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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 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 <    std::map<std::string, HydroProp> hydroPropMap;
56 <    if (simParams->haveHydroPropFile()) {
57 <        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
58 <    } else {
59 <        //error
54 >    simParams = info->getSimParams();
55 >    veloMunge = new Velocitizer(info);
56 >
57 >    sphericalBoundaryConditions_ = false;
58 >    if (simParams->getUseSphericalBoundaryConditions()) {
59 >      sphericalBoundaryConditions_ = true;
60 >      if (simParams->haveLangevinBufferRadius()) {
61 >        langevinBufferRadius_ = simParams->getLangevinBufferRadius();
62 >      } else {
63 >        sprintf( painCave.errMsg,
64 >                 "langevinBufferRadius must be specified "
65 >                 "when useSphericalBoundaryConditions is turned on.\n");
66 >        painCave.severity = OOPSE_ERROR;
67 >        painCave.isFatal = 1;
68 >        simError();  
69 >      }
70 >    
71 >      if (simParams->haveFrozenBufferRadius()) {
72 >        frozenBufferRadius_ = simParams->getFrozenBufferRadius();
73 >      } else {
74 >        sprintf( painCave.errMsg,
75 >                 "frozenBufferRadius must be specified "
76 >                 "when useSphericalBoundaryConditions is turned on.\n");
77 >        painCave.severity = OOPSE_ERROR;
78 >        painCave.isFatal = 1;
79 >        simError();  
80 >      }
81 >
82 >      if (frozenBufferRadius_ < langevinBufferRadius_) {
83 >        sprintf( painCave.errMsg,
84 >                 "frozenBufferRadius has been set smaller than the "
85 >                 "langevinBufferRadius.  This is probably an error.\n");
86 >        painCave.severity = OOPSE_WARNING;
87 >        painCave.isFatal = 0;
88 >        simError();  
89 >      }
90      }
91  
92 <    SimInfo::MoleculeIterator i;
93 <    Molecule::IntegrableObjectIterator  j;
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;
99 <              integrableObject = mol->nextIntegrableObject(j)) {
100 <            std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
101 <            if (iter != hydroPropMap.end()) {
102 <                hydroProps_.push_back(iter->second);
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 >        
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 <                //error
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 <           }
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 <
234 >      
235      }
236 <
236 >    
237      const unsigned int BufferSize = 65535;
238      char buffer[BufferSize];  
239      while (ifs.getline(buffer, BufferSize)) {
240 <        StringTokenizer tokenizer(buffer);
241 <        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 <        }
240 >      HydroProp* currProp = new HydroProp(buffer);
241 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
242      }
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 155 | Line 257 | namespace oopse {
257      Mat3x3d Atrans;
258      Vector3d Tb;
259      Vector3d ji;
158 –    double mass;
260      unsigned int index = 0;
261 +    bool doLangevinForces;
262 +    bool freezeMolecule;
263 +    int fdf;
264 +
265 +
266 +
267 +    fdf = 0;
268 +
269      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
161 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
162 –           integrableObject = mol->nextIntegrableObject(j)) {
270  
271 +      doLangevinForces = true;          
272 +      freezeMolecule = false;
273 +
274 +      if (sphericalBoundaryConditions_) {
275 +        
276 +        Vector3d molPos = mol->getCom();
277 +        RealType molRad = molPos.length();
278 +
279 +        doLangevinForces = false;
280 +        
281 +        if (molRad > langevinBufferRadius_) {
282 +          doLangevinForces = true;
283 +          freezeMolecule = false;
284 +        }
285 +        if (molRad > frozenBufferRadius_) {
286 +          doLangevinForces = false;
287 +          freezeMolecule = true;
288 +        }
289 +      }
290 +      
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();
303 <             Vector3d angMom = integrableObject->getJ();
304 <             Vector3d omega;
301 >            //calculate angular velocity in lab frame
302 >            Mat3x3d I = integrableObject->getI();
303 >            Vector3d angMom = integrableObject->getJ();
304 >            Vector3d omega;
305 >            
306 >            if (integrableObject->isLinear()) {
307 >              int linearAxis = integrableObject->linearAxis();
308 >              int l = (linearAxis +1 )%3;
309 >              int m = (linearAxis +2 )%3;
310 >              omega[l] = angMom[l] /I(l, l);
311 >              omega[m] = angMom[m] /I(m, m);
312 >              
313 >            } else {
314 >              omega[0] = angMom[0] /I(0, 0);
315 >              omega[1] = angMom[1] /I(1, 1);
316 >              omega[2] = angMom[2] /I(2, 2);
317 >            }
318  
319 <             if (integrableObject->isLinear()) {
172 <                int linearAxis = integrableObject->linearAxis();
173 <                int l = (linearAxis +1 )%3;
174 <                int m = (linearAxis +2 )%3;
175 <                omega[l] = angMom[l] /I(l, l);
176 <                omega[m] = angMom[m] /I(m, m);
177 <                
178 <             } else {
179 <                 omega[0] = angMom[0] /I(0, 0);
180 <                 omega[1] = angMom[1] /I(1, 1);
181 <                 omega[2] = angMom[2] /I(2, 2);
182 <             }
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;  
325 <             Vector3d vcdLab = vel + cross(omega, rcr);
326 <             Vector3d vcdBody = A* vcdLab;
327 <             Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
328 <             Vector3d frictionForceLab = Atrans*frictionForceBody;
329 <             integrableObject->addFrc(frictionForceLab);
330 <             Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
331 <             Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
332 <             integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
321 >            //apply friction force and torque at center of resistance
322 >            A = integrableObject->getA();
323 >            Atrans = A.transpose();
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 >            //std::cerr << "vcdB = " << vcdBody << "\n\n";
335 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
336  
337 <             //apply random force and torque at center of resistance
338 <             Vector3d randomForceBody;
339 <             Vector3d randomTorqueBody;
340 <             genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
341 <             Vector3d randomForceLab = Atrans*randomForceBody;
342 <             Vector3d randomTorqueLab = Atrans* randomTorqueBody;
343 <             integrableObject->addFrc(randomForceLab);            
344 <             integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
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 >            //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 >            //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 <             //spheric atom
370 <             Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
371 <             Vector3d randomForce;
372 <             Vector3d randomTorque;
373 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
374 <
375 <             integrableObject->addFrc(frictionForce+randomForce);            
369 >            //spherical atom
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 <
378 >        }
379 >          
380          ++index;
381      
382        }
383      }    
384  
385 <    ForceManager::postCalculation();
385 >    info_->setFdf(fdf);
386 >    veloMunge->removeComDrift();
387 >    // Remove angular drift if we are not using periodic boundary conditions.
388 >    if(!simParams->getUsePeriodicBoundaryConditions())
389 >      veloMunge->removeAngularDrift();
390  
391 <
224 <
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;
232 <
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 248 | 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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