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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 736 by tim, Thu Aug 28 21:09:47 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 +                  "PolicyByMass is used\n");
62 +        painCave.isFatal = 0;
63 +        simError();      
64 +        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
65 +      }  
66 +    }
67 +  }
68 +  
69 +  
70    //retrieve sample time of z-contraint
71    data = info->getProperty(ZCONSTIME_ID);
72    
# Line 69 | 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 83 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
124        this->zconsOutput = filename->getData();
125      }
126      
86 –
127    }
128  
129    //retrieve tolerance for z-constraint molecuels
# Line 113 | 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 154 | 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()].zconsIndex;
199 >      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
200  
201   #ifndef IS_MPI
202        totalNumMol = nMols;
# Line 175 | 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){
179 <
218 >        if(!(*parameters)[i].havingZPos){
219   #ifndef IS_MPI
220 <            for(int j = 0; j < nMols; j++){
221 <              if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 <                 molecules[i].getCOM(COM);
223 <                          break;
185 <              }
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
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 i = 0; i < nMols; i++)
240 <               if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 <                 molecules[i].getCOM(COM);
242 <                                         break;
243 <               }
244 <                                
245 <           }
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 238 | 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 <           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 252 | Line 293 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
293    }
294  
295    fz = new double[zconsMols.size()];
296 +  curZPos = new double[zconsMols.size()];
297    indexOfZConsMols = new int [zconsMols.size()];
298  
299 <  if(!fz || !indexOfZConsMols){
299 >  if(!fz || !curZPos || !indexOfZConsMols){
300      sprintf( painCave.errMsg,
301               "Memory allocation failure in class Zconstraint\n");
302      painCave.isFatal = 1;
303      simError();
304    }
305  
306 <  for(int i = 0; i < zconsMols.size(); i++)
306 >  //determine the states of z-constraint molecules
307 >  for(int i = 0; i < zconsMols.size(); i++){
308      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309 +
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);
315 +  }
316    
317   #endif
318  
319 +  //get total masss of unconstraint molecules
320 +  double totalMassOfUncons_local;
321 +  totalMassOfUncons_local = 0;
322 +  
323 +  for(int i = 0; i < unconsMols.size(); i++)
324 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
325 +    
326 + #ifndef IS_MPI
327 +  totalMassOfUncons = totalMassOfUncons_local;
328 + #else
329 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
330 +                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331 + #endif
332 +
333 +
334    //get total number of unconstrained atoms
335    int nUnconsAtoms_local;
336    nUnconsAtoms_local = 0;
# Line 275 | Line 340 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
340   #ifndef IS_MPI
341    totNumOfUnconsAtoms = nUnconsAtoms_local;
342   #else
343 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
344 < #endif
343 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
344 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
345 > #endif  
346  
347 <  checkZConsState();
348 <
283 <  //  
284 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
347 >  // creat zconsWriter  
348 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
349    
350    if(!fzOut){
351      sprintf( painCave.errMsg,
# Line 289 | Line 353 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
353      painCave.isFatal = 1;
354      simError();
355    }
356 <  
356 >
357 >  forcePolicy->update();
358   }
359  
360   template<typename T> ZConstraint<T>::~ZConstraint()
361   {
362    if(fz)
363      delete[] fz;
364 +
365 +  if(curZPos)
366 +    delete[] curZPos;
367    
368    if(indexOfZConsMols)
369      delete[] indexOfZConsMols;
370    
371    if(fzOut)
372      delete fzOut;
