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root/group/trunk/OOPSE-4/src/integrators/LDForceManager.cpp
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Comparing trunk/OOPSE-4/src/integrators/LDForceManager.cpp (file contents):
Revision 2634 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 2752 by gezelter, Tue May 16 02:06:37 2006 UTC

# Line 42 | Line 42 | namespace oopse {
42   #include "integrators/LDForceManager.hpp"
43   #include "math/CholeskyDecomposition.hpp"
44   #include "utils/OOPSEConstant.hpp"
45 + #include "hydrodynamics/Sphere.hpp"
46 + #include "hydrodynamics/Ellipsoid.hpp"
47 + #include "openbabel/mol.hpp"
48 +
49 + using namespace OpenBabel;
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
54 >        
55 >    sphericalBoundaryConditions_ = false;
56 >    if (simParams->getUseSphericalBoundaryConditions()) {
57 >      sphericalBoundaryConditions_ = true;
58 >      if (simParams->haveLangevinBufferRadius()) {
59 >        langevinBufferRadius_ = simParams->getLangevinBufferRadius();
60 >      } else {
61 >        sprintf( painCave.errMsg,
62 >                 "langevinBufferRadius must be specified "
63 >                 "when useSphericalBoundaryConditions is turned on.\n");
64 >        painCave.severity = OOPSE_ERROR;
65 >        painCave.isFatal = 1;
66 >        simError();  
67 >      }
68 >    
69 >      if (simParams->haveFrozenBufferRadius()) {
70 >        frozenBufferRadius_ = simParams->getFrozenBufferRadius();
71 >      } else {
72 >        sprintf( painCave.errMsg,
73 >                 "frozenBufferRadius must be specified "
74 >                 "when useSphericalBoundaryConditions is turned on.\n");
75 >        painCave.severity = OOPSE_ERROR;
76 >        painCave.isFatal = 1;
77 >        simError();  
78 >      }
79 >
80 >      if (frozenBufferRadius_ < langevinBufferRadius_) {
81 >        sprintf( painCave.errMsg,
82 >                 "frozenBufferRadius has been set smaller than the "
83 >                 "langevinBufferRadius.  This is probably an error.\n");
84 >        painCave.severity = OOPSE_WARNING;
85 >        painCave.isFatal = 0;
86 >        simError();  
87 >      }
88      }
89  
90 <    SimInfo::MoleculeIterator i;
91 <    Molecule::IntegrableObjectIterator  j;
90 >    // Build the hydroProp map:
91 >    std::map<std::string, HydroProp> hydroPropMap;
92 >
93      Molecule* mol;
94      StuntDouble* integrableObject;
95 <    for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
96 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
97 <              integrableObject = mol->nextIntegrableObject(j)) {
98 <            std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
99 <            if (iter != hydroPropMap.end()) {
100 <                hydroProps_.push_back(iter->second);
95 >    SimInfo::MoleculeIterator i;
96 >    Molecule::IntegrableObjectIterator  j;              
97 >    bool needHydroPropFile = false;
98 >    
99 >    for (mol = info->beginMolecule(i); mol != NULL;
100 >         mol = info->nextMolecule(i)) {
101 >      for (integrableObject = mol->beginIntegrableObject(j);
102 >           integrableObject != NULL;
103 >           integrableObject = mol->nextIntegrableObject(j)) {
104 >        
105 >        if (integrableObject->isRigidBody()) {
106 >          RigidBody* rb = static_cast<RigidBody*>(integrableObject);
107 >          if (rb->getNumAtoms() > 1) needHydroPropFile = true;
108 >        }
109 >        
110 >      }
111 >    }
112 >        
113 >
114 >    if (needHydroPropFile) {              
115 >      if (simParams->haveHydroPropFile()) {
116 >        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
117 >      } else {              
118 >        sprintf( painCave.errMsg,
119 >                 "HydroPropFile must be set to a file name if Langevin\n"
120 >                 "\tDynamics is specified for rigidBodies which contain more\n"
121 >                 "\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
122 >        painCave.severity = OOPSE_ERROR;
123 >        painCave.isFatal = 1;
124 >        simError();  
125 >      }      
126 >      std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
127 >      if (iter != hydroPropMap.end()) {
128 >        hydroProps_.push_back(iter->second);
129 >      } else {
130 >        sprintf( painCave.errMsg,
131 >                 "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
132 >        painCave.severity = OOPSE_ERROR;
133 >        painCave.isFatal = 1;
134 >        simError();  
135 >      }
136 >    } else {
137 >
138 >      std::map<std::string, HydroProp> hydroPropMap;
139 >      for (mol = info->beginMolecule(i); mol != NULL;
140 >           mol = info->nextMolecule(i)) {
141 >        for (integrableObject = mol->beginIntegrableObject(j);
142 >             integrableObject != NULL;
143 >             integrableObject = mol->nextIntegrableObject(j)) {
144 >          Shape* currShape = NULL;
145 >          if (integrableObject->isDirectionalAtom()) {
146 >            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
147 >            AtomType* atomType = dAtom->getAtomType();
