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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 696 by tim, Thu Aug 14 16:16:39 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() - 1].zconsIndex;
199  
# 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[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 <                 molecules[j].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 j = 0; j < nMols; j++)
239 <               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 <                 molecules[j].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;
# Line 265 | Line 306 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
306    for(int i = 0; i < zconsMols.size(); i++){
307      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
308  
309 <         zconsMols[i]->getCOM(COM);
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);
311 >      states.push_back(zcsFixed);
312 >    else
313 >      states.push_back(zcsMoving);
314    }
315    
316   #endif
# Line 284 | Line 325 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
325   #ifndef IS_MPI
326    totalMassOfUncons = totalMassOfUncons_local;
327   #else
328 <  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
328 >  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
329 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
330   #endif
331  
332  
# Line 297 | 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);  
342 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344   #endif  
345  
346    // creat zconsWriter  
347 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
347 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348    
349    if(!fzOut){
350      sprintf( painCave.errMsg,
# Line 309 | 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()
# Line 348 | 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 365 | Line 420 | template<typename T> void ZConstraint<T>::update()
420  
421    //determine the states of z-constraint molecules
422    for(int i = 0; i < zconsMols.size(); i++){
423 <           zconsMols[i]->getCOM(COM);
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);
425 >      states.push_back(zcsFixed);
426 >     else
427 >      states.push_back(zcsMoving);
428    }
429  
430      
# Line 377 | Line 432 | template<typename T> void ZConstraint<T>::update()
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 399 | 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 445 | Line 509 | template<typename T> void ZConstraint<T>::integrate(){
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 459 | Line 525 | template<typename T> void ZConstraint<T>::calcForce(in
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 <  cout << "---------------------------------------------------------------------" <<endl;
566 <  cout << "current time: " << info->getTime() << endl;
567 <  cout << "center of mass at z: " << zsys << endl;      
568 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
569 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
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 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
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 <  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
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 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
593 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
594 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
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 498 | Line 628 | template<typename T> double ZConstraint<T>::calcZSys()
628    double totalMZ;
629    double massOfCurMol;
630    double COM[3];
631 <        
631 >  
632    totalMass_local = 0;
633    totalMZ_local = 0;
634    
# Line 513 | Line 643 | template<typename T> double ZConstraint<T>::calcZSys()
643  
644    
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);  
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;
# Line 537 | Line 669 | template<typename T> void ZConstraint<T>::thermalize(
669  
670   /**
671   *
540 – *
541 – *
672   */
673  
674   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 546 | Line 676 | template<typename T> void ZConstraint<T>::zeroOutVel()
676    Atom** fixedZAtoms;  
677    double COMvel[3];
678    double vel[3];
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);      
688 <                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
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  
698 <                zconsMols[i]->getCOMvel(COMvel);
699 <                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
698 >    zconsMols[i]->getCOMvel(COMvel);
699 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
700      }
701 <        
701 >  
702    }
703  
704 <        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
705 <        cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;  
706 <                  
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 591 | Line 730 | template<typename T> void ZConstraint<T>::zeroOutVel()
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 627 | Line 766 | template<typename T> void ZConstraint<T>::zeroOutVel()
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);
773 <          }
774 <          
772 >       movingZAtoms[j]->setVel(vel);
773 >    }
774 >    
775     }
776  
777   }
778  
640 –        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
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 650 | Line 801 | template<typename T> void ZConstraint<T>::doZconstrain
801    double COM[3];
802    double force[3];
803  
804 <
654 <
655 <  //constrain the molecules which do not reach the specified positions  
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 670 | 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]
826 <                                <<"\tcurrent zpos: " << COM[whichDirection]
827 <                                << "\tcurrent fz: " <<fz[i] << 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 <        
833 >
834 >  //calculate total z-constraint force
835 > #ifdef IS_MPI
836 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
837 > #else
838 >  totalFZ = totalFZ_local;
839 > #endif
840 >
841 >  
842    // apply negative to fixed z-constrained molecues;
843    force[0]= 0;
844    force[1]= 0;
# Line 689 | Line 847 | template<typename T> void ZConstraint<T>::doZconstrain
847    for(int i = 0; i < zconsMols.size(); i++){
848  
849      if (states[i] == zcsFixed){  
850 <        
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;
855 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
856 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
857          zconsAtoms[j]->addFrc(force);
858        }
859 <                
