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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 763 by tim, Mon Sep 15 16:52:02 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), curZPos(NULL),
6 <                                                         indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
5 >                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL), fzOut(NULL),
6 >                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
9    //get properties from SimInfo
# Line 27 | 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
30 >  //creat force Subtraction 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");
34 >               "ZConstraint Warning: User does not set force Subtraction policy, "
35 >               "PolicyByMass is used\n");
36      painCave.isFatal = 0;
37      simError();      
38  
39 <    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
39 >    forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
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");
47 >                 "PolicyByMass 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{
51 >      forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
52 >    }
53 >    else{
54 >      if(policy->getData() == "BYNUMBER")
55 >        forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this);
56 >      else if(policy->getData() == "BYMASS")
57 >        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
58 >      else{
59          sprintf( painCave.errMsg,
60 <                  "ZConstraint Warning: unknown force substraction policy, "
61 <                  "average force substraction policy is used\n");
60 >                  "ZConstraint Warning: unknown force Subtraction policy, "
61 >                  "PolicyByMass is used\n");
62          painCave.isFatal = 0;
63          simError();      
64 <           }            
65 <         }
64 >        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
65 >      }  
66 >    }
67    }
67 –        
68    
69 <
69 >  
70    //retrieve sample time of z-contraint
71    data = info->getProperty(ZCONSTIME_ID);
72    
# Line 110 | Line 110 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
110    }
111    else{
112  
113 <     filename = dynamic_cast<StringData*>(data);
113 >    filename = dynamic_cast<StringData*>(data);
114      
115      if(!filename){
116  
# Line 124 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
124        this->zconsOutput = filename->getData();
125      }
126      
127 –
127    }
128  
129    //retrieve tolerance for z-constraint molecuels
# Line 154 | Line 153 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
153      }
154  
155    }
156 <        
156 >  
157    //retrieve index of z-constraint molecules
158    data = info->getProperty(ZCONSPARADATA_ID);
159    if(!data) {
# Line 195 | Line 194 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
194                 "ZConstraint error: index is out of range\n");
195          painCave.isFatal = 1;
196          simError();
197 <        }
197 >        }
198  
199        maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
200  
# Line 216 | Line 215 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
215        //its initial z coordinate  will be used as default
216        for(int i = 0; i < parameters->size(); i++){
217  
218 <              if(!(*parameters)[i].havingZPos){
220 <
218 >        if(!(*parameters)[i].havingZPos){
219   #ifndef IS_MPI
220 <            for(int j = 0; j < nMols; j++){
221 <              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 <                 molecules[j].getCOM(COM);
223 <                          break;
226 <              }
220 >          for(int j = 0; j < nMols; j++){
221 >            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 >              molecules[j].getCOM(COM);
223 >        break;
224              }
225 +          }
226   #else
227              //query which processor current zconstraint molecule belongs to
228 <           int *MolToProcMap;
229 <           int whichNode;
230 <                         double initZPos;
231 <           MolToProcMap = mpiSim->getMolToProcMap();
232 <           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233 <                          
234 <           //broadcast the zpos of current z-contraint molecule
235 <           //the node which contain this
236 <          
237 <           if (worldRank == whichNode ){
238 <                                                
239 <             for(int j = 0; j < nMols; j++)
240 <               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 <                 molecules[j].getCOM(COM);
