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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 738 by tim, Tue Sep 2 14:30:12 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 >      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
283        
284        molecules[i].getCOM(COM);
285      }
# 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);
397 <                        
396 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
397 >      
398        massOfZConsMols.push_back(molecules[i].getTotalMass());  
399        
400        molecules[i].getCOM(COM);
# Line 415 | Line 410 | template<typename T> void ZConstraint<T>::update()
410  
411    //determine the states of z-constraint molecules
412    for(int i = 0; i < zconsMols.size(); i++){
413 <           zconsMols[i]->getCOM(COM);
413 >     zconsMols[i]->getCOM(COM);
414        if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
415 <                  states.push_back(zcsFixed);
416 <           else
417 <                  states.push_back(zcsMoving);
415 >      states.push_back(zcsFixed);
416 >     else
417 >      states.push_back(zcsMoving);
418    }
419  
420      
# Line 427 | Line 422 | template<typename T> void ZConstraint<T>::update()
422    // that we want to make the MPI communication simple
423    if(fz)
424      delete[] fz;
425 <        
425 >  
426    if(curZPos)
427      delete[] curZPos;
428      
# Line 436 | Line 431 | template<typename T> void ZConstraint<T>::update()
431      
432    if (zconsMols.size() > 0){
433      fz = new double[zconsMols.size()];
434 <         curZPos = new double[zconsMols.size()];
434 >   curZPos = new double[zconsMols.size()];
435      indexOfZConsMols =  new int[zconsMols.size()];
436      
437      if(!fz || !curZPos || !indexOfZConsMols){
# Line 453 | Line 448 | template<typename T> void ZConstraint<T>::update()
448    }
449    else{
450      fz = NULL;
451 <         curZPos = NULL;
451 >   curZPos = NULL;
452      indexOfZConsMols = NULL;
453    }
454 <        
454 >  
455    //
456    forcePolicy->update();
457    
# Line 464 | Line 459 | template<typename T> void ZConstraint<T>::update()
459  
460   #endif
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
462 > /**
463 > *  Function Name: isZConstraintMol
464 > *  Parameter
465 > *    Molecule* mol
466 > *  Return value:
467 > *    -1, if the molecule is not z-constraint molecule,
468 > *    other non-negative values, its index in indexOfAllZConsMols vector
469   */
470  
471   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 499 | Line 495 | template<typename T> void ZConstraint<T>::integrate(){
495   }
496  
497   template<typename T> void ZConstraint<T>::integrate(){
498 +
499 +  // creat zconsWriter  
500 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
501    
502 +  if(!fzOut){
503 +    sprintf( painCave.errMsg,
504 +             "Memory allocation failure in class Zconstraint\n");
505 +    painCave.isFatal = 1;
506 +    simError();
507 +  }
508 +  
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 <    zeroOutVel();
536 <         forcePolicy->update();
534 >  if (checkZConsState()){    
535 >    zeroOutVel();    
536 >    forcePolicy->update();
537    }  
538 +  
539    zsys = calcZSys();
540 <  cout << "---------------------------------------------------------------------" <<endl;
541 <  cout << "current time: " << info->getTime() << endl;
542 <  cout << "center of mass at z: " << zsys << endl;      
543 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
544 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
540 >  zSysCOMVel = calcSysCOMVel();
541 > #ifdef IS_MPI
542 >  if(worldRank == 0){
543 > #endif
544 >     //cout << "---------------------------------------------------------------------" <<endl;
545 >     //cout << "current time: " << info->getTime() << endl;
546 >     //cout << "center of mass at z: " << zsys << endl;    
547 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
548  
549 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
549 > #ifdef IS_MPI
550 >  }
551 > #endif
552  
553    //do zconstraint force;
554    if (haveFixedZMols())
555      this->doZconstraintForce();
556 <    
556 >
557    //use harmonical poteintial to move the molecules to the specified positions
558    if (haveMovingZMols())
559      this->doHarmonic();
560  
546 –  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 –
561    //write out forces and current positions of z-constraint molecules
