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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 682 by tim, Tue Aug 12 17:51:33 2003 UTC vs.
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC

# Line 2 | Line 2 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
2   #include "simError.h"
3   #include <cmath>
4   template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5 <                                    : T(theInfo, the_ff), fz(NULL),
6 <                                      indexOfZConsMols(NULL)
5 >                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL),
6 >                                                         indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
9    //get properties from SimInfo
# Line 11 | Line 11 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
11    ZConsParaData* zConsParaData;
12    DoubleData* sampleTime;
13    DoubleData* tolerance;
14 +  StringData* policy;
15    StringData* filename;
16    double COM[3];
17  
# Line 26 | Line 27 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
27    double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2;
28    zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox);
29  
30 +  //creat force substraction policy
31 +  data = info->getProperty(ZCONSFORCEPOLICY_ID);
32 +  if(!data){
33 +    sprintf( painCave.errMsg,
34 +               "ZConstraint Warning: User does not set force substraction policy, "
35 +               "average force substraction policy is used\n");
36 +    painCave.isFatal = 0;
37 +    simError();      
38 +
39 +    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
40 +  }
41 +  else{
42 +    policy = dynamic_cast<StringData*>(data);
43 +                
44 +         if(!policy){
45 +      sprintf( painCave.errMsg,
46 +                 "ZConstraint Error: Convertion from GenericData to StringData failure, "
47 +                 "average force substraction policy is used\n");
48 +      painCave.isFatal = 0;
49 +      simError();      
50 +
51 +      forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
52 +         }
53 +         else{
54 +                if(policy->getData() == "BYNUMBER")
55 +         forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
56 +                else if(policy->getData() == "BYMASS")
57 +         forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
58 +                else{
59 +        sprintf( painCave.errMsg,
60 +                  "ZConstraint Warning: unknown force substraction policy, "
61 +                  "average force substraction policy is used\n");
62 +        painCave.isFatal = 0;
63 +        simError();      
64 +           }            
65 +         }
66 +  }
67 +        
68 +  
69 +
70    //retrieve sample time of z-contraint
71    data = info->getProperty(ZCONSTIME_ID);
72    
# Line 156 | Line 197 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
197          simError();
198          }
199  
200 <      maxIndex = (*parameters)[parameters->size()].zconsIndex;
200 >      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
201  
202   #ifndef IS_MPI
203        totalNumMol = nMols;
# Line 179 | Line 220 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
220  
221   #ifndef IS_MPI
222              for(int j = 0; j < nMols; j++){
223 <              if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
224 <                 molecules[i].getCOM(COM);
223 >              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
224 >                 molecules[j].getCOM(COM);
225                            break;
226                }
227              }
# Line 197 | Line 238 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
238            
239             if (worldRank == whichNode ){
240                                                  
241 <             for(int i = 0; i < nMols; i++)
242 <               if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
243 <                 molecules[i].getCOM(COM);
241 >             for(int j = 0; j < nMols; j++)
242 >               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
243 >                 molecules[j].getCOM(COM);
244                                           break;
245                 }
246                                  
# Line 238 | Line 279 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
279        massOfZConsMols.push_back(molecules[i].getTotalMass());  
280  
281        zPos.push_back((*parameters)[searchResult].zPos);
282 +                cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
