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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 2632 by tim, Thu Mar 16 22:50:48 2006 UTC vs.
Revision 2767 by tim, Wed May 24 16:18:00 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 >
127 >      for (mol = info->beginMolecule(i); mol != NULL;
128 >           mol = info->nextMolecule(i)) {
129 >        for (integrableObject = mol->beginIntegrableObject(j);
130 >             integrableObject != NULL;
131 >             integrableObject = mol->nextIntegrableObject(j)) {
132 >
133 >          std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
134 >          if (iter != hydroPropMap.end()) {
135 >            hydroProps_.push_back(iter->second);
136 >          } else {
137 >            sprintf( painCave.errMsg,
138 >                     "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
139 >            painCave.severity = OOPSE_ERROR;
140 >            painCave.isFatal = 1;
141 >            simError();  
142 >          }        
143 >        }
144 >      }
145 >    } else {
146 >
147 >      std::map<std::string, HydroProp> hydroPropMap;
148 >      for (mol = info->beginMolecule(i); mol != NULL;
149 >           mol = info->nextMolecule(i)) {
150 >        for (integrableObject = mol->beginIntegrableObject(j);
151 >             integrableObject != NULL;
152 >             integrableObject = mol->nextIntegrableObject(j)) {
153 >          Shape* currShape = NULL;
154 >          if (integrableObject->isDirectionalAtom()) {
155 >            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
156 >            AtomType* atomType = dAtom->getAtomType();
157 >            if (atomType->isGayBerne()) {
158 >              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
159 >              
160 >              GenericData* data = dAtomType->getPropertyByName("GayBerne");
161 >              if (data != NULL) {
162 >                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
163 >                
164 >                if (gayBerneData != NULL) {  
165 >                  GayBerneParam gayBerneParam = gayBerneData->getData();
166 >                  currShape = new Ellipsoid(V3Zero,
167 >                                            gayBerneParam.GB_sigma/2.0,
168 >                                            gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0,
169 >                                            Mat3x3d::identity());
170 >                } else {
171 >                  sprintf( painCave.errMsg,
172 >                           "Can not cast GenericData to GayBerneParam\n");
173 >                  painCave.severity = OOPSE_ERROR;
174 >                  painCave.isFatal = 1;
175 >                  simError();  
176 >                }
177 >              } else {
178 >                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
179 >                painCave.severity = OOPSE_ERROR;
180 >                painCave.isFatal = 1;
181 >                simError();    
182 >              }
183 >            }
184 >          } else {
185 >            Atom* atom = static_cast<Atom*>(integrableObject);
186 >            AtomType* atomType = atom->getAtomType();
187 >            if (atomType->isLennardJones()){
188 >              GenericData* data = atomType->getPropertyByName("LennardJones");
189 >              if (data != NULL) {
190 >                LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
191 >                
192 >                if (ljData != NULL) {
193 >                  LJParam ljParam = ljData->getData();
194 >                  currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
195 >                } else {
196 >                  sprintf( painCave.errMsg,
197 >                           "Can not cast GenericData to LJParam\n");
198 >                  painCave.severity = OOPSE_ERROR;
199 >                  painCave.isFatal = 1;
200 >                  simError();          
201 >                }      
202 >              }
203              } else {
204 <                //error
204 >              int obanum = etab.GetAtomicNum((atom->getType()).c_str());
205 >              if (obanum != 0) {
206 >                currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
207 >              } else {
208 >                sprintf( painCave.errMsg,
209 >                         "Could not find atom type in default element.txt\n");
210 >                painCave.severity = OOPSE_ERROR;
211 >                painCave.isFatal = 1;
212 >                simError();          
213 >              }
214              }
215 <            
216 <           }
215 >          }
216 >          HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
217 >          std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
218 >          if (iter != hydroPropMap.end())
219 >            hydroProps_.push_back(iter->second);
220 >          else {
221 >            HydroProp myProp;
222 >            myProp.cor = V3Zero;
223 >            for (int i1 = 0; i1 < 3; i1++) {
224 >              for (int j1 = 0; j1 < 3; j1++) {
225 >                myProp.Xirtt(i1,j1) = currHydroProp.Xi(i1,j1);
226 >                myProp.Xirrt(i1,j1) = currHydroProp.Xi(i1,j1+3);
227 >                myProp.Xirtr(i1,j1) = currHydroProp.Xi(i1+3,j1);
228 >                myProp.Xirrr(i1,j1) = currHydroProp.Xi(i1+3,j1+3);
229 >              }
230 >            }
231 >            CholeskyDecomposition(currHydroProp.Xi, myProp.S);
232 >            hydroPropMap.insert(std::map<std::string, HydroProp>::value_type(integrableObject->getType(), myProp));
233 >            hydroProps_.push_back(myProp);
234 >          }
235 >        }
236 >      }
237      }
238      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
239    }
240 +  
241 +  
242 +
243 +
244 +
245    std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
246      std::map<std::string, HydroProp> props;
