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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 711 by mmeineke, Fri Aug 22 20:04:39 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 +               "average force substraction policy is used\n");
36 +    painCave.isFatal = 0;
37 +    simError();      
38 +
39 +    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(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 +                 "average force substraction policy 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{
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  
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  
621 –  int nMovingZMols_local;
622 –  int nMovingZMols;
805  
624 –  //constrain the molecules which do not reach the specified positions  
806  
807 <   zsys = calcZSys();
627 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
807 >  //constrain the molecules which do not reach the specified positions  
808      
809    //Zero Out the force of z-contrained molecules    
810    totalFZ_local = 0;
811  
812    //calculate the total z-contrained force of fixed z-contrained molecules
813 <  cout << "Fixed Molecules" << endl;
813 >
814    for(int i = 0; i < zconsMols.size(); i++){
815 <                
815 >    
816      if (states[i] == zcsFixed){
817 <                
817 >      
818        zconsMols[i]->getCOM(COM);
819        zconsAtoms = zconsMols[i]->getMyAtoms();  
820  
# Line 642 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain
822        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
823          zconsAtoms[j]->getFrc(force);
824          fz[i] += force[whichDirection];      
825 <      }
825 >      }
826        totalFZ_local += fz[i];
827  
828 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
828 > //       cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
829 > //              <<"\tcurrent zpos: " << COM[whichDirection]
830 > //              << "\tcurrent fz: " <<fz[i] << endl;
831  
832      }
833 <          
833 >    
834    }
835  
836 <  //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 <  }
836 >  //calculate total z-constraint force
837   #ifdef IS_MPI
838    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);
839   #else
840    totalFZ = totalFZ_local;
665 –  nMovingZMols = nMovingZMols_local;
841   #endif
842  
843 <  force[0]= 0;
669 <  force[1]= 0;
670 <  force[2]= 0;
671 <  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
672 <
673 <  //modify the velocites of unconstrained molecules
674 <  for(int i = 0; i < unconsMols.size(); i++){
675 <    
676 <     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
677 <    
678 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
679 <       unconsAtoms[j]->addFrc(force);
680 <    
681 <  }      
682 <
683 < //modify the velocities of moving z-constrained molecules
684 <  for(int i = 0; i < zconsMols.size(); i++) {
685 <   if (states[i] == zcsMoving){
686 <                
687 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
688 <
689 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
690 <       movingZAtoms[j]->addFrc(force);
691 <     }
692 <  }
693 <
843 >  
844    // apply negative to fixed z-constrained molecues;
845    force[0]= 0;
846    force[1]= 0;
# Line 699 | Line 849 | template<typename T> void ZConstraint<T>::doZconstrain
849    for(int i = 0; i < zconsMols.size(); i++){
850  
851      if (states[i] == zcsFixed){  
852 <        
852 >  
853        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
854        zconsAtoms = zconsMols[i]->getMyAtoms();  
855      
856        for(int j =0; j < nAtomOfCurZConsMol; j++) {
857 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
857 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
858 >        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
859          zconsAtoms[j]->addFrc(force);
860        }
861 <                
861 >    
862      }
863 <        
863 >  
864    }
865  
866 + //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
867 + //        << "total force is " << calcTotalForce() << endl;
868 +
869 +  //calculate the number of atoms of moving z-constrained molecules
870 +  int nMovingZAtoms_local;
871 +  int nMovingZAtoms;
872 +  
873 +  nMovingZAtoms_local = 0;
874 +  for(int i = 0; i < zconsMols.size(); i++)
875 +    if(states[i] == zcsMoving)
876 +     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
877 +  
878 + #ifdef IS_MPI
879 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
880 +                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
881 + #else
882 +  nMovingZAtoms = nMovingZAtoms_local;
883 + #endif
884 +
885 +  force[0]= 0;
886 +  force[1]= 0;
887 +  force[2]= 0;
888 +
889 +  //modify the forces of unconstrained molecules
890 +  for(int i = 0; i < unconsMols.size(); i++){
891 +    
892 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
893 +    
894 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
895 +       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
896 +       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
897 +       unconsAtoms[j]->addFrc(force);
898 +     }
899 +    
900 +  }      
901 +
902 + //modify the forces of moving z-constrained molecules
903 +  for(int i = 0; i < zconsMols.size(); i++) {
904 +    if (states[i] == zcsMoving){
905 +    
906 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
907 +
908 +      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
909 +        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
910 +        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
