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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC

# Line 3 | Line 3 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
3   #include <cmath>
4   template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5                                      : T(theInfo, the_ff), fz(NULL), curZPos(NULL),
6 <                                                         indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
6 >                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
9    //get properties from SimInfo
# Line 32 | Line 32 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
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");
35 >               "PolicyByMass is used\n");
36      painCave.isFatal = 0;
37      simError();      
38  
39 <    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
39 >    forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
40    }
41    else{
42      policy = dynamic_cast<StringData*>(data);
43 <                
44 <         if(!policy){
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");
47 >                 "PolicyByMass 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{
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 <         }
64 >      }  
65 >    }
66    }
67 –        
67    
68 <
68 >  
69    //retrieve sample time of z-contraint
70    data = info->getProperty(ZCONSTIME_ID);
71    
# Line 110 | 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 124 | Line 123 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
123        this->zconsOutput = filename->getData();
124      }
125      
127 –
126    }
127  
128    //retrieve tolerance for z-constraint molecuels
# Line 154 | 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 195 | 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 216 | 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){
220 <
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;
226 <              }
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 279 | 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 <                cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
280 <           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 308 | 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 327 | 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 340 | 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_INT,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  
# Line 369 | Line 369 | template<typename T> ZConstraint<T>::~ZConstraint()
369    
370    if(fzOut)
371      delete fzOut;
372 <        
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 398 | 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 415 | 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 427 | 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 <        
435 >  
436    if(curZPos)
437      delete[] curZPos;
438      
# Line 436 | Line 441 | template<typename T> void ZConstraint<T>::update()
441      
442    if (zconsMols.size() > 0){
443      fz = new double[zconsMols.size()];
444 <         curZPos = new double[zconsMols.size()];
444 >   curZPos = new double[zconsMols.size()];
445      indexOfZConsMols =  new int[zconsMols.size()];
446      
447      if(!fz || !curZPos || !indexOfZConsMols){
# Line 453 | Line 458 | template<typename T> void ZConstraint<T>::update()
458    }
459    else{
460      fz = NULL;
461 <         curZPos = NULL;
461 >   curZPos = NULL;
462      indexOfZConsMols = NULL;
463    }
464 <        
464 >  
465    //
466    forcePolicy->update();
467    
# Line 464 | Line 469 | template<typename T> void ZConstraint<T>::update()
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 503 | 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 519 | Line 527 | template<typename T> void ZConstraint<T>::calcForce(in
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 +    
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 <         forcePolicy->update();
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  
546 –  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 –
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++){
587 >  if(info->getTime() >= curZconsTime){    
588 >   for(int i = 0; i < zconsMols.size(); i++){
589        zconsMols[i]->getCOM(COM);
590 <                curZPos[i] = COM[whichDirection];
590 >    curZPos[i] = COM[whichDirection];
591  
592 <                //if the z-constraint molecule is still moving, just record its force
593 <                if(states[i] == zcsMoving){
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++){
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 <         }
600 >      }
601 >     }
602 >   }
603      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
604 <         curZconsTime += zconsTime;
604 >   curZconsTime += zconsTime;
605    }
606 <        
607 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
608 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
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 579 | 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 594 | 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 618 | Line 669 | template<typename T> void ZConstraint<T>::thermalize(
669  
670   /**
671   *
621 – *
622 – *
672   */
673  
