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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 682 by tim, Tue Aug 12 17:51:33 2003 UTC vs.
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC

# Line 2 | Line 2 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
2   #include "simError.h"
3   #include <cmath>
4   template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5 <                                    : T(theInfo, the_ff), fz(NULL),
6 <                                      indexOfZConsMols(NULL)
5 >                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL),
6 >                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
9    //get properties from SimInfo
# Line 11 | Line 11 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
11    ZConsParaData* zConsParaData;
12    DoubleData* sampleTime;
13    DoubleData* tolerance;
14 +  StringData* policy;
15    StringData* filename;
16    double COM[3];
17  
# Line 26 | Line 27 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
27    double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2;
28    zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox);
29  
30 +  //creat force substraction policy
31 +  data = info->getProperty(ZCONSFORCEPOLICY_ID);
32 +  if(!data){
33 +    sprintf( painCave.errMsg,
34 +               "ZConstraint Warning: User does not set force substraction policy, "
35 +               "PolicyByMass is used\n");
36 +    painCave.isFatal = 0;
37 +    simError();      
38 +
39 +    forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
40 +  }
41 +  else{
42 +    policy = dynamic_cast<StringData*>(data);
43 +    
44 +    if(!policy){
45 +      sprintf( painCave.errMsg,
46 +                 "ZConstraint Error: Convertion from GenericData to StringData failure, "
47 +                 "PolicyByMass is used\n");
48 +      painCave.isFatal = 0;
49 +      simError();      
50 +
51 +      forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
52 +    }
53 +    else{
54 +      if(policy->getData() == "BYNUMBER")
55 +        forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
56 +      else if(policy->getData() == "BYMASS")
57 +        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
58 +      else{
59 +        sprintf( painCave.errMsg,
60 +                  "ZConstraint Warning: unknown force substraction policy, "
61 +                  "average force substraction policy is used\n");
62 +        painCave.isFatal = 0;
63 +        simError();      
64 +      }  
65 +    }
66 +  }
67 +  
68 +  
69    //retrieve sample time of z-contraint
70    data = info->getProperty(ZCONSTIME_ID);
71    
# Line 69 | 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 83 | Line 123 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
123        this->zconsOutput = filename->getData();
124      }
125      
86 –
126    }
127  
128    //retrieve tolerance for z-constraint molecuels
# Line 113 | 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 154 | 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()].zconsIndex;
198 >      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
199  
200   #ifndef IS_MPI
201        totalNumMol = nMols;
# Line 175 | 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){
179 <
217 >        if(!(*parameters)[i].havingZPos){
218   #ifndef IS_MPI
219 <            for(int j = 0; j < nMols; j++){
220 <              if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 <                 molecules[i].getCOM(COM);
222 <                          break;
185 <              }
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 i = 0; i < nMols; i++)
239 <               if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 <                 molecules[i].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 238 | 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 <           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 252 | Line 292 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
292    }
293  
294    fz = new double[zconsMols.size()];
295 +  curZPos = new double[zconsMols.size()];
296    indexOfZConsMols = new int [zconsMols.size()];
297  
298 <  if(!fz || !indexOfZConsMols){
298 >  if(!fz || !curZPos || !indexOfZConsMols){
299      sprintf( painCave.errMsg,
300               "Memory allocation failure in class Zconstraint\n");
301      painCave.isFatal = 1;
302      simError();
303    }
304  
305 <  for(int i = 0; i < zconsMols.size(); i++)
305 >  //determine the states of z-constraint molecules
306 >  for(int i = 0; i < zconsMols.size(); i++){
307      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
