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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 1120 by chuckv, Fri Feb 2 18:55:21 2007 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 "openbabel/mol.hpp"
49 +
50 + using namespace OpenBabel;
51   namespace oopse {
52  
53    LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
54 <    Globals* simParams = info->getSimParams();
55 <    std::map<std::string, HydroProp> hydroPropMap;
56 <    if (simParams->haveHydroPropFile()) {
57 <        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
58 <    } else {
59 <        //error
54 >    simParams = info->getSimParams();
55 >    veloMunge = new Velocitizer(info);
56 >
57 >    sphericalBoundaryConditions_ = false;
58 >    if (simParams->getUseSphericalBoundaryConditions()) {
59 >      sphericalBoundaryConditions_ = true;
60 >      if (simParams->haveLangevinBufferRadius()) {
61 >        langevinBufferRadius_ = simParams->getLangevinBufferRadius();
62 >      } else {
63 >        sprintf( painCave.errMsg,
64 >                 "langevinBufferRadius must be specified "
65 >                 "when useSphericalBoundaryConditions is turned on.\n");
66 >        painCave.severity = OOPSE_ERROR;
67 >        painCave.isFatal = 1;
68 >        simError();  
69 >      }
70 >    
71 >      if (simParams->haveFrozenBufferRadius()) {
72 >        frozenBufferRadius_ = simParams->getFrozenBufferRadius();
73 >      } else {
74 >        sprintf( painCave.errMsg,
75 >                 "frozenBufferRadius must be specified "
76 >                 "when useSphericalBoundaryConditions is turned on.\n");
77 >        painCave.severity = OOPSE_ERROR;
78 >        painCave.isFatal = 1;
79 >        simError();  
80 >      }
81 >
82 >      if (frozenBufferRadius_ < langevinBufferRadius_) {
83 >        sprintf( painCave.errMsg,
84 >                 "frozenBufferRadius has been set smaller than the "
85 >                 "langevinBufferRadius.  This is probably an error.\n");
86 >        painCave.severity = OOPSE_WARNING;
87 >        painCave.isFatal = 0;
88 >        simError();  
89 >      }
90      }
91  
92 <    SimInfo::MoleculeIterator i;
93 <    Molecule::IntegrableObjectIterator  j;
92 >    // Build the hydroProp map:
93 >    std::map<std::string, HydroProp*> hydroPropMap;
94 >
95      Molecule* mol;
96      StuntDouble* integrableObject;
97 <    for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
98 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
99 <              integrableObject = mol->nextIntegrableObject(j)) {
100 <            std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
101 <            if (iter != hydroPropMap.end()) {
102 <                hydroProps_.push_back(iter->second);
97 >    SimInfo::MoleculeIterator i;
98 >    Molecule::IntegrableObjectIterator  j;              
99 >    bool needHydroPropFile = false;
100 >    
101 >    for (mol = info->beginMolecule(i); mol != NULL;
102 >         mol = info->nextMolecule(i)) {
103 >      for (integrableObject = mol->beginIntegrableObject(j);
104 >           integrableObject != NULL;
105 >           integrableObject = mol->nextIntegrableObject(j)) {
106 >        
107 >        if (integrableObject->isRigidBody()) {
108 >          RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109 >          if (rb->getNumAtoms() > 1) needHydroPropFile = true;
110 >        }
111 >        
112 >      }
113 >    }
114 >        
115 >
116 >    if (needHydroPropFile) {              
117 >      if (simParams->haveHydroPropFile()) {
118 >        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
119 >      } else {              
120 >        sprintf( painCave.errMsg,
121 >                 "HydroPropFile must be set to a file name if Langevin\n"
122 >                 "\tDynamics is specified for rigidBodies which contain more\n"
123 >                 "\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
124 >        painCave.severity = OOPSE_ERROR;
125 >        painCave.isFatal = 1;
126 >        simError();  
127 >      }      
128 >
129 >      for (mol = info->beginMolecule(i); mol != NULL;
130 >           mol = info->nextMolecule(i)) {
131 >        for (integrableObject = mol->beginIntegrableObject(j);
132 >             integrableObject != NULL;
133 >             integrableObject = mol->nextIntegrableObject(j)) {
134 >
135 >          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
136 >          if (iter != hydroPropMap.end()) {
137 >            hydroProps_.push_back(iter->second);
138 >          } else {
139 >            sprintf( painCave.errMsg,
140 >                     "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
141 >            painCave.severity = OOPSE_ERROR;
142 >            painCave.isFatal = 1;
143 >            simError();  
144 >          }        
145 >        }
146 >      }
147 >    } else {
148 >      
149 >      std::map<std::string, HydroProp*> hydroPropMap;
150 >      for (mol = info->beginMolecule(i); mol != NULL;
151 >           mol = info->nextMolecule(i)) {
152 >        for (integrableObject = mol->beginIntegrableObject(j);
153 >             integrableObject != NULL;
154 >             integrableObject = mol->nextIntegrableObject(j)) {
155 >          Shape* currShape = NULL;
156 >          if (integrableObject->isDirectionalAtom()) {
157 >            DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
158 >            AtomType* atomType = dAtom->getAtomType();
159 >            if (atomType->isGayBerne()) {
160 >              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
161 >              
