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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 904 by tim, Thu Mar 16 22:50:48 2006 UTC vs.
Revision 1210 by gezelter, Wed Jan 23 03:45:33 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
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\n"
121 >                 "\tDynamics is specified for rigidBodies which contain more\n"
122 >                 "\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\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 obanum = etab.GetAtomicNum((atom->getType()).c_str());
202 >                if (obanum != 0) {
203 >                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
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() >= 67) {
87 <            std::string atomName = tokenizer.nextToken();
88 <            currProp.cod[0] = tokenizer.nextTokenAsDouble();
89 <            currProp.cod[1] = tokenizer.nextTokenAsDouble();
90 <            currProp.cod[2] = tokenizer.nextTokenAsDouble();
91 <
92 <            currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
93 <            currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
94 <            currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
95 <            currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
96 <            currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
97 <            currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
98 <            currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
99 <            currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
100 <            currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
101 <
102 <            currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
103 <            currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
104 <            currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
105 <            currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
106 <            currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
107 <            currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
108 <            currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
109 <            currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
110 <            currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
111 <
112 <            currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
113 <            currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
114 <            currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
115 <            currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
116 <            currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
117 <            currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
118 <            currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
119 <            currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
120 <            currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();                
121 <
122 <            currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
123 <            currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
124 <            currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
125 <            currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
126 <            currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
127 <            currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble();
128 <            currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble();
129 <            currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble();
130 <            currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble();
131 <
132 <            currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble();
133 <            currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble();
134 <            currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble();
135 <            currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble();
136 <            currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble();
137 <            currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble();
138 <            currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble();
139 <            currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble();
140 <            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 <        }
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 +    RealType mass;
252      Vector3d vel;
253      Vector3d pos;
254      Vector3d frc;
# Line 177 | Line 256 | namespace oopse {
256      Mat3x3d Atrans;
257      Vector3d Tb;
258      Vector3d ji;
180 –    double mass;
259      unsigned int index = 0;
260 +    bool doLangevinForces;
261 +    bool freezeMolecule;
262 +    int fdf;
263 +
264 +
265 +
266 +    fdf = 0;
267 +
268      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184 –           integrableObject = mol->nextIntegrableObject(j)) {
269  
270 +      doLangevinForces = true;          
271 +      freezeMolecule = false;
272 +
273 +      if (sphericalBoundaryConditions_) {
274 +        
275 +        Vector3d molPos = mol->getCom();
276 +        RealType molRad = molPos.length();
277 +
278 +        doLangevinForces = false;
279 +        
280 +        if (molRad > langevinBufferRadius_) {
281 +          doLangevinForces = true;
282 +          freezeMolecule = false;
283 +        }
284 +        if (molRad > frozenBufferRadius_) {
285 +          doLangevinForces = false;
286 +          freezeMolecule = true;
287 +        }
288 +      }
289 +      
290 +      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 +           integrableObject = mol->nextIntegrableObject(j)) {
292 +          
293 +        if (freezeMolecule)
294 +          fdf += integrableObject->freeze();
295 +        
296 +        if (doLangevinForces) {  
297            vel =integrableObject->getVel();
298 +          mass = integrableObject->getMass();
299            if (integrableObject->isDirectional()){
300 <             //calculate angular velocity in lab frame
301 <             Mat3x3d I = integrableObject->getI();
302 <             Vector3d angMom = integrableObject->getJ();
303 <             Vector3d omega;
300 >            //calculate angular velocity in lab frame
301 >            Mat3x3d I = integrableObject->getI();
302 >            Vector3d angMom = integrableObject->getJ();
303 >            Vector3d omega;
304 >            
305 >            if (integrableObject->isLinear()) {
306 >              int linearAxis = integrableObject->linearAxis();
307 >              int l = (linearAxis +1 )%3;
308 >              int m = (linearAxis +2 )%3;
309 >              omega[l] = angMom[l] /I(l, l);
310 >              omega[m] = angMom[m] /I(m, m);
311 >              
312 >            } else {
313 >              omega[0] = angMom[0] /I(0, 0);
314 >              omega[1] = angMom[1] /I(1, 1);
315 >              omega[2] = angMom[2] /I(2, 2);
316 >            }
317  
318 <             if (integrableObject->isLinear()) {
194 <                int linearAxis = integrableObject->linearAxis();
195 <                int l = (linearAxis +1 )%3;
196 <                int m = (linearAxis +2 )%3;
197 <                omega[l] = angMom[l] /I(l, l);