373 +  
374 +  if(forcePolicy)
375 +    delete forcePolicy;
376   }
377  
378 +
379 + /**
380 + *
381 + */
382 +
383   #ifdef IS_MPI
384   template<typename T> void ZConstraint<T>::update()
385   {
# Line 328 | Line 404 | template<typename T> void ZConstraint<T>::update()
404      
405        zconsMols.push_back(&molecules[i]);      
406        zPos.push_back((*parameters)[index].zPos);
407 <        kz.push_back((*parameters)[index].kRatio * zForceConst);
408 <
407 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
408 >      
409        massOfZConsMols.push_back(molecules[i].getTotalMass());  
410        
411        molecules[i].getCOM(COM);
# Line 342 | Line 418 | template<typename T> void ZConstraint<T>::update()
418  
419      }
420    }
421 +
422 +  //determine the states of z-constraint molecules
423 +  for(int i = 0; i < zconsMols.size(); i++){
424 +     zconsMols[i]->getCOM(COM);
425 +      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
426 +      states.push_back(zcsFixed);
427 +     else
428 +      states.push_back(zcsMoving);
429 +  }
430 +
431      
432    //The reason to declare fz and indexOfZconsMols as pointer to array is
433    // that we want to make the MPI communication simple
434    if(fz)
435      delete[] fz;
436 +  
437 +  if(curZPos)
438 +    delete[] curZPos;
439      
440    if(indexOfZConsMols)
441      delete[] indexOfZConsMols;
442      
443    if (zconsMols.size() > 0){
444      fz = new double[zconsMols.size()];
445 +   curZPos = new double[zconsMols.size()];
446      indexOfZConsMols =  new int[zconsMols.size()];
447      
448 <    if(!fz || !indexOfZConsMols){
448 >    if(!fz || !curZPos || !indexOfZConsMols){
449        sprintf( painCave.errMsg,
450                 "Memory allocation failure in class Zconstraint\n");
451        painCave.isFatal = 1;
# Line 369 | Line 459 | template<typename T> void ZConstraint<T>::update()
459    }
460    else{
461      fz = NULL;
462 +   curZPos = NULL;
463      indexOfZConsMols = NULL;
464    }
465    
466 +  //
467 +  forcePolicy->update();
468 +  
469   }
470  
471   #endif
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
473 > /**
474 > *  Function Name: isZConstraintMol
475 > *  Parameter
476 > *    Molecule* mol
477 > *  Return value:
478 > *    -1, if the molecule is not z-constraint molecule,
479 > *    other non-negative values, its index in indexOfAllZConsMols vector
480   */
481  
482   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 410 | Line 505 | template<typename T> int ZConstraint<T>::isZConstraint
505    return -1;
506   }
507  
413 – /**
414 – * Description:
415 – *  Reset the z coordinates
416 – */
508   template<typename T> void ZConstraint<T>::integrate(){
509    
510    //zero out the velocities of center of mass of unconstrained molecules
511    //and the velocities of center of mass of every single z-constrained molecueles
512    zeroOutVel();
513 +
514 +  curZconsTime = zconsTime + info->getTime();
515    
516    T::integrate();
517  
# Line 430 | Line 523 | template<typename T> void ZConstraint<T>::integrate(){
523   *
524   *
525   *
526 < */
434 <
435 <
526 > */
527   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
528 +  double zsys;
529 +  double COM[3];
530 +  double force[3];
531 +  double zSysCOMVel;
532  
533    T::calcForce(calcPot, calcStress);
534  
535 <  if (checkZConsState())
535 >  if (checkZConsState()){
536 >    
537 > #ifdef IS_MPI
538 >    if(worldRank == 0){
539 > #endif
540 > //       std::cerr << "\n"
541 > //              << "*******************************************\n"
542 > //              << " about to call zeroOutVel()\n"
543 > //              << "*******************************************\n"
544 > //              << "\n";
545 > #ifdef IS_MPI
546 >    }
547 > #endif
548      zeroOutVel();
549  
550 + #ifdef IS_MPI
551 +    if(worldRank == 0){
552 + #endif
553 + //       std::cerr << "\n"
554 + //              << "*******************************************\n"
555 + //              << " finished zeroOutVel()\n"
556 + //              << "*******************************************\n"
557 + //              << "\n";
558 + #ifdef IS_MPI
559 +    }
560 + #endif
561 +    
562 +    forcePolicy->update();
563 +  }  
564 +  
565 +  zsys = calcZSys();
566 +  zSysCOMVel = calcSysCOMVel();
567 + #ifdef IS_MPI
568 +  if(worldRank == 0){
569 + #endif
570 + //     cout << "---------------------------------------------------------------------" <<endl;