162 >              GenericData* data = dAtomType->getPropertyByName("GayBerne");
163 >              if (data != NULL) {
164 >                GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
165 >                
166 >                if (gayBerneData != NULL) {  
167 >                  GayBerneParam gayBerneParam = gayBerneData->getData();
168 >                  currShape = new Ellipsoid(V3Zero,
169 >                                            gayBerneParam.GB_d / 2.0,
170 >                                            gayBerneParam.GB_l / 2.0,
171 >                                            Mat3x3d::identity());
172 >                } else {
173 >                  sprintf( painCave.errMsg,
174 >                           "Can not cast GenericData to GayBerneParam\n");
175 >                  painCave.severity = OOPSE_ERROR;
176 >                  painCave.isFatal = 1;
177 >                  simError();  
178 >                }
179 >              } else {
180 >                sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
181 >                painCave.severity = OOPSE_ERROR;
182 >                painCave.isFatal = 1;
183 >                simError();    
184 >              }
185 >            }
186 >          } else {
187 >            Atom* atom = static_cast<Atom*>(integrableObject);
188 >            AtomType* atomType = atom->getAtomType();
189 >            if (atomType->isLennardJones()){
190 >              GenericData* data = atomType->getPropertyByName("LennardJones");
191 >              if (data != NULL) {
192 >                LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
193 >                
194 >                if (ljData != NULL) {
195 >                  LJParam ljParam = ljData->getData();
196 >                  currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
197 >                } else {
198 >                  sprintf( painCave.errMsg,
199 >                           "Can not cast GenericData to LJParam\n");
200 >                  painCave.severity = OOPSE_ERROR;
201 >                  painCave.isFatal = 1;
202 >                  simError();          
203 >                }      
204 >              }
205              } else {
206 <                //error
206 >              int obanum = etab.GetAtomicNum((atom->getType()).c_str());
207 >              if (obanum != 0) {
208 >                currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
209 >              } else {
210 >                sprintf( painCave.errMsg,
211 >                         "Could not find atom type in default element.txt\n");
212 >                painCave.severity = OOPSE_ERROR;
213 >                painCave.isFatal = 1;
214 >                simError();          
215 >              }
216              }
217 <            
218 <           }
217 >          }
218 >          HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
219 >          std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
220 >          if (iter != hydroPropMap.end())
221 >            hydroProps_.push_back(iter->second);
222 >          else {
223 >            currHydroProp->complete();
224 >            hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
225 >            hydroProps_.push_back(currHydroProp);
226 >          }
227 >        }
228 >      }
229      }
230      variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
231 <  }
232 <  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
233 <    std::map<std::string, HydroProp> props;
231 >  }  
232 >
233 >  std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
234 >    std::map<std::string, HydroProp*> props;
235      std::ifstream ifs(filename.c_str());
236      if (ifs.is_open()) {
237 <
237 >      
238      }
239 <
239 >    
240      const unsigned int BufferSize = 65535;
241      char buffer[BufferSize];  
242      while (ifs.getline(buffer, BufferSize)) {
243 <        StringTokenizer tokenizer(buffer);
244 <        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 <        }
243 >      HydroProp* currProp = new HydroProp(buffer);
244 >      props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
245      }
246  
247      return props;
248    }
249 <  
249 >  
250    void LDForceManager::postCalculation() {
251      SimInfo::MoleculeIterator i;
252      Molecule::IntegrableObjectIterator  j;
# Line 155 | Line 259 | namespace oopse {
259      Mat3x3d Atrans;
260      Vector3d Tb;
261      Vector3d ji;
262 <    double mass;
262 >    RealType mass;
263      unsigned int index = 0;
264 <    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
265 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266 <           integrableObject = mol->nextIntegrableObject(j)) {
264 >    bool doLangevinForces;
265 >    bool freezeMolecule;
266 >    int fdf;
267 >    int nIntegrated;
268 >    int nFrozen;
269  
270 <          vel =integrableObject->getVel();
165 <          if (integrableObject->isDirectional()){
166 <             //calculate angular velocity in lab frame
167 <             Mat3x3d I = integrableObject->getI();
168 <             Vector3d angMom = integrableObject->getJ();
169 <             Vector3d omega;
270 >    fdf = 0;
271  
272 <             if (integrableObject->isLinear()) {
172 <                int linearAxis = integrableObject->linearAxis();
173 <                int l = (linearAxis +1 )%3;
174 <                int m = (linearAxis +2 )%3;
175 <                omega[l] = angMom[l] /I(l, l);
176 <                omega[m] = angMom[m] /I(m, m);
177 <                
178 <             } else {
179 <                 omega[0] = angMom[0] /I(0, 0);
180 <                 omega[1] = angMom[1] /I(1, 1);