308 +
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);
314 +  }
315    
316   #endif
317  
318 +  //get total masss of unconstraint molecules
319 +  double totalMassOfUncons_local;
320 +  totalMassOfUncons_local = 0;
321 +  
322 +  for(int i = 0; i < unconsMols.size(); i++)
323 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
324 +    
325 + #ifndef IS_MPI
326 +  totalMassOfUncons = totalMassOfUncons_local;
327 + #else
328 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
329 +                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
330 + #endif
331 +
332 +
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
# Line 275 | 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_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
343 < #endif
342 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344 > #endif  
345  
346 <  checkZConsState();
347 <
283 <  //  
284 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
346 >  // creat zconsWriter  
347 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348    
349    if(!fzOut){
350      sprintf( painCave.errMsg,
# Line 289 | Line 352 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
352      painCave.isFatal = 1;
353      simError();
354    }
355 <  
355 >
356 >  forcePolicy->update();
357   }
358  
359   template<typename T> ZConstraint<T>::~ZConstraint()
360   {
361    if(fz)
362      delete[] fz;
363 +
364 +  if(curZPos)
365 +    delete[] curZPos;
366    
367    if(indexOfZConsMols)
368      delete[] indexOfZConsMols;
369    
370    if(fzOut)
371      delete fzOut;
372 +  
373 +  if(forcePolicy)
374 +    delete forcePolicy;
375   }
376  
377 +
378 + /**
379 + *
380 + */
381 +
382   #ifdef IS_MPI
383   template<typename T> void ZConstraint<T>::update()
384   {
# Line 328 | 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 342 | Line 417 | template<typename T> void ZConstraint<T>::update()
417  
418      }
419    }
420 +
421 +  //determine the states of z-constraint molecules
422 +  for(int i = 0; i < zconsMols.size(); i++){
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);
428 +  }
429 +
430      
431    //The reason to declare fz and indexOfZconsMols as pointer to array is
432    // that we want to make the MPI communication simple
433    if(fz)
434      delete[] fz;
435 +  
436 +  if(curZPos)
437 +    delete[] curZPos;
438      
439    if(indexOfZConsMols)
440      delete[] indexOfZConsMols;
441      
442    if (zconsMols.size() > 0){
443      fz = new double[zconsMols.size()];
444 +   curZPos = new double[zconsMols.size()];
445      indexOfZConsMols =  new int[zconsMols.size()];
446      
447 <    if(!fz || !indexOfZConsMols){
447 >    if(!fz || !curZPos || !indexOfZConsMols){
448        sprintf( painCave.errMsg,
449                 "Memory allocation failure in class Zconstraint\n");
450        painCave.isFatal = 1;
# Line 369 | Line 458 | template<typename T> void ZConstraint<T>::update()
458    }
459    else{
460      fz = NULL;
461 +   curZPos = NULL;
462      indexOfZConsMols = NULL;
463    }
464    
465 +  //
466 +  forcePolicy->update();
467 +  
468   }
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 410 | Line 504 | template<typename T> int ZConstraint<T>::isZConstraint
504    return -1;
505   }
506  
413 – /**
414 – * Description:
415 – *  Reset the z coordinates
416 – */
507   template<typename T> void ZConstraint<T>::integrate(){
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 430 | Line 522 | template<typename T> void ZConstraint<T>::integrate(){
522   *
523   *
524   *
525 < */
434 <
435 <
525 > */
526   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
527 +  double zsys;
528 +  double COM[3];
529 +  double force[3];
530 +  double zSysCOMVel;
531  
532    T::calcForce(calcPot, calcStress);
533  
534 <  if (checkZConsState())
534 >  if (checkZConsState()){
535 >    
536 > #ifdef IS_MPI
537 >    if(worldRank == 0){
538 > #endif
539 > //       std::cerr << "\n"
540 > //              << "*******************************************\n"
541 > //              << " about to call zeroOutVel()\n"
542 > //              << "*******************************************\n"
543 > //              << "\n";
544 > #ifdef IS_MPI
545 >    }
546 > #endif
547      zeroOutVel();
548  
549 + #ifdef IS_MPI
550 +    if(worldRank == 0){
551 + #endif
552 + //       std::cerr << "\n"
553 + //              << "*******************************************\n"
554 + //              << " finished zeroOutVel()\n"
555 + //              << "*******************************************\n"
556 + //              << "\n";