283             kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284        
285        molecules[i].getCOM(COM);
# Line 252 | Line 294 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
294    }
295  
296    fz = new double[zconsMols.size()];
297 +  curZPos = new double[zconsMols.size()];
298    indexOfZConsMols = new int [zconsMols.size()];
299  
300 <  if(!fz || !indexOfZConsMols){
300 >  if(!fz || !curZPos || !indexOfZConsMols){
301      sprintf( painCave.errMsg,
302               "Memory allocation failure in class Zconstraint\n");
303      painCave.isFatal = 1;
304      simError();
305    }
306  
307 <  for(int i = 0; i < zconsMols.size(); i++)
307 >  //determine the states of z-constraint molecules
308 >  for(int i = 0; i < zconsMols.size(); i++){
309      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
310 +
311 +         zconsMols[i]->getCOM(COM);
312 +    if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
313 +                states.push_back(zcsFixed);
314 +         else
315 +                states.push_back(zcsMoving);
316 +  }
317    
318   #endif
319  
320 +  //get total masss of unconstraint molecules
321 +  double totalMassOfUncons_local;
322 +  totalMassOfUncons_local = 0;
323 +  
324 +  for(int i = 0; i < unconsMols.size(); i++)
325 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
326 +    
327 + #ifndef IS_MPI
328 +  totalMassOfUncons = totalMassOfUncons_local;
329 + #else
330 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331 + #endif
332 +
333 +
334    //get total number of unconstrained atoms
335    int nUnconsAtoms_local;
336    nUnconsAtoms_local = 0;
# Line 275 | Line 340 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
340   #ifndef IS_MPI
341    totNumOfUnconsAtoms = nUnconsAtoms_local;
342   #else
343 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
344 < #endif
343 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344 > #endif  
345  
346 <  checkZConsState();
347 <
283 <  //  
284 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
346 >  // creat zconsWriter  
347 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348    
349    if(!fzOut){
350      sprintf( painCave.errMsg,
# Line 289 | Line 352 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
352      painCave.isFatal = 1;
353      simError();
354    }
355 <  
355 >
356 >  forcePolicy->update();
357   }
358  
359   template<typename T> ZConstraint<T>::~ZConstraint()
360   {
361    if(fz)
362      delete[] fz;
363 +
364 +  if(curZPos)
365 +    delete[] curZPos;
366    
367    if(indexOfZConsMols)
368      delete[] indexOfZConsMols;
369    
370    if(fzOut)
371      delete fzOut;
372 +        
373 +  if(forcePolicy)
374 +    delete forcePolicy;
375   }
376  
377   #ifdef IS_MPI
# Line 328 | Line 398 | template<typename T> void ZConstraint<T>::update()
398      
399        zconsMols.push_back(&molecules[i]);      
400        zPos.push_back((*parameters)[index].zPos);
401 <        kz.push_back((*parameters)[index].kRatio * zForceConst);
402 <
401 >        kz.push_back((*parameters)[index].kRatio * zForceConst);
402 >                        
403        massOfZConsMols.push_back(molecules[i].getTotalMass());  
404        
405        molecules[i].getCOM(COM);
# Line 342 | Line 412 | template<typename T> void ZConstraint<T>::update()
412  
413      }
414    }
415 +
416 +  //determine the states of z-constraint molecules
417 +  for(int i = 0; i < zconsMols.size(); i++){
418 +           zconsMols[i]->getCOM(COM);
419 +      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
420 +                  states.push_back(zcsFixed);
421 +           else
422 +                  states.push_back(zcsMoving);
423 +  }
424 +
425      
426    //The reason to declare fz and indexOfZconsMols as pointer to array is
427    // that we want to make the MPI communication simple
428    if(fz)
429      delete[] fz;
430 +        
431 +  if(curZPos)
432 +    delete[] curZPos;
433      
434    if(indexOfZConsMols)
435      delete[] indexOfZConsMols;
436      
437    if (zconsMols.size() > 0){
438      fz = new double[zconsMols.size()];
439 +         curZPos = new double[zconsMols.size()];
440      indexOfZConsMols =  new int[zconsMols.size()];
441      
442 <    if(!fz || !indexOfZConsMols){
442 >    if(!fz || !curZPos || !indexOfZConsMols){
443        sprintf( painCave.errMsg,
444                 "Memory allocation failure in class Zconstraint\n");
445        painCave.isFatal = 1;
# Line 369 | Line 453 | template<typename T> void ZConstraint<T>::update()
453    }