562 <  if(info->getTime() >= curZconsTime){          
563 <         for(int i = 0; i < zconsMols.size(); i++){
562 >  if(info->getTime() >= curZconsTime){    
563 >   for(int i = 0; i < zconsMols.size(); i++){
564        zconsMols[i]->getCOM(COM);
565 <                curZPos[i] = COM[whichDirection];
565 >    curZPos[i] = COM[whichDirection];
566  
567 <                //if the z-constraint molecule is still moving, just record its force
568 <                if(states[i] == zcsMoving){
567 >    //if the z-constraint molecule is still moving, just record its force
568 >    if(states[i] == zcsMoving){
569           fz[i] = 0;
570 <                  Atom** movingZAtoms;
571 <                  movingZAtoms = zconsMols[i]->getMyAtoms();
572 <                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
570 >      Atom** movingZAtoms;
571 >      movingZAtoms = zconsMols[i]->getMyAtoms();
572 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
573             movingZAtoms[j]->getFrc(force);
574             fz[i] += force[whichDirection];
575 <                  }
576 <           }
577 <         }
575 >      }
576 >     }
577 >   }
578      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
579 <         curZconsTime += zconsTime;
579 >   curZconsTime += zconsTime;
580    }
581 <        
582 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
583 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
581 >
582 >  zSysCOMVel = calcSysCOMVel();  
583 > #ifdef IS_MPI
584 >  if(worldRank == 0){
585 > #endif
586 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
587 > #ifdef IS_MPI
588 >  }
589 > #endif
590   }
591 +
592 +
593 + /**
594 + *
595 + */
596  
597   template<typename T> double ZConstraint<T>::calcZSys()
598   {
# Line 579 | Line 603 | template<typename T> double ZConstraint<T>::calcZSys()
603    double totalMZ;
604    double massOfCurMol;
605    double COM[3];
606 <        
606 >  
607    totalMass_local = 0;
608    totalMZ_local = 0;
609    
# Line 594 | Line 618 | template<typename T> double ZConstraint<T>::calcZSys()
618  
619    
620   #ifdef IS_MPI  
621 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
622 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
621 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
622 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
623 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
624 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
625   #else
626    totalMass = totalMass_local;
627    totalMZ = totalMZ_local;
# Line 618 | Line 644 | template<typename T> void ZConstraint<T>::thermalize(
644  
645   /**
646   *
621 – *
622 – *
647   */
648  
649   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 627 | Line 651 | template<typename T> void ZConstraint<T>::zeroOutVel()
651    Atom** fixedZAtoms;  
652    double COMvel[3];
653    double vel[3];
654 +  double zSysCOMVel;
655  
656    //zero out the velocities of center of mass of fixed z-constrained molecules
657    
658    for(int i = 0; i < zconsMols.size(); i++){
659  
660 <    if (states[i] == zcsFixed){
660 >    if (states[i] == zcsFixed){
661  
662 <           zconsMols[i]->getCOMvel(COMvel);      
663 <                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
662 >     zconsMols[i]->getCOMvel(COMvel);      
663 >     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
664  
665        fixedZAtoms = zconsMols[i]->getMyAtoms();
666 <          
666 >    
667        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
668          fixedZAtoms[j]->getVel(vel);
669 <             vel[whichDirection] -= COMvel[whichDirection];
670 <             fixedZAtoms[j]->setVel(vel);
669 >       vel[whichDirection] -= COMvel[whichDirection];
670 >       fixedZAtoms[j]->setVel(vel);
671        }
672  
673 <                zconsMols[i]->getCOMvel(COMvel);
674 <                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
673 >    zconsMols[i]->getCOMvel(COMvel);
674 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
675      }
676 <        
676 >  
677    }
678  
679 <        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
679 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
680  
681 +  zSysCOMVel = calcSysCOMVel();
682   #ifdef IS_MPI
683 <  if (worldRank == 0){
683 >  if(worldRank == 0){
684   #endif
685 <    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
685 >     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