148 >            if (atomType->isGayBerne()) {
149 >              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
150 >              
151 >              GenericData* data = dAtomType->getPropertyByName("GayBerne");
152 >              if (data != NULL) {
153 >                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
154 >                
155 >                if (gayBerneData != NULL) {  
156 >                  GayBerneParam gayBerneParam = gayBerneData->getData();
157 >                  currShape = new Ellipsoid(V3Zero,
158 >                                            gayBerneParam.GB_sigma/2.0,
159 >                                            gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0,
160 >                                            Mat3x3d::identity());
161 >                } else {
162 >                  sprintf( painCave.errMsg,
163 >                           "Can not cast GenericData to GayBerneParam\n");
164 >                  painCave.severity = OOPSE_ERROR;
165 >                  painCave.isFatal = 1;
166 >                  simError();  
167 >                }
168 >              } else {
169 >                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
170 >                painCave.severity = OOPSE_ERROR;
171 >                painCave.isFatal = 1;
172 >                simError();    
173 >              }
174 >            }
175 >          } else {
176 >            Atom* atom = static_cast<Atom*>(integrableObject);
177 >            AtomType* atomType = atom->getAtomType();
178 >            if (atomType->isLennardJones()){
179 >              GenericData* data = atomType->getPropertyByName("LennardJones");
180 >              if (data != NULL) {
181 >                LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
182 >                
183 >                if (ljData != NULL) {
184 >                  LJParam ljParam = ljData->getData();
185 >                  currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
186 >                } else {
187 >                  sprintf( painCave.errMsg,
188 >                           "Can not cast GenericData to LJParam\n");
189 >                  painCave.severity = OOPSE_ERROR;
190 >                  painCave.isFatal = 1;
191 >                  simError();          
192 >                }      
193 >              }
194              } else {
195 <                //error
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 >              }
205              }
206 <            
207 <           }
206 >          }
207 >          HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
208 >          std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
209 >          if (iter != hydroPropMap.end())
210 >            hydroProps_.push_back(iter->second);
211 >          else {
212 >            HydroProp myProp;
213 >            myProp.cor = V3Zero;
214 >            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);
225 >          }
226 >        }
227 >      }
228      }
229      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
230    }
231 +  
232 +  
233 +
234 +
235 +
236    std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237      std::map<std::string, HydroProp> props;
238      std::ifstream ifs(filename.c_str());
239      if (ifs.is_open()) {
240 <
240 >      
241      }
242 <
242 >    
243      const unsigned int BufferSize = 65535;
244      char buffer[BufferSize];  
83 –    Mat3x3d Ddtt;
84 –    Mat3x3d Ddtr;
85 –    Mat3x3d Ddrr;
245      while (ifs.getline(buffer, BufferSize)) {
246 <        StringTokenizer tokenizer(buffer);
247 <        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 <
255 <            Ddtt(0,0) = tokenizer.nextTokenAsDouble();
256 <            Ddtt(0,1) = tokenizer.nextTokenAsDouble();
257 <            Ddtt(0,2) = tokenizer.nextTokenAsDouble();
258 <            Ddtt(1,0) = tokenizer.nextTokenAsDouble();
259 <            Ddtt(1,1) = tokenizer.nextTokenAsDouble();
260 <            Ddtt(1,2) = tokenizer.nextTokenAsDouble();
261 <            Ddtt(2,0) = tokenizer.nextTokenAsDouble();
262 <            Ddtt(2,1) = tokenizer.nextTokenAsDouble();
263 <            Ddtt(2,2) = tokenizer.nextTokenAsDouble();
264 <
265 <            Ddtr(0,0) = tokenizer.nextTokenAsDouble();
266 <            Ddtr(0,1) = tokenizer.nextTokenAsDouble();
267 <            Ddtr(0,2) = tokenizer.nextTokenAsDouble();
268 <            Ddtr(1,0) = tokenizer.nextTokenAsDouble();
269 <            Ddtr(1,1) = tokenizer.nextTokenAsDouble();
270 <            Ddtr(1,2) = tokenizer.nextTokenAsDouble();
271 <            Ddtr(2,0) = tokenizer.nextTokenAsDouble();
272 <            Ddtr(2,1) = tokenizer.nextTokenAsDouble();
273 <            Ddtr(2,2) = tokenizer.nextTokenAsDouble();
274 <
275 <            Ddrr(0,0) = tokenizer.nextTokenAsDouble();
276 <            Ddrr(0,1) = tokenizer.nextTokenAsDouble();
277 <            Ddrr(0,2) = tokenizer.nextTokenAsDouble();
278 <            Ddrr(1,0) = tokenizer.nextTokenAsDouble();
279 <            Ddrr(1,1) = tokenizer.nextTokenAsDouble();
280 <            Ddrr(1,2) = tokenizer.nextTokenAsDouble();
