300 >        if (doLangevinForces) {  
301            vel =integrableObject->getVel();
302            if (integrableObject->isDirectional()){
303              //calculate angular velocity in lab frame
# Line 374 | Line 321 | namespace oopse {
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 >            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
325              Vector3d vcdLab = vel + cross(omega, rcr);
326              Vector3d vcdBody = A* vcdLab;
327 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
327 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
328              Vector3d frictionForceLab = Atrans*frictionForceBody;
329              integrableObject->addFrc(frictionForceLab);
330 <            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
330 >            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
331              Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
332              integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
333              
# Line 395 | Line 342 | namespace oopse {
342              
343            } else {
344              //spherical atom
345 <            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
345 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
346              Vector3d randomForce;
347              Vector3d randomTorque;
348              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
# Line 408 | Line 355 | namespace oopse {
355      
356        }
357      }    
358 +
359      info_->setFdf(fdf);
360 <    
360 >    veloMunge->removeComDrift();
361 >    // Remove angular drift if we are not using periodic boundary conditions.
362 >    if(!simParams->getUsePeriodicBoundaryConditions())
363 >      veloMunge->removeAngularDrift();
364 >
365      ForceManager::postCalculation();  
366    }
367  
# Line 428 | Line 380 | void LDForceManager::genRandomForceAndTorque(Vector3d&
380      Z[5] = randNumGen_.randNorm(0, variance);
381      
382  
383 <    generalForce = hydroProps_[index].S*Z;
383 >    generalForce = hydroProps_[index]->getS()*Z;
384      
385      force[0] = generalForce[0];
386      force[1] = generalForce[1];

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