557 + #ifdef IS_MPI
558 +    }
559 + #endif
560 +    
561 +    forcePolicy->update();
562 +  }  
563 +  
564 +  zsys = calcZSys();
565 +  zSysCOMVel = calcSysCOMVel();
566 + #ifdef IS_MPI
567 +  if(worldRank == 0){
568 + #endif
569 + //     cout << "---------------------------------------------------------------------" <<endl;
570 + //     cout << "current time: " << info->getTime() << endl;
571 + //     cout << "center of mass at z: " << zsys << endl;    
572 + //     cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
573 +
574 + #ifdef IS_MPI
575 +  }
576 + #endif
577 +
578    //do zconstraint force;
579    if (haveFixedZMols())
580      this->doZconstraintForce();
581 <  
581 >
582    //use harmonical poteintial to move the molecules to the specified positions
583    if (haveMovingZMols())
584 <    //this->doHarmonic();
585 <  
586 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
587 <      
584 >    this->doHarmonic();
585 >
586 >  //write out forces and current positions of z-constraint molecules
587 >  if(info->getTime() >= curZconsTime){    
588 >   for(int i = 0; i < zconsMols.size(); i++){
589 >      zconsMols[i]->getCOM(COM);
590 >    curZPos[i] = COM[whichDirection];
591 >
592 >    //if the z-constraint molecule is still moving, just record its force
593 >    if(states[i] == zcsMoving){
594 >         fz[i] = 0;
595 >      Atom** movingZAtoms;
596 >      movingZAtoms = zconsMols[i]->getMyAtoms();
597 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
598 >           movingZAtoms[j]->getFrc(force);
599 >           fz[i] += force[whichDirection];
600 >      }
601 >     }
602 >   }
603 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
604 >   curZconsTime += zconsTime;
605 >  }
606 >
607 >  zSysCOMVel = calcSysCOMVel();  
608 > #ifdef IS_MPI
609 >  if(worldRank == 0){
610 > #endif
611 > //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
612 > #ifdef IS_MPI
613 >  }
614 > #endif
615   }
616 +
617 +
618 + /**
619 + *
620 + */
621  
622   template<typename T> double ZConstraint<T>::calcZSys()
623   {
# Line 459 | Line 626 | template<typename T> double ZConstraint<T>::calcZSys()
626    double totalMass;
627    double totalMZ_local;
628    double totalMZ;
462 –  double massOfUncons_local;
629    double massOfCurMol;
630    double COM[3];
631    
632    totalMass_local = 0;
467 –  totalMass = 0;
633    totalMZ_local = 0;
469 –  totalMZ = 0;
470 –  massOfUncons_local = 0;
471 –    
634    
635    for(int i = 0; i < nMols; i++){
636      massOfCurMol = molecules[i].getTotalMass();
# Line 476 | Line 638 | template<typename T> double ZConstraint<T>::calcZSys()
638      
639      totalMass_local += massOfCurMol;
640      totalMZ_local += massOfCurMol * COM[whichDirection];
641 <    
480 <    if(isZConstraintMol(&molecules[i]) == -1){
481 <    
482 <      massOfUncons_local += massOfCurMol;
483 <    }  
484 <    
641 >
642    }
643 +
644    
487 –  
645   #ifdef IS_MPI  
646 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
647 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
648 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
649 < #else
646 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
647 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
648 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
649 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
650 > #else
651    totalMass = totalMass_local;
652    totalMZ = totalMZ_local;
653 <  totalMassOfUncons = massOfUncons_local;
496 < #endif  
653 > #endif  
654  
655    double zsys;
656    zsys = totalMZ / totalMass;
# Line 512 | Line 669 | template<typename T> void ZConstraint<T>::thermalize(
669  
670   /**
671   *
515 – *
516 – *
672   */
673  
674   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 521 | Line 676 | template<typename T> void ZConstraint<T>::zeroOutVel()
676    Atom** fixedZAtoms;  
677    double COMvel[3];
678    double vel[3];
679 <  
679 >  double zSysCOMVel;
680 >
681    //zero out the velocities of center of mass of fixed z-constrained molecules
682    
683    for(int i = 0; i < zconsMols.size(); i++){
684  
685 <    if (states[i] == zcsFixed){
685 >    if (states[i] == zcsFixed){
686  
687 <        zconsMols[i]->getCOMvel(COMvel);      
687 >     zconsMols[i]->getCOMvel(COMvel);      
688 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
689 >
690        fixedZAtoms = zconsMols[i]->getMyAtoms();
691 <          
691 >    
692        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
693          fixedZAtoms[j]->getVel(vel);
694 <          vel[whichDirection] -= COMvel[whichDirection];
695 <          fixedZAtoms[j]->setVel(vel);