281 <            Ddrr(2,0) = tokenizer.nextTokenAsDouble();
282 <            Ddrr(2,1) = tokenizer.nextTokenAsDouble();
283 <            Ddrr(2,2) = tokenizer.nextTokenAsDouble();                
284 <
285 <            currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
286 <            currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
287 <            currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
288 <            currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
289 <            currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
290 <            currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
291 <            currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
292 <            currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
293 <            currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
294 <
295 <            currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
296 <            currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
297 <            currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
298 <            currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
299 <            currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
300 <            currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
301 <            currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
302 <            currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
144 <            currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
145 <        
146 <            currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
147 <            currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
148 <            currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
149 <            currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
150 <            currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
151 <            currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
152 <            currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
153 <            currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
154 <            currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
155 <
156 <            currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
157 <            currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
158 <            currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
159 <            currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
160 <            currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
161 <            currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
162 <            currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
163 <            currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
164 <            currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
165 <
166 <            SquareMatrix<double, 6> Xir;
167 <            Xir.setSubMatrix(0, 0, currProp.Xirtt);
168 <            Xir.setSubMatrix(0, 3, currProp.Xirrt);
169 <            Xir.setSubMatrix(3, 0, currProp.Xirtr);
170 <            Xir.setSubMatrix(3, 3, currProp.Xirrr);
171 <            CholeskyDecomposition(Xir, currProp.S);            
172 <
173 <            props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
174 <        }
246 >      StringTokenizer tokenizer(buffer);
247 >      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<double, 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 >      }
303      }
304 <
304 >    
305      return props;
306    }
307    
# Line 191 | Line 319 | namespace oopse {
319      Vector3d ji;
320      double mass;
321      unsigned int index = 0;
322 +    bool doLangevinForces;
323 +    bool freezeMolecule;
324 +    int fdf;
325 +    
326 +    fdf = 0;
327      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
328 +      
329 +      if (sphericalBoundaryConditions_) {
330 +        
331 +        Vector3d molPos = mol->getCom();
332 +        double molRad = molPos.length();
333 +        
334 +        doLangevinForces = false;
335 +        freezeMolecule = false;
336 +        
337 +        if (molRad > langevinBufferRadius_) {
338 +          doLangevinForces = true;
339 +          freezeMolecule = false;
340 +        }
341 +        if (molRad > frozenBufferRadius_) {
342 +          doLangevinForces = false;
343 +          freezeMolecule = true;
344 +        }
345 +      }
346 +      
347        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
348 <           integrableObject = mol->nextIntegrableObject(j)) {
349 <
348 >           integrableObject = mol->nextIntegrableObject(j)) {
349 >          
350 >        if (freezeMolecule)
351 >          fdf += integrableObject->freeze();
352 >        
353 >        if (doLangevinForces) {          
354            vel =integrableObject->getVel();
355            if (integrableObject->isDirectional()){
356 <             //calculate angular velocity in lab frame
357 <             Mat3x3d I = integrableObject->getI();
358 <             Vector3d angMom = integrableObject->getJ();
