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root/OpenMD/trunk/src/constraints/ZconstraintForceManager.cpp
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Comparing trunk/src/constraints/ZconstraintForceManager.cpp (file contents):
Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 111 | Line 111 | namespace oopse {
111  
112      //estimate the force constant of harmonical potential
113      Mat3x3d hmat = currSnapshot_->getHmat();
114 <    double halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2;        
115 <    double targetTemp;
114 >    RealType halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2;      
115 >    RealType targetTemp;
116      if (simParam->haveTargetTemp()) {
117        targetTemp = simParam->getTargetTemp();
118      } else {
119        targetTemp = 298.0;
120      }
121 <    double zforceConstant = OOPSEConstant::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox);
121 >    RealType zforceConstant = OOPSEConstant::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox);
122          
123 <    int nZconstraints = simParam->getNZconstraints();
124 <    ZconStamp** stamp = simParam->getZconStamp();
123 >    int nZconstraints = simParam->getNZconsStamps();
124 >    std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
125      //
126      for (int i = 0; i < nZconstraints; i++){
127  
# Line 148 | Line 148 | namespace oopse {
148      update();
149      
150      //calculate masss of unconstraint molecules in the whole system (never change during the simulation)
151 <    double totMassUnconsMols_local = 0.0;    
151 >    RealType totMassUnconsMols_local = 0.0;    
152      std::vector<Molecule*>::iterator j;
153      for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
154        totMassUnconsMols_local += (*j)->getMass();
# Line 156 | Line 156 | namespace oopse {
156   #ifndef IS_MPI
157      totMassUnconsMols_ = totMassUnconsMols_local;
158   #else
159 <    MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_DOUBLE,
159 >    MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_REALTYPE,
160                    MPI_SUM, MPI_COMM_WORLD);  
161   #endif
162  
# Line 194 | Line 194 | namespace oopse {
194          zmol.param = i->second;
195          zmol.cantPos = zmol.param.zTargetPos; /**@todo fixed me when zmol migrate, it is incorrect*/
196          Vector3d com = zmol.mol->getCom();
197 <        double diff = fabs(zmol.param.zTargetPos - com[whichDirection]);
197 >        RealType diff = fabs(zmol.param.zTargetPos - com[whichDirection]);
198          if (diff < zconsTol_) {
199            fixedZMols_.push_back(zmol);
200          } else {
# Line 299 | Line 299 | namespace oopse {
299  
300      // calculate the vz of center of mass of moving molecules(include unconstrained molecules
301      // and moving z-constrained molecules)  
302 <    double pzMovingMols_local = 0.0;
303 <    double pzMovingMols;
302 >    RealType pzMovingMols_local = 0.0;
303 >    RealType pzMovingMols;
304      
305      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
306        mol = i->mol;        
# Line 318 | Line 318 | namespace oopse {
318   #ifndef IS_MPI
319      pzMovingMols = pzMovingMols_local;
320   #else
321 <    MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_DOUBLE,
321 >    MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_REALTYPE,
322                    MPI_SUM, MPI_COMM_WORLD);
323   #endif
324  
325 <    double vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_);
325 >    RealType vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_);
326  
327      //modify the velocities of moving z-constrained molecuels
328      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
# Line 352 | Line 352 | namespace oopse {
352  
353  
354    void ZconstraintForceManager::doZconstraintForce(){
355 <    double totalFZ;
356 <    double totalFZ_local;
355 >    RealType totalFZ;
356 >    RealType totalFZ_local;
357      Vector3d com;
358      Vector3d force(0.0);
359  
# Line 383 | Line 383 | namespace oopse {
383  
384      //calculate total z-constraint force
385   #ifdef IS_MPI
386 <    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
386 >    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
387   #else
388      totalFZ = totalFZ_local;
389   #endif
# Line 427 | Line 427 | namespace oopse {
427  
428  
429    void ZconstraintForceManager::doHarmonic(){
430 <    double totalFZ;
430 >    RealType totalFZ;
431      Vector3d force(0.0);
