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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 726 by tim, Tue Aug 26 20:37:30 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()
384   {
# 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 456 | Line 522 | template<typename T> void ZConstraint<T>::integrate(){
522   *
523   *
524   *
525 < */
460 <
461 <
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())
535 <  zeroOutVel();
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() <<"\tcenter of mass at z: " << zsys << endl;      
567 <  cout << "before calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
568 <        
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 <
480 <
481 <      
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 <  cout << "after calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
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 494 | Line 627 | template<typename T> double ZConstraint<T>::calcZSys()
627    double totalMass;
628    double totalMZ_local;
629    double totalMZ;
497 –  double massOfUncons_local;
630    double massOfCurMol;
631    double COM[3];
632    
633    totalMass_local = 0;
502 –  totalMass = 0;
634    totalMZ_local = 0;
504 –  totalMZ = 0;
505 –  massOfUncons_local = 0;
506 –    
635    
636    for(int i = 0; i < nMols; i++){
637      massOfCurMol = molecules[i].getTotalMass();
# Line 511 | Line 639 | template<typename T> double ZConstraint<T>::calcZSys()
639      
640      totalMass_local += massOfCurMol;
641      totalMZ_local += massOfCurMol * COM[whichDirection];
642 <    
515 <    if(isZConstraintMol(&molecules[i]) == -1){
516 <    
517 <      massOfUncons_local += massOfCurMol;
518 <    }  
519 <    
642 >
643    }
644 +
645    
522 –  
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;
531 < #endif  
654 > #endif  
655  
656    double zsys;
657    zsys = totalMZ / totalMass;
# Line 547 | Line 670 | template<typename T> void ZConstraint<T>::thermalize(
670  
671   /**
672   *
550 – *
551 – *
673   */
674  
675   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 556 | Line 677 | template<typename T> void ZConstraint<T>::zeroOutVel()
677    Atom** fixedZAtoms;  
678    double COMvel[3];
679    double vel[3];
680 +  double zSysCOMVel;
681  
560 –  double tempMass = 0;
561 –  double tempMVz =0;
562 –  double tempVz = 0;
563 –  for(int i = 0; i < nMols; i++){
564 –    molecules[i].getCOMvel(COMvel);
565 –    tempMass +=molecules[i].getTotalMass();  
566 –         tempMVz += molecules[i].getTotalMass() * COMvel[whichDirection];
567 –         tempVz += COMvel[whichDirection];
568 –  }
569 –  cout << "initial velocity of center of mass is " << tempMVz / tempMass << endl;
570 –
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);      
689 <                cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
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  
699 <                zconsMols[i]->getCOMvel(COMvel);
700 <                cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
699 >    zconsMols[i]->getCOMvel(COMvel);
700 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
701      }
702 <        
702 >  
703    }
704  
705 <        cout << "before resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;    
706 <                  
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 611 | Line 731 | template<typename T> void ZConstraint<T>::zeroOutVel()
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 647 | Line 767 | template<typename T> void ZConstraint<T>::zeroOutVel()
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);
774 <          }
775 <          
773 >       movingZAtoms[j]->setVel(vel);
774 >    }
775 >    
776     }
777  
778   }
779  
660 –        cout << "after resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
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 670 | Line 802 | template<typename T> void ZConstraint<T>::doZconstrain
802    double COM[3];
803    double force[3];
804  
673 –  int nMovingZMols_local;
674 –  int nMovingZMols;
805  
806 <  //constrain the molecules which do not reach the specified positions  
806 >
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 691 | 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      }
834 <          
834 >    
835    }
836  
837 <  //calculate the number of atoms of moving z-constrained molecules
704 <  nMovingZMols_local = 0;
705 <  for(int i = 0; i < zconsMols.size(); i++)
706 <    if(states[i] == zcsMoving)
707 <           nMovingZMols_local += massOfZConsMols[i];
708 <  
837 >  //calculate total z-constraint force
838   #ifdef IS_MPI
839    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
711 –  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
840   #else
841    totalFZ = totalFZ_local;
714 –  nMovingZMols = nMovingZMols_local;
842   #endif
843  
844 <  force[0]= 0;
718 <  force[1]= 0;
719 <  force[2]= 0;