242 <                                         break;
243 <               }
244 <                                
245 <           }
228 >          int *MolToProcMap;
229 >          int whichNode;
230 >    double initZPos;
231 >          MolToProcMap = mpiSim->getMolToProcMap();
232 >          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233 >        
234 >          //broadcast the zpos of current z-contraint molecule
235 >          //the node which contain this
236 >          
237 >          if (worldRank == whichNode ){
238 >            
239 >            for(int j = 0; j < nMols; j++)
240 >              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 >                molecules[j].getCOM(COM);
242 >          break;
243 >              }
244 >        
245 >          }
246  
247 <            MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);                          
247 >          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
248   #endif
249              
250 <                 (*parameters)[i].zPos = COM[whichDirection];
250 >          (*parameters)[i].zPos = COM[whichDirection];
251  
252 <            sprintf( painCave.errMsg,
253 <                     "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
252 >          sprintf( painCave.errMsg,
253 >                     "ZConstraint warning: Does not specify zpos for z-constraint molecule "
254                       "initial z coornidate will be used \n");
255 <            painCave.isFatal = 0;
256 <            simError();  
257 <          
258 <              }
259 <            }
260 <                        
255 >           painCave.isFatal = 0;
256 >           simError();  
257 >    
258 >  }
259 >      }
260 >      
261      }//end if (!zConsParaData)
262    }//end  if (!data)
263              
# Line 279 | Line 277 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
277        massOfZConsMols.push_back(molecules[i].getTotalMass());  
278  
279        zPos.push_back((*parameters)[searchResult].zPos);
280 <                cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
281 <           kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
280 > //       cout << "index: "<< (*parameters)[searchResult].zconsIndex
281 > //              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
282        
283 +      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284        molecules[i].getCOM(COM);
285      }
286      else
# Line 308 | Line 307 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
307    for(int i = 0; i < zconsMols.size(); i++){
308      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309  
310 <         zconsMols[i]->getCOM(COM);
310 >    zconsMols[i]->getCOM(COM);
311      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
312 <                states.push_back(zcsFixed);
313 <         else
314 <                states.push_back(zcsMoving);
312 >      states.push_back(zcsFixed);
313 >    else
314 >      states.push_back(zcsMoving);
315    }
316    
317   #endif
# Line 327 | Line 326 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
326   #ifndef IS_MPI
327    totalMassOfUncons = totalMassOfUncons_local;
328   #else
329 <  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
329 >  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
330 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331   #endif
332  
333 –
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
# 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  
347 –  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348 –  
349 –  if(!fzOut){
350 –    sprintf( painCave.errMsg,
351 –             "Memory allocation failure in class Zconstraint\n");
352 –    painCave.isFatal = 1;
353 –    simError();
354 –  }
355 –
346    forcePolicy->update();
347   }
348  
# Line 369 | Line 359 | template<typename T> ZConstraint<T>::~ZConstraint()
359    
360    if(fzOut)
361      delete fzOut;
362 <        
362 >  
363    if(forcePolicy)
364      delete forcePolicy;
365   }
366  
367 +
368 + /**
369 + *
370 + */
371 +
372   #ifdef IS_MPI
373   template<typename T> void ZConstraint<T>::update()
374   {
# Line 398 | Line 393 | template<typename T> void ZConstraint<T>::update()
393      
394        zconsMols.push_back(&molecules[i]);      
395        zPos.push_back((*parameters)[index].zPos);
396 <        kz.push_back((*parameters)[index].kRatio * zForceConst);
402 <                        
396 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
397        massOfZConsMols.push_back(molecules[i].getTotalMass());  
398        
399        molecules[i].getCOM(COM);
# Line 415 | Line 409 | template<typename T> void ZConstraint<T>::update()
409  