571 + //     cout << "current time: " << info->getTime() << endl;
572 + //     cout << "center of mass at z: " << zsys << endl;    
573 + //     cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
574 +
575 + #ifdef IS_MPI
576 +  }
577 + #endif
578 +
579    //do zconstraint force;
580    if (haveFixedZMols())
581      this->doZconstraintForce();
582 <  
582 >
583    //use harmonical poteintial to move the molecules to the specified positions
584    if (haveMovingZMols())
585 <    //this->doHarmonic();
586 <  
587 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
588 <      
585 >    this->doHarmonic();
586 >
587 >  //write out forces and current positions of z-constraint molecules
588 >  if(info->getTime() >= curZconsTime){    
589 >   for(int i = 0; i < zconsMols.size(); i++){
590 >      zconsMols[i]->getCOM(COM);
591 >    curZPos[i] = COM[whichDirection];
592 >
593 >    //if the z-constraint molecule is still moving, just record its force
594 >    if(states[i] == zcsMoving){
595 >         fz[i] = 0;
596 >      Atom** movingZAtoms;
597 >      movingZAtoms = zconsMols[i]->getMyAtoms();
598 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
599 >           movingZAtoms[j]->getFrc(force);
600 >           fz[i] += force[whichDirection];
601 >      }
602 >     }
603 >   }
604 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
605 >   curZconsTime += zconsTime;
606 >  }
607 >
608 >  zSysCOMVel = calcSysCOMVel();  
609 > #ifdef IS_MPI
610 >  if(worldRank == 0){
611 > #endif
612 > //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
613 > #ifdef IS_MPI
614 >  }
615 > #endif
616   }
617 +
618 +
619 + /**
620 + *
621 + */
622  
623   template<typename T> double ZConstraint<T>::calcZSys()
624   {
# Line 459 | Line 627 | template<typename T> double ZConstraint<T>::calcZSys()
627    double totalMass;
628    double totalMZ_local;
629    double totalMZ;
462 –  double massOfUncons_local;
630    double massOfCurMol;
631    double COM[3];
632    
633    totalMass_local = 0;
467 –  totalMass = 0;
634    totalMZ_local = 0;
469 –  totalMZ = 0;
470 –  massOfUncons_local = 0;
471 –    
635    
636    for(int i = 0; i < nMols; i++){
637      massOfCurMol = molecules[i].getTotalMass();
# Line 476 | Line 639 | template<typename T> double ZConstraint<T>::calcZSys()
639      
640      totalMass_local += massOfCurMol;
641      totalMZ_local += massOfCurMol * COM[whichDirection];
642 <    
480 <    if(isZConstraintMol(&molecules[i]) == -1){
481 <    
482 <      massOfUncons_local += massOfCurMol;
483 <    }  
484 <    
642 >
643    }
644 +
645    
487 –  
646   #ifdef IS_MPI  
647 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
648 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
649 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
650 < #else
647 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
648 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
649 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
650 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
651 > #else
652    totalMass = totalMass_local;
653    totalMZ = totalMZ_local;
654 <  totalMassOfUncons = massOfUncons_local;
496 < #endif  
654 > #endif  
655  
656    double zsys;
657    zsys = totalMZ / totalMass;
# Line 512 | Line 670 | template<typename T> void ZConstraint<T>::thermalize(
670  
671   /**
672   *
515 – *
516 – *
673   */
674  
675   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 521 | Line 677 | template<typename T> void ZConstraint<T>::zeroOutVel()
677    Atom** fixedZAtoms;  
678    double COMvel[3];
679    double vel[3];
680 <  
680 >  double zSysCOMVel;
681 >
682    //zero out the velocities of center of mass of fixed z-constrained molecules
683    
684    for(int i = 0; i < zconsMols.size(); i++){
685  
686 <    if (states[i] == zcsFixed){
686 >    if (states[i] == zcsFixed){
687  
688 <        zconsMols[i]->getCOMvel(COMvel);      
688 >     zconsMols[i]->getCOMvel(COMvel);      
689 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
690 >
691        fixedZAtoms = zconsMols[i]->getMyAtoms();
692 <          
692 >    
693        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
694          fixedZAtoms[j]->getVel(vel);
695 <          vel[whichDirection] -= COMvel[whichDirection];
696 <          fixedZAtoms[j]->setVel(vel);
695 >       vel[whichDirection] -= COMvel[whichDirection];
696 >       fixedZAtoms[j]->setVel(vel);
697        }
698 <          
698 >