674   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 627 | 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;      
704 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
705  
706 +  zSysCOMVel = calcSysCOMVel();
707   #ifdef IS_MPI
708 <  if (worldRank == 0){
708 >  if(worldRank == 0){
709   #endif
710 <    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
710 > //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
711   #ifdef IS_MPI
712    }
713   #endif
714 <                  
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 679 | 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 715 | 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  
779 +
780 +  zSysCOMVel = calcSysCOMVel();
781   #ifdef IS_MPI
782 <  if (worldRank == 0){
782 >  if(worldRank == 0){
783   #endif
784 <        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
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 744 | Line 801 | template<typename T> void ZConstraint<T>::doZconstrain
801    double COM[3];
802    double force[3];
803  
804 <
748 <
749 <  //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  
756 – #ifdef IS_MPI
757 –  if (worldRank == 0){
758 – #endif
759 –    cout << "Fixed Molecules" << endl;
760 – #ifdef IS_MPI
761 –  }
762 – #endif
763 –
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 772 | 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  
834    //calculate total z-constraint force
# Line 790 | Line 838 | template<typename T> void ZConstraint<T>::doZconstrain
838    totalFZ = totalFZ_local;
839   #endif
840  
841 <        
841 >  
842    // apply negative to fixed z-constrained molecues;
843    force[0]= 0;
844    force[1]= 0;
# Line 799 | 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;
856 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
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;
864 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
865 > //        << "total force is " << calcTotalForce() << endl;
866  
819 –  //calculate the number of atoms of moving z-constrained molecules
820 –  int nMovingZAtoms_local;
821 –  int nMovingZAtoms;
822 –        
823 –  nMovingZAtoms_local = 0;
824 –  for(int i = 0; i < zconsMols.size(); i++)
825 –    if(states[i] == zcsMoving)
826 –           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
827 –  
828 – #ifdef IS_MPI
829 –  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
830 – #else
831 –  nMovingZAtoms = nMovingZAtoms_local;
832 – #endif
833 –
867    force[0]= 0;
868    force[1]= 0;
869    force[2]= 0;
# Line 841 | Line 874 | template<typename T> void ZConstraint<T>::doZconstrain
874       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
875      
876       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
877 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
878 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
877 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
878 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
879         unconsAtoms[j]->addFrc(force);
880       }
881      
# Line 851 | Line 884 | template<typename T> void ZConstraint<T>::doZconstrain
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++){
891 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
892 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
891 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
892 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
893          movingZAtoms[j]->addFrc(force);
894        }
895      }
896    }
897  
898    //cout << "after substracting z-constraint force from moving molecuels "
899 <  //              << "total force is " << calcTotalForce()  << endl;
899 >  //      << "total force is " << calcTotalForce()  << endl;
900 >
901 > }
902 >
903 > /**
904 >  *
905 >  *
906 >  */
907 >
908 > template<typename T> void ZConstraint<T>::doHarmonic(){
909 >  double force[3];
910 >  double harmonicU;
911 >  double harmonicF;
912 >  double COM[3];
913 >  double diff;
914 >  double totalFZ_local;
915 >  double totalFZ;
916 >  
917 >  force[0] = 0;
918 >  force[1] = 0;
919 >  force[2] = 0;
920 >
921 >  totalFZ_local = 0;
922 >
923 >  for(int i = 0; i < zconsMols.size(); i++) {
924 >
925 >    if (states[i] == zcsMoving){
926 >      zconsMols[i]->getCOM(COM);
927 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
928 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
929 >
930 >      diff = COM[whichDirection] -zPos[i];
931 >    
932 >      harmonicU = 0.5 * kz[i] * diff * diff;  
933 >      info->lrPot += harmonicU;
934 >
935 >      harmonicF =  - kz[i] * diff;
936 >      totalFZ_local += harmonicF;
937 >
938 >       //adjust force
939 >    
940 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
941 >
942 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
943 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
944 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
945 >         movingZAtoms[j]->addFrc(force);
946 >       }
947 >    }
948 >
949 >  }
950 >
951 > #ifndef IS_MPI
952 >  totalFZ = totalFZ_local;
953 > #else
954 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
955 > #endif
956 >
957 >  force[0]= 0;
958 >  force[1]= 0;
959 >  force[2]= 0;
960 >
961 >  //modify the forces of unconstrained molecules
962 >  for(int i = 0; i < unconsMols.size(); i++){
963 >    