454    else{
455      fz = NULL;
456 +         curZPos = NULL;
457      indexOfZConsMols = NULL;
458    }
459 +        
460 +  //
461 +  forcePolicy->update();
462    
463   }
464  
# Line 410 | Line 498 | template<typename T> int ZConstraint<T>::isZConstraint
498    return -1;
499   }
500  
413 – /**
414 – * Description:
415 – *  Reset the z coordinates
416 – */
501   template<typename T> void ZConstraint<T>::integrate(){
502    
503    //zero out the velocities of center of mass of unconstrained molecules
# Line 430 | Line 514 | template<typename T> void ZConstraint<T>::integrate(){
514   *
515   *
516   *
517 < */
434 <
435 <
517 > */
518   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
519 +  double zsys;
520 +  double COM[3];
521 +  double force[3];
522  
523    T::calcForce(calcPot, calcStress);
524  
525 <  if (checkZConsState())
525 >  if (checkZConsState()){
526      zeroOutVel();
527 +         forcePolicy->update();
528 +  }  
529 +  zsys = calcZSys();
530 +  cout << "---------------------------------------------------------------------" <<endl;
531 +  cout << "current time: " << info->getTime() << endl;
532 +  cout << "center of mass at z: " << zsys << endl;      
533 +  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
534 +  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
535  
536 +  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
537 +
538    //do zconstraint force;
539    if (haveFixedZMols())
540      this->doZconstraintForce();
541 <  
541 >    
542    //use harmonical poteintial to move the molecules to the specified positions
543    if (haveMovingZMols())
544 <    //this->doHarmonic();
545 <  
546 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
547 <      
544 >    this->doHarmonic();
545 >
546 >  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 >
548 >  //write out forces and current positions of z-constraint molecules
549 >  if(info->getTime() >= curZconsTime){          
550 >         for(int i = 0; i < zconsMols.size(); i++){
551 >      zconsMols[i]->getCOM(COM);
552 >                curZPos[i] = COM[whichDirection];
553 >
554 >                //if the z-constraint molecule is still moving, just record its force
555 >                if(states[i] == zcsMoving){
556 >         fz[i] = 0;
557 >                  Atom** movingZAtoms;
558 >                  movingZAtoms = zconsMols[i]->getMyAtoms();
559 >                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
560 >           movingZAtoms[j]->getFrc(force);
561 >           fz[i] += force[whichDirection];
562 >                  }
563 >           }
564 >         }
565 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
566 >         curZconsTime += zconsTime;
567 >  }
568 >        
569 >  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
570 >  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
571   }
572  
573   template<typename T> double ZConstraint<T>::calcZSys()
# Line 459 | Line 577 | template<typename T> double ZConstraint<T>::calcZSys()
577    double totalMass;
578    double totalMZ_local;
579    double totalMZ;
462 –  double massOfUncons_local;
580    double massOfCurMol;
581    double COM[3];
582 <  
582 >        
583    totalMass_local = 0;
467 –  totalMass = 0;
584    totalMZ_local = 0;
469 –  totalMZ = 0;
470 –  massOfUncons_local = 0;
471 –    
585    
586    for(int i = 0; i < nMols; i++){
587      massOfCurMol = molecules[i].getTotalMass();
# Line 476 | Line 589 | template<typename T> double ZConstraint<T>::calcZSys()
589      
590      totalMass_local += massOfCurMol;
591      totalMZ_local += massOfCurMol * COM[whichDirection];
592 <    
480 <    if(isZConstraintMol(&molecules[i]) == -1){
481 <    
482 <      massOfUncons_local += massOfCurMol;
483 <    }  
484 <    
592 >
593    }
594 +
595    
487 –  
596   #ifdef IS_MPI  
597 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
598 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
599 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
492 < #else
597 >  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
598 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
599 > #else
600    totalMass = totalMass_local;
601    totalMZ = totalMZ_local;
602 <  totalMassOfUncons = massOfUncons_local;
496 < #endif  
602 > #endif  
603  
604    double zsys;
605    zsys = totalMZ / totalMass;
# Line 521 | Line 627 | template<typename T> void ZConstraint<T>::zeroOutVel()
627    Atom** fixedZAtoms;  
628    double COMvel[3];
629    double vel[3];
630 <  