699 >    zconsMols[i]->getCOMvel(COMvel);
700 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
701      }
541 –        
542 –  }
702    
703 +  }
704 +
705 +    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
706 +
707 +  zSysCOMVel = calcSysCOMVel();
708 + #ifdef IS_MPI
709 +  if(worldRank == 0){
710 + #endif
711 + //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
712 + #ifdef IS_MPI
713 +  }
714 + #endif
715 +      
716    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
717    double MVzOfMovingMols_local;
718    double MVzOfMovingMols;
# Line 555 | Line 727 | template<typename T> void ZConstraint<T>::zeroOutVel()
727      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
728    }
729  
730 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
559 <
730 >  for(int i = 0; i < zconsMols.size(); i++){
731      if (states[i] == zcsMoving){
732        zconsMols[i]->getCOMvel(COMvel);
733        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
734 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
734 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
735      }
736 <                
736 >    
737    }
738  
739   #ifndef IS_MPI
# Line 591 | Line 762 | template<typename T> void ZConstraint<T>::zeroOutVel()
762  
763    //modify the velocities of moving z-constrained molecuels
764    Atom** movingZAtoms;
765 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
765 >  for(int i = 0; i < zconsMols.size(); i++){
766  
767      if (states[i] ==zcsMoving){
768    
769        movingZAtoms = zconsMols[i]->getMyAtoms();
770 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
770 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
771          movingZAtoms[j]->getVel(vel);
772          vel[whichDirection] -= vzOfMovingMols;
773 <          movingZAtoms[j]->setVel(vel);
603 <        }
604 <          
773 >       movingZAtoms[j]->setVel(vel);
774      }
775 +    
776 +   }
777  
778 + }
779 +
780 +
781 +  zSysCOMVel = calcSysCOMVel();
782 + #ifdef IS_MPI
783 +  if(worldRank == 0){
784 + #endif
785 + //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
786 + #ifdef IS_MPI
787    }
788 + #endif
789  
790   }
791  
792 + /**
793 + *
794 + */
795 +
796   template<typename T> void ZConstraint<T>::doZconstraintForce(){
797  
798    Atom** zconsAtoms;
# Line 616 | Line 801 | template<typename T> void ZConstraint<T>::doZconstrain
801    double COMvel[3];  
802    double COM[3];
803    double force[3];
619 –  double zsys;
804  
805 <  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;  
805 >  //constrain the molecules which do not reach the specified positions  
806      
807    //Zero Out the force of z-contrained molecules    
808    totalFZ_local = 0;
809  
810    //calculate the total z-contrained force of fixed z-contrained molecules
811 <  cout << "Fixed Molecules" << endl;
811 >
812    for(int i = 0; i < zconsMols.size(); i++){
813 <                
813 >    
814      if (states[i] == zcsFixed){
815 <                
815 >      
816        zconsMols[i]->getCOM(COM);
817        zconsAtoms = zconsMols[i]->getMyAtoms();  
818  
# Line 642 | Line 820 | template<typename T> void ZConstraint<T>::doZconstrain
820        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
821          zconsAtoms[j]->getFrc(force);
822          fz[i] += force[whichDirection];      
823 <      }
823 >      }
824        totalFZ_local += fz[i];
825  
826 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
826 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
827 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
828 >      //       << "\tcurrent fz: " <<fz[i] << endl;
829  
830 +
831      }
832 <          
832 >    
833    }
834  
835 <  //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 <  }
835 >  //calculate total z-constraint force
836   #ifdef IS_MPI
837    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);
838   #else
839    totalFZ = totalFZ_local;
665 –  nMovingZMols = nMovingZMols_local;
840   #endif
841  
842 +  
843 +  // apply negative to fixed z-constrained molecues;
844    force[0]= 0;
845    force[1]= 0;
846    force[2]= 0;
671 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
847  
848 <  //modify the velocites of unconstrained molecules
848 >  for(int i = 0; i < zconsMols.size(); i++){
849 >
850 >    if (states[i] == zcsFixed){  
851 >  
852 >      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
853 >      zconsAtoms = zconsMols[i]->getMyAtoms();  
854 >    
