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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 908 by tim, Mon Mar 20 19:12:14 2006 UTC vs.
Revision 1237 by gezelter, Fri Apr 18 16:55:15 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 <    std::map<std::string, HydroProp> hydroPropMap;
55 <    if (simParams->haveHydroPropFile()) {
56 <        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
57 <    } else {
58 <        //error
52 >  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
53 >    simParams = info->getSimParams();
54 >    veloMunge = new Velocitizer(info);
55 >
56 >    sphericalBoundaryConditions_ = false;
57 >    if (simParams->getUseSphericalBoundaryConditions()) {
58 >      sphericalBoundaryConditions_ = true;
59 >      if (simParams->haveLangevinBufferRadius()) {
60 >        langevinBufferRadius_ = simParams->getLangevinBufferRadius();
61 >      } else {
62 >        sprintf( painCave.errMsg,
63 >                 "langevinBufferRadius must be specified "
64 >                 "when useSphericalBoundaryConditions is turned on.\n");
65 >        painCave.severity = OOPSE_ERROR;
66 >        painCave.isFatal = 1;
67 >        simError();  
68 >      }
69 >    
70 >      if (simParams->haveFrozenBufferRadius()) {
71 >        frozenBufferRadius_ = simParams->getFrozenBufferRadius();
72 >      } else {
73 >        sprintf( painCave.errMsg,
74 >                 "frozenBufferRadius must be specified "
75 >                 "when useSphericalBoundaryConditions is turned on.\n");
76 >        painCave.severity = OOPSE_ERROR;
77 >        painCave.isFatal = 1;
78 >        simError();  
79 >      }
80 >
81 >      if (frozenBufferRadius_ < langevinBufferRadius_) {
82 >        sprintf( painCave.errMsg,
83 >                 "frozenBufferRadius has been set smaller than the "
84 >                 "langevinBufferRadius.  This is probably an error.\n");
85 >        painCave.severity = OOPSE_WARNING;
86 >        painCave.isFatal = 0;
87 >        simError();  
88 >      }
89      }
90  
91 <    SimInfo::MoleculeIterator i;
92 <    Molecule::IntegrableObjectIterator  j;
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;
98 <              integrableObject = mol->nextIntegrableObject(j)) {
99 <            std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
100 <            if (iter != hydroPropMap.end()) {
101 <                hydroProps_.push_back(iter->second);
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 >        
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 Dynamics\n"
121 >                 "\tis specified for rigidBodies which contain more than one atom\n"
122 >                 "\tTo create a HydroPropFile, run the \"Hydro\" program.\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 <                //error
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 aNum = etab.GetAtomicNum((atom->getType()).c_str());
202 >                if (aNum != 0) {
203 >                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
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 <           }
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 <
233 >      
234      }
235 <
235 >    
236      const unsigned int BufferSize = 65535;
237      char buffer[BufferSize];  
238      while (ifs.getline(buffer, BufferSize)) {
239 <        StringTokenizer tokenizer(buffer);
240 <        HydroProp currProp;
86 <        if (tokenizer.countTokens() >= 40) {
87 <            std::string atomName = tokenizer.nextToken();
88 <            currProp.cor[0] = tokenizer.nextTokenAsDouble();
89 <            currProp.cor[1] = tokenizer.nextTokenAsDouble();
90 <            currProp.cor[2] = tokenizer.nextTokenAsDouble();
91 <            
92 <            currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
93 <            currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
94 <            currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
95 <            currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
96 <            currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
97 <            currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
98 <            currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
99 <            currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
100 <            currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
101 <
102 <            currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
103 <            currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
104 <            currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
105 <            currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
106 <            currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
107 <            currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
108 <            currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
109 <            currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
110 <            currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
111 <        
112 <            currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
113 <            currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
114 <            currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
115 <            currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
116 <            currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
117 <            currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
118 <            currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
119 <            currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
120 <            currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
121 <
122 <            currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
123 <            currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
124 <            currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
125 <            currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
126 <            currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
127 <            currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
128 <            currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
