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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
Revision 983 by gezelter, Tue Jun 6 17:43:28 2006 UTC

# Line 42 | Line 42
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 <    
55 <    std::map<std::string, HydroProp> hydroPropMap;
51 <    if (simParams->haveHydroPropFile()) {
52 <      hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
53 <    } else {
54 <      sprintf( painCave.errMsg,
55 <               "HydroPropFile must be set if Langevin Dynamics is specified.\n");
56 <      painCave.severity = OOPSE_ERROR;
57 <      painCave.isFatal = 1;
58 <      simError();  
59 <    }
60 <    
53 >    simParams = info->getSimParams();
54 >    veloMunge = new Velocitizer(info);
55 >
56      sphericalBoundaryConditions_ = false;
57      if (simParams->getUseSphericalBoundaryConditions()) {
58        sphericalBoundaryConditions_ = true;
# Line 92 | Line 87 | namespace oopse {
87          simError();  
88        }
89      }
90 <      
91 <    SimInfo::MoleculeIterator i;
92 <    Molecule::IntegrableObjectIterator  j;
90 >
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;
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 <        std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
106 <        if (iter != hydroPropMap.end()) {
107 <          hydroProps_.push_back(iter->second);
108 <        } else {
107 <          sprintf( painCave.errMsg,
108 <                   "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
109 <          painCave.severity = OOPSE_ERROR;
110 <          painCave.isFatal = 1;
111 <          simError();  
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 +          if (integrableObject->isDirectionalAtom()) {
156 +            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
157 +            AtomType* atomType = dAtom->getAtomType();
158 +            if (atomType->isGayBerne()) {
159 +              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
160 +              
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_d / 2.0,
169 +                                            gayBerneParam.GB_l / 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 +            }
185 +          } else {
186 +            Atom* atom = static_cast<Atom*>(integrableObject);
187 +            AtomType* atomType = atom->getAtomType();
188 +            if (atomType->isLennardJones()){
189 +              GenericData* data = atomType->getPropertyByName("LennardJones");
190 +              if (data != NULL) {
191 +                LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
192 +                
193 +                if (ljData != NULL) {
194 +                  LJParam ljParam = ljData->getData();
195 +                  currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
196 +                } else {
197 +                  sprintf( painCave.errMsg,
198 +                           "Can not cast GenericData to LJParam\n");
199 +                  painCave.severity = OOPSE_ERROR;
200 +                  painCave.isFatal = 1;
201 +                  simError();          
202 +                }      
203 +              }
204 +            } else {
205 +              int obanum = etab.GetAtomicNum((atom->getType()).c_str());
206 +              if (obanum != 0) {
207 +                currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
208 +              } else {
209 +                sprintf( painCave.errMsg,
210 +                         "Could not find atom type in default element.txt\n");
211 +                painCave.severity = OOPSE_ERROR;
212 +                painCave.isFatal = 1;
213 +                simError();          
214 +              }
215 +            }
216 +          }
217 +          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
218 +          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
219 +          if (iter != hydroPropMap.end())
220 +            hydroProps_.push_back(iter->second);
221 +          else {
222 +            currHydroProp->complete();
223 +            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
224 +            hydroProps_.push_back(currHydroProp);
225 +          }
226 +        }
227        }
228      }
229      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
230 <  }
231 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
232 <    std::map<std::string, HydroProp> props;
230 >  }  
231 >
232 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
233 >    std::map<std::string, HydroProp*> props;
234      std::ifstream ifs(filename.c_str());
235      if (ifs.is_open()) {
236        
# Line 125 | Line 239 | namespace oopse {
239      const unsigned int BufferSize = 65535;
240      char buffer[BufferSize];  
241      while (ifs.getline(buffer, BufferSize)) {
242 <      StringTokenizer tokenizer(buffer);
243 <      HydroProp currProp;
130 <      if (tokenizer.countTokens() >= 40) {
131 <        std::string atomName = tokenizer.nextToken();
132 <        currProp.cor[0] = tokenizer.nextTokenAsDouble();
133 <        currProp.cor[1] = tokenizer.nextTokenAsDouble();
134 <        currProp.cor[2] = tokenizer.nextTokenAsDouble();
135 <        
136 <        currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
137 <        currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
138 <        currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
139 <        currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
140 <        currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
141 <        currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
142 <        currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
143 <        currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
144 <        currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
145 <        
146 <        currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
147 <        currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
148 <        currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
149 <        currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
150 <        currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
151 <        currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
152 <        currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
153 <        currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