855 >      for(int j =0; j < nAtomOfCurZConsMol; j++) {
856 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
857 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
858 >        zconsAtoms[j]->addFrc(force);
859 >      }
860 >    
861 >    }
862 >  
863 >  }
864 >
865 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
866 > //        << "total force is " << calcTotalForce() << endl;
867 >
868 >  force[0]= 0;
869 >  force[1]= 0;
870 >  force[2]= 0;
871 >
872 >  //modify the forces of unconstrained molecules
873    for(int i = 0; i < unconsMols.size(); i++){
874      
875       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
876      
877 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
877 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
878 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
879 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
880         unconsAtoms[j]->addFrc(force);
881 +     }
882      
883    }      
884  
885 < //modify the velocities of moving z-constrained molecules
885 > //modify the forces of moving z-constrained molecules
886    for(int i = 0; i < zconsMols.size(); i++) {
887 <   if (states[i] == zcsMoving){
888 <                
889 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
887 >    if (states[i] == zcsMoving){
888 >    
889 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
890  
891 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
892 <       movingZAtoms[j]->addFrc(force);
893 <     }
891 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
892 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
893 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
894 >        movingZAtoms[j]->addFrc(force);
895 >      }
896 >    }
897    }
898  
899 <  // apply negative to fixed z-constrained molecues;
900 <  force[0]= 0;
696 <  force[1]= 0;
697 <  force[2]= 0;
899 >  //cout << "after substracting z-constraint force from moving molecuels "
900 >  //      << "total force is " << calcTotalForce()  << endl;
901  
902 <  for(int i = 0; i < zconsMols.size(); i++){
902 > }
903  
904 <    if (states[i] == zcsFixed){  
905 <        
906 <      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
907 <      zconsAtoms = zconsMols[i]->getMyAtoms();  
904 > /**
905 >  *
906 >  *
907 >  */
908 >
909 > template<typename T> void ZConstraint<T>::doHarmonic(){
910 >  double force[3];
911 >  double harmonicU;
912 >  double harmonicF;
913 >  double COM[3];
914 >  double diff;
915 >  double totalFZ_local;
916 >  double totalFZ;
917 >  
918 >  force[0] = 0;
919 >  force[1] = 0;
920 >  force[2] = 0;
921 >
922 >  totalFZ_local = 0;
923 >
924 >  for(int i = 0; i < zconsMols.size(); i++) {
925 >
926 >    if (states[i] == zcsMoving){
927 >      zconsMols[i]->getCOM(COM);
928 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
929 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
930 >
931 >      diff = COM[whichDirection] -zPos[i];
932      
933 <      for(int j =0; j < nAtomOfCurZConsMol; j++) {
934 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
935 <        zconsAtoms[j]->addFrc(force);
936 <      }
937 <                
933 >      harmonicU = 0.5 * kz[i] * diff * diff;  
934 >      info->lrPot += harmonicU;
935 >
936 >      harmonicF =  - kz[i] * diff;
937 >      totalFZ_local += harmonicF;
938 >
939 >       //adjust force
940 >    
941 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
942 >
943 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
944 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
945 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
946 >         movingZAtoms[j]->addFrc(force);
947 >       }
948      }
712 –        
713 –  }
949  
950 +  }
951 +
952 + #ifndef IS_MPI
953 +  totalFZ = totalFZ_local;
954 + #else
955 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
956 + #endif
957 +
958 +  force[0]= 0;
959 +  force[1]= 0;
960 +  force[2]= 0;
961 +
962 +  //modify the forces of unconstrained molecules
963 +  for(int i = 0; i < unconsMols.size(); i++){
964 +    
965 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
966 +    
967 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
968 +       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
969 +       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
970 +       unconsAtoms[j]->addFrc(force);    
971 +     }
972 +  }  
973 +
974   }
975  
976 + /**
977 + *
978 + */
979 +
980   template<typename T> bool ZConstraint<T>::checkZConsState(){