694 >       vel[whichDirection] -= COMvel[whichDirection];
695 >       fixedZAtoms[j]->setVel(vel);
696        }
697 <          
697 >
698 >    zconsMols[i]->getCOMvel(COMvel);
699 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
700      }
541 –        
542 –  }
701    
702 +  }
703 +
704 +    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
705 +
706 +  zSysCOMVel = calcSysCOMVel();
707 + #ifdef IS_MPI
708 +  if(worldRank == 0){
709 + #endif
710 + //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
711 + #ifdef IS_MPI
712 +  }
713 + #endif
714 +      
715    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
716    double MVzOfMovingMols_local;
717    double MVzOfMovingMols;
# Line 555 | Line 726 | template<typename T> void ZConstraint<T>::zeroOutVel()
726      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
727    }
728  
729 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
559 <
729 >  for(int i = 0; i < zconsMols.size(); i++){
730      if (states[i] == zcsMoving){
731        zconsMols[i]->getCOMvel(COMvel);
732        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
733 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
733 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
734      }
735 <                
735 >    
736    }
737  
738   #ifndef IS_MPI
# Line 591 | Line 761 | template<typename T> void ZConstraint<T>::zeroOutVel()
761  
762    //modify the velocities of moving z-constrained molecuels
763    Atom** movingZAtoms;
764 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
764 >  for(int i = 0; i < zconsMols.size(); i++){
765  
766      if (states[i] ==zcsMoving){
767    
768        movingZAtoms = zconsMols[i]->getMyAtoms();
769 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
769 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
770          movingZAtoms[j]->getVel(vel);
771          vel[whichDirection] -= vzOfMovingMols;
772 <          movingZAtoms[j]->setVel(vel);
603 <        }
604 <          
772 >       movingZAtoms[j]->setVel(vel);
773      }
774 +    
775 +   }
776  
777 + }
778 +
779 +
780 +  zSysCOMVel = calcSysCOMVel();
781 + #ifdef IS_MPI
782 +  if(worldRank == 0){
783 + #endif
784 + //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
785 + #ifdef IS_MPI
786    }
787 + #endif
788  
789   }
790  
791 + /**
792 + *
793 + */
794 +
795   template<typename T> void ZConstraint<T>::doZconstraintForce(){
796  
797    Atom** zconsAtoms;
# Line 616 | Line 800 | template<typename T> void ZConstraint<T>::doZconstrain
800    double COMvel[3];  
801    double COM[3];
802    double force[3];
619 –  double zsys;
803  
804 <  int nMovingZMols_local;
622 <  int nMovingZMols;
623 <
624 <  //constrain the molecules which do not reach the specified positions  
625 <
626 <   zsys = calcZSys();
627 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
804 >  //constrain the molecules which do not reach the specified positions  
805      
806    //Zero Out the force of z-contrained molecules    
807    totalFZ_local = 0;
808  
809    //calculate the total z-contrained force of fixed z-contrained molecules
810 <  cout << "Fixed Molecules" << endl;
810 >
811    for(int i = 0; i < zconsMols.size(); i++){
812 <                
812 >    
813      if (states[i] == zcsFixed){
814 <                
814 >      
815        zconsMols[i]->getCOM(COM);
816        zconsAtoms = zconsMols[i]->getMyAtoms();  
817  
# Line 642 | Line 819 | template<typename T> void ZConstraint<T>::doZconstrain
819        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
820          zconsAtoms[j]->getFrc(force);
821          fz[i] += force[whichDirection];      
822 <      }
822 >      }
823        totalFZ_local += fz[i];
824  
825 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
825 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
826 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
827 >      //       << "\tcurrent fz: " <<fz[i] << endl;
828  
829 +
830      }
831 <          
831 >    
832    }
833  
834 <  //calculate the number of atoms of moving z-constrained molecules
655 <  nMovingZMols_local = 0;
656 <  for(int i = 0; zconsMols.size(); i++){
657 <    if(states[i] == zcsMoving)
658 <        nMovingZMols_local += massOfZConsMols[i];
659 <  }
834 >  //calculate total z-constraint force
835   #ifdef IS_MPI
836    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
662 –  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
837   #else
838    totalFZ = totalFZ_local;
665 –  nMovingZMols = nMovingZMols_local;
839   #endif
840  
841 +  
842 +  // apply negative to fixed z-constrained molecues;