720 <  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
721 <
722 <  //modify the forces of unconstrained molecules
723 <  for(int i = 0; i < unconsMols.size(); i++){
724 <    
725 <     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
726 <    
727 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
728 <       unconsAtoms[j]->addFrc(force);
729 <    
730 <  }      
731 <
732 < //modify the forces of moving z-constrained molecules
733 <  for(int i = 0; i < zconsMols.size(); i++) {
734 <   if (states[i] == zcsMoving){
735 <                
736 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
737 <
738 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
739 <       movingZAtoms[j]->addFrc(force);
740 <     }
741 <  }
742 <
844 >  
845    // apply negative to fixed z-constrained molecues;
846    force[0]= 0;
847    force[1]= 0;
# Line 748 | Line 850 | template<typename T> void ZConstraint<T>::doZconstrain
850    for(int i = 0; i < zconsMols.size(); i++){
851  
852      if (states[i] == zcsFixed){  
853 <        
853 >  
854        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
855        zconsAtoms = zconsMols[i]->getMyAtoms();  
856      
857        for(int j =0; j < nAtomOfCurZConsMol; j++) {
858 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
858 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
859 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
860          zconsAtoms[j]->addFrc(force);
861        }
862 <                
862 >    
863      }
864 <        
864 >  
865    }
866  
867 < }
867 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
868 > //        << "total force is " << calcTotalForce() << endl;
869  
870 < template<typename T> bool ZConstraint<T>::checkZConsState(){
871 <  double COM[3];
872 <  double diff;
870 >  //calculate the number of atoms of moving z-constrained molecules
871 >  int nMovingZAtoms_local;
872 >  int nMovingZAtoms;
873    
874 <  bool changed;
874 >  nMovingZAtoms_local = 0;
875 >  for(int i = 0; i < zconsMols.size(); i++)
876 >    if(states[i] == zcsMoving)
877 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
878    
879 <  changed = false;
880 <  
881 <  for(int i =0; i < zconsMols.size(); i++){
879 > #ifdef IS_MPI
880 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
881 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
882 > #else
883 >  nMovingZAtoms = nMovingZAtoms_local;
884 > #endif
885  
886 <    zconsMols[i]->getCOM(COM);
887 <    diff = fabs(COM[whichDirection] - zPos[i]);  
888 <    if (  diff <= zconsTol && states[i] == zcsMoving){
779 <      states[i] = zcsFixed;
780 <        changed = true;
781 <    }
782 <    else if ( diff > zconsTol && states[i] == zcsFixed){
783 <      states[i] = zcsMoving;
784 <        changed = true;  
785 <    }
786 <  
787 <  }
886 >  force[0]= 0;
887 >  force[1]= 0;
888 >  force[2]= 0;
889  
890 <  return changed;
891 < }
890 >  //modify the forces of unconstrained molecules
891 >  for(int i = 0; i < unconsMols.size(); i++){
892 >    
893 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
894 >    
895 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
896 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
897 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
898 >       unconsAtoms[j]->addFrc(force);
899 >     }
900 >    
901 >  }      
902  
903 < template<typename T> bool ZConstraint<T>::haveFixedZMols(){
904 <  for(int i = 0; i < zconsMols.size(); i++)
905 <    if (states[i] == zcsFixed)
906 <      return true;
903 > //modify the forces of moving z-constrained molecules
904 >  for(int i = 0; i < zconsMols.size(); i++) {
905 >    if (states[i] == zcsMoving){
906 >    
907 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
908  
909 <  return false;
910 < }
909 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
910 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
911 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
912 >        movingZAtoms[j]->addFrc(force);
913 >      }
914 >    }
915 >  }
916  
917 +  //cout << "after substracting z-constraint force from moving molecuels "
918 +  //      << "total force is " << calcTotalForce()  << endl;
919  
801 – /**
802 – *
803 – */
804 – template<typename T> bool ZConstraint<T>::haveMovingZMols(){
805 –  for(int i = 0; i < zconsMols.size(); i++)
806 –    if (states[i] == zcsMoving)
807 –      return true;
808 –
809 –  return false;
810 –  
920   }
921  
922   /**
# Line 821 | Line 930 | template<typename T> void ZConstraint<T>::doHarmonic()
930    double harmonicF;
931    double COM[3];
932    double diff;
933 +  double totalFZ_local;
934    double totalFZ;
935 <        
935 >  
936    force[0] = 0;
937    force[1] = 0;
938    force[2] = 0;
939  
940 <  totalFZ = 0;
940 >  totalFZ_local = 0;
941  
832 –  cout << "Moving Molecules" << endl;  
942    for(int i = 0; i < zconsMols.size(); i++) {
943  