432      Vector3d com;
433 <    double totalFZ_local = 0;
433 >    RealType totalFZ_local = 0;
434      std::list<ZconstraintMol>::iterator i;
435      StuntDouble* integrableObject;
436      Molecule::IntegrableObjectIterator ii;
# Line 438 | Line 438 | namespace oopse {
438      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
439        mol = i->mol;
440        com = mol->getCom();  
441 <      double resPos = usingSMD_? i->cantPos : i->param.zTargetPos;
442 <      double diff = com[whichDirection] - resPos;
443 <      double harmonicU = 0.5 * i->param.kz * diff * diff;
441 >      RealType resPos = usingSMD_? i->cantPos : i->param.zTargetPos;
442 >      RealType diff = com[whichDirection] - resPos;
443 >      RealType harmonicU = 0.5 * i->param.kz * diff * diff;
444        currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU;
445 <      double harmonicF = -i->param.kz * diff;
445 >      RealType harmonicF = -i->param.kz * diff;
446        totalFZ_local += harmonicF;
447  
448        //adjust force
# Line 457 | Line 457 | namespace oopse {
457   #ifndef IS_MPI
458      totalFZ = totalFZ_local;
459   #else
460 <    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
460 >    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);  
461   #endif
462  
463      //modify the forces of unconstrained molecules
# Line 476 | Line 476 | namespace oopse {
476  
477    bool ZconstraintForceManager::checkZConsState(){
478      Vector3d com;
479 <    double diff;
479 >    RealType diff;
480      int changed_local = 0;
481  
482      std::list<ZconstraintMol>::iterator i;
# Line 566 | Line 566 | namespace oopse {
566  
567    void ZconstraintForceManager::calcTotalMassMovingZMols(){
568  
569 <    double totMassMovingZMols_local = 0.0;
569 >    RealType totMassMovingZMols_local = 0.0;
570      std::list<ZconstraintMol>::iterator i;
571      for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
572        totMassMovingZMols_local += i->mol->getMass();
573      }
574      
575   #ifdef IS_MPI
576 <    MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_DOUBLE,
576 >    MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_REALTYPE,
577                    MPI_SUM, MPI_COMM_WORLD);
578   #else
579      totMassMovingZMols_ = totMassMovingZMols_local;
# Line 581 | Line 581 | namespace oopse {
581  
582    }
583  
584 <  double ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce){
584 >  RealType ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce){
585      return totalForce * sd->getMass() / mol->getMass();
586    }
587  
588 <  double ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, double totalForce){
588 >  RealType ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, RealType totalForce){
589      return totalForce * mol->getMass() / (totMassUnconsMols_ + totMassMovingZMols_);
590    }
591  
592 <  double ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, double totalForce){
592 >  RealType ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, RealType totalForce){
593      return totalForce * sd->getMass() / mol->getMass();
594    }
595  
596 <  double ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, double totalForce){
596 >  RealType ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, RealType totalForce){
597      return totalForce * mol->getMass() / totMassUnconsMols_;
598    }
599  
600    void ZconstraintForceManager::updateZPos(){
601 <    double curTime = currSnapshot_->getTime();
601 >    RealType curTime = currSnapshot_->getTime();
602      std::list<ZconstraintMol>::iterator i;
603      for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
604        i->param.zTargetPos += zconsGap_;    
# Line 612 | Line 612 | namespace oopse {
612      }
613    }
614  
615 <  double ZconstraintForceManager::getZTargetPos(int index){
616 <    double zTargetPos;
615 >  RealType ZconstraintForceManager::getZTargetPos(int index){
616 >    RealType zTargetPos;
617   #ifndef IS_MPI    
618      Molecule* mol = info_->getMoleculeByGlobalIndex(index);
619      assert(mol);
# Line 621 | Line 621 | namespace oopse {
621      zTargetPos = com[whichDirection];
622   #else
623      int whicProc = info_->getMolToProc(index);
624 <    MPI_Bcast(&zTargetPos, 1, MPI_DOUBLE, whicProc, MPI_COMM_WORLD);
624 >    MPI_Bcast(&zTargetPos, 1, MPI_REALTYPE, whicProc, MPI_COMM_WORLD);
625   #endif
626      return zTargetPos;
627    }

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