630 >
631    //zero out the velocities of center of mass of fixed z-constrained molecules
632    
633    for(int i = 0; i < zconsMols.size(); i++){
634  
635      if (states[i] == zcsFixed){
636  
637 <        zconsMols[i]->getCOMvel(COMvel);      
637 >           zconsMols[i]->getCOMvel(COMvel);      
638 >                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
639 >
640        fixedZAtoms = zconsMols[i]->getMyAtoms();
641            
642        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
643          fixedZAtoms[j]->getVel(vel);
644 <          vel[whichDirection] -= COMvel[whichDirection];
645 <          fixedZAtoms[j]->setVel(vel);
644 >             vel[whichDirection] -= COMvel[whichDirection];
645 >             fixedZAtoms[j]->setVel(vel);
646        }
647 <          
647 >
648 >                zconsMols[i]->getCOMvel(COMvel);
649 >                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
650      }
651          
652    }
653 <  
653 >
654 >        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
655 >
656 > #ifdef IS_MPI
657 >  if (worldRank == 0){
658 > #endif
659 >    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
660 > #ifdef IS_MPI
661 >  }
662 > #endif
663 >                  
664    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
665    double MVzOfMovingMols_local;
666    double MVzOfMovingMols;
# Line 555 | Line 675 | template<typename T> void ZConstraint<T>::zeroOutVel()
675      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
676    }
677  
678 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
559 <
678 >  for(int i = 0; i < zconsMols.size(); i++){
679      if (states[i] == zcsMoving){
680        zconsMols[i]->getCOMvel(COMvel);
681        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
# Line 591 | Line 710 | template<typename T> void ZConstraint<T>::zeroOutVel()
710  
711    //modify the velocities of moving z-constrained molecuels
712    Atom** movingZAtoms;
713 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
713 >  for(int i = 0; i < zconsMols.size(); i++){
714  
715      if (states[i] ==zcsMoving){
716    
717        movingZAtoms = zconsMols[i]->getMyAtoms();
718 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
718 >           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
719          movingZAtoms[j]->getVel(vel);
720          vel[whichDirection] -= vzOfMovingMols;
721 <          movingZAtoms[j]->setVel(vel);
722 <        }
721 >             movingZAtoms[j]->setVel(vel);
722 >          }
723            
724 <    }
724 >   }
725  
726 + }
727 +
728 + #ifdef IS_MPI
729 +  if (worldRank == 0){
730 + #endif
731 +        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
732 + #ifdef IS_MPI
733    }
734 + #endif
735  
736   }
737  
# Line 616 | Line 743 | template<typename T> void ZConstraint<T>::doZconstrain
743    double COMvel[3];  
744    double COM[3];
745    double force[3];
619 –  double zsys;
746  
621 –  int nMovingZMols_local;
622 –  int nMovingZMols;
747  
624 –  //constrain the molecules which do not reach the specified positions  
748  
749 <   zsys = calcZSys();
627 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
749 >  //constrain the molecules which do not reach the specified positions  
750      
751    //Zero Out the force of z-contrained molecules    
752    totalFZ_local = 0;
753  
754    //calculate the total z-contrained force of fixed z-contrained molecules
755 <  cout << "Fixed Molecules" << endl;
755 >
756 > #ifdef IS_MPI
757 >  if (worldRank == 0){
758 > #endif
759 >    cout << "Fixed Molecules" << endl;
760 > #ifdef IS_MPI
761 >  }
762 > #endif
763 >
764    for(int i = 0; i < zconsMols.size(); i++){
765                  
766      if (states[i] == zcsFixed){
# Line 645 | Line 775 | template<typename T> void ZConstraint<T>::doZconstrain
775        }
776        totalFZ_local += fz[i];
777  
778 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
778 >      cout << "index: " << indexOfZConsMols[i]
779 >                                <<"\tcurrent zpos: " << COM[whichDirection]
780 >                                << "\tcurrent fz: " <<fz[i] << endl;
781  
782      }
783            
784    }
785  
786 <  //calculate the number of atoms of moving z-constrained molecules
655 <  nMovingZMols_local = 0;
656 <  for(int i = 0; zconsMols.size(); i++){
657 <    if(states[i] == zcsMoving)
658 <        nMovingZMols_local += massOfZConsMols[i];
659 <  }
786 >  //calculate total z-constraint force
787   #ifdef IS_MPI