181 <                 omega[2] = angMom[2] /I(2, 2);
182 <             }
272 >    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
273  
274 <             //apply friction force and torque at center of resistance
275 <             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));
274 >      doLangevinForces = true;          
275 >      freezeMolecule = false;
276  
277 <             //apply random force and torque at center of resistance
278 <             Vector3d randomForceBody;
279 <             Vector3d randomTorqueBody;
280 <             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 ));            
277 >      if (sphericalBoundaryConditions_) {
278 >        
279 >        Vector3d molPos = mol->getCom();
280 >        RealType molRad = molPos.length();
281  
282 +        doLangevinForces = false;
283 +        
284 +        if (molRad > langevinBufferRadius_) {
285 +          doLangevinForces = true;
286 +          freezeMolecule = false;
287 +        }
288 +        if (molRad > frozenBufferRadius_) {
289 +          doLangevinForces = false;
290 +          freezeMolecule = true;
291 +        }
292 +      }
293 +      
294 +      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
295 +           integrableObject = mol->nextIntegrableObject(j)) {
296 +          
297 +        if (freezeMolecule)
298 +          fdf += integrableObject->freeze();
299 +        
300 +        if (doLangevinForces) {  
301 +          vel =integrableObject->getVel();
302 +          if (integrableObject->isDirectional()){
303 +            //calculate angular velocity in lab frame
304 +            Mat3x3d I = integrableObject->getI();
305 +            Vector3d angMom = integrableObject->getJ();
306 +            Vector3d omega;
307 +            
308 +            if (integrableObject->isLinear()) {
309 +              int linearAxis = integrableObject->linearAxis();
310 +              int l = (linearAxis +1 )%3;
311 +              int m = (linearAxis +2 )%3;
312 +              omega[l] = angMom[l] /I(l, l);
313 +              omega[m] = angMom[m] /I(m, m);
314 +              
315 +            } else {
316 +              omega[0] = angMom[0] /I(0, 0);
317 +              omega[1] = angMom[1] /I(1, 1);
318 +              omega[2] = angMom[2] /I(2, 2);
319 +            }
320 +            
321 +            //apply friction force and torque at center of resistance
322 +            A = integrableObject->getA();
323 +            Atrans = A.transpose();
324 +            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
325 +            Vector3d vcdLab = vel + cross(omega, rcr);
326 +            Vector3d vcdBody = A* vcdLab;
327 +            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
328 +            Vector3d frictionForceLab = Atrans*frictionForceBody;
329 +            integrableObject->addFrc(frictionForceLab);
330 +            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
331 +            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
332 +            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
333 +            
334 +            //apply random force and torque at center of resistance
335 +            Vector3d randomForceBody;
336 +            Vector3d randomTorqueBody;
337 +            genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
338 +            Vector3d randomForceLab = Atrans*randomForceBody;
339 +            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
340 +            integrableObject->addFrc(randomForceLab);            
341 +            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
342 +            
343            } else {
344 <             //spheric atom
345 <             Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);    
346 <             Vector3d randomForce;
347 <             Vector3d randomTorque;
348 <             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
349 <
350 <             integrableObject->addFrc(frictionForce+randomForce);            
344 >            //spherical atom
345 >            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
346 >            Vector3d randomForce;
347 >            Vector3d randomTorque;
348 >            genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
349 >            
350 >            integrableObject->addFrc(frictionForce+randomForce);            
351            }
352 <
352 >        }
353 >          
354          ++index;
355      
356        }
357      }    
358  
359 <    ForceManager::postCalculation();
359 >    info_->setFdf(fdf);
360 >    veloMunge->removeComDrift();
361 >    // Remove angular drift if we are not using periodic boundary conditions.
362 >    if(!simParams->getUsePeriodicBoundaryConditions())
363 >      veloMunge->removeAngularDrift();
364  
365 <
224 <
365 >    ForceManager::postCalculation();  
366    }
367  
368 < void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
368 > void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
369  
370  
371 <    Vector<double, 6> Z;
372 <    Vector<double, 6> generalForce;
371 >    Vector<RealType, 6> Z;
372 >    Vector<RealType, 6> generalForce;
373  
374          
375      Z[0] = randNumGen_.randNorm(0, variance);
# Line 239 | Line 380 | void LDForceManager::genRandomForceAndTorque(Vector3d&
380      Z[5] = randNumGen_.randNorm(0, variance);
381      
382  
383 <    generalForce = hydroProps_[index].S*Z;
383 >    generalForce = hydroProps_[index]->getS()*Z;
384      
385      force[0] = generalForce[0];
386      force[1] = generalForce[1];

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