911 +        movingZAtoms[j]->addFrc(force);
912 +      }
913 +    }
914 +  }
915 +
916 +  //cout << "after substracting z-constraint force from moving molecuels "
917 +  //      << "total force is " << calcTotalForce()  << endl;
918 +
919   }
920  
921 + /**
922 +  *
923 +  *
924 +  */
925 +
926 + template<typename T> void ZConstraint<T>::doHarmonic(){
927 +  double force[3];
928 +  double harmonicU;
929 +  double harmonicF;
930 +  double COM[3];
931 +  double diff;
932 +  double totalFZ_local;
933 +  double totalFZ;
934 +  
935 +  force[0] = 0;
936 +  force[1] = 0;
937 +  force[2] = 0;
938 +
939 +  totalFZ_local = 0;
940 +
941 +  for(int i = 0; i < zconsMols.size(); i++) {
942 +
943 +    if (states[i] == zcsMoving){
944 +      zconsMols[i]->getCOM(COM);
945 +      cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
946 +           << "\tcurrent zpos: " << COM[whichDirection] << endl;
947 +    
948 +    diff = COM[whichDirection] -zPos[i];
949 +    
950 +      harmonicU = 0.5 * kz[i] * diff * diff;  
951 +    info->lrPot += harmonicU;
952 +
953 +      harmonicF =  - kz[i] * diff;
954 +      totalFZ_local += harmonicF;
955 +
956 +       //adjust force
957 +    
958 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
959 +
960 +       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
961 +        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
962 +         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
963 +         movingZAtoms[j]->addFrc(force);
964 +       }
965 +    }
966 +
967 +  }
968 +
969 + #ifndef IS_MPI
970 +  totalFZ = totalFZ_local;
971 + #else
972 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
973 + #endif
974 +
975 +  force[0]= 0;
976 +  force[1]= 0;
977 +  force[2]= 0;
978 +
979 +  //modify the forces of unconstrained molecules
980 +  for(int i = 0; i < unconsMols.size(); i++){
981 +    
982 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
983 +    
984 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
985 +       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
986 +       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
987 +       unconsAtoms[j]->addFrc(force);    
988 +     }
989 +  }  
990 +
991 + }
992 +
993 + /**
994 + *
995 + */
996 +
997   template<typename T> bool ZConstraint<T>::checkZConsState(){
998    double COM[3];
999    double diff;
1000    
1001 <  bool changed;
1001 >  int changed_local;
1002 >  int changed;
1003    
1004 <  changed = false;
1004 >  changed_local = 0;
1005    
1006    for(int i =0; i < zconsMols.size(); i++){
1007  
# Line 728 | Line 1009 | template<typename T> bool ZConstraint<T>::checkZConsSt
1009      diff = fabs(COM[whichDirection] - zPos[i]);  
1010      if (  diff <= zconsTol && states[i] == zcsMoving){
1011        states[i] = zcsFixed;
1012 <        changed = true;
1012 >     changed_local = 1;
1013      }
1014      else if ( diff > zconsTol && states[i] == zcsFixed){
1015        states[i] = zcsMoving;
1016 <        changed = true;  
1016 >     changed_local = 1;  
1017      }
1018    
1019    }
1020  
1021 <  return changed;
1021 > #ifndef IS_MPI
1022 >  changed =changed_local;
1023 > #else
1024 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1025 > #endif
1026 >  
1027 >  return (changed > 0);
1028   }
1029  
1030   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1031 +
1032 +  int havingFixed_local;
1033 +  int havingFixed;
1034 +
1035 +  havingFixed_local = 0;
1036 +
1037    for(int i = 0; i < zconsMols.size(); i++)
1038 <    if (states[i] == zcsFixed)
1039 <      return true;
1038 >    if (states[i] == zcsFixed){
1039 >      havingFixed_local = 1;
1040 >    break;
1041 >    }
1042  
1043 <  return false;
1043 > #ifndef IS_MPI
1044 >  havingFixed = havingFixed_local;
1045 > #else
1046 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1047 > #endif
1048 >
1049 >  return havingFixed > 0 ? true : false;
1050   }
1051  
1052  
# Line 753 | Line 1054 | template<typename T> bool ZConstraint<T>::haveMovingZM
1054   *
1055   */
1056   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1057 +
1058 +  int havingMoving_local;
1059 +  int havingMoving;
1060 +
1061 +  havingMoving_local = 0;
1062 +
1063    for(int i = 0; i < zconsMols.size(); i++)
1064 <    if (states[i] == zcsMoving)
1065 <      return true;
1064 >    if (states[i] == zcsMoving){
1065 >      havingMoving_local = 1;
1066 >    break;
1067 >    }
1068  
1069 <  return false;
1069 > #ifndef IS_MPI
1070 >  havingMoving = havingMoving_local;
1071 > #else
1072 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1073 > #endif
1074 >
1075 >  return havingMoving > 0 ? true : false;
1076    
1077   }
1078  
1079   /**
1080 <  *
1081 <  *
767 <  */
1080 > *
1081 > */
1082  
1083 < template<typename T> void ZConstraint<T>::doHarmonic(){
1084 <  double force[3];
1085 <  double harmonicU;
1086 <  double COM[3];
1087 <  double diff;
1088 <        
1089 <  force[0] = 0;
1090 <  force[1] = 0;
1091 <  force[2] = 0;
1083 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1084 > {
1085 >  double MVzOfMovingMols_local;
1086 >  double MVzOfMovingMols;
1087 >  double totalMassOfMovingZMols_local;
1088 >  double totalMassOfMovingZMols;
1089 >  double COMvel[3];
1090 >      
1091 >  MVzOfMovingMols_local = 0;
1092 >  totalMassOfMovingZMols_local = 0;
1093  
1094 <  cout << "Moving Molecules" << endl;  
1095 <  for(int i = 0; i < zconsMols.size(); i++) {
1094 >  for(int i =0; i < unconsMols.size(); i++){
1095 >    unconsMols[i]->getCOMvel(COMvel);
1096 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1097 >  }
1098  
1099 +  for(int i = 0; i < zconsMols.size(); i++){