410    //determine the states of z-constraint molecules
411    for(int i = 0; i < zconsMols.size(); i++){
412 <           zconsMols[i]->getCOM(COM);
412 >     zconsMols[i]->getCOM(COM);
413        if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
414 <                  states.push_back(zcsFixed);
415 <           else
416 <                  states.push_back(zcsMoving);
414 >      states.push_back(zcsFixed);
415 >     else
416 >      states.push_back(zcsMoving);
417    }
418  
419      
# Line 427 | Line 421 | template<typename T> void ZConstraint<T>::update()
421    // that we want to make the MPI communication simple
422    if(fz)
423      delete[] fz;
424 <        
424 >  
425    if(curZPos)
426      delete[] curZPos;
427      
# Line 436 | Line 430 | template<typename T> void ZConstraint<T>::update()
430      
431    if (zconsMols.size() > 0){
432      fz = new double[zconsMols.size()];
433 <         curZPos = new double[zconsMols.size()];
433 >   curZPos = new double[zconsMols.size()];
434      indexOfZConsMols =  new int[zconsMols.size()];
435      
436      if(!fz || !curZPos || !indexOfZConsMols){
# Line 453 | Line 447 | template<typename T> void ZConstraint<T>::update()
447    }
448    else{
449      fz = NULL;
450 <         curZPos = NULL;
450 >   curZPos = NULL;
451      indexOfZConsMols = NULL;
452    }
453 <        
453 >  
454    //
455    forcePolicy->update();
456    
# Line 464 | Line 458 | template<typename T> void ZConstraint<T>::update()
458  
459   #endif
460  
461 < /**  Function Name: isZConstraintMol
462 < **  Parameter
463 < **    Molecule* mol
464 < **  Return value:
465 < **    -1, if the molecule is not z-constraint molecule,
466 < **    other non-negative values, its index in indexOfAllZConsMols vector
461 > /**
462 > *  Function Name: isZConstraintMol
463 > *  Parameter
464 > *    Molecule* mol
465 > *  Return value:
466 > *    -1, if the molecule is not z-constraint molecule,
467 > *    other non-negative values, its index in indexOfAllZConsMols vector
468   */
469  
470   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 499 | Line 494 | template<typename T> void ZConstraint<T>::integrate(){
494   }
495  
496   template<typename T> void ZConstraint<T>::integrate(){
497 +
498 +  // creat zconsWriter  
499 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
500    
501 +  if(!fzOut){
502 +    sprintf( painCave.errMsg,
503 +             "Memory allocation failure in class Zconstraint\n");
504 +    painCave.isFatal = 1;
505 +    simError();
506 +  }
507 +  
508    //zero out the velocities of center of mass of unconstrained molecules
509    //and the velocities of center of mass of every single z-constrained molecueles
510    zeroOutVel();
511 +
512 +  curZconsTime = zconsTime + info->getTime();
513    
514    T::integrate();
515  
# Line 519 | Line 526 | template<typename T> void ZConstraint<T>::calcForce(in
526    double zsys;
527    double COM[3];
528    double force[3];
529 +  double zSysCOMVel;
530  
531    T::calcForce(calcPot, calcStress);
532  
533 <  if (checkZConsState()){
534 <    zeroOutVel();
535 <         forcePolicy->update();
533 >  if (checkZConsState()){    
534 >    zeroOutVel();    
535 >    forcePolicy->update();
536    }  
537 +  
538    zsys = calcZSys();
539 <  cout << "---------------------------------------------------------------------" <<endl;
540 <  cout << "current time: " << info->getTime() << endl;
541 <  cout << "center of mass at z: " << zsys << endl;      
542 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
543 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
539 >  zSysCOMVel = calcSysCOMVel();
540 > #ifdef IS_MPI
541 >  if(worldRank == 0){
542 > #endif
543 >     //cout << "---------------------------------------------------------------------" <<endl;
544 >     //cout << "current time: " << info->getTime() << endl;
545 >     //cout << "center of mass at z: " << zsys << endl;    
546 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
547  
548 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
548 > #ifdef IS_MPI
549 >  }
550 > #endif
551  
552    //do zconstraint force;
553    if (haveFixedZMols())
554      this->doZconstraintForce();
555 <    
555 >
556    //use harmonical poteintial to move the molecules to the specified positions
557    if (haveMovingZMols())
558      this->doHarmonic();
559  
546 –  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 –
560    //write out forces and current positions of z-constraint molecules
561 <  if(info->getTime() >= curZconsTime){          
562 <         for(int i = 0; i < zconsMols.size(); i++){
561 >  if(info->getTime() >= curZconsTime){    
562 >   for(int i = 0; i < zconsMols.size(); i++){