788    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
662 –  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
789   #else
790    totalFZ = totalFZ_local;
665 –  nMovingZMols = nMovingZMols_local;
791   #endif
792  
793 <  force[0]= 0;
669 <  force[1]= 0;
670 <  force[2]= 0;
671 <  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
672 <
673 <  //modify the velocites of unconstrained molecules
674 <  for(int i = 0; i < unconsMols.size(); i++){
675 <    
676 <     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
677 <    
678 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
679 <       unconsAtoms[j]->addFrc(force);
680 <    
681 <  }      
682 <
683 < //modify the velocities of moving z-constrained molecules
684 <  for(int i = 0; i < zconsMols.size(); i++) {
685 <   if (states[i] == zcsMoving){
686 <                
687 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
688 <
689 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
690 <       movingZAtoms[j]->addFrc(force);
691 <     }
692 <  }
693 <
793 >        
794    // apply negative to fixed z-constrained molecues;
795    force[0]= 0;
796    force[1]= 0;
# Line 704 | Line 804 | template<typename T> void ZConstraint<T>::doZconstrain
804        zconsAtoms = zconsMols[i]->getMyAtoms();  
805      
806        for(int j =0; j < nAtomOfCurZConsMol; j++) {
807 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
807 >                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
808 >        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
809          zconsAtoms[j]->addFrc(force);
810        }
811                  
812      }
813          
814    }
815 +
816 +  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
817 +  //               << "total force is " << calcTotalForce() << endl;
818 +
819 +  //calculate the number of atoms of moving z-constrained molecules
820 +  int nMovingZAtoms_local;
821 +  int nMovingZAtoms;
822 +        
823 +  nMovingZAtoms_local = 0;
824 +  for(int i = 0; i < zconsMols.size(); i++)
825 +    if(states[i] == zcsMoving)
826 +           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
827 +  
828 + #ifdef IS_MPI
829 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
830 + #else
831 +  nMovingZAtoms = nMovingZAtoms_local;
832 + #endif
833  
834 +  force[0]= 0;
835 +  force[1]= 0;
836 +  force[2]= 0;
837 +
838 +  //modify the forces of unconstrained molecules
839 +  for(int i = 0; i < unconsMols.size(); i++){
840 +    
841 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
842 +    
843 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
844 +       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
845 +       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
846 +       unconsAtoms[j]->addFrc(force);
847 +     }
848 +    
849 +  }      
850 +
851 + //modify the forces of moving z-constrained molecules
852 +  for(int i = 0; i < zconsMols.size(); i++) {
853 +    if (states[i] == zcsMoving){
854 +                
855 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
856 +
857 +      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
858 +        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
859 +        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
860 +        movingZAtoms[j]->addFrc(force);
861 +      }
862 +    }
863 +  }
864 +
865 +  //cout << "after substracting z-constraint force from moving molecuels "
866 +  //              << "total force is " << calcTotalForce()  << endl;
867 +
868   }
869  
870   template<typename T> bool ZConstraint<T>::checkZConsState(){
871    double COM[3];
872    double diff;
873    
874 <  bool changed;
874 >  int changed_local;
875 >  int changed;
876 >        
877 >  changed_local = 0;
878    
723 –  changed = false;
724 –  
879    for(int i =0; i < zconsMols.size(); i++){
880  
881      zconsMols[i]->getCOM(COM);
882      diff = fabs(COM[whichDirection] - zPos[i]);  
883      if (  diff <= zconsTol && states[i] == zcsMoving){
884        states[i] = zcsFixed;
885 <        changed = true;
885 >           changed_local = 1;
886      }
887      else if ( diff > zconsTol && states[i] == zcsFixed){
888        states[i] = zcsMoving;
889 <        changed = true;  
889 >           changed_local = 1;    
890      }
891    
892    }
893  
894 <  return changed;
894 > #ifndef IS_MPI
895 >  changed =changed_local;
896 > #else
897 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
898 > #endif
899 >
900 >  return changed > 0 ? true : false;
901   }
902  
903   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