1100 +
1101      if (states[i] == zcsMoving){
1102 <      zconsMols[i]->getCOM(COM):
1103 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
1104 <                
1105 <                diff = COM[whichDirection] -zPos[i];
1106 <                
1107 <      harmonicU = 0.5 * kz[i] * diff * diff;  
789 <                info->ltPot += harmonicU;
1102 >      zconsMols[i]->getCOMvel(COMvel);
1103 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1104 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1105 >    }
1106 >    
1107 >  }
1108  
1109 <                force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms();
1110 <                
1111 <      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
1109 > #ifndef IS_MPI
1110 >  MVzOfMovingMols = MVzOfMovingMols_local;
1111 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1112 > #else
1113 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1115 > #endif
1116  
1117 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
1118 <         movingZAtoms[j]->addFrc(force);
797 <    }
1117 >  double vzOfMovingMols;
1118 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1119  
1120 +  return vzOfMovingMols;
1121 + }
1122 +
1123 + /**
1124 + *
1125 + */
1126 +
1127 + template<typename T> double ZConstraint<T>::calcSysCOMVel()
1128 + {
1129 +  double COMvel[3];
1130 +  double tempMVz_local;
1131 +  double tempMVz;
1132 +  double massOfZCons_local;
1133 +  double massOfZCons;
1134 +
1135 +
1136 + tempMVz_local = 0;
1137 +
1138 +  for(int i =0 ; i < nMols; i++){
1139 +    molecules[i].getCOMvel(COMvel);
1140 +   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1141    }
1142  
1143 +  massOfZCons_local = 0;
1144 +  
1145 +  for(int i = 0; i < massOfZConsMols.size(); i++){
1146 +    massOfZCons_local += massOfZConsMols[i];
1147 +  }
1148 + #ifndef IS_MPI
1149 +  massOfZCons = massOfZCons_local;
1150 +  tempMVz = tempMVz_local;
1151 + #else
1152 +  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1153 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1154 + #endif
1155 +
1156 +  return tempMVz /(totalMassOfUncons + massOfZCons);
1157   }
1158 +
1159 + /**
1160 + *
1161 + */
1162 +
1163 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1164 +
1165 +  double force[3];  
1166 +  double totalForce_local;
1167 +  double totalForce;
1168 +
1169 +  totalForce_local = 0;
1170 +
1171 +  for(int i = 0; i < nAtoms; i++){
1172 +    atoms[i]->getFrc(force);
1173 +    totalForce_local += force[whichDirection];
1174 +  }
1175 +
1176 + #ifndef IS_MPI
1177 +  totalForce = totalForce_local;
1178 + #else
1179 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1180 + #endif
1181 +
1182 +  return totalForce;
1183 +
1184 + }
1185 +
1186 + /**
1187 + *
1188 + */
1189 +
1190 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1191 +  //calculate the number of atoms of moving z-constrained molecules
1192 +  int nMovingZAtoms_local;
1193 +  int nMovingZAtoms;
1194 +  
1195 +  nMovingZAtoms_local = 0;
1196 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1197 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1198 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1199 +  
1200 + #ifdef IS_MPI
1201 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1202 + #else
1203 +  nMovingZAtoms = nMovingZAtoms_local;
1204 + #endif
1205 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1206 +
1207 + #ifdef IS_MPI
1208 +  if(worldRank == 0){
1209 + #endif
1210 +    std::cerr << "\n"
1211 +              << "*******************************************\n"
1212 +              << " fiished Policy by numbr()\n"
1213 +              << "*******************************************\n"
1214 +              << "\n";
1215 + #ifdef IS_MPI
1216 +  }
1217 + #endif
1218 + }
1219 +
1220 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1221 +  return totalForce / mol->getNAtoms();
1222 + }
1223 +
1224 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1225 +  return totalForce / totNumOfMovingAtoms;
1226 + }
1227 +
1228 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1229 +    return totalForce / mol->getNAtoms();
1230 + }
1231 +
1232 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1233 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1234 + }
1235 +
1236 + /**
1237 + *
1238 + */
1239 +
1240 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1241 +  //calculate the number of atoms of moving z-constrained molecules
1242 +  double massOfMovingZAtoms_local;
1243 +  double massOfMovingZAtoms;
1244 +  
1245 +  massOfMovingZAtoms_local = 0;
1246 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1247 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1248 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1249 +  
1250 + #ifdef IS_MPI
1251 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1252 + #else
1253 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1254 + #endif
1255 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1256 + }
1257 +
1258 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1259 +  return totalForce * atom->getMass() / mol->getTotalMass();
1260 + }
1261 +
1262 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1263 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1264 + }
1265 +
1266 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1267 +  return totalForce * atom->getMass() / mol->getTotalMass();
1268 + }
1269 +
1270 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1271 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1272 + }
1273 +

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