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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 908 by tim, Mon Mar 20 19:12:14 2006 UTC vs.
Revision 1216 by xsun, Wed Jan 23 21:22:50 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() >= 40) {
87 <            std::string atomName = tokenizer.nextToken();
88 <            currProp.cor[0] = tokenizer.nextTokenAsDouble();
89 <            currProp.cor[1] = tokenizer.nextTokenAsDouble();
90 <            currProp.cor[2] = tokenizer.nextTokenAsDouble();
91 <            
92 <            currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
93 <            currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
94 <            currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
95 <            currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
96 <            currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
97 <            currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
98 <            currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
99 <            currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
100 <            currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
101 <
102 <            currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
103 <            currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
104 <            currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
105 <            currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
106 <            currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
107 <            currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
108 <            currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
109 <            currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
110 <            currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
111 <        
112 <            currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
113 <            currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
114 <            currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
115 <            currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
116 <            currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
117 <            currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
118 <            currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
119 <            currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
120 <            currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
121 <
122 <            currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
123 <            currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
124 <            currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
125 <            currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
126 <            currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
127 <            currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
128 <            currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
129 <            currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
130 <            currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
131 <
132 <            SquareMatrix<double, 6> Xir;
133 <            Xir.setSubMatrix(0, 0, currProp.Xirtt);
134 <            Xir.setSubMatrix(0, 3, currProp.Xirrt);
135 <            Xir.setSubMatrix(3, 0, currProp.Xirtr);
136 <            Xir.setSubMatrix(3, 3, currProp.Xirrr);
137 <            CholeskyDecomposition(Xir, currProp.S);            
138 <
139 <            props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
140 <        }
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 155 | Line 256 | namespace oopse {
256      Mat3x3d Atrans;
257      Vector3d Tb;
258      Vector3d ji;
158 –    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)) {
161 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
162 –           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 >            Mat3x3d I = integrableObject->getI();
301 >            Vector3d angMom = integrableObject->getJ();
302 >            A = integrableObject->getA();
303 >            Atrans = A.transpose();
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 <             }
305 >            Vector3d omegaBody;
306 >            
307 >            if (integrableObject->isLinear()) {
308 >              int linearAxis = integrableObject->linearAxis();
309 >              int l = (linearAxis +1 )%3;
310 >              int m = (linearAxis +2 )%3;
311 >              omegaBody[l] = angMom[l] /I(l, l);
312 >              omegaBody[m] = angMom[m] /I(m, m);
313 >              
314 >            } else {
315 >              omegaBody[0] = angMom[0] /I(0, 0);
316 >              omegaBody[1] = angMom[1] /I(1, 1);
317 >              omegaBody[2] = angMom[2] /I(2, 2);
318 >            }
319  
320 <             //apply friction force and torque at center of resistance
185 <             A = integrableObject->getA();
186 <             Atrans = A.transpose();
187 <             Vector3d rcr = Atrans * hydroProps_[index].cor;  
188 <             Vector3d vcdLab = vel + cross(omega, rcr);
189 <             Vector3d vcdBody = A* vcdLab;
190 <             Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
191 <             Vector3d frictionForceLab = Atrans*frictionForceBody;
192 <             integrableObject->addFrc(frictionForceLab);
193 <             Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
194 <             Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
195 <             integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
320 >            Vector3d omegaLab = Atrans * omegaBody;
321  
322 <             //apply random force and torque at center of resistance
198 <             Vector3d randomForceBody;
199 <             Vector3d randomTorqueBody;
200 <             genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
201 <             Vector3d randomForceLab = Atrans*randomForceBody;
202 <             Vector3d randomTorqueLab = Atrans* randomTorqueBody;
203 <             integrableObject->addFrc(randomForceLab);            
204 <             integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
322 >            // apply friction force and torque at center of resistance
323  
324 <          } else {
325 <             //spheric atom
326 <             Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
327 <             Vector3d randomForce;
328 <             Vector3d randomTorque;
211 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
324 >            Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
325 >            Vector3d vcdLab = vel + cross(omegaLab, rcrLab);
326 >        
327 >            Vector3d vcdBody = A * vcdLab;
328 >            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
329  
330 <             integrableObject->addFrc(frictionForce+randomForce);            
331 <          }
330 >            Vector3d frictionForceLab = Atrans * frictionForceBody;
331 >            integrableObject->addFrc(frictionForceLab);
332 >            Vector3d frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
333 >            Vector3d frictionTorqueLab = Atrans * frictionTorqueBody;
334 >            integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
335  
336 +            //apply random force and torque at center of resistance
337 +            Vector3d randomForceBody;
338 +            Vector3d randomTorqueBody;
339 +            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
340 +            Vector3d randomForceLab = Atrans * randomForceBody;
341 +            Vector3d randomTorqueLab = Atrans * randomTorqueBody;
342 +            integrableObject->addFrc(randomForceLab);            
343 +            integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));            
344 +            
345 +          } else {
346 +            //spherical atom
347 +            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
348 +            Vector3d randomForce;
349 +            Vector3d randomTorque;
350 +            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
351 +            
352 +            integrableObject->addFrc(frictionForce+randomForce);            
353 +          }
354 +        }
355 +          
356          ++index;
357      
358        }
359      }    
360  
361 <    ForceManager::postCalculation();
361 >    info_->setFdf(fdf);
362 >    veloMunge->removeComDrift();
363 >    // Remove angular drift if we are not using periodic boundary conditions.
364 >    if(!simParams->getUsePeriodicBoundaryConditions())
365 >      veloMunge->removeAngularDrift();
366  
367 <
224 <
367 >    ForceManager::postCalculation(needStress);  
368    }
369  
370 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
370 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
371  
372  
373 <    Vector<double, 6> Z;
374 <    Vector<double, 6> generalForce;
232 <
373 >    Vector<RealType, 6> Z;
374 >    Vector<RealType, 6> generalForce;
375          
376      Z[0] = randNumGen_.randNorm(0, variance);
377      Z[1] = randNumGen_.randNorm(0, variance);
# Line 238 | Line 380 | void LDForceManager::genRandomForceAndTorque(Vector3d&
380      Z[4] = randNumGen_.randNorm(0, variance);
381      Z[5] = randNumGen_.randNorm(0, variance);
382      
383 <
242 <    generalForce = hydroProps_[index].S*Z;
383 >    generalForce = hydroProps_[index]->getS()*Z;
384      
385      force[0] = generalForce[0];
386      force[1] = generalForce[1];
# Line 248 | Line 389 | void LDForceManager::genRandomForceAndTorque(Vector3d&
389      torque[1] = generalForce[4];
390      torque[2] = generalForce[5];
391      
392 < }
392 > }
393  
394   }

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