904 +
905 +  int havingFixed_local;
906 +  int havingFixed;
907 +
908 +  havingFixed_local = 0;
909 +
910    for(int i = 0; i < zconsMols.size(); i++)
911 <    if (states[i] == zcsFixed)
912 <      return true;
911 >    if (states[i] == zcsFixed){
912 >      havingFixed_local = 1;
913 >                break;
914 >    }
915  
916 <  return false;
916 > #ifndef IS_MPI
917 >  havingFixed = havingFixed_local;
918 > #else
919 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
920 > #endif
921 >
922 >  return havingFixed > 0 ? true : false;
923   }
924  
925  
# Line 753 | Line 927 | template<typename T> bool ZConstraint<T>::haveMovingZM
927   *
928   */
929   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
930 +
931 +  int havingMoving_local;
932 +  int havingMoving;
933 +
934 +  havingMoving_local = 0;
935 +
936    for(int i = 0; i < zconsMols.size(); i++)
937 <    if (states[i] == zcsMoving)
938 <      return true;
937 >    if (states[i] == zcsMoving){
938 >      havingMoving_local = 1;
939 >                break;
940 >    }
941  
942 <  return false;
942 > #ifndef IS_MPI
943 >  havingMoving = havingMoving_local;
944 > #else
945 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
946 > #endif
947 >
948 >  return havingMoving > 0 ? true : false;
949    
950   }
951  
# Line 769 | Line 957 | template<typename T> void ZConstraint<T>::doHarmonic()
957   template<typename T> void ZConstraint<T>::doHarmonic(){
958    double force[3];
959    double harmonicU;
960 +  double harmonicF;
961    double COM[3];
962    double diff;
963 +  double totalFZ_local;
964 +  double totalFZ;
965          
966    force[0] = 0;
967    force[1] = 0;
968    force[2] = 0;
969  
970 <  cout << "Moving Molecules" << endl;  
970 >  totalFZ_local = 0;
971 >
972 > #ifdef IS_MPI
973 >  if (worldRank == 0){
974 > #endif
975 >    cout << "Moving Molecules" << endl;
976 > #ifdef IS_MPI
977 >  }
978 > #endif
979 >
980 >
981    for(int i = 0; i < zconsMols.size(); i++) {
982  
983      if (states[i] == zcsMoving){
984 <      zconsMols[i]->getCOM(COM):
984 >      zconsMols[i]->getCOM(COM);
985        cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
986                  
987                  diff = COM[whichDirection] -zPos[i];
988                  
989        harmonicU = 0.5 * kz[i] * diff * diff;  
990 <                info->ltPot += harmonicU;
990 >                info->lrPot += harmonicU;
991  
992 <                force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms();
992 >      harmonicF =  - kz[i] * diff;
993 >      totalFZ_local += harmonicF;
994 >
995 >       //adjust force
996                  
997        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
998  
999 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
999 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
1000 >                  force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
1001 >         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
1002           movingZAtoms[j]->addFrc(force);
1003 +       }
1004      }
1005  
1006    }
1007  
1008 + #ifndef IS_MPI
1009 +  totalFZ = totalFZ_local;
1010 + #else
1011 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1012 + #endif
1013 +
1014 +  force[0]= 0;
1015 +  force[1]= 0;
1016 +  force[2]= 0;
1017 +
1018 +  //modify the forces of unconstrained molecules
1019 +  for(int i = 0; i < unconsMols.size(); i++){
1020 +    
1021 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
1022 +    
1023 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
1024 +       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
1025 +       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
1026 +       unconsAtoms[j]->addFrc(force);    
1027 +     }
1028 +  }  
1029 +
1030   }
1031 +
1032 + template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1033 + {
1034 +  double MVzOfMovingMols_local;
1035 +  double MVzOfMovingMols;
1036 +  double totalMassOfMovingZMols_local;
1037 +  double totalMassOfMovingZMols;
1038 +  double COMvel[3];
1039 +      
1040 +  MVzOfMovingMols_local = 0;
1041 +  totalMassOfMovingZMols_local = 0;
1042 +
1043 +  for(int i =0; i < unconsMols.size(); i++){
1044 +    unconsMols[i]->getCOMvel(COMvel);
1045 +    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1046 +  }
1047 +
1048 +  for(int i = 0; i < zconsMols.size(); i++){
1049 +
1050 +    if (states[i] == zcsMoving){
1051 +      zconsMols[i]->getCOMvel(COMvel);
1052 +      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1053 +      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1054 +    }