843    force[0]= 0;
844    force[1]= 0;
845    force[2]= 0;
671 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
846  
847 <  //modify the velocites of unconstrained molecules
847 >  for(int i = 0; i < zconsMols.size(); i++){
848 >
849 >    if (states[i] == zcsFixed){  
850 >  
851 >      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
852 >      zconsAtoms = zconsMols[i]->getMyAtoms();  
853 >    
854 >      for(int j =0; j < nAtomOfCurZConsMol; j++) {
855 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
856 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
857 >        zconsAtoms[j]->addFrc(force);
858 >      }
859 >    
860 >    }
861 >  
862 >  }
863 >
864 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
865 > //        << "total force is " << calcTotalForce() << endl;
866 >
867 >  force[0]= 0;
868 >  force[1]= 0;
869 >  force[2]= 0;
870 >
871 >  //modify the forces of unconstrained molecules
872    for(int i = 0; i < unconsMols.size(); i++){
873      
874       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
875      
876 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
876 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
877 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
878 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
879         unconsAtoms[j]->addFrc(force);
880 +     }
881      
882    }      
883  
884 < //modify the velocities of moving z-constrained molecules
884 > //modify the forces of moving z-constrained molecules
885    for(int i = 0; i < zconsMols.size(); i++) {
886 <   if (states[i] == zcsMoving){
887 <                
888 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
886 >    if (states[i] == zcsMoving){
887 >    
888 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
889  
890 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
891 <       movingZAtoms[j]->addFrc(force);
892 <     }
890 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
891 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
892 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
893 >        movingZAtoms[j]->addFrc(force);
894 >      }
895 >    }
896    }
897  
898 <  // apply negative to fixed z-constrained molecues;
899 <  force[0]= 0;
696 <  force[1]= 0;
697 <  force[2]= 0;
898 >  //cout << "after substracting z-constraint force from moving molecuels "
899 >  //      << "total force is " << calcTotalForce()  << endl;
900  
901 <  for(int i = 0; i < zconsMols.size(); i++){
901 > }
902  
903 <    if (states[i] == zcsFixed){  
904 <        
905 <      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
906 <      zconsAtoms = zconsMols[i]->getMyAtoms();  
903 > /**
904 >  *
905 >  *
906 >  */
907 >
908 > template<typename T> void ZConstraint<T>::doHarmonic(){
909 >  double force[3];
910 >  double harmonicU;
911 >  double harmonicF;
912 >  double COM[3];
913 >  double diff;
914 >  double totalFZ_local;
915 >  double totalFZ;
916 >  
917 >  force[0] = 0;
918 >  force[1] = 0;
919 >  force[2] = 0;
920 >
921 >  totalFZ_local = 0;
922 >
923 >  for(int i = 0; i < zconsMols.size(); i++) {
924 >
925 >    if (states[i] == zcsMoving){
926 >      zconsMols[i]->getCOM(COM);
927 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
928 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
929 >
930 >      diff = COM[whichDirection] -zPos[i];
931      
932 <      for(int j =0; j < nAtomOfCurZConsMol; j++) {
933 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
934 <        zconsAtoms[j]->addFrc(force);
935 <      }
936 <                
932 >      harmonicU = 0.5 * kz[i] * diff * diff;  
933 >      info->lrPot += harmonicU;
934 >
935 >      harmonicF =  - kz[i] * diff;
936 >      totalFZ_local += harmonicF;
937 >
938 >       //adjust force
939 >    
940 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
941 >
942 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
943 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
944 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
945 >         movingZAtoms[j]->addFrc(force);
946 >       }
947      }
712 –        
713 –  }
948  
949 +  }
950 +
951 + #ifndef IS_MPI
952 +  totalFZ = totalFZ_local;
953 + #else
954 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
955 + #endif
956 +
957 +  force[0]= 0;
958 +  force[1]= 0;
959 +  force[2]= 0;
960 +
961 +  //modify the forces of unconstrained molecules
962 +  for(int i = 0; i < unconsMols.size(); i++){
963 +    
964 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
965 +    
966 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
