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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 711 by mmeineke, Fri Aug 22 20:04:39 2003 UTC

# Line 3 | Line 3 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
3   #include <cmath>
4   template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5                                      : T(theInfo, the_ff), fz(NULL), curZPos(NULL),
6 <                                                         indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
6 >                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
9    //get properties from SimInfo
# Line 40 | Line 40 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
40    }
41    else{
42      policy = dynamic_cast<StringData*>(data);
43 <                
44 <         if(!policy){
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");
# Line 49 | Line 49 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
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{
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 <         }
64 >      }  
65 >    }
66    }
67 –        
67    
68 <
68 >  
69    //retrieve sample time of z-contraint
70    data = info->getProperty(ZCONSTIME_ID);
71    
# Line 110 | Line 109 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
109    }
110    else{
111  
112 <     filename = dynamic_cast<StringData*>(data);
112 >    filename = dynamic_cast<StringData*>(data);
113      
114      if(!filename){
115  
# Line 124 | Line 123 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
123        this->zconsOutput = filename->getData();
124      }
125      
127 –
126    }
127  
128    //retrieve tolerance for z-constraint molecuels
# Line 154 | Line 152 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
152      }
153  
154    }
155 <        
155 >  
156    //retrieve index of z-constraint molecules
157    data = info->getProperty(ZCONSPARADATA_ID);
158    if(!data) {
# Line 195 | Line 193 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
193                 "ZConstraint error: index is out of range\n");
194          painCave.isFatal = 1;
195          simError();
196 <        }
196 >        }
197  
198        maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
199  
# Line 216 | Line 214 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
214        //its initial z coordinate  will be used as default
215        for(int i = 0; i < parameters->size(); i++){
216  
217 <              if(!(*parameters)[i].havingZPos){
220 <
217 >        if(!(*parameters)[i].havingZPos){
218   #ifndef IS_MPI
219 <            for(int j = 0; j < nMols; j++){
220 <              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 <                 molecules[j].getCOM(COM);
222 <                          break;
226 <              }
219 >          for(int j = 0; j < nMols; j++){
220 >            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 >              molecules[j].getCOM(COM);
222 >        break;
223              }
224 +          }
225   #else
226              //query which processor current zconstraint molecule belongs to
227 <           int *MolToProcMap;
228 <           int whichNode;
229 <                         double initZPos;
230 <           MolToProcMap = mpiSim->getMolToProcMap();
231 <           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
232 <                          
233 <           //broadcast the zpos of current z-contraint molecule
234 <           //the node which contain this
227 >          int *MolToProcMap;
228 >          int whichNode;
229 >    double initZPos;
230 >          MolToProcMap = mpiSim->getMolToProcMap();
231 >          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
232 >        
233 >          //broadcast the zpos of current z-contraint molecule
234 >          //the node which contain this
235            
236 <           if (worldRank == whichNode ){
237 <                                                
238 <             for(int j = 0; j < nMols; j++)
239 <               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 <                 molecules[j].getCOM(COM);
241 <                                         break;
242 <               }
243 <                                
244 <           }
236 >          if (worldRank == whichNode ){
237 >            
238 >            for(int j = 0; j < nMols; j++)
239 >              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 >                molecules[j].getCOM(COM);
241 >          break;
242 >              }
243 >        
244 >          }
245  
246 <            MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);                          
246 >          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
247   #endif
248              
249 <                 (*parameters)[i].zPos = COM[whichDirection];
249 >          (*parameters)[i].zPos = COM[whichDirection];
250  
251 <            sprintf( painCave.errMsg,
251 >          sprintf( painCave.errMsg,
252                       "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
253                       "initial z coornidate will be used \n");
254 <            painCave.isFatal = 0;
255 <            simError();  
256 <          
257 <              }
258 <            }
259 <                        
254 >           painCave.isFatal = 0;
255 >           simError();  
256 >    
257 >  }
258 >      }
259 >      
260      }//end if (!zConsParaData)
261    }//end  if (!data)
262              
# Line 279 | Line 276 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
276        massOfZConsMols.push_back(molecules[i].getTotalMass());  
277  
278        zPos.push_back((*parameters)[searchResult].zPos);
279 <                cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
280 <           kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
279 >      cout << "index: "<< (*parameters)[searchResult].zconsIndex
280 >             <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
281 >      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
282        
283        molecules[i].getCOM(COM);
284      }
# Line 308 | Line 306 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
306    for(int i = 0; i < zconsMols.size(); i++){
307      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
308  
309 <         zconsMols[i]->getCOM(COM);
309 >    zconsMols[i]->getCOM(COM);
310      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
311 <                states.push_back(zcsFixed);
312 <         else
313 <                states.push_back(zcsMoving);
311 >      states.push_back(zcsFixed);
312 >    else
313 >      states.push_back(zcsMoving);
314    }
315    
316   #endif
# Line 327 | Line 325 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
325   #ifndef IS_MPI
326    totalMassOfUncons = totalMassOfUncons_local;
327   #else
328 <  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
328 >  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
329 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
330   #endif
331  
332  
# Line 340 | Line 339 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
339   #ifndef IS_MPI
340    totNumOfUnconsAtoms = nUnconsAtoms_local;
341   #else
342 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
342 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344   #endif  
345  
346    // creat zconsWriter  
# Line 369 | Line 369 | template<typename T> ZConstraint<T>::~ZConstraint()
369    
370    if(fzOut)
371      delete fzOut;
372 <        
372 >  
373    if(forcePolicy)
374      delete forcePolicy;
375   }
376  
377 +
378 + /**
379 + *
380 + */
381 +
382   #ifdef IS_MPI
383   template<typename T> void ZConstraint<T>::update()
384   {
# Line 398 | Line 403 | template<typename T> void ZConstraint<T>::update()
403      
404        zconsMols.push_back(&molecules[i]);      
405        zPos.push_back((*parameters)[index].zPos);
406 <        kz.push_back((*parameters)[index].kRatio * zForceConst);
407 <                        
406 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
407 >      
408        massOfZConsMols.push_back(molecules[i].getTotalMass());  
409        
410        molecules[i].getCOM(COM);
# Line 415 | Line 420 | template<typename T> void ZConstraint<T>::update()
420  
421    //determine the states of z-constraint molecules
422    for(int i = 0; i < zconsMols.size(); i++){
423 <           zconsMols[i]->getCOM(COM);
423 >     zconsMols[i]->getCOM(COM);
424        if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
425 <                  states.push_back(zcsFixed);
426 <           else
427 <                  states.push_back(zcsMoving);
425 >      states.push_back(zcsFixed);
426 >     else
427 >      states.push_back(zcsMoving);
428    }
429  
430      
# Line 427 | Line 432 | template<typename T> void ZConstraint<T>::update()
432    // that we want to make the MPI communication simple
433    if(fz)
434      delete[] fz;
435 <        
435 >  
436    if(curZPos)
437      delete[] curZPos;
438      
# Line 436 | Line 441 | template<typename T> void ZConstraint<T>::update()
441      
442    if (zconsMols.size() > 0){
443      fz = new double[zconsMols.size()];
444 <         curZPos = new double[zconsMols.size()];
444 >   curZPos = new double[zconsMols.size()];
445      indexOfZConsMols =  new int[zconsMols.size()];
446      
447      if(!fz || !curZPos || !indexOfZConsMols){
# Line 453 | Line 458 | template<typename T> void ZConstraint<T>::update()
458    }
459    else{
460      fz = NULL;
461 <         curZPos = NULL;
461 >   curZPos = NULL;
462      indexOfZConsMols = NULL;
463    }
464 <        
464 >  
465    //
466    forcePolicy->update();
467    
# Line 464 | Line 469 | template<typename T> void ZConstraint<T>::update()
469  
470   #endif
471  
472 < /**  Function Name: isZConstraintMol
473 < **  Parameter
474 < **    Molecule* mol
475 < **  Return value:
476 < **    -1, if the molecule is not z-constraint molecule,
477 < **    other non-negative values, its index in indexOfAllZConsMols vector
472 > /**
473 > *  Function Name: isZConstraintMol
474 > *  Parameter
475 > *    Molecule* mol
476 > *  Return value:
477 > *    -1, if the molecule is not z-constraint molecule,
478 > *    other non-negative values, its index in indexOfAllZConsMols vector
479   */
480  
481   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 503 | Line 509 | template<typename T> void ZConstraint<T>::integrate(){
509    //zero out the velocities of center of mass of unconstrained molecules
510    //and the velocities of center of mass of every single z-constrained molecueles
511    zeroOutVel();
512 +
513 +  curZconsTime = zconsTime + info->getTime();
514    
515    T::integrate();
516  
# Line 519 | Line 527 | template<typename T> void ZConstraint<T>::calcForce(in
527    double zsys;
528    double COM[3];
529    double force[3];
530 +  double zSysCOMVel;
531  
532    T::calcForce(calcPot, calcStress);
533  
534    if (checkZConsState()){
535 +    
536 + #ifdef IS_MPI
537 +    if(worldRank == 0){
538 + #endif
539 +      std::cerr << "\n"
540 +                << "*******************************************\n"
541 +                << " about to call zeroOutVel()\n"
542 +                << "*******************************************\n"
543 +                << "\n";
544 + #ifdef IS_MPI
545 +    }
546 + #endif
547      zeroOutVel();
548 <         forcePolicy->update();
548 >
549 > #ifdef IS_MPI
550 >    if(worldRank == 0){
551 > #endif
552 >      std::cerr << "\n"
553 >                << "*******************************************\n"
554 >                << " finished zeroOutVel()\n"
555 >                << "*******************************************\n"
556 >                << "\n";
557 > #ifdef IS_MPI
558 >    }
559 > #endif
560 >    
561 >    forcePolicy->update();
562    }  
563 +  
564    zsys = calcZSys();
565 <  cout << "---------------------------------------------------------------------" <<endl;
566 <  cout << "current time: " << info->getTime() << endl;
567 <  cout << "center of mass at z: " << zsys << endl;      
568 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
569 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
565 >  zSysCOMVel = calcSysCOMVel();
566 > #ifdef IS_MPI
567 >  if(worldRank == 0){
568 > #endif
569 >    cout << "---------------------------------------------------------------------" <<endl;
570 >    cout << "current time: " << info->getTime() << endl;
571 >    cout << "center of mass at z: " << zsys << endl;    
572 >    cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
573  
574 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
574 > #ifdef IS_MPI
575 >  }
576 > #endif
577  
578    //do zconstraint force;
579    if (haveFixedZMols())
# Line 543 | Line 583 | template<typename T> void ZConstraint<T>::calcForce(in
583    if (haveMovingZMols())
584      this->doHarmonic();
585  
546 –  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 –
586    //write out forces and current positions of z-constraint molecules
587 <  if(info->getTime() >= curZconsTime){          
588 <         for(int i = 0; i < zconsMols.size(); i++){
587 >  if(info->getTime() >= curZconsTime){    
588 >   for(int i = 0; i < zconsMols.size(); i++){
589        zconsMols[i]->getCOM(COM);
590 <                curZPos[i] = COM[whichDirection];
590 >    curZPos[i] = COM[whichDirection];
591  
592 <                //if the z-constraint molecule is still moving, just record its force
593 <                if(states[i] == zcsMoving){
592 >    //if the z-constraint molecule is still moving, just record its force
593 >    if(states[i] == zcsMoving){
594           fz[i] = 0;
595 <                  Atom** movingZAtoms;
596 <                  movingZAtoms = zconsMols[i]->getMyAtoms();
597 <                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
595 >      Atom** movingZAtoms;
596 >      movingZAtoms = zconsMols[i]->getMyAtoms();
597 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
598             movingZAtoms[j]->getFrc(force);
599             fz[i] += force[whichDirection];
600 <                  }
601 <           }
602 <         }
600 >      }
601 >     }
602 >   }
603      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
604 <         curZconsTime += zconsTime;
604 >   curZconsTime += zconsTime;
605    }
606 <        
607 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
608 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
606 >
607 >  zSysCOMVel = calcSysCOMVel();  
608 > #ifdef IS_MPI
609 >  if(worldRank == 0){
610 > #endif
611 >    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
612 > #ifdef IS_MPI
613 >  }
614 > #endif
615 >
616   }
617 +
618 +
619 + /**
620 + *
621 + */
622  
623   template<typename T> double ZConstraint<T>::calcZSys()
624   {
# Line 579 | Line 629 | template<typename T> double ZConstraint<T>::calcZSys()
629    double totalMZ;
630    double massOfCurMol;
631    double COM[3];
632 <        
632 >  
633    totalMass_local = 0;
634    totalMZ_local = 0;
635    
# Line 594 | Line 644 | template<typename T> double ZConstraint<T>::calcZSys()
644  
645    
646   #ifdef IS_MPI  
647 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
648 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
647 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
648 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
649 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
650 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
651   #else
652    totalMass = totalMass_local;
653    totalMZ = totalMZ_local;
# Line 618 | Line 670 | template<typename T> void ZConstraint<T>::thermalize(
670  
671   /**
672   *
621 – *
622 – *
673   */
674  
675   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 627 | Line 677 | template<typename T> void ZConstraint<T>::zeroOutVel()
677    Atom** fixedZAtoms;  
678    double COMvel[3];
679    double vel[3];
680 +  double zSysCOMVel;
681  
682    //zero out the velocities of center of mass of fixed z-constrained molecules
683    
684    for(int i = 0; i < zconsMols.size(); i++){
685  
686 <    if (states[i] == zcsFixed){
686 >    if (states[i] == zcsFixed){
687  
688 <           zconsMols[i]->getCOMvel(COMvel);      
689 <                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
688 >     zconsMols[i]->getCOMvel(COMvel);      
689 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
690  
691        fixedZAtoms = zconsMols[i]->getMyAtoms();
692 <          
692 >    
693        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
694          fixedZAtoms[j]->getVel(vel);
695 <             vel[whichDirection] -= COMvel[whichDirection];
696 <             fixedZAtoms[j]->setVel(vel);
695 >       vel[whichDirection] -= COMvel[whichDirection];
696 >       fixedZAtoms[j]->setVel(vel);
697        }
698  
699 <                zconsMols[i]->getCOMvel(COMvel);
700 <                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
699 >    zconsMols[i]->getCOMvel(COMvel);
700 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
701      }
702 <        
702 >  
703    }
704  
705 <        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
705 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
706  
707 +  zSysCOMVel = calcSysCOMVel();
708   #ifdef IS_MPI
709 <  if (worldRank == 0){
709 >  if(worldRank == 0){
710   #endif
711 <    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
711 >    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
712   #ifdef IS_MPI
713    }
714   #endif
715 <                  
715 >      
716    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
717    double MVzOfMovingMols_local;
718    double MVzOfMovingMols;
# Line 679 | Line 731 | template<typename T> void ZConstraint<T>::zeroOutVel()
731      if (states[i] == zcsMoving){
732        zconsMols[i]->getCOMvel(COMvel);
733        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
734 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
734 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
735      }
736 <                
736 >    
737    }
738  
739   #ifndef IS_MPI
# Line 715 | Line 767 | template<typename T> void ZConstraint<T>::zeroOutVel()
767      if (states[i] ==zcsMoving){
768    
769        movingZAtoms = zconsMols[i]->getMyAtoms();
770 <           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
770 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
771          movingZAtoms[j]->getVel(vel);
772          vel[whichDirection] -= vzOfMovingMols;
773 <             movingZAtoms[j]->setVel(vel);
774 <          }
775 <          
773 >       movingZAtoms[j]->setVel(vel);
774 >    }
775 >    
776     }
777  
778   }
779  
780 +
781 +  zSysCOMVel = calcSysCOMVel();
782   #ifdef IS_MPI
783 <  if (worldRank == 0){
783 >  if(worldRank == 0){
784   #endif
785 <        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
785 >    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
786   #ifdef IS_MPI
787    }
788   #endif
789  
790   }
791  
792 + /**
793 + *
794 + */
795 +
796   template<typename T> void ZConstraint<T>::doZconstraintForce(){
797  
798    Atom** zconsAtoms;
# Line 746 | Line 804 | template<typename T> void ZConstraint<T>::doZconstrain
804  
805  
806  
807 <  //constrain the molecules which do not reach the specified positions  
807 >  //constrain the molecules which do not reach the specified positions  
808      
809    //Zero Out the force of z-contrained molecules    
810    totalFZ_local = 0;
811  
812    //calculate the total z-contrained force of fixed z-contrained molecules
813  
756 – #ifdef IS_MPI
757 –  if (worldRank == 0){
758 – #endif
759 –    cout << "Fixed Molecules" << endl;
760 – #ifdef IS_MPI
761 –  }
762 – #endif
763 –
814    for(int i = 0; i < zconsMols.size(); i++){
815 <                
815 >    
816      if (states[i] == zcsFixed){
817 <                
817 >      
818        zconsMols[i]->getCOM(COM);
819        zconsAtoms = zconsMols[i]->getMyAtoms();  
820  
# Line 772 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain
822        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
823          zconsAtoms[j]->getFrc(force);
824          fz[i] += force[whichDirection];      
825 <      }
825 >      }
826        totalFZ_local += fz[i];
827  
828 <      cout << "index: " << indexOfZConsMols[i]
829 <                                <<"\tcurrent zpos: " << COM[whichDirection]
830 <                                << "\tcurrent fz: " <<fz[i] << endl;
828 > //       cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
829 > //              <<"\tcurrent zpos: " << COM[whichDirection]
830 > //              << "\tcurrent fz: " <<fz[i] << endl;
831  
832      }
833 <          
833 >    
834    }
835  
836    //calculate total z-constraint force
# Line 790 | Line 840 | template<typename T> void ZConstraint<T>::doZconstrain
840    totalFZ = totalFZ_local;
841   #endif
842  
843 <        
843 >  
844    // apply negative to fixed z-constrained molecues;
845    force[0]= 0;
846    force[1]= 0;
# Line 799 | Line 849 | template<typename T> void ZConstraint<T>::doZconstrain
849    for(int i = 0; i < zconsMols.size(); i++){
850  
851      if (states[i] == zcsFixed){  
852 <        
852 >  
853        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
854        zconsAtoms = zconsMols[i]->getMyAtoms();  
855      
856        for(int j =0; j < nAtomOfCurZConsMol; j++) {
857 <                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
857 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
858          //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
859          zconsAtoms[j]->addFrc(force);
860        }
861 <                
861 >    
862      }
863 <        
863 >  
864    }
865  
866 <  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
867 <  //               << "total force is " << calcTotalForce() << endl;
866 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
867 > //        << "total force is " << calcTotalForce() << endl;
868  
869    //calculate the number of atoms of moving z-constrained molecules
870    int nMovingZAtoms_local;
871    int nMovingZAtoms;
872 <        
872 >  
873    nMovingZAtoms_local = 0;
874    for(int i = 0; i < zconsMols.size(); i++)
875      if(states[i] == zcsMoving)
876 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
876 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
877    
878   #ifdef IS_MPI
879 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
879 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
880 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
881   #else
882    nMovingZAtoms = nMovingZAtoms_local;
883   #endif
# Line 851 | Line 902 | template<typename T> void ZConstraint<T>::doZconstrain
902   //modify the forces of moving z-constrained molecules
903    for(int i = 0; i < zconsMols.size(); i++) {
904      if (states[i] == zcsMoving){
905 <                
905 >    
906        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
907  
908        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
# Line 863 | Line 914 | template<typename T> void ZConstraint<T>::doZconstrain
914    }
915  
916    //cout << "after substracting z-constraint force from moving molecuels "
917 <  //              << "total force is " << calcTotalForce()  << endl;
917 >  //      << "total force is " << calcTotalForce()  << endl;
918 >
919 > }
920 >
921 > /**
922 >  *
923 >  *
924 >  */
925 >
926 > template<typename T> void ZConstraint<T>::doHarmonic(){
927 >  double force[3];
928 >  double harmonicU;
929 >  double harmonicF;
930 >  double COM[3];
931 >  double diff;
932 >  double totalFZ_local;
933 >  double totalFZ;
934 >  
935 >  force[0] = 0;
936 >  force[1] = 0;
937 >  force[2] = 0;
938 >
939 >  totalFZ_local = 0;
940 >
941 >  for(int i = 0; i < zconsMols.size(); i++) {
942 >
943 >    if (states[i] == zcsMoving){
944 >      zconsMols[i]->getCOM(COM);
945 >      cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
946 >           << "\tcurrent zpos: " << COM[whichDirection] << endl;
947 >    
948 >    diff = COM[whichDirection] -zPos[i];
949 >    
950 >      harmonicU = 0.5 * kz[i] * diff * diff;  
951 >    info->lrPot += harmonicU;
952 >
953 >      harmonicF =  - kz[i] * diff;
954 >      totalFZ_local += harmonicF;
955 >
956 >       //adjust force
957 >    
958 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
959 >
960 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
961 >        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
962 >         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
963 >         movingZAtoms[j]->addFrc(force);
964 >       }
965 >    }
966 >
967 >  }
968 >
969 > #ifndef IS_MPI
970 >  totalFZ = totalFZ_local;
971 > #else
972 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
973 > #endif
974 >
975 >  force[0]= 0;
976 >  force[1]= 0;
977 >  force[2]= 0;
978 >
979 >  //modify the forces of unconstrained molecules
980 >  for(int i = 0; i < unconsMols.size(); i++){
981 >    
982 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
983 >    
984 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
985 >       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
986 >       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
987 >       unconsAtoms[j]->addFrc(force);    
988 >     }
989 >  }  
990  
991   }
992  
993 + /**
994 + *
995 + */
996 +
997   template<typename T> bool ZConstraint<T>::checkZConsState(){
998    double COM[3];
999    double diff;
1000    
1001    int changed_local;
1002    int changed;
1003 <        
1003 >  
1004    changed_local = 0;
1005    
1006    for(int i =0; i < zconsMols.size(); i++){
# Line 882 | Line 1009 | template<typename T> bool ZConstraint<T>::checkZConsSt
1009      diff = fabs(COM[whichDirection] - zPos[i]);  
1010      if (  diff <= zconsTol && states[i] == zcsMoving){
1011        states[i] = zcsFixed;
1012 <           changed_local = 1;
1012 >     changed_local = 1;
1013      }
1014      else if ( diff > zconsTol && states[i] == zcsFixed){
1015        states[i] = zcsMoving;
1016 <           changed_local = 1;    
1016 >     changed_local = 1;  
1017      }
1018    
1019    }
# Line 896 | Line 1023 | template<typename T> bool ZConstraint<T>::checkZConsSt
1023   #else
1024    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1025   #endif
1026 <
1027 <  return changed > 0 ? true : false;
1026 >  
1027 >  return (changed > 0);
1028   }
1029  
1030   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 910 | Line 1037 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1037    for(int i = 0; i < zconsMols.size(); i++)
1038      if (states[i] == zcsFixed){
1039        havingFixed_local = 1;
1040 <                break;
1040 >    break;
1041      }
1042  
1043   #ifndef IS_MPI
# Line 936 | Line 1063 | template<typename T> bool ZConstraint<T>::haveMovingZM
1063    for(int i = 0; i < zconsMols.size(); i++)
1064      if (states[i] == zcsMoving){
1065        havingMoving_local = 1;
1066 <                break;
1066 >    break;
1067      }
1068  
1069   #ifndef IS_MPI
# Line 950 | Line 1077 | template<typename T> bool ZConstraint<T>::haveMovingZM
1077   }
1078  
1079   /**
1080 <  *
1081 <  *
955 <  */
956 <
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 <  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);
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->lrPot += harmonicU;
991 <
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++){          
1000 <                  force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
1001 <         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
1002 <         movingZAtoms[j]->addFrc(force);
1003 <       }
1004 <    }
1080 > *
1081 > */
1082  
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 –
1083   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1084   {
1085    double MVzOfMovingMols_local;
# Line 1050 | Line 1101 | template<typename T> double ZConstraint<T>::calcMoving
1101      if (states[i] == zcsMoving){
1102        zconsMols[i]->getCOMvel(COMvel);
1103        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1104 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1104 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1105      }
1106 <                
1106 >    
1107    }
1108  
1109   #ifndef IS_MPI
# Line 1069 | Line 1120 | template<typename T> double ZConstraint<T>::calcMoving
1120    return vzOfMovingMols;
1121   }
1122  
1123 + /**
1124 + *
1125 + */
1126  
1127   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1128   {
# Line 1083 | Line 1137 | template<typename T> double ZConstraint<T>::calcSysCOM
1137  
1138    for(int i =0 ; i < nMols; i++){
1139      molecules[i].getCOMvel(COMvel);
1140 <         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1140 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1141    }
1142  
1143    massOfZCons_local = 0;
1144 <        
1144 >  
1145    for(int i = 0; i < massOfZConsMols.size(); i++){
1146      massOfZCons_local += massOfZConsMols[i];
1147    }
# Line 1102 | Line 1156 | template<typename T> double ZConstraint<T>::calcTotalF
1156    return tempMVz /(totalMassOfUncons + massOfZCons);
1157   }
1158  
1159 + /**
1160 + *
1161 + */
1162 +
1163   template<typename T> double ZConstraint<T>::calcTotalForce(){
1164  
1165    double force[3];  
# Line 1133 | Line 1191 | template<typename T> void ZConstraint<T>::PolicyByNumb
1191    //calculate the number of atoms of moving z-constrained molecules
1192    int nMovingZAtoms_local;
1193    int nMovingZAtoms;
1194 <        
1194 >  
1195    nMovingZAtoms_local = 0;
1196    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1197      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1198 <           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1198 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1199    
1200   #ifdef IS_MPI
1201    MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 1145 | Line 1203 | template<typename T> void ZConstraint<T>::PolicyByNumb
1203    nMovingZAtoms = nMovingZAtoms_local;
1204   #endif
1205    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1206 +
1207 + #ifdef IS_MPI
1208 +  if(worldRank == 0){
1209 + #endif
1210 +    std::cerr << "\n"
1211 +              << "*******************************************\n"
1212 +              << " fiished Policy by numbr()\n"
1213 +              << "*******************************************\n"
1214 +              << "\n";
1215 + #ifdef IS_MPI
1216 +  }
1217 + #endif
1218   }
1219  
1220 < template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1220 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1221    return totalForce / mol->getNAtoms();
1222   }
1223  
# Line 1171 | Line 1241 | template<typename T> void ZConstraint<T>::PolicyByMass
1241    //calculate the number of atoms of moving z-constrained molecules
1242    double massOfMovingZAtoms_local;
1243    double massOfMovingZAtoms;
1244 <        
1244 >  
1245    massOfMovingZAtoms_local = 0;
1246    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1247      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1248 <           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1248 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1249    
1250   #ifdef IS_MPI
1251    MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);

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