1055 +                
1056 +  }
1057 +
1058 + #ifndef IS_MPI
1059 +  MVzOfMovingMols = MVzOfMovingMols_local;
1060 +  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1061 + #else
1062 +  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1063 +  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1064 + #endif
1065 +
1066 +  double vzOfMovingMols;
1067 +  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1068 +
1069 +  return vzOfMovingMols;
1070 + }
1071 +
1072 +
1073 + template<typename T> double ZConstraint<T>::calcSysCOMVel()
1074 + {
1075 +  double COMvel[3];
1076 +  double tempMVz_local;
1077 +  double tempMVz;
1078 +  double massOfZCons_local;
1079 +  double massOfZCons;
1080 +
1081 +
1082 + tempMVz_local = 0;
1083 +
1084 +  for(int i =0 ; i < nMols; i++){
1085 +    molecules[i].getCOMvel(COMvel);
1086 +         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1087 +  }
1088 +
1089 +  massOfZCons_local = 0;
1090 +        
1091 +  for(int i = 0; i < massOfZConsMols.size(); i++){
1092 +    massOfZCons_local += massOfZConsMols[i];
1093 +  }
1094 + #ifndef IS_MPI
1095 +  massOfZCons = massOfZCons_local;
1096 +  tempMVz = tempMVz_local;
1097 + #else
1098 +  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1099 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1100 + #endif
1101 +
1102 +  return tempMVz /(totalMassOfUncons + massOfZCons);
1103 + }
1104 +
1105 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1106 +
1107 +  double force[3];  
1108 +  double totalForce_local;
1109 +  double totalForce;
1110 +
1111 +  totalForce_local = 0;
1112 +
1113 +  for(int i = 0; i < nAtoms; i++){
1114 +    atoms[i]->getFrc(force);
1115 +    totalForce_local += force[whichDirection];
1116 +  }
1117 +
1118 + #ifndef IS_MPI
1119 +  totalForce = totalForce_local;
1120 + #else
1121 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1122 + #endif
1123 +
1124 +  return totalForce;
1125 +
1126 + }
1127 +
1128 + /**
1129 + *
1130 + */
1131 +
1132 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1133 +  //calculate the number of atoms of moving z-constrained molecules
1134 +  int nMovingZAtoms_local;
1135 +  int nMovingZAtoms;
1136 +        
1137 +  nMovingZAtoms_local = 0;
1138 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1139 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1140 +           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1141 +  
1142 + #ifdef IS_MPI
1143 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1144 + #else
1145 +  nMovingZAtoms = nMovingZAtoms_local;
1146 + #endif
1147 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1148 + }
1149 +
1150 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1151 +  return totalForce / mol->getNAtoms();
1152 + }
1153 +
1154 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1155 +  return totalForce / totNumOfMovingAtoms;
1156 + }
1157 +
1158 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1159 +    return totalForce / mol->getNAtoms();
1160 + }
1161 +
1162 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1163 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1164 + }
1165 +
1166 + /**
1167 + *
1168 + */
1169 +
1170 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1171 +  //calculate the number of atoms of moving z-constrained molecules
1172 +  double massOfMovingZAtoms_local;
1173 +  double massOfMovingZAtoms;
1174 +        
1175 +  massOfMovingZAtoms_local = 0;
1176 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1177 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1178 +           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1179 +  
1180 + #ifdef IS_MPI
1181 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1182 + #else
1183 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1184 + #endif
1185 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1186 + }
1187 +
1188 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1189 +  return totalForce * atom->getMass() / mol->getTotalMass();
1190 + }
1191 +
1192 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1193 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1194 + }
1195 +
1196 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1197 +  return totalForce * atom->getMass() / mol->getTotalMass();
1198 + }
1199 +
1200 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1201 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1202 + }
1203 +

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