981    double COM[3];
982    double diff;
983    
984 <  bool changed;
984 >  int changed_local;
985 >  int changed;
986    
987 <  changed = false;
987 >  changed_local = 0;
988    
989    for(int i =0; i < zconsMols.size(); i++){
990  
# Line 728 | Line 992 | template<typename T> bool ZConstraint<T>::checkZConsSt
992      diff = fabs(COM[whichDirection] - zPos[i]);  
993      if (  diff <= zconsTol && states[i] == zcsMoving){
994        states[i] = zcsFixed;
995 <        changed = true;
995 >     changed_local = 1;
996      }
997      else if ( diff > zconsTol && states[i] == zcsFixed){
998        states[i] = zcsMoving;
999 <        changed = true;  
999 >     changed_local = 1;  
1000      }
1001    
1002    }
1003  
1004 <  return changed;
1004 > #ifndef IS_MPI
1005 >  changed =changed_local;
1006 > #else
1007 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1008 > #endif
1009 >
1010 >  return (changed > 0);
1011 >
1012   }
1013  
1014   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1015 +
1016 +  int havingFixed_local;
1017 +  int havingFixed;
1018 +
1019 +  havingFixed_local = 0;
1020 +
1021    for(int i = 0; i < zconsMols.size(); i++)
1022 <    if (states[i] == zcsFixed)
1023 <      return true;
1022 >    if (states[i] == zcsFixed){
1023 >      havingFixed_local = 1;
1024 >    break;
1025 >    }
1026  
1027 <  return false;
1027 > #ifndef IS_MPI
1028 >  havingFixed = havingFixed_local;
1029 > #else
1030 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1031 > #endif
1032 >
1033 >  return (havingFixed > 0);
1034   }
1035  
1036  
# Line 753 | Line 1038 | template<typename T> bool ZConstraint<T>::haveMovingZM
1038   *
1039   */
1040   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1041 +
1042 +  int havingMoving_local;
1043 +  int havingMoving;
1044 +
1045 +  havingMoving_local = 0;
1046 +
1047    for(int i = 0; i < zconsMols.size(); i++)
1048 <    if (states[i] == zcsMoving)
1049 <      return true;
1048 >    if (states[i] == zcsMoving){
1049 >      havingMoving_local = 1;
1050 >    break;
1051 >    }
1052  
1053 <  return false;
1053 > #ifndef IS_MPI
1054 >  havingMoving = havingMoving_local;
1055 > #else
1056 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1057 > #endif
1058 >
1059 >  return (havingMoving > 0);
1060    
1061   }
1062  
1063   /**
1064 <  *
1065 <  *
767 <  */
1064 > *
1065 > */
1066  
1067 < template<typename T> void ZConstraint<T>::doHarmonic(){
1068 <  double force[3];
1069 <  double harmonicU;
1070 <  double COM[3];
1071 <  double diff;
1072 <        
1073 <  force[0] = 0;
1074 <  force[1] = 0;
1075 <  force[2] = 0;
1067 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1068 > {
1069 >  double MVzOfMovingMols_local;
1070 >  double MVzOfMovingMols;
1071 >  double totalMassOfMovingZMols_local;
1072 >  double totalMassOfMovingZMols;
1073 >  double COMvel[3];
1074 >      
1075 >  MVzOfMovingMols_local = 0;
1076 >  totalMassOfMovingZMols_local = 0;
1077  
1078 <  cout << "Moving Molecules" << endl;  
1079 <  for(int i = 0; i < zconsMols.size(); i++) {
1078 >  for(int i =0; i < unconsMols.size(); i++){
1079 >    unconsMols[i]->getCOMvel(COMvel);
1080 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1081 >  }
1082  
1083 +  for(int i = 0; i < zconsMols.size(); i++){
1084 +
1085      if (states[i] == zcsMoving){
1086 <      zconsMols[i]->getCOM(COM):
1087 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
1088 <                
1089 <                diff = COM[whichDirection] -zPos[i];
1090 <                
1091 <      harmonicU = 0.5 * kz[i] * diff * diff;  
789 <                info->ltPot += harmonicU;
1086 >      zconsMols[i]->getCOMvel(COMvel);
1087 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1088 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1089 >    }
1090 >    
1091 >  }
1092  
1093 <                force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms();
1094 <                
1095 <      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
1093 > #ifndef IS_MPI
1094 >  MVzOfMovingMols = MVzOfMovingMols_local;
1095 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1096 > #else
1097 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1098 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1099 > #endif
1100  
1101 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
1102 <         movingZAtoms[j]->addFrc(force);
797 <    }
1101 >  double vzOfMovingMols;