154 <        currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
155 <        
156 <        currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
157 <        currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
158 <        currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
159 <        currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
160 <        currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
161 <        currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
162 <        currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
163 <        currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
164 <        currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
165 <        
166 <        currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
167 <        currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
168 <        currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
169 <        currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
170 <        currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
171 <        currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
172 <        currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
173 <        currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
174 <        currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
175 <        
176 <        SquareMatrix<double, 6> Xir;
177 <        Xir.setSubMatrix(0, 0, currProp.Xirtt);
178 <        Xir.setSubMatrix(0, 3, currProp.Xirrt);
179 <        Xir.setSubMatrix(3, 0, currProp.Xirtr);
180 <        Xir.setSubMatrix(3, 3, currProp.Xirrr);
181 <        CholeskyDecomposition(Xir, currProp.S);            
182 <        
183 <        props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
184 <      }
242 >      HydroProp* currProp = new HydroProp(buffer);
243 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
244      }
245 <    
245 >
246      return props;
247    }
248 <  
248 >  
249    void LDForceManager::postCalculation() {
250      SimInfo::MoleculeIterator i;
251      Molecule::IntegrableObjectIterator  j;
# Line 199 | Line 258 | namespace oopse {
258      Mat3x3d Atrans;
259      Vector3d Tb;
260      Vector3d ji;
261 <    double mass;
261 >    RealType mass;
262      unsigned int index = 0;
263      bool doLangevinForces;
264      bool freezeMolecule;
265      int fdf;
266 <    
266 >
267 >
268      fdf = 0;
269      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
270 <      
270 >
271 >      doLangevinForces = true;          
272 >      freezeMolecule = false;
273 >
274        if (sphericalBoundaryConditions_) {
275          
276          Vector3d molPos = mol->getCom();
277 <        double molRad = molPos.length();
277 >        RealType molRad = molPos.length();
278          
279          doLangevinForces = false;
217 –        freezeMolecule = false;
280          
281          if (molRad > langevinBufferRadius_) {
282            doLangevinForces = true;
# Line 226 | Line 288 | namespace oopse {
288          }
289        }
290        
291 <      if (doLangevinForces) {
292 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
231 <             integrableObject = mol->nextIntegrableObject(j)) {
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            if (integrableObject->isDirectional()){
300              //calculate angular velocity in lab frame
# Line 253 | Line 318 | namespace oopse {
318              //apply friction force and torque at center of resistance
319              A = integrableObject->getA();
320              Atrans = A.transpose();
321 <            Vector3d rcr = Atrans * hydroProps_[index].cor;  
321 >            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
322              Vector3d vcdLab = vel + cross(omega, rcr);
323              Vector3d vcdBody = A* vcdLab;
324 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
324 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
325              Vector3d frictionForceLab = Atrans*frictionForceBody;
326              integrableObject->addFrc(frictionForceLab);
327 <            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
327 >            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
328              Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
329              integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
330              
# Line 274 | Line 339 | namespace oopse {
339              
340            } else {
341              //spherical atom
342 <            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
342 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
343              Vector3d randomForce;
344              Vector3d randomTorque;
345              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
346              
347              integrableObject->addFrc(frictionForce+randomForce);            
348            }
349 +        }
350            
351 <          ++index;
351 >        ++index;
352      
287 –        }
353        }
354 <      if (freezeMolecule)
290 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 <             integrableObject = mol->nextIntegrableObject(j)) {          
292 <          fdf += integrableObject->freeze();
293 <        }
294 <    }
295 <    
354 >    }    
355      info_->setFdf(fdf);
356 <    
356 >
357 >    veloMunge->removeComDrift();
358 >    // Remove angular drift if we are not using periodic boundary conditions.
359 >    if(!simParams->getUsePeriodicBoundaryConditions())
360 >      veloMunge->removeAngularDrift();
361 >
362      ForceManager::postCalculation();  
363    }
364  
365 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
365 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
366  
367  
368 <    Vector<double, 6> Z;
369 <    Vector<double, 6> generalForce;
368 >    Vector<RealType, 6> Z;
369 >    Vector<RealType, 6> generalForce;
370  
371          
372      Z[0] = randNumGen_.randNorm(0, variance);
# Line 313 | Line 377 | void LDForceManager::genRandomForceAndTorque(Vector3d&
377      Z[5] = randNumGen_.randNorm(0, variance);
378      
379  
380 <    generalForce = hydroProps_[index].S*Z;
380 >    generalForce = hydroProps_[index]->getS()*Z;
381      
382      force[0] = generalForce[0];
383      force[1] = generalForce[1];

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