359 <             Vector3d omega;
360 <
361 <             if (integrableObject->isLinear()) {
362 <                int linearAxis = integrableObject->linearAxis();
363 <                int l = (linearAxis +1 )%3;
364 <                int m = (linearAxis +2 )%3;
365 <                omega[l] = angMom[l] /I(l, l);
366 <                omega[m] = angMom[m] /I(m, m);
367 <                
368 <             } else {
369 <                 omega[0] = angMom[0] /I(0, 0);
370 <                 omega[1] = angMom[1] /I(1, 1);
371 <                 omega[2] = angMom[2] /I(2, 2);
372 <             }
373 <
374 <             //apply friction force and torque at center of resistance
375 <             A = integrableObject->getA();
376 <             Atrans = A.transpose();
377 <             Vector3d rcr = Atrans * hydroProps_[index].cor;  
378 <             Vector3d vcdLab = vel + cross(omega, rcr);
379 <             Vector3d vcdBody = A* vcdLab;
380 <             Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
381 <             Vector3d frictionForceLab = Atrans*frictionForceBody;
382 <             integrableObject->addFrc(frictionForceLab);
383 <             Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
384 <             Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
385 <             integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
386 <
387 <             //apply random force and torque at center of resistance
388 <             Vector3d randomForceBody;
389 <             Vector3d randomTorqueBody;
390 <             genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
391 <             Vector3d randomForceLab = Atrans*randomForceBody;
392 <             Vector3d randomTorqueLab = Atrans* randomTorqueBody;
393 <             integrableObject->addFrc(randomForceLab);            
394 <             integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
395 <
356 >            //calculate angular velocity in lab frame
357 >            Mat3x3d I = integrableObject->getI();
358 >            Vector3d angMom = integrableObject->getJ();
359 >            Vector3d omega;
360 >            
361 >            if (integrableObject->isLinear()) {
362 >              int linearAxis = integrableObject->linearAxis();
363 >              int l = (linearAxis +1 )%3;
364 >              int m = (linearAxis +2 )%3;
365 >              omega[l] = angMom[l] /I(l, l);
366 >              omega[m] = angMom[m] /I(m, m);
367 >              
368 >            } else {
369 >              omega[0] = angMom[0] /I(0, 0);
370 >              omega[1] = angMom[1] /I(1, 1);
371 >              omega[2] = angMom[2] /I(2, 2);
372 >            }
373 >            
374 >            //apply friction force and torque at center of resistance
375 >            A = integrableObject->getA();
376 >            Atrans = A.transpose();
377 >            Vector3d rcr = Atrans * hydroProps_[index].cor;  
378 >            Vector3d vcdLab = vel + cross(omega, rcr);
379 >            Vector3d vcdBody = A* vcdLab;
380 >            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
381 >            Vector3d frictionForceLab = Atrans*frictionForceBody;
382 >            integrableObject->addFrc(frictionForceLab);
383 >            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
384 >            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
385 >            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
386 >            
387 >            //apply random force and torque at center of resistance
388 >            Vector3d randomForceBody;
389 >            Vector3d randomTorqueBody;
390 >            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
391 >            Vector3d randomForceLab = Atrans*randomForceBody;
392 >            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
393 >            integrableObject->addFrc(randomForceLab);            
394 >            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
395 >            
396            } else {
397 <             //spheric atom
398 <             Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
399 <             Vector3d randomForce;
400 <             Vector3d randomTorque;
401 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
402 <
403 <             integrableObject->addFrc(frictionForce+randomForce);            
397 >            //spherical atom
398 >            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
399 >            Vector3d randomForce;
400 >            Vector3d randomTorque;
401 >            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
402 >            
403 >            integrableObject->addFrc(frictionForce+randomForce);            
404            }
405 <
405 >        }
406 >          
407          ++index;
408      
409        }
410      }    
411 <
412 <    ForceManager::postCalculation();
413 <
257 <
258 <
411 >    info_->setFdf(fdf);
412 >    
413 >    ForceManager::postCalculation();  
414    }
415  
416   void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {

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