859 >    
860      }
861 <        
861 >  
862    }
863  
864 <  cout << "after zero out z-constraint force on fixed z-constraint molecuels "
865 <                  << "total force is " << calcTotalForce() << endl;
707 <  //calculate the number of atoms of moving z-constrained molecules
708 <  int nMovingZAtoms_local;
709 <  int nMovingZAtoms;
710 <        
711 <  nMovingZAtoms_local = 0;
712 <  for(int i = 0; i < zconsMols.size(); i++)
713 <    if(states[i] == zcsMoving)
714 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
715 <  
716 < #ifdef IS_MPI
717 <  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
718 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
719 < #else
720 <  totalFZ = totalFZ_local;
721 <  nMovingZAtoms = nMovingZAtoms_local;
722 < #endif
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;
727 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
870  
871    //modify the forces of unconstrained molecules
730 –  int accessCount = 0;
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 forces of moving z-constrained molecules
885    for(int i = 0; i < zconsMols.size(); i++) {
886      if (states[i] == zcsMoving){
887 <                
887 >    
888        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
889  
890 <      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
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    }
750 –        
751 –  cout << "after substracting z-constraint force from moving molecuels "
752 –                  << "total force is " << calcTotalForce()  << endl;
897  
898 < }
898 >  //cout << "after substracting z-constraint force from moving molecuels "
899 >  //      << "total force is " << calcTotalForce()  << endl;
900  
756 – template<typename T> bool ZConstraint<T>::checkZConsState(){
757 –  double COM[3];
758 –  double diff;
759 –  
760 –  bool changed;
761 –  
762 –  changed = false;
763 –  
764 –  for(int i =0; i < zconsMols.size(); i++){
765 –
766 –    zconsMols[i]->getCOM(COM);
767 –    diff = fabs(COM[whichDirection] - zPos[i]);  
768 –    if (  diff <= zconsTol && states[i] == zcsMoving){
769 –      states[i] = zcsFixed;
770 –        changed = true;
771 –    }
772 –    else if ( diff > zconsTol && states[i] == zcsFixed){
773 –      states[i] = zcsMoving;
774 –        changed = true;  
775 –    }
776 –  
777 –  }
778 –
779 –  return changed;
901   }
902  
782 – template<typename T> bool ZConstraint<T>::haveFixedZMols(){
783 –  for(int i = 0; i < zconsMols.size(); i++)
784 –    if (states[i] == zcsFixed)
785 –      return true;
786 –
787 –  return false;
788 – }
789 –
790 –
903   /**
792 – *
793 – */
794 – template<typename T> bool ZConstraint<T>::haveMovingZMols(){
795 –  for(int i = 0; i < zconsMols.size(); i++)
796 –    if (states[i] == zcsMoving)
797 –      return true;
798 –
799 –  return false;
800 –  
801 – }
802 –
803 – /**
904    *
905    *
906    */
# Line 811 | Line 911 | template<typename T> void ZConstraint<T>::doHarmonic()
911    double harmonicF;
912    double COM[3];
913    double diff;
914 +  double totalFZ_local;
915    double totalFZ;
916 <        
916 >  
917    force[0] = 0;
918    force[1] = 0;
919    force[2] = 0;
920  
921 <  totalFZ = 0;
921 >  totalFZ_local = 0;
922  
822 –  cout << "Moving Molecules" << endl;  
923    for(int i = 0; i < zconsMols.size(); i++) {
924  
925      if (states[i] == zcsMoving){
926        zconsMols[i]->getCOM(COM);
927 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
928 <                
929 <                diff = COM[whichDirection] -zPos[i];
930 <                
927 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
928 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
929 >
930 >      diff = COM[whichDirection] -zPos[i];
931 >    
932        harmonicU = 0.5 * kz[i] * diff * diff;  
933 <                info->lrPot += harmonicU;
933 >      info->lrPot += harmonicU;
934  
935        harmonicF =  - kz[i] * diff;
936 <      totalFZ += harmonicF;
936 >      totalFZ_local += harmonicF;
937  
938 <       //
939 <                force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
839 <                
938 >       //adjust force
939 >    
940        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
941  
942 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
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      }
948  
949    }
950 <        
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;
851 –  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
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++)          
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 +  int changed_local;
984 +  int changed;
985 +  
986 +  changed_local = 0;
987 +  
988 +  for(int i =0; i < zconsMols.size(); i++){
989 +
990 +    zconsMols[i]->getCOM(COM);
991 +    diff = fabs(COM[whichDirection] - zPos[i]);  
992 +    if (  diff <= zconsTol && states[i] == zcsMoving){
993 +      states[i] = zcsFixed;
994 +     changed_local = 1;
995 +    }
996 +    else if ( diff > zconsTol && states[i] == zcsFixed){
997 +      states[i] = zcsMoving;
998 +     changed_local = 1;  
999 +    }
1000 +  
1001 +  }
1002 +
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 +      havingFixed_local = 1;
1023 +    break;
1024 +    }
1025 +
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 +
1036 + /**
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 +      havingMoving_local = 1;
1049 +    break;
1050 +    }
1051 +
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 + */
1065 +
1066   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1067   {
1068    double MVzOfMovingMols_local;
# Line 882 | Line 1084 | template<typename T> double ZConstraint<T>::calcMoving
1084      if (states[i] == zcsMoving){
1085        zconsMols[i]->getCOMvel(COMvel);
1086        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1087 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1087 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1088      }
1089 <                
1089 >    
1090    }
1091  
1092   #ifndef IS_MPI
# Line 901 | Line 1103 | template<typename T> double ZConstraint<T>::calcMoving
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 = 0;
1114 <                
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 += molecules[i].getTotalMass()*COMvel[whichDirection];
1123 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1124    }
1125  
915 –  double massOfZCons_local;
916 –  double massOfZCons;
917 –
1126    massOfZCons_local = 0;
1127 <        
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];  
# Line 951 | Line 1165 | template<typename T> double ZConstraint<T>::calcTotalF
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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