247      std::ifstream ifs(filename.c_str());
248      if (ifs.is_open()) {
249 <
249 >      
250      }
251 <
251 >    
252      const unsigned int BufferSize = 65535;
253      char buffer[BufferSize];  
254      while (ifs.getline(buffer, BufferSize)) {
255 <        StringTokenizer tokenizer(buffer);
256 <        HydroProp currProp;
257 <        if (tokenizer.countTokens() >= 67) {
258 <            std::string atomName = tokenizer.nextToken();
259 <            currProp.cod[0] = tokenizer.nextTokenAsDouble();
260 <            currProp.cod[1] = tokenizer.nextTokenAsDouble();
261 <            currProp.cod[2] = tokenizer.nextTokenAsDouble();
262 <
263 <            currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
264 <            currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
265 <            currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
266 <            currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
267 <            currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
268 <            currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
269 <            currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
270 <            currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
271 <            currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
272 <
273 <            currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
274 <            currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
275 <            currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
276 <            currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
277 <            currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
278 <            currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
279 <            currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
280 <            currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
281 <            currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
282 <
283 <            currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
284 <            currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
285 <            currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
286 <            currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
287 <            currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
288 <            currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
289 <            currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
290 <            currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
291 <            currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();                
292 <
293 <            currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
294 <            currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
295 <            currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
296 <            currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
297 <            currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
298 <            currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble();
299 <            currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble();
300 <            currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble();
301 <            currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble();
302 <
303 <            currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble();
304 <            currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble();
305 <            currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble();
306 <            currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble();
307 <            currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble();
308 <            currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble();
309 <            currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble();
310 <            currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble();
311 <            currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble();
141 <            
142 <            currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble();
143 <            currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble();
144 <            currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble();
145 <            currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble();
146 <            currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble();
147 <            currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble();
148 <            currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble();
149 <            currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble();
150 <            currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble();
151 <
152 <            currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
153 <            currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
154 <            currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
155 <            currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
156 <            currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
157 <            currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
158 <            currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
159 <            currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
160 <            currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
161 <            props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
162 <        }
255 >      StringTokenizer tokenizer(buffer);
256 >      HydroProp currProp;
257 >      if (tokenizer.countTokens() >= 40) {
258 >        std::string atomName = tokenizer.nextToken();
259 >        currProp.cor[0] = tokenizer.nextTokenAsDouble();