129 <            currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
130 <            currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
131 <
132 <            SquareMatrix<double, 6> Xir;
133 <            Xir.setSubMatrix(0, 0, currProp.Xirtt);
134 <            Xir.setSubMatrix(0, 3, currProp.Xirrt);
135 <            Xir.setSubMatrix(3, 0, currProp.Xirtr);
136 <            Xir.setSubMatrix(3, 3, currProp.Xirrr);
137 <            CholeskyDecomposition(Xir, currProp.S);            
138 <
139 <            props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
140 <        }
239 >      HydroProp* currProp = new HydroProp(buffer);
240 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
241      }
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 <    Vector3d vel;
251 >    RealType mass;
252      Vector3d pos;
253      Vector3d frc;
254      Mat3x3d A;
255      Mat3x3d Atrans;
256      Vector3d Tb;
257      Vector3d ji;
158 –    double mass;
258      unsigned int index = 0;
259 +    bool doLangevinForces;
260 +    bool freezeMolecule;
261 +    int fdf;
262 +
263 +    fdf = 0;
264 +
265      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
161 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
162 –           integrableObject = mol->nextIntegrableObject(j)) {
266  
267 <          vel =integrableObject->getVel();
267 >      doLangevinForces = true;          
268 >      freezeMolecule = false;
269 >
270 >      if (sphericalBoundaryConditions_) {
271 >        
272 >        Vector3d molPos = mol->getCom();
273 >        RealType molRad = molPos.length();
274 >
275 >        doLangevinForces = false;
276 >        
277 >        if (molRad > langevinBufferRadius_) {
278 >          doLangevinForces = true;
279 >          freezeMolecule = false;
280 >        }
281 >        if (molRad > frozenBufferRadius_) {
282 >          doLangevinForces = false;
283 >          freezeMolecule = true;
284 >        }
285 >      }
286 >      
287 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
288 >           integrableObject = mol->nextIntegrableObject(j)) {
289 >          
290 >        if (freezeMolecule)
291 >          fdf += integrableObject->freeze();
292 >        
293 >        if (doLangevinForces) {  
294 >          mass = integrableObject->getMass();
295            if (integrableObject->isDirectional()){
166 –             //calculate angular velocity in lab frame
167 –             Mat3x3d I = integrableObject->getI();
168 –             Vector3d angMom = integrableObject->getJ();
169 –             Vector3d omega;
296  
297 <             if (integrableObject->isLinear()) {
297 >            // preliminaries for directional objects:
298 >
299 >            A = integrableObject->getA();
300 >            Atrans = A.transpose();
301 >            Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
302 >
303 >            //apply random force and torque at center of resistance
304 >
305 >            Vector3d randomForceBody;
306 >            Vector3d randomTorqueBody;
307 >            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
308 >            Vector3d randomForceLab = Atrans * randomForceBody;
309 >            Vector3d randomTorqueLab = Atrans * randomTorqueBody;
310 >            integrableObject->addFrc(randomForceLab);            
311 >            integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));            
312 >
313 >            Mat3x3d I = integrableObject->getI();
314 >            Vector3d omegaBody;
315 >
316 >            // What remains contains velocity explicitly, but the velocity required
317 >            // is at the full step: v(t + h), while we have initially the velocity
318 >            // at the half step: v(t + h/2).  We need to iterate to converge the
319 >            // friction force and friction torque vectors.
320 >
321 >            // this is the velocity at the half-step:
322 >            
323 >            Vector3d vel =integrableObject->getVel();
324 >            Vector3d angMom = integrableObject->getJ();
325 >
326 >            //estimate velocity at full-step using everything but friction forces:          
327 >
328 >            frc = integrableObject->getFrc();
329 >            Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
330 >
331 >            Tb = integrableObject->lab2Body(integrableObject->getTrq());
332 >            Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;                            
333 >
334 >            Vector3d omegaLab;
335 >            Vector3d vcdLab;
336 >            Vector3d vcdBody;
337 >            Vector3d frictionForceBody;
338 >            Vector3d frictionForceLab(0.0);
339 >            Vector3d oldFFL;  // used to test for convergence
340 >            Vector3d frictionTorqueBody(0.0);
341 >            Vector3d oldFTB;  // used to test for convergence
342 >            Vector3d frictionTorqueLab;
343 >            RealType fdot;
344 >            RealType tdot;
345 >
346 >            //iteration starts here:
347 >
348 >            for (int k = 0; k < maxIterNum_; k++) {
349 >                            
350 >              if (integrableObject->isLinear()) {
351                  int linearAxis = integrableObject->linearAxis();
352                  int l = (linearAxis +1 )%3;
353                  int m = (linearAxis +2 )%3;
354 <                omega[l] = angMom[l] /I(l, l);
355 <                omega[m] = angMom[m] /I(m, m);
354 >                omegaBody[l] = angMomStep[l] /I(l, l);
355 >                omegaBody[m] = angMomStep[m] /I(m, m);
356                  
357 <             } else {
358 <                 omega[0] = angMom[0] /I(0, 0);
359 <                 omega[1] = angMom[1] /I(1, 1);
360 <                 omega[2] = angMom[2] /I(2, 2);
361 <             }
357 >              } else {
358 >                omegaBody[0] = angMomStep[0] /I(0, 0);
359 >                omegaBody[1] = angMomStep[1] /I(1, 1);
360 >                omegaBody[2] = angMomStep[2] /I(2, 2);
361 >              }
362 >              
363 >              omegaLab = Atrans * omegaBody;
364 >              
365 >              // apply friction force and torque at center of resistance
366 >              
367 >              vcdLab = velStep + cross(omegaLab, rcrLab);      
368 >              vcdBody = A * vcdLab;
369 >              frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