563        zconsMols[i]->getCOM(COM);
564 <                curZPos[i] = COM[whichDirection];
564 >    curZPos[i] = COM[whichDirection];
565  
566 <                //if the z-constraint molecule is still moving, just record its force
567 <                if(states[i] == zcsMoving){
566 >    //if the z-constraint molecule is still moving, just record its force
567 >    if(states[i] == zcsMoving){
568           fz[i] = 0;
569 <                  Atom** movingZAtoms;
570 <                  movingZAtoms = zconsMols[i]->getMyAtoms();
571 <                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
569 >      Atom** movingZAtoms;
570 >      movingZAtoms = zconsMols[i]->getMyAtoms();
571 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
572             movingZAtoms[j]->getFrc(force);
573             fz[i] += force[whichDirection];
574 <                  }
575 <           }
576 <         }
574 >      }
575 >     }
576 >   }
577      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
578 <         curZconsTime += zconsTime;
578 >   curZconsTime += zconsTime;
579    }
580 <        
581 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
582 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
580 >
581 >  zSysCOMVel = calcSysCOMVel();  
582 > #ifdef IS_MPI
583 >  if(worldRank == 0){
584 > #endif
585 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
586 > #ifdef IS_MPI
587 >  }
588 > #endif
589   }
590 +
591 +
592 + /**
593 + *
594 + */
595  
596   template<typename T> double ZConstraint<T>::calcZSys()
597   {
# Line 579 | Line 602 | template<typename T> double ZConstraint<T>::calcZSys()
602    double totalMZ;
603    double massOfCurMol;
604    double COM[3];
605 <        
605 >  
606    totalMass_local = 0;
607    totalMZ_local = 0;
608    
# Line 594 | Line 617 | template<typename T> double ZConstraint<T>::calcZSys()
617  
618    
619   #ifdef IS_MPI  
620 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
621 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
620 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
621 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
622 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
623 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
624   #else
625    totalMass = totalMass_local;
626    totalMZ = totalMZ_local;
# Line 618 | Line 643 | template<typename T> void ZConstraint<T>::thermalize(
643  
644   /**
645   *
621 – *
622 – *
646   */
647  
648   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 627 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel()
650    Atom** fixedZAtoms;  
651    double COMvel[3];
652    double vel[3];
653 +  double zSysCOMVel;
654  
655    //zero out the velocities of center of mass of fixed z-constrained molecules
656    
657    for(int i = 0; i < zconsMols.size(); i++){
658  
659 <    if (states[i] == zcsFixed){
659 >    if (states[i] == zcsFixed){
660  
661 <           zconsMols[i]->getCOMvel(COMvel);      
662 <                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
661 >     zconsMols[i]->getCOMvel(COMvel);      
662 >     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663  
664        fixedZAtoms = zconsMols[i]->getMyAtoms();
665 <          
665 >    
666        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
667          fixedZAtoms[j]->getVel(vel);
668 <             vel[whichDirection] -= COMvel[whichDirection];
669 <             fixedZAtoms[j]->setVel(vel);
668 >       vel[whichDirection] -= COMvel[whichDirection];
669 >       fixedZAtoms[j]->setVel(vel);
670        }
671  
672 <                zconsMols[i]->getCOMvel(COMvel);
673 <                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
672 >    zconsMols[i]->getCOMvel(COMvel);
673 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
674      }
675 <        
675 >  
676    }
677  
678 <        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
678 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
679  
680 +  zSysCOMVel = calcSysCOMVel();
681   #ifdef IS_MPI
682 <  if (worldRank == 0){
682 >  if(worldRank == 0){
683   #endif
684 <    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
684 >     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
685   #ifdef IS_MPI
686    }
687   #endif
688 <                  
688 >      
689    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
690    double MVzOfMovingMols_local;
691    double MVzOfMovingMols;
# Line 679 | Line 704 | template<typename T> void ZConstraint<T>::zeroOutVel()
704      if (states[i] == zcsMoving){
705        zconsMols[i]->getCOMvel(COMvel);
706        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