260 >        currProp.cor[1] = tokenizer.nextTokenAsDouble();
261 >        currProp.cor[2] = tokenizer.nextTokenAsDouble();
262 >        
263 >        currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
264 >        currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
265 >        currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
266 >        currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
267 >        currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
268 >        currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
269 >        currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
270 >        currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
271 >        currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
272 >        
273 >        currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
274 >        currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
275 >        currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
276 >        currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
277 >        currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
278 >        currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
279 >        currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
280 >        currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
281 >        currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
282 >        
283 >        currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
284 >        currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
285 >        currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
286 >        currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
287 >        currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
288 >        currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
289 >        currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
290 >        currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
291 >        currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
292 >        
293 >        currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
294 >        currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
295 >        currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
296 >        currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
297 >        currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
298 >        currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
299 >        currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
300 >        currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
301 >        currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
302 >        
303 >        SquareMatrix<RealType, 6> Xir;
304 >        Xir.setSubMatrix(0, 0, currProp.Xirtt);
305 >        Xir.setSubMatrix(0, 3, currProp.Xirrt);
306 >        Xir.setSubMatrix(3, 0, currProp.Xirtr);
307 >        Xir.setSubMatrix(3, 3, currProp.Xirrr);
308 >        CholeskyDecomposition(Xir, currProp.S);            
309 >        
310 >        props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
311 >      }
312      }
313 <
313 >    
314      return props;
315    }
316    
# Line 177 | Line 326 | namespace oopse {
326      Mat3x3d Atrans;
327      Vector3d Tb;
328      Vector3d ji;
329 <    double mass;
329 >    RealType mass;
330      unsigned int index = 0;
331 +    bool doLangevinForces;
332 +    bool freezeMolecule;
333 +    int fdf;
334 +    
335 +    fdf = 0;
336      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184 –           integrableObject = mol->nextIntegrableObject(j)) {
337  
338 +      doLangevinForces = true;          
339 +      freezeMolecule = false;
340 +
341 +      if (sphericalBoundaryConditions_) {
342 +        
343 +        Vector3d molPos = mol->getCom();
344 +        RealType molRad = molPos.length();
345 +        
346 +        doLangevinForces = false;
347 +        
348 +        if (molRad > langevinBufferRadius_) {
349 +          doLangevinForces = true;
350 +          freezeMolecule = false;
351 +        }
352 +        if (molRad > frozenBufferRadius_) {
353 +          doLangevinForces = false;
354 +          freezeMolecule = true;
355 +        }
356 +      }
357 +      
358 +      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
359 +           integrableObject = mol->nextIntegrableObject(j)) {
360 +          
361 +        if (freezeMolecule)
362 +          fdf += integrableObject->freeze();
363 +        
364 +        if (doLangevinForces) {          
365            vel =integrableObject->getVel();
366            if (integrableObject->isDirectional()){
367 <             //calculate angular velocity in lab frame
368 <             Mat3x3d I = integrableObject->getI();
369 <             Vector3d angMom = integrableObject->getJ();
370 <             Vector3d omega;
371 <
372 <             if (integrableObject->isLinear()) {
373 <                int linearAxis = integrableObject->linearAxis();
374 <                int l = (linearAxis +1 )%3;
375 <                int m = (linearAxis +2 )%3;
376 <                omega[l] = angMom[l] /I(l, l);
377 <                omega[m] = angMom[m] /I(m, m);
378 <                
379 <             } else {
380 <                 omega[0] = angMom[0] /I(0, 0);
381 <                 omega[1] = angMom[1] /I(1, 1);
382 <                 omega[2] = angMom[2] /I(2, 2);
383 <             }
384 <
385 <             //apply friction force and torque at center of diffusion
386 <             A = integrableObject->getA();
387 <             Atrans = A.transpose();
388 <             Vector3d rcd = Atrans * hydroProps_[index].cod;  
389 <             Vector3d vcd = vel + cross(omega, rcd);
390 <             vcd = A* vcd;
391 <             Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
392 <             frictionForce = Atrans*frictionForce;