944      if (states[i] == zcsMoving){
945        zconsMols[i]->getCOM(COM);
946 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
947 <                
948 <                diff = COM[whichDirection] -zPos[i];
949 <                
946 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
947 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
948 >
949 >      diff = COM[whichDirection] -zPos[i];
950 >    
951        harmonicU = 0.5 * kz[i] * diff * diff;  
952 <                info->lrPot += harmonicU;
952 >      info->lrPot += harmonicU;
953  
954 <      harmonicF =  - kz[i] * diff / zconsMols[i]->getNAtoms();
955 <                force[whichDirection] = harmonicF;
956 <      totalFZ += harmonicF;
957 <                
954 >      harmonicF =  - kz[i] * diff;
955 >      totalFZ_local += harmonicF;
956 >
957 >       //adjust force
958 >    
959        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
960  
961 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
961 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
962 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
963 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
964           movingZAtoms[j]->addFrc(force);
965 +       }
966      }
967  
968    }
969  
970 + #ifndef IS_MPI
971 +  totalFZ = totalFZ_local;
972 + #else
973 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
974 + #endif
975 +
976    force[0]= 0;
977    force[1]= 0;
978    force[2]= 0;
859 –  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
979  
980    //modify the forces of unconstrained molecules
981    for(int i = 0; i < unconsMols.size(); i++){
982      
983       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
984      
985 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
985 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
986 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
987 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
988         unconsAtoms[j]->addFrc(force);    
989 +     }
990    }  
991  
992   }
993  
994 < template<typename T> double ZConstraint<T>::calcCOMVel()
994 > /**
995 > *
996 > */
997 >
998 > template<typename T> bool ZConstraint<T>::checkZConsState(){
999 >  double COM[3];
1000 >  double diff;
1001 >  
1002 >  int changed_local;
1003 >  int changed;
1004 >  
1005 >  changed_local = 0;
1006 >  
1007 >  for(int i =0; i < zconsMols.size(); i++){
1008 >
1009 >    zconsMols[i]->getCOM(COM);
1010 >    diff = fabs(COM[whichDirection] - zPos[i]);  
1011 >    if (  diff <= zconsTol && states[i] == zcsMoving){
1012 >      states[i] = zcsFixed;
1013 >     changed_local = 1;
1014 >    }
1015 >    else if ( diff > zconsTol && states[i] == zcsFixed){
1016 >      states[i] = zcsMoving;
1017 >     changed_local = 1;  
1018 >    }
1019 >  
1020 >  }
1021 >
1022 > #ifndef IS_MPI
1023 >  changed =changed_local;
1024 > #else
1025 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1026 > #endif
1027 >
1028 >  return (changed > 0);
1029 >
1030 > }
1031 >
1032 > template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1033 >
1034 >  int havingFixed_local;
1035 >  int havingFixed;
1036 >
1037 >  havingFixed_local = 0;
1038 >
1039 >  for(int i = 0; i < zconsMols.size(); i++)
1040 >    if (states[i] == zcsFixed){
1041 >      havingFixed_local = 1;
1042 >    break;
1043 >    }
1044 >
1045 > #ifndef IS_MPI
1046 >  havingFixed = havingFixed_local;
1047 > #else
1048 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1049 > #endif
1050 >
1051 >  return (havingFixed > 0);
1052 > }
1053 >
1054 >
1055 > /**
1056 > *
1057 > */
1058 > template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1059 >
1060 >  int havingMoving_local;
1061 >  int havingMoving;
1062 >
1063 >  havingMoving_local = 0;
1064 >
1065 >  for(int i = 0; i < zconsMols.size(); i++)
1066 >    if (states[i] == zcsMoving){
1067 >      havingMoving_local = 1;
1068 >    break;
1069 >    }
1070 >
1071 > #ifndef IS_MPI
1072 >  havingMoving = havingMoving_local;
1073 > #else
1074 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1075 > #endif
1076 >
1077 >  return (havingMoving > 0);
1078 >  
1079 > }
1080 >
1081 > /**
1082 > *
1083 > */
1084 >
1085 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1086   {
1087    double MVzOfMovingMols_local;
1088    double MVzOfMovingMols;
# Line 890 | Line 1103 | template<typename T> double ZConstraint<T>::calcCOMVel
1103      if (states[i] == zcsMoving){
1104        zconsMols[i]->getCOMvel(COMvel);
1105        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1106 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1106 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1107      }
1108 <                
1108 >    
1109    }
1110  
1111   #ifndef IS_MPI
# Line 909 | Line 1122 | template<typename T> double ZConstraint<T>::calcCOMVel
1122    return vzOfMovingMols;
1123   }
1124  
1125 + /**
1126 + *
1127 + */
1128  
1129 < template<typename T> double ZConstraint<T>::calcCOMVel2()