707 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
707 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
708      }
709 <                
709 >    
710    }
711  
712   #ifndef IS_MPI
# Line 715 | Line 740 | template<typename T> void ZConstraint<T>::zeroOutVel()
740      if (states[i] ==zcsMoving){
741    
742        movingZAtoms = zconsMols[i]->getMyAtoms();
743 <           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
743 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
744          movingZAtoms[j]->getVel(vel);
745          vel[whichDirection] -= vzOfMovingMols;
746 <             movingZAtoms[j]->setVel(vel);
747 <          }
748 <          
746 >       movingZAtoms[j]->setVel(vel);
747 >    }
748 >    
749     }
750  
751   }
752  
753 +
754 +  zSysCOMVel = calcSysCOMVel();
755   #ifdef IS_MPI
756 <  if (worldRank == 0){
756 >  if(worldRank == 0){
757   #endif
758 <        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
758 >     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
759   #ifdef IS_MPI
760    }
761   #endif
762  
763   }
764  
765 + /**
766 + *
767 + */
768 +
769   template<typename T> void ZConstraint<T>::doZconstraintForce(){
770  
771    Atom** zconsAtoms;
# Line 744 | Line 775 | template<typename T> void ZConstraint<T>::doZconstrain
775    double COM[3];
776    double force[3];
777  
778 <
748 <
749 <  //constrain the molecules which do not reach the specified positions  
778 >  //constrain the molecules which do not reach the specified positions  
779      
780    //Zero Out the force of z-contrained molecules    
781    totalFZ_local = 0;
782  
783    //calculate the total z-contrained force of fixed z-contrained molecules
784 +  
785 +  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
786 +  //       << "total force is " << calcTotalForce() << endl;
787  
756 – #ifdef IS_MPI
757 –  if (worldRank == 0){
758 – #endif
759 –    cout << "Fixed Molecules" << endl;
760 – #ifdef IS_MPI
761 –  }
762 – #endif
763 –
788    for(int i = 0; i < zconsMols.size(); i++){
789 <                
789 >    
790      if (states[i] == zcsFixed){
791 <                
791 >      
792        zconsMols[i]->getCOM(COM);
793        zconsAtoms = zconsMols[i]->getMyAtoms();  
794  
# Line 772 | Line 796 | template<typename T> void ZConstraint<T>::doZconstrain
796        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
797          zconsAtoms[j]->getFrc(force);
798          fz[i] += force[whichDirection];      
799 <      }
799 >      }
800        totalFZ_local += fz[i];
801  
802 <      cout << "index: " << indexOfZConsMols[i]
803 <                                <<"\tcurrent zpos: " << COM[whichDirection]
804 <                                << "\tcurrent fz: " <<fz[i] << endl;
802 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
803 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
804 >      //      << "\tcurrent fz: " <<fz[i] << endl;
805  
806 +
807      }
808 <          
808 >    
809    }
810  
811    //calculate total z-constraint force
# Line 790 | Line 815 | template<typename T> void ZConstraint<T>::doZconstrain
815    totalFZ = totalFZ_local;
816   #endif
817  
818 <        
818 >  
819    // apply negative to fixed z-constrained molecues;
820    force[0]= 0;
821    force[1]= 0;
# Line 799 | Line 824 | template<typename T> void ZConstraint<T>::doZconstrain
824    for(int i = 0; i < zconsMols.size(); i++){
825  
826      if (states[i] == zcsFixed){  
827 <        
827 >  
828        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
829        zconsAtoms = zconsMols[i]->getMyAtoms();  
830      
831        for(int j =0; j < nAtomOfCurZConsMol; j++) {
832 <                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
833 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
832 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
833 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
834          zconsAtoms[j]->addFrc(force);
835        }
836 <                
836 >    
837      }
838 <        
838 >  
839    }
840  
841    //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
842 <  //               << "total force is " << calcTotalForce() << endl;
842 >  //      << "total force is " << calcTotalForce() << endl;
843 >  
844  
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 –
845    force[0]= 0;
846    force[1]= 0;
847    force[2]= 0;
# Line 841 | Line 852 | template<typename T> void ZConstraint<T>::doZconstrain
852       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
853      
854       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
855 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
856 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