393 <             integrableObject->addFrc(frictionForce);
394 <             Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
395 <             frictionTorque = Atrans*frictionTorque;
396 <             integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
397 <            
398 <             //apply random force and torque at center of diffustion
399 <             Vector3d randomForce;
400 <             Vector3d randomTorque;
401 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
402 <             randomForce = Atrans*randomForce;
403 <             randomTorque = Atrans* randomTorque;
404 <             integrableObject->addFrc(randomForce);            
405 <             integrableObject->addTrq(randomTorque + cross(rcd, randomForce ));
406 <            
367 >            //calculate angular velocity in lab frame
368 >            Mat3x3d I = integrableObject->getI();
369 >            Vector3d angMom = integrableObject->getJ();
370 >            Vector3d omega;
371 >            
372 >            if (integrableObject->isLinear()) {
373 >              int linearAxis = integrableObject->linearAxis();
374 >              int l = (linearAxis +1 )%3;
375 >              int m = (linearAxis +2 )%3;
376 >              omega[l] = angMom[l] /I(l, l);
377 >              omega[m] = angMom[m] /I(m, m);
378 >              
379 >            } else {
380 >              omega[0] = angMom[0] /I(0, 0);
381 >              omega[1] = angMom[1] /I(1, 1);
382 >              omega[2] = angMom[2] /I(2, 2);
383 >            }
384 >            
385 >            //apply friction force and torque at center of resistance
386 >            A = integrableObject->getA();
387 >            Atrans = A.transpose();
388 >            Vector3d rcr = Atrans * hydroProps_[index].cor;  
389 >            Vector3d vcdLab = vel + cross(omega, rcr);
390 >            Vector3d vcdBody = A* vcdLab;
391 >            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
392 >            Vector3d frictionForceLab = Atrans*frictionForceBody;
393 >            integrableObject->addFrc(frictionForceLab);
394 >            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
395 >            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
396 >            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
397 >            
398 >            //apply random force and torque at center of resistance
399 >            Vector3d randomForceBody;
400 >            Vector3d randomTorqueBody;
401 >            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
402 >            Vector3d randomForceLab = Atrans*randomForceBody;
403 >            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
404 >            integrableObject->addFrc(randomForceLab);            
405 >            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
406 >            
407            } else {
408 <             //spheric atom
409 <             Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);    
410 <             Vector3d randomForce;
411 <             Vector3d randomTorque;
412 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
413 <
414 <             //randomForce /= OOPSEConstant::energyConvert;
236 <             //randomTorque /= OOPSEConstant::energyConvert;
237 <             integrableObject->addFrc(frictionForce+randomForce);            
408 >            //spherical atom
409 >            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
410 >            Vector3d randomForce;
411 >            Vector3d randomTorque;
412 >            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
413 >            
414 >            integrableObject->addFrc(frictionForce+randomForce);            
415            }
416 <
416 >        }
417 >          
418          ++index;
419      
420        }
421      }    
422 <
423 <    ForceManager::postCalculation();
424 <
247 <
248 <
422 >    info_->setFdf(fdf);
423 >    
424 >    ForceManager::postCalculation();  
425    }
426  
427 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
252 <    /*
253 <    SquareMatrix<double, 6> Dd;
254 <    SquareMatrix<double, 6> S;
255 <    Vector<double, 6> Z;
256 <    Vector<double, 6> generalForce;
257 <    Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt);
258 <    Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose());
259 <    Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr);
260 <    Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr);
261 <    CholeskyDecomposition(Dd, S);
262 <    */
427 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
428  
264 –    SquareMatrix<double, 6> Xid;
265 –    SquareMatrix<double, 6> S;
266 –    Vector<double, 6> Z;
267 –    Vector<double, 6> generalForce;
268 –    Xid.setSubMatrix(0, 0, hydroProps_[index].Xidtt);
269 –    Xid.setSubMatrix(0, 3, hydroProps_[index].Xidrt);
270 –    Xid.setSubMatrix(3, 0, hydroProps_[index].Xidtr);
271 –    Xid.setSubMatrix(3, 3, hydroProps_[index].Xidrr);
272 –    CholeskyDecomposition(Xid, S);
429  
430 <    /*
431 <    Xid *= variance;
432 <    Z[0] = randNumGen_.randNorm(0, 1.0);
277 <    Z[1] = randNumGen_.randNorm(0, 1.0);
278 <    Z[2] = randNumGen_.randNorm(0, 1.0);
279 <    Z[3] = randNumGen_.randNorm(0, 1.0);
280 <    Z[4] = randNumGen_.randNorm(0, 1.0);
281 <    Z[5] = randNumGen_.randNorm(0, 1.0);
282 <    */
430 >    Vector<RealType, 6> Z;
431 >    Vector<RealType, 6> generalForce;
432 >
433          
434      Z[0] = randNumGen_.randNorm(0, variance);
435      Z[1] = randNumGen_.randNorm(0, variance);
# Line 289 | Line 439 | void LDForceManager::genRandomForceAndTorque(Vector3d&
439      Z[5] = randNumGen_.randNorm(0, variance);
440      
441  
442 <    generalForce = S*Z;
442 >    generalForce = hydroProps_[index].S*Z;
443      
444      force[0] = generalForce[0];
445      force[1] = generalForce[1];

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