686   #ifdef IS_MPI
687    }
688   #endif
689 <                  
689 >      
690    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
691    double MVzOfMovingMols_local;
692    double MVzOfMovingMols;
# Line 679 | Line 705 | template<typename T> void ZConstraint<T>::zeroOutVel()
705      if (states[i] == zcsMoving){
706        zconsMols[i]->getCOMvel(COMvel);
707        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
708 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
708 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
709      }
710 <                
710 >    
711    }
712  
713   #ifndef IS_MPI
# Line 715 | Line 741 | template<typename T> void ZConstraint<T>::zeroOutVel()
741      if (states[i] ==zcsMoving){
742    
743        movingZAtoms = zconsMols[i]->getMyAtoms();
744 <           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
744 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
745          movingZAtoms[j]->getVel(vel);
746          vel[whichDirection] -= vzOfMovingMols;
747 <             movingZAtoms[j]->setVel(vel);
748 <          }
749 <          
747 >       movingZAtoms[j]->setVel(vel);
748 >    }
749 >    
750     }
751  
752   }
753  
754 +
755 +  zSysCOMVel = calcSysCOMVel();
756   #ifdef IS_MPI
757 <  if (worldRank == 0){
757 >  if(worldRank == 0){
758   #endif
759 <        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
759 >     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
760   #ifdef IS_MPI
761    }
762   #endif
763  
764   }
765  
766 + /**
767 + *
768 + */
769 +
770   template<typename T> void ZConstraint<T>::doZconstraintForce(){
771  
772    Atom** zconsAtoms;
# Line 744 | Line 776 | template<typename T> void ZConstraint<T>::doZconstrain
776    double COM[3];
777    double force[3];
778  
779 <
748 <
749 <  //constrain the molecules which do not reach the specified positions  
779 >  //constrain the molecules which do not reach the specified positions  
780      
781    //Zero Out the force of z-contrained molecules    
782    totalFZ_local = 0;
783  
784    //calculate the total z-contrained force of fixed z-contrained molecules
785 +  
786 +  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
787 +  //       << "total force is " << calcTotalForce() << endl;
788  
756 – #ifdef IS_MPI
757 –  if (worldRank == 0){
758 – #endif
759 –    cout << "Fixed Molecules" << endl;
760 – #ifdef IS_MPI
761 –  }
762 – #endif
763 –
789    for(int i = 0; i < zconsMols.size(); i++){
790 <                
790 >    
791      if (states[i] == zcsFixed){
792 <                
792 >      
793        zconsMols[i]->getCOM(COM);
794        zconsAtoms = zconsMols[i]->getMyAtoms();  
795  
# Line 772 | Line 797 | template<typename T> void ZConstraint<T>::doZconstrain
797        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
798          zconsAtoms[j]->getFrc(force);
799          fz[i] += force[whichDirection];      
800 <      }
800 >      }
801        totalFZ_local += fz[i];
802  
803 <      cout << "index: " << indexOfZConsMols[i]
804 <                                <<"\tcurrent zpos: " << COM[whichDirection]
805 <                                << "\tcurrent fz: " <<fz[i] << endl;
803 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
804 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
805 >      //      << "\tcurrent fz: " <<fz[i] << endl;
806  
807 +
808      }
809 <          
809 >    
810    }
811  
812    //calculate total z-constraint force
# Line 790 | Line 816 | template<typename T> void ZConstraint<T>::doZconstrain
816    totalFZ = totalFZ_local;
817   #endif
818  
819 <        
819 >  
820    // apply negative to fixed z-constrained molecues;
821    force[0]= 0;
822    force[1]= 0;
# Line 799 | Line 825 | template<typename T> void ZConstraint<T>::doZconstrain
825    for(int i = 0; i < zconsMols.size(); i++){
826  
827      if (states[i] == zcsFixed){  
828 <        
828 >  
829        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
830        zconsAtoms = zconsMols[i]->getMyAtoms();  
831      
832        for(int j =0; j < nAtomOfCurZConsMol; j++) {
833 <                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
834 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
833 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
834 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
835          zconsAtoms[j]->addFrc(force);
836        }
837 <                
837 >    