967 +       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
968 +       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
969 +       unconsAtoms[j]->addFrc(force);    
970 +     }
971 +  }  
972 +
973   }
974  
975 + /**
976 + *
977 + */
978 +
979   template<typename T> bool ZConstraint<T>::checkZConsState(){
980    double COM[3];
981    double diff;
982    
983 <  bool changed;
983 >  int changed_local;
984 >  int changed;
985    
986 <  changed = false;
986 >  changed_local = 0;
987    
988    for(int i =0; i < zconsMols.size(); i++){
989  
# Line 728 | Line 991 | template<typename T> bool ZConstraint<T>::checkZConsSt
991      diff = fabs(COM[whichDirection] - zPos[i]);  
992      if (  diff <= zconsTol && states[i] == zcsMoving){
993        states[i] = zcsFixed;
994 <        changed = true;
994 >     changed_local = 1;
995      }
996      else if ( diff > zconsTol && states[i] == zcsFixed){
997        states[i] = zcsMoving;
998 <        changed = true;  
998 >     changed_local = 1;  
999      }
1000    
1001    }
1002  
1003 <  return changed;
1003 > #ifndef IS_MPI
1004 >  changed =changed_local;
1005 > #else
1006 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1007 > #endif
1008 >
1009 >  return (changed > 0);
1010 >
1011   }
1012  
1013   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1014 +
1015 +  int havingFixed_local;
1016 +  int havingFixed;
1017 +
1018 +  havingFixed_local = 0;
1019 +
1020    for(int i = 0; i < zconsMols.size(); i++)
1021 <    if (states[i] == zcsFixed)
1022 <      return true;
1021 >    if (states[i] == zcsFixed){
1022 >      havingFixed_local = 1;
1023 >    break;
1024 >    }
1025  
1026 <  return false;
1026 > #ifndef IS_MPI
1027 >  havingFixed = havingFixed_local;
1028 > #else
1029 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1030 > #endif
1031 >
1032 >  return (havingFixed > 0);
1033   }
1034  
1035  
# Line 753 | Line 1037 | template<typename T> bool ZConstraint<T>::haveMovingZM
1037   *
1038   */
1039   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1040 +
1041 +  int havingMoving_local;
1042 +  int havingMoving;
1043 +
1044 +  havingMoving_local = 0;
1045 +
1046    for(int i = 0; i < zconsMols.size(); i++)
1047 <    if (states[i] == zcsMoving)
1048 <      return true;
1047 >    if (states[i] == zcsMoving){
1048 >      havingMoving_local = 1;
1049 >    break;
1050 >    }
1051  
1052 <  return false;
1052 > #ifndef IS_MPI
1053 >  havingMoving = havingMoving_local;
1054 > #else
1055 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1056 > #endif
1057 >
1058 >  return (havingMoving > 0);
1059    
1060   }
1061  
1062   /**
1063 <  *
1064 <  *
767 <  */
1063 > *
1064 > */
1065  
1066 < template<typename T> void ZConstraint<T>::doHarmonic(){
1067 <  double force[3];
1068 <  double harmonicU;
1069 <  double COM[3];
1070 <  double diff;
1071 <        
1072 <  force[0] = 0;
1073 <  force[1] = 0;
1074 <  force[2] = 0;
1066 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1067 > {
1068 >  double MVzOfMovingMols_local;
1069 >  double MVzOfMovingMols;
1070 >  double totalMassOfMovingZMols_local;
1071 >  double totalMassOfMovingZMols;
1072 >  double COMvel[3];
1073 >      
1074 >  MVzOfMovingMols_local = 0;
1075 >  totalMassOfMovingZMols_local = 0;
1076  
1077 <  cout << "Moving Molecules" << endl;  
1078 <  for(int i = 0; i < zconsMols.size(); i++) {
1077 >  for(int i =0; i < unconsMols.size(); i++){
1078 >    unconsMols[i]->getCOMvel(COMvel);
1079 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1080 >  }
1081  
1082 +  for(int i = 0; i < zconsMols.size(); i++){
1083 +
1084      if (states[i] == zcsMoving){
1085 <      zconsMols[i]->getCOM(COM):
1086 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
1087 <                
1088 <                diff = COM[whichDirection] -zPos[i];
1089 <                
1090 <      harmonicU = 0.5 * kz[i] * diff * diff;  
789 <                info->ltPot += harmonicU;
1085 >      zconsMols[i]->getCOMvel(COMvel);
1086 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1087 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1088 >    }
1089 >    
1090 >  }
1091  
1092 <                force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms();
1093 <                
1094 <      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
1092 > #ifndef IS_MPI
1093 >  MVzOfMovingMols = MVzOfMovingMols_local;
1094 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1095 > #else
1096 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1097 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1098 > #endif
1099  
1100 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