198 <                omega[m] = angMom[m] /I(m, m);
199 <                
200 <             } else {
201 <                 omega[0] = angMom[0] /I(0, 0);
202 <                 omega[1] = angMom[1] /I(1, 1);
203 <                 omega[2] = angMom[2] /I(2, 2);
204 <             }
318 >            //std::cerr << "I = " << I(0,0) << "\t" << I(1,1) << "\t" << I(2,2) << "\n\n";
319  
320 <             //apply friction force and torque at center of diffusion
321 <             A = integrableObject->getA();
322 <             Atrans = A.transpose();
323 <             Vector3d rcd = Atrans * hydroProps_[index].cod;  
324 <             Vector3d vcd = vel + cross(omega, rcd);
325 <             vcd = A* vcd;
326 <             Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
327 <             frictionForce = Atrans*frictionForce;
328 <             integrableObject->addFrc(frictionForce);
329 <             Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
330 <             frictionTorque = Atrans*frictionTorque;
331 <             integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
332 <            
333 <             //apply random force and torque at center of diffustion
334 <             Vector3d randomForce;
221 <             Vector3d randomTorque;
222 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
223 <             randomForce = Atrans*randomForce;
224 <             randomTorque = Atrans* randomTorque;
225 <             integrableObject->addFrc(randomForce);            
226 <             integrableObject->addTrq(randomTorque + cross(rcd, randomForce ));
227 <            
228 <          } else {
229 <             //spheric atom
230 <             Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);    
231 <             Vector3d randomForce;
232 <             Vector3d randomTorque;
233 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
320 >            //apply friction force and torque at center of resistance
321 >            A = integrableObject->getA();
322 >            Atrans = A.transpose();
323 >            //std::cerr << "A = " << integrableObject->getA() << "\n";
324 >            //std::cerr << "Atrans = " << A.transpose() << "\n\n";
325 >            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
326 >            //std::cerr << "cor = " << hydroProps_[index]->getCOR() << "\n\n\n\n";
327 >            //std::cerr << "rcr = " << rcr << "\n\n";
328 >            Vector3d vcdLab = vel + cross(omega, rcr);
329 >        
330 >            //std::cerr << "velL = " << vel << "\n\n";
331 >            //std::cerr << "vcdL = " << vcdLab << "\n\n";
332 >            Vector3d vcdBody = A* vcdLab;
333 >            //std::cerr << "vcdB = " << vcdBody << "\n\n";
334 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
335  
336 <             //randomForce /= OOPSEConstant::energyConvert;
337 <             //randomTorque /= OOPSEConstant::energyConvert;
338 <             integrableObject->addFrc(frictionForce+randomForce);            
339 <          }
336 >            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
337 >            //std::cerr << "ffB = " << frictionForceBody << "\n\n";
338 >            Vector3d frictionForceLab = Atrans*frictionForceBody;
339 >            //std::cerr << "ffL = " << frictionForceLab << "\n\n";
340 >            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
341 >            integrableObject->addFrc(frictionForceLab);
342 >            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
343 >            //std::cerr << "ome = " << omega << "\n\n";
344 >            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
345 >            //std::cerr << "ftB = " << frictionTorqueBody << "\n\n";
346 >            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
347 >            //std::cerr << "ftL = " << frictionTorqueLab << "\n\n";
348 >            //std::cerr << "ftL2 = " << frictionTorqueLab+cross(rcr,frictionForceLab) << "\n\n";
349 >            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
350 >            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
351 >            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
352  
353 +            //apply random force and torque at center of resistance
354 +            Vector3d randomForceBody;
355 +            Vector3d randomTorqueBody;
356 +            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
357 +            //std::cerr << "rfB = " << randomForceBody << "\n\n";
358 +            //std::cerr << "rtB = " << randomTorqueBody << "\n\n";
359 +            Vector3d randomForceLab = Atrans*randomForceBody;
360 +            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
361 +            integrableObject->addFrc(randomForceLab);            
362 +            //std::cerr << "rfL = " << randomForceLab << "\n\n";
363 +            //std::cerr << "rtL = " << randomTorqueLab << "\n\n";
364 +            //std::cerr << "rtL2 = " << randomTorqueLab + cross(rcr, randomForceLab) << "\n\n";
365 +            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
366 +            
367 +          } else {
368 +            //spherical atom
369 +            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
370 +            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
371 +            Vector3d randomForce;
372 +            Vector3d randomTorque;
373 +            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
374 +            
375 +            integrableObject->addFrc(frictionForce+randomForce);            
376 +          }
377 +        }
378 +          
379          ++index;
380      
381        }
382      }    
383  
384 <    ForceManager::postCalculation();
384 >    info_->setFdf(fdf);
385 >    veloMunge->removeComDrift();
386 >    // Remove angular drift if we are not using periodic boundary conditions.
387 >    if(!simParams->getUsePeriodicBoundaryConditions())
388 >      veloMunge->removeAngularDrift();
389  
390 <
248 <
390 >    ForceManager::postCalculation(needStress);  
391    }
392  
393 < 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 <    */
393 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
394  
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);
395  
396 <    /*
397 <    Xid *= variance;
276 <    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 <    */
396 >    Vector<RealType, 6> Z;
397 >    Vector<RealType, 6> generalForce;
398          
399      Z[0] = randNumGen_.randNorm(0, variance);
400      Z[1] = randNumGen_.randNorm(0, variance);
401      Z[2] = randNumGen_.randNorm(0, variance);
402 +    //Z[3] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
403 +    //Z[4] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
404 +    //Z[5] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
405      Z[3] = randNumGen_.randNorm(0, variance);
406      Z[4] = randNumGen_.randNorm(0, variance);
407      Z[5] = randNumGen_.randNorm(0, variance);
408      
409  
410 <    generalForce = S*Z;
410 >    generalForce = hydroProps_[index]->getS()*Z;
411      
412      force[0] = generalForce[0];
413      force[1] = generalForce[1];
# Line 298 | Line 416 | void LDForceManager::genRandomForceAndTorque(Vector3d&
416      torque[1] = generalForce[4];
417      torque[2] = generalForce[5];
418      
419 < }
419 > }
420  
421   }

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