855 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
856 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
857         unconsAtoms[j]->addFrc(force);
858       }
859      
# Line 851 | Line 862 | template<typename T> void ZConstraint<T>::doZconstrain
862   //modify the forces of moving z-constrained molecules
863    for(int i = 0; i < zconsMols.size(); i++) {
864      if (states[i] == zcsMoving){
865 <                
865 >    
866        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
867  
868        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
869 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
870 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
869 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
870 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
871          movingZAtoms[j]->addFrc(force);
872        }
873      }
874    }
875 + //  cout << "after substracting z-constraint force from moving molecuels "
876 + //        << "total force is " << calcTotalForce()  << endl;
877  
878 <  //cout << "after substracting z-constraint force from moving molecuels "
866 <  //              << "total force is " << calcTotalForce()  << endl;
878 > }
879  
880 + /**
881 +  *
882 +  *
883 +  */
884 +
885 + template<typename T> void ZConstraint<T>::doHarmonic(){
886 +  double force[3];
887 +  double harmonicU;
888 +  double harmonicF;
889 +  double COM[3];
890 +  double diff;
891 +  double totalFZ_local;
892 +  double totalFZ;
893 +  
894 +  force[0] = 0;
895 +  force[1] = 0;
896 +  force[2] = 0;
897 +
898 +  totalFZ_local = 0;
899 +
900 +  for(int i = 0; i < zconsMols.size(); i++) {
901 +
902 +    if (states[i] == zcsMoving){
903 +      zconsMols[i]->getCOM(COM);
904 + //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
905 + //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
906 +
907 +      diff = COM[whichDirection] -zPos[i];
908 +    
909 +      harmonicU = 0.5 * kz[i] * diff * diff;  
910 +      info->lrPot += harmonicU;
911 +
912 +      harmonicF =  - kz[i] * diff;
913 +      totalFZ_local += harmonicF;
914 +
915 +       //adjust force
916 +    
917 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
918 +
919 +       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
920 +        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
921 +        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
922 +         movingZAtoms[j]->addFrc(force);
923 +       }
924 +    }
925 +
926 +  }
927 +
928 + #ifndef IS_MPI
929 +  totalFZ = totalFZ_local;
930 + #else
931 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
932 + #endif
933 +
934 +  //cout << "before substracting harmonic force from moving molecuels "
935 +  //      << "total force is " << calcTotalForce()  << endl;
936 +
937 +  force[0]= 0;
938 +  force[1]= 0;
939 +  force[2]= 0;
940 +
941 +  //modify the forces of unconstrained molecules
942 +  for(int i = 0; i < unconsMols.size(); i++){
943 +    
944 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
945 +    
946 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
947 +       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
948 +       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
949 +       unconsAtoms[j]->addFrc(force);    
950 +     }
951 +  }  
952 +
953 +  //cout << "after substracting harmonic force from moving molecuels "
954 +  //      << "total force is " << calcTotalForce()  << endl;
955 +
956   }
957  
958 + /**
959 + *
960 + */
961 +
962   template<typename T> bool ZConstraint<T>::checkZConsState(){
963    double COM[3];
964    double diff;
965    
966    int changed_local;
967    int changed;
968 <        
968 >  
969    changed_local = 0;
970    
971    for(int i =0; i < zconsMols.size(); i++){
# Line 882 | Line 974 | template<typename T> bool ZConstraint<T>::checkZConsSt
974      diff = fabs(COM[whichDirection] - zPos[i]);  
975      if (  diff <= zconsTol && states[i] == zcsMoving){
976        states[i] = zcsFixed;
977 <           changed_local = 1;
977 >     changed_local = 1;
978      }
979      else if ( diff > zconsTol && states[i] == zcsFixed){
980        states[i] = zcsMoving;
981 <           changed_local = 1;    
981 >     changed_local = 1;  
982      }
983    
984    }
# Line 897 | Line 989 | template<typename T> bool ZConstraint<T>::checkZConsSt
989    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
990   #endif
991  
992 <  return changed > 0 ? true : false;
992 >  return (changed > 0);
993 >
994   }
995  
996   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 910 | Line 1003 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1003    for(int i = 0; i < zconsMols.size(); i++)