1101 <         movingZAtoms[j]->addFrc(force);
797 <    }
1100 >  double vzOfMovingMols;
1101 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1102  
1103 +  return vzOfMovingMols;
1104 + }
1105 +
1106 + /**
1107 + *
1108 + */
1109 +
1110 + template<typename T> double ZConstraint<T>::calcSysCOMVel()
1111 + {
1112 +  double COMvel[3];
1113 +  double tempMVz_local;
1114 +  double tempMVz;
1115 +  double massOfZCons_local;
1116 +  double massOfZCons;
1117 +
1118 +
1119 + tempMVz_local = 0;
1120 +
1121 +  for(int i =0 ; i < nMols; i++){
1122 +    molecules[i].getCOMvel(COMvel);
1123 +   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1124    }
1125  
1126 +  massOfZCons_local = 0;
1127 +  
1128 +  for(int i = 0; i < massOfZConsMols.size(); i++){
1129 +    massOfZCons_local += massOfZConsMols[i];
1130 +  }
1131 + #ifndef IS_MPI
1132 +  massOfZCons = massOfZCons_local;
1133 +  tempMVz = tempMVz_local;
1134 + #else
1135 +  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1136 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1137 + #endif
1138 +
1139 +  return tempMVz /(totalMassOfUncons + massOfZCons);
1140   }
1141 +
1142 + /**
1143 + *
1144 + */
1145 +
1146 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1147 +
1148 +  double force[3];  
1149 +  double totalForce_local;
1150 +  double totalForce;
1151 +
1152 +  totalForce_local = 0;
1153 +
1154 +  for(int i = 0; i < nAtoms; i++){
1155 +    atoms[i]->getFrc(force);
1156 +    totalForce_local += force[whichDirection];
1157 +  }
1158 +
1159 + #ifndef IS_MPI
1160 +  totalForce = totalForce_local;
1161 + #else
1162 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1163 + #endif
1164 +
1165 +  return totalForce;
1166 +
1167 + }
1168 +
1169 + /**
1170 + *
1171 + */
1172 +
1173 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1174 +  //calculate the number of atoms of moving z-constrained molecules
1175 +  int nMovingZAtoms_local;
1176 +  int nMovingZAtoms;
1177 +  
1178 +  nMovingZAtoms_local = 0;
1179 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1180 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1181 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1182 +  
1183 + #ifdef IS_MPI
1184 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1185 + #else
1186 +  nMovingZAtoms = nMovingZAtoms_local;
1187 + #endif
1188 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1189 +
1190 + #ifdef IS_MPI
1191 +  if(worldRank == 0){
1192 + #endif
1193 + //    std::cerr << "\n"
1194 + //            << "*******************************************\n"
1195 + //            << " fiished Policy by numbr()\n"
1196 + //            << "*******************************************\n"
1197 + //            << "\n";
1198 + #ifdef IS_MPI
1199 +  }
1200 + #endif
1201 + }
1202 +
1203 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1204 +  return totalForce / mol->getNAtoms();
1205 + }
1206 +
1207 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1208 +  return totalForce / totNumOfMovingAtoms;
1209 + }
1210 +
1211 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1212 +    return totalForce / mol->getNAtoms();
1213 + }
1214 +
1215 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1216 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1217 + }
1218 +
1219 + /**
1220 + *
1221 + */
1222 +
1223 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1224 +  //calculate the number of atoms of moving z-constrained molecules
1225 +  double massOfMovingZAtoms_local;
1226 +  double massOfMovingZAtoms;
1227 +  
1228 +  massOfMovingZAtoms_local = 0;
1229 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1230 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1231 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1232 +  
1233 + #ifdef IS_MPI
1234 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1235 + #else
1236 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1237 + #endif
1238 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1239 + }
1240 +
1241 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1242 +  return totalForce * atom->getMass() / mol->getTotalMass();
1243 + }
1244 +
1245 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1246 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1247 + }
1248 +
1249 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1250 +  return totalForce * atom->getMass() / mol->getTotalMass();
1251 + }
1252 +
1253 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1254 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1255 + }
1256 +

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