ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/integrators/LDForceManager.cpp
(Generate patch)

Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 1120 by chuckv, Fri Feb 2 18:55:21 2007 UTC vs.
Revision 1237 by gezelter, Fri Apr 18 16:55:15 2008 UTC

# Line 45 | Line 45
45   #include "utils/OOPSEConstant.hpp"
46   #include "hydrodynamics/Sphere.hpp"
47   #include "hydrodynamics/Ellipsoid.hpp"
48 < #include "openbabel/mol.hpp"
48 > #include "utils/ElementsTable.hpp"
49  
50 – using namespace OpenBabel;
50   namespace oopse {
51  
52 <  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
52 >  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
53      simParams = info->getSimParams();
54      veloMunge = new Velocitizer(info);
55  
# Line 118 | Line 117 | namespace oopse {
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");
120 >                 "HydroPropFile must be set to a file name if Langevin Dynamics\n"
121 >                 "\tis specified for rigidBodies which contain more than one atom\n"
122 >                 "\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
123          painCave.severity = OOPSE_ERROR;
124          painCave.isFatal = 1;
125          simError();  
# Line 153 | Line 152 | namespace oopse {
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();
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 <              
160 >              DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);              
161                GenericData* data = dAtomType->getPropertyByName("GayBerne");
162                if (data != NULL) {
163                  GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
# Line 166 | Line 165 | namespace oopse {
165                  if (gayBerneData != NULL) {  
166                    GayBerneParam gayBerneParam = gayBerneData->getData();
167                    currShape = new Ellipsoid(V3Zero,
169 –                                            gayBerneParam.GB_d / 2.0,
168                                              gayBerneParam.GB_l / 2.0,
169 +                                            gayBerneParam.GB_d / 2.0,
170                                              Mat3x3d::identity());
171                  } else {
172                    sprintf( painCave.errMsg,
# Line 182 | Line 181 | namespace oopse {
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);
184 >            } else {
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 aNum = etab.GetAtomicNum((atom->getType()).c_str());
202 >                if (aNum != 0) {
203 >                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
204                  } else {
205                    sprintf( painCave.errMsg,
206 <                           "Can not cast GenericData to LJParam\n");
206 >                           "Could not find atom type in default element.txt\n");
207                    painCave.severity = OOPSE_ERROR;
208                    painCave.isFatal = 1;
209                    simError();          
210 <                }      
204 <              }
205 <            } else {
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();          
210 >                }
211                }
212              }
213            }
# Line 247 | Line 243 | namespace oopse {
243      return props;
244    }
245    
246 <  void LDForceManager::postCalculation() {
246 >  void LDForceManager::postCalculation(bool needStress){
247      SimInfo::MoleculeIterator i;
248      Molecule::IntegrableObjectIterator  j;
249      Molecule* mol;
250      StuntDouble* integrableObject;
251 <    Vector3d vel;
251 >    RealType mass;
252      Vector3d pos;
253      Vector3d frc;
254      Mat3x3d A;
255      Mat3x3d Atrans;
256      Vector3d Tb;
257      Vector3d ji;
262 –    RealType mass;
258      unsigned int index = 0;
259      bool doLangevinForces;
260      bool freezeMolecule;
261      int fdf;
267 –    int nIntegrated;
268 –    int nFrozen;
262  
263      fdf = 0;
264  
# Line 298 | Line 291 | namespace oopse {
291            fdf += integrableObject->freeze();
292          
293          if (doLangevinForces) {  
294 <          vel =integrableObject->getVel();
294 >          mass = integrableObject->getMass();
295            if (integrableObject->isDirectional()){
296 <            //calculate angular velocity in lab frame
297 <            Mat3x3d I = integrableObject->getI();
298 <            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
296 >
297 >            // preliminaries for directional objects:
298 >
299              A = integrableObject->getA();
300              Atrans = A.transpose();
301 <            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
302 <            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 <            
301 >            Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
302 >
303              //apply random force and torque at center of resistance
304 +
305              Vector3d randomForceBody;
306              Vector3d randomTorqueBody;
307              genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
308 <            Vector3d randomForceLab = Atrans*randomForceBody;
309 <            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
308 >            Vector3d randomForceLab = Atrans * randomForceBody;
309 >            Vector3d randomTorqueLab = Atrans * randomTorqueBody;
310              integrableObject->addFrc(randomForceLab);            
311 <            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
311 >            integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));            
312 >
313 >            Mat3x3d I = integrableObject->getI();
314 >            Vector3d omegaBody;
315 >
316 >            // What remains contains velocity explicitly, but the velocity required
317 >            // is at the full step: v(t + h), while we have initially the velocity
318 >            // at the half step: v(t + h/2).  We need to iterate to converge the
319 >            // friction force and friction torque vectors.