838      }
839 <        
839 >  
840    }
841  
842    //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
843 <  //               << "total force is " << calcTotalForce() << endl;
843 >  //      << "total force is " << calcTotalForce() << endl;
844 >  
845  
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 –
846    force[0]= 0;
847    force[1]= 0;
848    force[2]= 0;
# Line 841 | Line 853 | template<typename T> void ZConstraint<T>::doZconstrain
853       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
854      
855       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
856 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
857 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
856 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
857 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
858         unconsAtoms[j]->addFrc(force);
859       }
860      
# 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++){
870 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
871 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
870 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
871 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
872          movingZAtoms[j]->addFrc(force);
873        }
874      }
875    }
876 + //  cout << "after substracting z-constraint force from moving molecuels "
877 + //        << "total force is " << calcTotalForce()  << endl;
878  
879 <  //cout << "after substracting z-constraint force from moving molecuels "
880 <  //              << "total force is " << calcTotalForce()  << endl;
879 > }
880 >
881 > /**
882 >  *
883 >  *
884 >  */
885 >
886 > template<typename T> void ZConstraint<T>::doHarmonic(){
887 >  double force[3];
888 >  double harmonicU;
889 >  double harmonicF;
890 >  double COM[3];
891 >  double diff;
892 >  double totalFZ_local;
893 >  double totalFZ;
894 >  
895 >  force[0] = 0;
896 >  force[1] = 0;
897 >  force[2] = 0;
898 >
899 >  totalFZ_local = 0;
900 >
901 >  for(int i = 0; i < zconsMols.size(); i++) {
902 >
903 >    if (states[i] == zcsMoving){
904 >      zconsMols[i]->getCOM(COM);
905 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
906 > //         << "\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 >  cout << "before substracting harmonic force from moving molecuels "
936 >        << "total force is " << calcTotalForce()  << endl;
937  
938 +  force[0]= 0;
939 +  force[1]= 0;
940 +  force[2]= 0;
941 +
942 +  //modify the forces of unconstrained molecules
943 +  for(int i = 0; i < unconsMols.size(); i++){
944 +    
945 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
946 +    
947 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
948 +       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
949 +       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
950 +       unconsAtoms[j]->addFrc(force);    
951 +     }
952 +  }  
953 +
954 +  cout << "after substracting harmonic force from moving molecuels "
955 +        << "total force is " << calcTotalForce()  << endl;
956 +
957   }
958  
959 + /**
960 + *
961 + */
962 +
963   template<typename T> bool ZConstraint<T>::checkZConsState(){
964    double COM[3];
965    double diff;
966    
967    int changed_local;
968    int changed;
969 <        
969 >  
970    changed_local = 0;
971    
972    for(int i =0; i < zconsMols.size(); i++){
# Line 882 | Line 975 | template<typename T> bool ZConstraint<T>::checkZConsSt
975      diff = fabs(COM[whichDirection] - zPos[i]);  
976      if (  diff <= zconsTol && states[i] == zcsMoving){
977        states[i] = zcsFixed;
978 <           changed_local = 1;
978 >     changed_local = 1;
979      }
980      else if ( diff > zconsTol && states[i] == zcsFixed){
981        states[i] = zcsMoving;
982 <           changed_local = 1;    
982 >     changed_local = 1;  
983      }
984    
985    }
# Line 897 | Line 990 | template<typename T> bool ZConstraint<T>::checkZConsSt
990    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
991   #endif
992  
993 <  return changed > 0 ? true : false;
993 >  return (changed > 0);
994 >
995   }
996  
997   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 910 | Line 1004 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1004    for(int i = 0; i < zconsMols.size(); i++)
1005      if (states[i] == zcsFixed){
1006        havingFixed_local = 1;
1007 <                break;
1007 >    break;
1008      }
1009  
1010   #ifndef IS_MPI