1129 > template<typename T> double ZConstraint<T>::calcSysCOMVel()
1130   {
1131    double COMvel[3];
1132 <  double tempMVz = 0;
1133 <  int index;
1134 <                
1132 >  double tempMVz_local;
1133 >  double tempMVz;
1134 >  double massOfZCons_local;
1135 >  double massOfZCons;
1136 >
1137 >
1138 > tempMVz_local = 0;
1139 >
1140    for(int i =0 ; i < nMols; i++){
1141 <         index = isZConstraintMol(&molecules[i]);
1142 <    if( index == -1){
922 <       molecules[i].getCOMvel(COMvel);
923 <            tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
924 <    }
925 <         else if(states[i] == zcsMoving){
926 <       zconsMols[index]->getCOMvel(COMvel);
927 <            tempMVz += massOfZConsMols[index]*COMvel[whichDirection];    
928 <         }
1141 >    molecules[i].getCOMvel(COMvel);
1142 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1143    }
1144 <        
1145 <  return tempMVz /totalMassOfUncons;
1144 >
1145 >  massOfZCons_local = 0;
1146 >  
1147 >  for(int i = 0; i < massOfZConsMols.size(); i++){
1148 >    massOfZCons_local += massOfZConsMols[i];
1149 >  }
1150 > #ifndef IS_MPI
1151 >  massOfZCons = massOfZCons_local;
1152 >  tempMVz = tempMVz_local;
1153 > #else
1154 >  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1155 >  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1156 > #endif
1157 >
1158 >  return tempMVz /(totalMassOfUncons + massOfZCons);
1159   }
1160 +
1161 + /**
1162 + *
1163 + */
1164 +
1165 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1166 +
1167 +  double force[3];  
1168 +  double totalForce_local;
1169 +  double totalForce;
1170 +
1171 +  totalForce_local = 0;
1172 +
1173 +  for(int i = 0; i < nAtoms; i++){
1174 +    atoms[i]->getFrc(force);
1175 +    totalForce_local += force[whichDirection];
1176 +  }
1177 +
1178 + #ifndef IS_MPI
1179 +  totalForce = totalForce_local;
1180 + #else
1181 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1182 + #endif
1183 +
1184 +  return totalForce;
1185 +
1186 + }
1187 +
1188 + /**
1189 + *
1190 + */
1191 +
1192 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1193 +  //calculate the number of atoms of moving z-constrained molecules
1194 +  int nMovingZAtoms_local;
1195 +  int nMovingZAtoms;
1196 +  
1197 +  nMovingZAtoms_local = 0;
1198 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1199 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1200 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1201 +  
1202 + #ifdef IS_MPI
1203 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1204 + #else
1205 +  nMovingZAtoms = nMovingZAtoms_local;
1206 + #endif
1207 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1208 +
1209 + #ifdef IS_MPI
1210 +  if(worldRank == 0){
1211 + #endif
1212 + //    std::cerr << "\n"
1213 + //            << "*******************************************\n"
1214 + //            << " fiished Policy by numbr()\n"
1215 + //            << "*******************************************\n"
1216 + //            << "\n";
1217 + #ifdef IS_MPI
1218 +  }
1219 + #endif
1220 + }
1221 +
1222 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1223 +  return totalForce / mol->getNAtoms();
1224 + }
1225 +
1226 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1227 +  return totalForce / totNumOfMovingAtoms;
1228 + }
1229 +
1230 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1231 +    return totalForce / mol->getNAtoms();
1232 + }
1233 +
1234 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1235 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1236 + }
1237 +
1238 + /**
1239 + *
1240 + */
1241 +
1242 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1243 +  //calculate the number of atoms of moving z-constrained molecules
1244 +  double massOfMovingZAtoms_local;
1245 +  double massOfMovingZAtoms;
1246 +  
1247 +  massOfMovingZAtoms_local = 0;
1248 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1249 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1250 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1251 +  
1252 + #ifdef IS_MPI
1253 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1254 + #else
1255 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1256 + #endif
1257 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1258 + }
1259 +
1260 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1261 +  return totalForce * atom->getMass() / mol->getTotalMass();
1262 + }
1263 +
1264 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1265 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1266 + }
1267 +
1268 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1269 +  return totalForce * atom->getMass() / mol->getTotalMass();
1270 + }
1271 +
1272 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1273 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1274 + }
1275 +

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