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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 981 by gezelter, Mon Jun 5 18:24:45 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 <    
50 <    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 <    
54 >        
55      sphericalBoundaryConditions_ = false;
56      if (simParams->getUseSphericalBoundaryConditions()) {
57        sphericalBoundaryConditions_ = true;
# Line 92 | Line 86 | namespace oopse {
86          simError();  
87        }
88      }
89 <      
90 <    SimInfo::MoleculeIterator i;
91 <    Molecule::IntegrableObjectIterator  j;
89 >
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;
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 <        std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
105 <        if (iter != hydroPropMap.end()) {
106 <          hydroProps_.push_back(iter->second);
107 <        } 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();  
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_d / 2.0,
168 +                                            gayBerneParam.GB_l / 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 +              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 +          HydroProp* currHydroProp = currShape->getHydroProp(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 +            currHydroProp->complete();
222 +            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
223 +            hydroProps_.push_back(currHydroProp);
224 +          }
225 +        }
226 +      }
227 +    }
228      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
229 <  }
230 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
231 <    std::map<std::string, HydroProp> props;
229 >  }  
230 >
231 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
232 >    std::map<std::string, HydroProp*> props;
233      std::ifstream ifs(filename.c_str());
234      if (ifs.is_open()) {
235        
# Line 125 | Line 238 | namespace oopse {
238      const unsigned int BufferSize = 65535;
239      char buffer[BufferSize];  
240      while (ifs.getline(buffer, BufferSize)) {
241 <      StringTokenizer tokenizer(buffer);
242 <      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 <      }
241 >      HydroProp* currProp = new HydroProp(buffer);
242 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
243      }
244 <    
244 >
245      return props;
246    }
247 <  
247 >  
248    void LDForceManager::postCalculation() {
249      SimInfo::MoleculeIterator i;
250      Molecule::IntegrableObjectIterator  j;
# Line 199 | Line 257 | namespace oopse {
257      Mat3x3d Atrans;
258      Vector3d Tb;
259      Vector3d ji;
260 <    double mass;
260 >    RealType mass;
261      unsigned int index = 0;
262      bool doLangevinForces;
263      bool freezeMolecule;
# Line 207 | Line 265 | namespace oopse {
265      
266      fdf = 0;
267      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
268 <      
268 >
269 >      doLangevinForces = true;          
270 >      freezeMolecule = false;
271 >
272        if (sphericalBoundaryConditions_) {
273          
274          Vector3d molPos = mol->getCom();
275 <        double molRad = molPos.length();
275 >        RealType molRad = molPos.length();
276          
277          doLangevinForces = false;
217 –        freezeMolecule = false;
278          
279          if (molRad > langevinBufferRadius_) {
280            doLangevinForces = true;
# Line 226 | Line 286 | namespace oopse {
286          }
287        }
288        
289 <      if (doLangevinForces) {
290 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
231 <             integrableObject = mol->nextIntegrableObject(j)) {
289 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290 >           integrableObject = mol->nextIntegrableObject(j)) {
291            
292 +        if (freezeMolecule)
293 +          fdf += integrableObject->freeze();
294 +        
295 +        if (doLangevinForces) {          
296            vel =integrableObject->getVel();
297            if (integrableObject->isDirectional()){
298              //calculate angular velocity in lab frame
# Line 253 | Line 316 | namespace oopse {
316              //apply friction force and torque at center of resistance
317              A = integrableObject->getA();
318              Atrans = A.transpose();
319 <            Vector3d rcr = Atrans * hydroProps_[index].cor;  
319 >            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
320              Vector3d vcdLab = vel + cross(omega, rcr);
321              Vector3d vcdBody = A* vcdLab;
322 <            Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
322 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
323              Vector3d frictionForceLab = Atrans*frictionForceBody;
324              integrableObject->addFrc(frictionForceLab);
325 <            Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
325 >            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
326              Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
327              integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
328              
# Line 274 | Line 337 | namespace oopse {
337              
338            } else {
339              //spherical atom
340 <            Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
340 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
341              Vector3d randomForce;
342              Vector3d randomTorque;
343              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
344              
345              integrableObject->addFrc(frictionForce+randomForce);            
346            }
347 +        }
348            
349 <          ++index;
349 >        ++index;
350      
287 –        }
351        }
352 <      if (freezeMolecule)
290 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 <             integrableObject = mol->nextIntegrableObject(j)) {          
292 <          fdf += integrableObject->freeze();
293 <        }
294 <    }
295 <    
352 >    }    
353      info_->setFdf(fdf);
354      
355      ForceManager::postCalculation();  
356    }
357  
358 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
358 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
359  
360  
361 <    Vector<double, 6> Z;
362 <    Vector<double, 6> generalForce;
361 >    Vector<RealType, 6> Z;
362 >    Vector<RealType, 6> generalForce;
363  
364          
365      Z[0] = randNumGen_.randNorm(0, variance);
# Line 313 | Line 370 | void LDForceManager::genRandomForceAndTorque(Vector3d&
370      Z[5] = randNumGen_.randNorm(0, variance);
371      
372  
373 <    generalForce = hydroProps_[index].S*Z;
373 >    generalForce = hydroProps_[index]->getS()*Z;
374      
375      force[0] = generalForce[0];
376      force[1] = generalForce[1];

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