370 >              oldFFL = frictionForceLab;
371 >              frictionForceLab = Atrans * frictionForceBody;
372 >              oldFTB = frictionTorqueBody;
373 >              frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
374 >              frictionTorqueLab = Atrans * frictionTorqueBody;
375 >              
376 >              // re-estimate velocities at full-step using friction forces:
377 >              
378 >              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
379 >              angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
380  
381 <             //apply friction force and torque at center of resistance
382 <             A = integrableObject->getA();
383 <             Atrans = A.transpose();
384 <             Vector3d rcr = Atrans * hydroProps_[index].cor;  
385 <             Vector3d vcdLab = vel + cross(omega, rcr);
386 <             Vector3d vcdBody = A* vcdLab;
387 <             Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
388 <             Vector3d frictionForceLab = Atrans*frictionForceBody;
192 <             integrableObject->addFrc(frictionForceLab);
193 <             Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
194 <             Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
195 <             integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
381 >              // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
382 >              
383 >              fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
384 >              tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
385 >              
386 >              if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
387 >                break; // iteration ends here
388 >            }
389  
390 <             //apply random force and torque at center of resistance
391 <             Vector3d randomForceBody;
199 <             Vector3d randomTorqueBody;
200 <             genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
201 <             Vector3d randomForceLab = Atrans*randomForceBody;
202 <             Vector3d randomTorqueLab = Atrans* randomTorqueBody;
203 <             integrableObject->addFrc(randomForceLab);            
204 <             integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
390 >            integrableObject->addFrc(frictionForceLab);
391 >            integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
392  
393 +            
394            } else {
395 <             //spheric atom
208 <             Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
209 <             Vector3d randomForce;
210 <             Vector3d randomTorque;
211 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
395 >            //spherical atom
396  
397 <             integrableObject->addFrc(frictionForce+randomForce);            
398 <          }
397 >            Vector3d randomForce;
398 >            Vector3d randomTorque;
399 >            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
400 >            integrableObject->addFrc(randomForce);            
401  
402 +            // What remains contains velocity explicitly, but the velocity required
403 +            // is at the full step: v(t + h), while we have initially the velocity
404 +            // at the half step: v(t + h/2).  We need to iterate to converge the
405 +            // friction force vector.
406 +
407 +            // this is the velocity at the half-step:
408 +            
409 +            Vector3d vel =integrableObject->getVel();
410 +
411 +            //estimate velocity at full-step using everything but friction forces:          
412 +
413 +            frc = integrableObject->getFrc();
414 +            Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
415 +
416 +            Vector3d frictionForce(0.0);
417 +            Vector3d oldFF;  // used to test for convergence
418 +            RealType fdot;
419 +
420 +            //iteration starts here:
421 +
422 +            for (int k = 0; k < maxIterNum_; k++) {
423 +
424 +              oldFF = frictionForce;                            
425 +              frictionForce = -hydroProps_[index]->getXitt() * velStep;
426 +
427 +              // re-estimate velocities at full-step using friction forces:
428 +              
429 +              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
430 +
431 +              // check for convergence (if the vector has converged, fdot will be 1.0):
432 +              
433 +              fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
434 +              
435 +              if (fabs(1.0 - fdot) <= forceTolerance_)
436 +                break; // iteration ends here
437 +            }
438 +
439 +            integrableObject->addFrc(frictionForce);
440 +
441 +          }
442 +        }
443 +          
444          ++index;
445      
446        }
447      }    
448  
449 <    ForceManager::postCalculation();
449 >    info_->setFdf(fdf);
450 >    veloMunge->removeComDrift();
451 >    // Remove angular drift if we are not using periodic boundary conditions.
452 >    if(!simParams->getUsePeriodicBoundaryConditions())
453 >      veloMunge->removeAngularDrift();
454  
455 <
224 <
455 >    ForceManager::postCalculation(needStress);  
456    }
457  
458 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
458 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
459  
460  
461 <    Vector<double, 6> Z;
462 <    Vector<double, 6> generalForce;
232 <
461 >    Vector<RealType, 6> Z;
462 >    Vector<RealType, 6> generalForce;
463          
464      Z[0] = randNumGen_.randNorm(0, variance);
465      Z[1] = randNumGen_.randNorm(0, variance);
# Line 238 | Line 468 | void LDForceManager::genRandomForceAndTorque(Vector3d&
468      Z[4] = randNumGen_.randNorm(0, variance);
469      Z[5] = randNumGen_.randNorm(0, variance);
470      
471 <
242 <    generalForce = hydroProps_[index].S*Z;
471 >    generalForce = hydroProps_[index]->getS()*Z;
472      
473      force[0] = generalForce[0];
474      force[1] = generalForce[1];
# Line 248 | Line 477 | void LDForceManager::genRandomForceAndTorque(Vector3d&
477      torque[1] = generalForce[4];
478      torque[2] = generalForce[5];
479      
480 < }
480 > }
481  
482   }

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