1004      if (states[i] == zcsFixed){
1005        havingFixed_local = 1;
1006 <                break;
1006 >    break;
1007      }
1008  
1009   #ifndef IS_MPI
# Line 919 | Line 1012 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1012    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1013   #endif
1014  
1015 <  return havingFixed > 0 ? true : false;
1015 >  return (havingFixed > 0);
1016   }
1017  
1018  
# Line 936 | Line 1029 | template<typename T> bool ZConstraint<T>::haveMovingZM
1029    for(int i = 0; i < zconsMols.size(); i++)
1030      if (states[i] == zcsMoving){
1031        havingMoving_local = 1;
1032 <                break;
1032 >    break;
1033      }
1034  
1035   #ifndef IS_MPI
# Line 945 | Line 1038 | template<typename T> bool ZConstraint<T>::haveMovingZM
1038    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1039   #endif
1040  
1041 <  return havingMoving > 0 ? true : false;
1041 >  return (havingMoving > 0);
1042    
1043   }
1044  
1045   /**
1046 <  *
1047 <  *
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;
1046 > *
1047 > */
1048  
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 –    }
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 –
1049   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1050   {
1051    double MVzOfMovingMols_local;
# Line 1050 | Line 1067 | template<typename T> double ZConstraint<T>::calcMoving
1067      if (states[i] == zcsMoving){
1068        zconsMols[i]->getCOMvel(COMvel);
1069        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1070 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1070 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1071      }
1072 <                
1072 >    
1073    }
1074  
1075   #ifndef IS_MPI
# Line 1069 | Line 1086 | template<typename T> double ZConstraint<T>::calcMoving
1086    return vzOfMovingMols;
1087   }
1088  
1089 + /**
1090 + *
1091 + */
1092  
1093   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1094   {
# Line 1083 | Line 1103 | template<typename T> double ZConstraint<T>::calcSysCOM
1103  
1104    for(int i =0 ; i < nMols; i++){
1105      molecules[i].getCOMvel(COMvel);
1106 <         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1106 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1107    }
1108  
1109    massOfZCons_local = 0;
1110 <        
1110 >  
1111    for(int i = 0; i < massOfZConsMols.size(); i++){
1112      massOfZCons_local += massOfZConsMols[i];
1113    }
# Line 1102 | Line 1122 | template<typename T> double ZConstraint<T>::calcTotalF
1122    return tempMVz /(totalMassOfUncons + massOfZCons);
1123   }
1124  
1125 + /**
1126 + *
1127 + */
1128 +
1129   template<typename T> double ZConstraint<T>::calcTotalForce(){
1130  
1131    double force[3];  
# Line 1133 | Line 1157 | template<typename T> void ZConstraint<T>::PolicyByNumb
1157    //calculate the number of atoms of moving z-constrained molecules
1158    int nMovingZAtoms_local;
1159    int nMovingZAtoms;
1160 <        
1160 >  
1161    nMovingZAtoms_local = 0;
1162    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1163      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1164 <           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1164 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1165    
1166   #ifdef IS_MPI
1167    MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 1147 | Line 1171 | template<typename T> double ZConstraint<T>::PolicyByNu
1171    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1172   }
1173  
1174 < template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1174 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1175    return totalForce / mol->getNAtoms();
1176   }
1177  
# Line 1171 | Line 1195 | template<typename T> void ZConstraint<T>::PolicyByMass
1195    //calculate the number of atoms of moving z-constrained molecules
1196    double massOfMovingZAtoms_local;
1197    double massOfMovingZAtoms;
1198 <        
1198 >  
1199    massOfMovingZAtoms_local = 0;
1200    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1201      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1202 <           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1202 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1203    
1204   #ifdef IS_MPI
1205    MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1206   #else
1207    massOfMovingZAtoms = massOfMovingZAtoms_local;
1208   #endif
1209 <  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1209 >  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1210   }
1211  
1212   template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){

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