# Line 919 | Line 1013 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1013    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1014   #endif
1015  
1016 <  return havingFixed > 0 ? true : false;
1016 >  return (havingFixed > 0);
1017   }
1018  
1019  
# Line 936 | Line 1030 | template<typename T> bool ZConstraint<T>::haveMovingZM
1030    for(int i = 0; i < zconsMols.size(); i++)
1031      if (states[i] == zcsMoving){
1032        havingMoving_local = 1;
1033 <                break;
1033 >    break;
1034      }
1035  
1036   #ifndef IS_MPI
# Line 945 | Line 1039 | template<typename T> bool ZConstraint<T>::haveMovingZM
1039    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1040   #endif
1041  
1042 <  return havingMoving > 0 ? true : false;
1042 >  return (havingMoving > 0);
1043    
1044   }
1045  
1046   /**
1047 <  *
1048 <  *
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;
1047 > *
1048 > */
1049  
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 –
1050   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1051   {
1052    double MVzOfMovingMols_local;
# Line 1050 | Line 1068 | template<typename T> double ZConstraint<T>::calcMoving
1068      if (states[i] == zcsMoving){
1069        zconsMols[i]->getCOMvel(COMvel);
1070        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1071 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1071 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1072      }
1073 <                
1073 >    
1074    }
1075  
1076   #ifndef IS_MPI
# Line 1069 | Line 1087 | template<typename T> double ZConstraint<T>::calcMoving
1087    return vzOfMovingMols;
1088   }
1089  
1090 + /**
1091 + *
1092 + */
1093  
1094   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1095   {
# Line 1083 | Line 1104 | template<typename T> double ZConstraint<T>::calcSysCOM
1104  
1105    for(int i =0 ; i < nMols; i++){
1106      molecules[i].getCOMvel(COMvel);
1107 <         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1107 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1108    }
1109  
1110    massOfZCons_local = 0;
1111 <        
1111 >  
1112    for(int i = 0; i < massOfZConsMols.size(); i++){
1113      massOfZCons_local += massOfZConsMols[i];
1114    }
# Line 1102 | Line 1123 | template<typename T> double ZConstraint<T>::calcTotalF
1123    return tempMVz /(totalMassOfUncons + massOfZCons);
1124   }
1125  
1126 + /**
1127 + *
1128 + */
1129 +
1130   template<typename T> double ZConstraint<T>::calcTotalForce(){
1131  
1132    double force[3];  
# Line 1133 | Line 1158 | template<typename T> void ZConstraint<T>::PolicyByNumb
1158    //calculate the number of atoms of moving z-constrained molecules
1159    int nMovingZAtoms_local;
1160    int nMovingZAtoms;
1161 <        
1161 >  
1162    nMovingZAtoms_local = 0;
1163    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1164      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1165 <           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1165 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1166    
1167   #ifdef IS_MPI
1168    MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 1147 | Line 1172 | template<typename T> double ZConstraint<T>::PolicyByNu
1172    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1173   }
1174  
1175 < template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1175 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1176    return totalForce / mol->getNAtoms();
1177   }
1178  
# Line 1171 | Line 1196 | template<typename T> void ZConstraint<T>::PolicyByMass
1196    //calculate the number of atoms of moving z-constrained molecules
1197    double massOfMovingZAtoms_local;
1198    double massOfMovingZAtoms;
1199 <        
1199 >  
1200    massOfMovingZAtoms_local = 0;
1201    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1202      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1203 <           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1203 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1204    
1205   #ifdef IS_MPI
1206    MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1207   #else
1208    massOfMovingZAtoms = massOfMovingZAtoms_local;
1209   #endif
1210 <  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1210 >  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1211   }
1212  
1213   template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){

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