320 >
321 >            // this is the velocity at the half-step:
322              
323 +            Vector3d vel =integrableObject->getVel();
324 +            Vector3d angMom = integrableObject->getJ();
325 +
326 +            //estimate velocity at full-step using everything but friction forces:          
327 +
328 +            frc = integrableObject->getFrc();
329 +            Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
330 +
331 +            Tb = integrableObject->lab2Body(integrableObject->getTrq());
332 +            Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;                            
333 +
334 +            Vector3d omegaLab;
335 +            Vector3d vcdLab;
336 +            Vector3d vcdBody;
337 +            Vector3d frictionForceBody;
338 +            Vector3d frictionForceLab(0.0);
339 +            Vector3d oldFFL;  // used to test for convergence
340 +            Vector3d frictionTorqueBody(0.0);
341 +            Vector3d oldFTB;  // used to test for convergence
342 +            Vector3d frictionTorqueLab;
343 +            RealType fdot;
344 +            RealType tdot;
345 +
346 +            //iteration starts here:
347 +
348 +            for (int k = 0; k < maxIterNum_; k++) {
349 +                            
350 +              if (integrableObject->isLinear()) {
351 +                int linearAxis = integrableObject->linearAxis();
352 +                int l = (linearAxis +1 )%3;
353 +                int m = (linearAxis +2 )%3;
354 +                omegaBody[l] = angMomStep[l] /I(l, l);
355 +                omegaBody[m] = angMomStep[m] /I(m, m);
356 +                
357 +              } else {
358 +                omegaBody[0] = angMomStep[0] /I(0, 0);
359 +                omegaBody[1] = angMomStep[1] /I(1, 1);
360 +                omegaBody[2] = angMomStep[2] /I(2, 2);
361 +              }
362 +              
363 +              omegaLab = Atrans * omegaBody;
364 +              
365 +              // apply friction force and torque at center of resistance
366 +              
367 +              vcdLab = velStep + cross(omegaLab, rcrLab);      
368 +              vcdBody = A * vcdLab;
369 +              frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
370 +              oldFFL = frictionForceLab;
371 +              frictionForceLab = Atrans * frictionForceBody;
372 +              oldFTB = frictionTorqueBody;
373 +              frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
374 +              frictionTorqueLab = Atrans * frictionTorqueBody;
375 +              
376 +              // re-estimate velocities at full-step using friction forces:
377 +              
378 +              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
379 +              angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
380 +
381 +              // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
382 +              
383 +              fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
384 +              tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
385 +              
386 +              if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
387 +                break; // iteration ends here
388 +            }
389 +
390 +            integrableObject->addFrc(frictionForceLab);
391 +            integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
392 +
393 +            
394            } else {
395              //spherical atom
396 <            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
396 >
397              Vector3d randomForce;
398              Vector3d randomTorque;
399              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
400 +            integrableObject->addFrc(randomForce);            
401 +
402 +            // What remains contains velocity explicitly, but the velocity required
403 +            // is at the full step: v(t + h), while we have initially the velocity
404 +            // at the half step: v(t + h/2).  We need to iterate to converge the
405 +            // friction force vector.
406 +
407 +            // this is the velocity at the half-step:
408              
409 <            integrableObject->addFrc(frictionForce+randomForce);            
409 >            Vector3d vel =integrableObject->getVel();
410 >
411 >            //estimate velocity at full-step using everything but friction forces:          
412 >
413 >            frc = integrableObject->getFrc();
414 >            Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
415 >
416 >            Vector3d frictionForce(0.0);
417 >            Vector3d oldFF;  // used to test for convergence
418 >            RealType fdot;
419 >
420 >            //iteration starts here:
421 >
422 >            for (int k = 0; k < maxIterNum_; k++) {
423 >
424 >              oldFF = frictionForce;                            
425 >              frictionForce = -hydroProps_[index]->getXitt() * velStep;
426 >
427 >              // re-estimate velocities at full-step using friction forces:
428 >              
429 >              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
430 >
431 >              // check for convergence (if the vector has converged, fdot will be 1.0):
432 >              
433 >              fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
434 >              
435 >              if (fabs(1.0 - fdot) <= forceTolerance_)
436 >                break; // iteration ends here
437 >            }
438 >
439 >            integrableObject->addFrc(frictionForce);
440 >
441            }
442          }
443            
# Line 362 | Line 452 | namespace oopse {
452      if(!simParams->getUsePeriodicBoundaryConditions())
453        veloMunge->removeAngularDrift();
454  
455 <    ForceManager::postCalculation();  
455 >    ForceManager::postCalculation(needStress);  
456    }
457  
458   void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
# Line 370 | Line 460 | void LDForceManager::genRandomForceAndTorque(Vector3d&
460  
461      Vector<RealType, 6> Z;
462      Vector<RealType, 6> generalForce;
373 –
463          
464      Z[0] = randNumGen_.randNorm(0, variance);
465      Z[1] = randNumGen_.randNorm(0, variance);
# Line 379 | Line 468 | void LDForceManager::genRandomForceAndTorque(Vector3d&
468      Z[4] = randNumGen_.randNorm(0, variance);
469      Z[5] = randNumGen_.randNorm(0, variance);
470      
382 –
471      generalForce = hydroProps_[index]->getS()*Z;
472      
473      force[0] = generalForce[0];
# Line 389 | Line 477 | void LDForceManager::genRandomForceAndTorque(Vector3d&
477      torque[1] = generalForce[4];
478      torque[2] = generalForce[5];
479      
480 < }
480 > }
481  
482   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines