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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 700 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 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 524 | Line 530 | template<typename T> void ZConstraint<T>::calcForce(in
530  
531    if (checkZConsState()){
532      zeroOutVel();
533 <         forcePolicy->update();
533 >   forcePolicy->update();
534    }  
535    zsys = calcZSys();
536    cout << "---------------------------------------------------------------------" <<endl;
537    cout << "current time: " << info->getTime() << endl;
538 <  cout << "center of mass at z: " << zsys << endl;      
538 >  cout << "center of mass at z: " << zsys << endl;    
539    //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
540    cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
541  
542 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
542 >  //cout <<  "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
543  
544    //do zconstraint force;
545    if (haveFixedZMols())
# Line 543 | Line 549 | template<typename T> void ZConstraint<T>::calcForce(in
549    if (haveMovingZMols())
550      this->doHarmonic();
551  
552 <  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
552 >  //cout <<  "after doHarmonic, totalForce is " << calcTotalForce() << endl;
553  
554    //write out forces and current positions of z-constraint molecules
555 <  if(info->getTime() >= curZconsTime){          
556 <         for(int i = 0; i < zconsMols.size(); i++){
555 >  if(info->getTime() >= curZconsTime){    
556 >   for(int i = 0; i < zconsMols.size(); i++){
557        zconsMols[i]->getCOM(COM);
558 <                curZPos[i] = COM[whichDirection];
558 >    curZPos[i] = COM[whichDirection];
559  
560 <                //if the z-constraint molecule is still moving, just record its force
561 <                if(states[i] == zcsMoving){
560 >    //if the z-constraint molecule is still moving, just record its force
561 >    if(states[i] == zcsMoving){
562           fz[i] = 0;
563 <                  Atom** movingZAtoms;
564 <                  movingZAtoms = zconsMols[i]->getMyAtoms();
565 <                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
563 >      Atom** movingZAtoms;
564 >      movingZAtoms = zconsMols[i]->getMyAtoms();
565 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
566             movingZAtoms[j]->getFrc(force);
567             fz[i] += force[whichDirection];
568 <                  }
569 <           }
570 <         }
568 >      }
569 >     }
570 >   }
571      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
572 <         curZconsTime += zconsTime;
572 >   curZconsTime += zconsTime;
573    }
574 <        
574 >  
575    //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
576    cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
577   }
578 +
579 +
580 + /**
581 + *
582 + */
583  
584   template<typename T> double ZConstraint<T>::calcZSys()
585   {
# Line 579 | Line 590 | template<typename T> double ZConstraint<T>::calcZSys()
590    double totalMZ;
591    double massOfCurMol;
592    double COM[3];
593 <        
593 >  
594    totalMass_local = 0;
595    totalMZ_local = 0;
596    
# Line 594 | Line 605 | template<typename T> double ZConstraint<T>::calcZSys()
605  
606    
607   #ifdef IS_MPI  
608 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
609 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
608 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
609 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
610 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
611 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
612   #else
613    totalMass = totalMass_local;
614    totalMZ = totalMZ_local;
# Line 618 | Line 631 | template<typename T> void ZConstraint<T>::thermalize(
631  
632   /**
633   *
621 – *
622 – *
634   */
635  
636   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 627 | Line 638 | template<typename T> void ZConstraint<T>::zeroOutVel()
638    Atom** fixedZAtoms;  
639    double COMvel[3];
640    double vel[3];
641 +  double zSysCOMVel;
642  
643    //zero out the velocities of center of mass of fixed z-constrained molecules
644    
645    for(int i = 0; i < zconsMols.size(); i++){
646  
647 <    if (states[i] == zcsFixed){
647 >    if (states[i] == zcsFixed){
648  
649 <           zconsMols[i]->getCOMvel(COMvel);      
650 <                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
649 >     zconsMols[i]->getCOMvel(COMvel);      
650 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
651  
652        fixedZAtoms = zconsMols[i]->getMyAtoms();
653 <          
653 >    
654        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
655          fixedZAtoms[j]->getVel(vel);
656 <             vel[whichDirection] -= COMvel[whichDirection];
657 <             fixedZAtoms[j]->setVel(vel);
656 >       vel[whichDirection] -= COMvel[whichDirection];
657 >       fixedZAtoms[j]->setVel(vel);
658        }
659  
660 <                zconsMols[i]->getCOMvel(COMvel);
661 <                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
660 >    zconsMols[i]->getCOMvel(COMvel);
661 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
662      }
663 <        
663 >  
664    }
665  
666 <        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
666 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
667  
668 +  zSysCOMVel = calcSysCOMVel();
669   #ifdef IS_MPI
670 <  if (worldRank == 0){
670 >  if(worldRank == 0){
671   #endif
672 <    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
672 >    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
673   #ifdef IS_MPI
674    }
675   #endif
676 <                  
676 >      
677    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
678    double MVzOfMovingMols_local;
679    double MVzOfMovingMols;
# Line 679 | Line 692 | template<typename T> void ZConstraint<T>::zeroOutVel()
692      if (states[i] == zcsMoving){
693        zconsMols[i]->getCOMvel(COMvel);
694        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
695 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
695 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
696      }
697 <                
697 >    
698    }
699  
700   #ifndef IS_MPI
# Line 715 | Line 728 | template<typename T> void ZConstraint<T>::zeroOutVel()
728      if (states[i] ==zcsMoving){
729    
730        movingZAtoms = zconsMols[i]->getMyAtoms();
731 <           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
731 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
732          movingZAtoms[j]->getVel(vel);
733          vel[whichDirection] -= vzOfMovingMols;
734 <             movingZAtoms[j]->setVel(vel);
735 <          }
736 <          
734 >       movingZAtoms[j]->setVel(vel);
735 >    }
736 >    
737     }
738  
739   }
740  
741 +
742 +  zSysCOMVel = calcSysCOMVel();
743   #ifdef IS_MPI
744 <  if (worldRank == 0){
744 >  if(worldRank == 0){
745   #endif
746 <        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
746 >    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
747   #ifdef IS_MPI
748    }
749   #endif
750  
751   }
752  
753 + /**
754 + *
755 + */
756 +
757   template<typename T> void ZConstraint<T>::doZconstraintForce(){
758  
759    Atom** zconsAtoms;
# Line 746 | Line 765 | template<typename T> void ZConstraint<T>::doZconstrain
765  
766  
767  
768 <  //constrain the molecules which do not reach the specified positions  
768 >  //constrain the molecules which do not reach the specified positions  
769      
770    //Zero Out the force of z-contrained molecules    
771    totalFZ_local = 0;
772  
773    //calculate the total z-contrained force of fixed z-contrained molecules
774  
756 – #ifdef IS_MPI
757 –  if (worldRank == 0){
758 – #endif
759 –    cout << "Fixed Molecules" << endl;
760 – #ifdef IS_MPI
761 –  }
762 – #endif
763 –
775    for(int i = 0; i < zconsMols.size(); i++){
776 <                
776 >    
777      if (states[i] == zcsFixed){
778 <                
778 >      
779        zconsMols[i]->getCOM(COM);
780        zconsAtoms = zconsMols[i]->getMyAtoms();  
781  
# Line 772 | Line 783 | template<typename T> void ZConstraint<T>::doZconstrain
783        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
784          zconsAtoms[j]->getFrc(force);
785          fz[i] += force[whichDirection];      
786 <      }
786 >      }
787        totalFZ_local += fz[i];
788  
789 <      cout << "index: " << indexOfZConsMols[i]
790 <                                <<"\tcurrent zpos: " << COM[whichDirection]
791 <                                << "\tcurrent fz: " <<fz[i] << endl;
789 >      cout << "Fixed Molecule --\tindex: " << indexOfZConsMols[i]
790 >             <<"\tcurrent zpos: " << COM[whichDirection]
791 >             << "\tcurrent fz: " <<fz[i] << endl;
792  
793      }
794 <          
794 >    
795    }
796  
797    //calculate total z-constraint force
# Line 790 | Line 801 | template<typename T> void ZConstraint<T>::doZconstrain
801    totalFZ = totalFZ_local;
802   #endif
803  
804 <        
804 >  
805    // apply negative to fixed z-constrained molecues;
806    force[0]= 0;
807    force[1]= 0;
# Line 799 | Line 810 | template<typename T> void ZConstraint<T>::doZconstrain
810    for(int i = 0; i < zconsMols.size(); i++){
811  
812      if (states[i] == zcsFixed){  
813 <        
813 >  
814        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
815        zconsAtoms = zconsMols[i]->getMyAtoms();  
816      
817        for(int j =0; j < nAtomOfCurZConsMol; j++) {
818 <                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
818 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
819          //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
820          zconsAtoms[j]->addFrc(force);
821        }
822 <                
822 >    
823      }
824 <        
824 >  
825    }
826  
827    //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
828 <  //               << "total force is " << calcTotalForce() << endl;
828 >  //       << "total force is " << calcTotalForce() << endl;
829  
830    //calculate the number of atoms of moving z-constrained molecules
831    int nMovingZAtoms_local;
832    int nMovingZAtoms;
833 <        
833 >  
834    nMovingZAtoms_local = 0;
835    for(int i = 0; i < zconsMols.size(); i++)
836      if(states[i] == zcsMoving)
837 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
837 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
838    
839   #ifdef IS_MPI
840 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
840 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
841 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
842   #else
843    nMovingZAtoms = nMovingZAtoms_local;
844   #endif
# Line 851 | Line 863 | template<typename T> void ZConstraint<T>::doZconstrain
863   //modify the forces of moving z-constrained molecules
864    for(int i = 0; i < zconsMols.size(); i++) {
865      if (states[i] == zcsMoving){
866 <                
866 >    
867        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
868  
869        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
# Line 863 | Line 875 | template<typename T> void ZConstraint<T>::doZconstrain
875    }
876  
877    //cout << "after substracting z-constraint force from moving molecuels "
878 <  //              << "total force is " << calcTotalForce()  << endl;
878 >  //      << "total force is " << calcTotalForce()  << endl;
879  
880   }
881  
882 + /**
883 +  *
884 +  *
885 +  */
886 +
887 + template<typename T> void ZConstraint<T>::doHarmonic(){
888 +  double force[3];
889 +  double harmonicU;
890 +  double harmonicF;
891 +  double COM[3];
892 +  double diff;
893 +  double totalFZ_local;
894 +  double totalFZ;
895 +  
896 +  force[0] = 0;
897 +  force[1] = 0;
898 +  force[2] = 0;
899 +
900 +  totalFZ_local = 0;
901 +
902 +  for(int i = 0; i < zconsMols.size(); i++) {
903 +
904 +    if (states[i] == zcsMoving){
905 +      zconsMols[i]->getCOM(COM);
906 +      cout << "Moving Molecule --\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
907 +    
908 +    diff = COM[whichDirection] -zPos[i];
909 +    
910 +      harmonicU = 0.5 * kz[i] * diff * diff;  
911 +    info->lrPot += harmonicU;
912 +
913 +      harmonicF =  - kz[i] * diff;
914 +      totalFZ_local += harmonicF;
915 +
916 +       //adjust force
917 +    
918 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
919 +
920 +       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
921 +        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
922 +         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
923 +         movingZAtoms[j]->addFrc(force);
924 +       }
925 +    }
926 +
927 +  }
928 +
929 + #ifndef IS_MPI
930 +  totalFZ = totalFZ_local;
931 + #else
932 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
933 + #endif
934 +
935 +  force[0]= 0;
936 +  force[1]= 0;
937 +  force[2]= 0;
938 +
939 +  //modify the forces of unconstrained molecules
940 +  for(int i = 0; i < unconsMols.size(); i++){
941 +    
942 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
943 +    
944 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
945 +       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
946 +       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
947 +       unconsAtoms[j]->addFrc(force);    
948 +     }
949 +  }  
950 +
951 + }
952 +
953 + /**
954 + *
955 + */
956 +
957   template<typename T> bool ZConstraint<T>::checkZConsState(){
958    double COM[3];
959    double diff;
960    
961    int changed_local;
962    int changed;
963 <        
963 >  
964    changed_local = 0;
965    
966    for(int i =0; i < zconsMols.size(); i++){
# Line 882 | Line 969 | template<typename T> bool ZConstraint<T>::checkZConsSt
969      diff = fabs(COM[whichDirection] - zPos[i]);  
970      if (  diff <= zconsTol && states[i] == zcsMoving){
971        states[i] = zcsFixed;
972 <           changed_local = 1;
972 >     changed_local = 1;
973      }
974      else if ( diff > zconsTol && states[i] == zcsFixed){
975        states[i] = zcsMoving;
976 <           changed_local = 1;    
976 >     changed_local = 1;  
977      }
978    
979    }
# Line 910 | Line 997 | template<typename T> bool ZConstraint<T>::haveFixedZMo
997    for(int i = 0; i < zconsMols.size(); i++)
998      if (states[i] == zcsFixed){
999        havingFixed_local = 1;
1000 <                break;
1000 >    break;
1001      }
1002  
1003   #ifndef IS_MPI
# Line 936 | Line 1023 | template<typename T> bool ZConstraint<T>::haveMovingZM
1023    for(int i = 0; i < zconsMols.size(); i++)
1024      if (states[i] == zcsMoving){
1025        havingMoving_local = 1;
1026 <                break;
1026 >    break;
1027      }
1028  
1029   #ifndef IS_MPI
# Line 950 | Line 1037 | template<typename T> bool ZConstraint<T>::haveMovingZM
1037   }
1038  
1039   /**
1040 <  *
1041 <  *
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 <    }
1040 > *
1041 > */
1042  
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 –
1043   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1044   {
1045    double MVzOfMovingMols_local;
# Line 1050 | Line 1061 | template<typename T> double ZConstraint<T>::calcMoving
1061      if (states[i] == zcsMoving){
1062        zconsMols[i]->getCOMvel(COMvel);
1063        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1064 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1064 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1065      }
1066 <                
1066 >    
1067    }
1068  
1069   #ifndef IS_MPI
# Line 1069 | Line 1080 | template<typename T> double ZConstraint<T>::calcMoving
1080    return vzOfMovingMols;
1081   }
1082  
1083 + /**
1084 + *
1085 + */
1086  
1087   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1088   {
# Line 1083 | Line 1097 | template<typename T> double ZConstraint<T>::calcSysCOM
1097  
1098    for(int i =0 ; i < nMols; i++){
1099      molecules[i].getCOMvel(COMvel);
1100 <         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1100 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1101    }
1102  
1103    massOfZCons_local = 0;
1104 <        
1104 >  
1105    for(int i = 0; i < massOfZConsMols.size(); i++){
1106      massOfZCons_local += massOfZConsMols[i];
1107    }
# Line 1102 | Line 1116 | template<typename T> double ZConstraint<T>::calcTotalF
1116    return tempMVz /(totalMassOfUncons + massOfZCons);
1117   }
1118  
1119 + /**
1120 + *
1121 + */
1122 +
1123   template<typename T> double ZConstraint<T>::calcTotalForce(){
1124  
1125    double force[3];  
# Line 1133 | Line 1151 | template<typename T> void ZConstraint<T>::PolicyByNumb
1151    //calculate the number of atoms of moving z-constrained molecules
1152    int nMovingZAtoms_local;
1153    int nMovingZAtoms;
1154 <        
1154 >  
1155    nMovingZAtoms_local = 0;
1156    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1157      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1158 <           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1158 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1159    
1160   #ifdef IS_MPI
1161    MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 1147 | Line 1165 | template<typename T> double ZConstraint<T>::PolicyByNu
1165    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1166   }
1167  
1168 < template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1168 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1169    return totalForce / mol->getNAtoms();
1170   }
1171  
# Line 1171 | Line 1189 | template<typename T> void ZConstraint<T>::PolicyByMass
1189    //calculate the number of atoms of moving z-constrained molecules
1190    double massOfMovingZAtoms_local;
1191    double massOfMovingZAtoms;
1192 <        
1192 >  
1193    massOfMovingZAtoms_local = 0;
1194    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1195      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1196 <           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1196 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1197    
1198   #ifdef IS_MPI
1199    MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);

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