1102 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1103  
1104 +  return vzOfMovingMols;
1105 + }
1106 +
1107 + /**
1108 + *
1109 + */
1110 +
1111 + template<typename T> double ZConstraint<T>::calcSysCOMVel()
1112 + {
1113 +  double COMvel[3];
1114 +  double tempMVz_local;
1115 +  double tempMVz;
1116 +  double massOfZCons_local;
1117 +  double massOfZCons;
1118 +
1119 +
1120 + tempMVz_local = 0;
1121 +
1122 +  for(int i =0 ; i < nMols; i++){
1123 +    molecules[i].getCOMvel(COMvel);
1124 +   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1125    }
1126  
1127 +  massOfZCons_local = 0;
1128 +  
1129 +  for(int i = 0; i < massOfZConsMols.size(); i++){
1130 +    massOfZCons_local += massOfZConsMols[i];
1131 +  }
1132 + #ifndef IS_MPI
1133 +  massOfZCons = massOfZCons_local;
1134 +  tempMVz = tempMVz_local;
1135 + #else
1136 +  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1137 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1138 + #endif
1139 +
1140 +  return tempMVz /(totalMassOfUncons + massOfZCons);
1141   }
1142 +
1143 + /**
1144 + *
1145 + */
1146 +
1147 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1148 +
1149 +  double force[3];  
1150 +  double totalForce_local;
1151 +  double totalForce;
1152 +
1153 +  totalForce_local = 0;
1154 +
1155 +  for(int i = 0; i < nAtoms; i++){
1156 +    atoms[i]->getFrc(force);
1157 +    totalForce_local += force[whichDirection];
1158 +  }
1159 +
1160 + #ifndef IS_MPI
1161 +  totalForce = totalForce_local;
1162 + #else
1163 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1164 + #endif
1165 +
1166 +  return totalForce;
1167 +
1168 + }
1169 +
1170 + /**
1171 + *
1172 + */
1173 +
1174 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1175 +  //calculate the number of atoms of moving z-constrained molecules
1176 +  int nMovingZAtoms_local;
1177 +  int nMovingZAtoms;
1178 +  
1179 +  nMovingZAtoms_local = 0;
1180 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1181 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1182 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1183 +  
1184 + #ifdef IS_MPI
1185 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1186 + #else
1187 +  nMovingZAtoms = nMovingZAtoms_local;
1188 + #endif
1189 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1190 +
1191 + #ifdef IS_MPI
1192 +  if(worldRank == 0){
1193 + #endif
1194 + //    std::cerr << "\n"
1195 + //            << "*******************************************\n"
1196 + //            << " fiished Policy by numbr()\n"
1197 + //            << "*******************************************\n"
1198 + //            << "\n";
1199 + #ifdef IS_MPI
1200 +  }
1201 + #endif
1202 + }
1203 +
1204 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1205 +  return totalForce / mol->getNAtoms();
1206 + }
1207 +
1208 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1209 +  return totalForce / totNumOfMovingAtoms;
1210 + }
1211 +
1212 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1213 +    return totalForce / mol->getNAtoms();
1214 + }
1215 +
1216 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1217 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1218 + }
1219 +
1220 + /**
1221 + *
1222 + */
1223 +
1224 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1225 +  //calculate the number of atoms of moving z-constrained molecules
1226 +  double massOfMovingZAtoms_local;
1227 +  double massOfMovingZAtoms;
1228 +  
1229 +  massOfMovingZAtoms_local = 0;
1230 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1231 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1232 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1233 +  
1234 + #ifdef IS_MPI
1235 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1236 + #else
1237 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1238 + #endif
1239 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1240 + }
1241 +
1242 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1243 +  return totalForce * atom->getMass() / mol->getTotalMass();
1244 + }
1245 +
1246 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1247 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1248 + }
1249 +
1250 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1251 +  return totalForce * atom->getMass() / mol->getTotalMass();
1252 + }
1253 +
1254 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1255 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1256 + }
1257 +

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