964 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
965 >    
966 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
967 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
968 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
969 >       unconsAtoms[j]->addFrc(force);    
970 >     }
971 >  }  
972  
973   }
974  
975 + /**
976 + *
977 + */
978 +
979   template<typename T> bool ZConstraint<T>::checkZConsState(){
980    double COM[3];
981    double diff;
982    
983    int changed_local;
984    int changed;
985 <        
985 >  
986    changed_local = 0;
987    
988    for(int i =0; i < zconsMols.size(); i++){
# Line 882 | Line 991 | template<typename T> bool ZConstraint<T>::checkZConsSt
991      diff = fabs(COM[whichDirection] - zPos[i]);  
992      if (  diff <= zconsTol && states[i] == zcsMoving){
993        states[i] = zcsFixed;
994 <           changed_local = 1;
994 >     changed_local = 1;
995      }
996      else if ( diff > zconsTol && states[i] == zcsFixed){
997        states[i] = zcsMoving;
998 <           changed_local = 1;    
998 >     changed_local = 1;  
999      }
1000    
1001    }
# Line 897 | Line 1006 | template<typename T> bool ZConstraint<T>::checkZConsSt
1006    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1007   #endif
1008  
1009 <  return changed > 0 ? true : false;
1009 >  return (changed > 0);
1010 >
1011   }
1012  
1013   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 910 | Line 1020 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1020    for(int i = 0; i < zconsMols.size(); i++)
1021      if (states[i] == zcsFixed){
1022        havingFixed_local = 1;
1023 <                break;
1023 >    break;
1024      }
1025  
1026   #ifndef IS_MPI
# Line 919 | Line 1029 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1029    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1030   #endif
1031  
1032 <  return havingFixed > 0 ? true : false;
1032 >  return (havingFixed > 0);
1033   }
1034  
1035  
# Line 936 | Line 1046 | template<typename T> bool ZConstraint<T>::haveMovingZM
1046    for(int i = 0; i < zconsMols.size(); i++)
1047      if (states[i] == zcsMoving){
1048        havingMoving_local = 1;
1049 <                break;
1049 >    break;
1050      }
1051  
1052   #ifndef IS_MPI
# Line 945 | Line 1055 | template<typename T> bool ZConstraint<T>::haveMovingZM
1055    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1056   #endif
1057  
1058 <  return havingMoving > 0 ? true : false;
1058 >  return (havingMoving > 0);
1059    
1060   }
1061  
1062   /**
1063 <  *
1064 <  *
955 <  */
956 <
957 < template<typename T> void ZConstraint<T>::doHarmonic(){
958 <  double force[3];
959 <  double harmonicU;
960 <  double harmonicF;
961 <  double COM[3];
962 <  double diff;
963 <  double totalFZ_local;
964 <  double totalFZ;
965 <        
966 <  force[0] = 0;
967 <  force[1] = 0;
968 <  force[2] = 0;
969 <
970 <  totalFZ_local = 0;
971 <
972 < #ifdef IS_MPI
973 <  if (worldRank == 0){
974 < #endif
975 <    cout << "Moving Molecules" << endl;
976 < #ifdef IS_MPI
977 <  }
978 < #endif
979 <
980 <
981 <  for(int i = 0; i < zconsMols.size(); i++) {
982 <
983 <    if (states[i] == zcsMoving){
984 <      zconsMols[i]->getCOM(COM);
985 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
986 <                
987 <                diff = COM[whichDirection] -zPos[i];
988 <                
989 <      harmonicU = 0.5 * kz[i] * diff * diff;  
990 <                info->lrPot += harmonicU;
991 <
992 <      harmonicF =  - kz[i] * diff;
993 <      totalFZ_local += harmonicF;
994 <
995 <       //adjust force
996 <                
997 <      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
998 <
999 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
1000 <                  force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
1001 <         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
1002 <         movingZAtoms[j]->addFrc(force);
1003 <       }
1004 <    }
1063 > *
1064 > */
1065  
1006 –  }
1007 –
1008 – #ifndef IS_MPI
1009 –  totalFZ = totalFZ_local;
1010 – #else
1011 –  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1012 – #endif
1013 –
1014 –  force[0]= 0;
1015 –  force[1]= 0;
1016 –  force[2]= 0;
1017 –
1018 –  //modify the forces of unconstrained molecules
1019 –  for(int i = 0; i < unconsMols.size(); i++){
1020 –    
1021 –     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
1022 –    
1023 –     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
1024 –       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
1025 –       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
1026 –       unconsAtoms[j]->addFrc(force);    
1027 –     }
1028 –  }  
1029 –
1030 – }
1031 –
1066   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1067   {
1068    double MVzOfMovingMols_local;
# Line 1050 | 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 1069 | 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   {
# Line 1083 | Line 1120 | template<typename T> double ZConstraint<T>::calcSysCOM
1120  
1121    for(int i =0 ; i < nMols; i++){
1122      molecules[i].getCOMvel(COMvel);
1123 <         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1123 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1124    }
1125  
1126    massOfZCons_local = 0;
1127 <        
1127 >  
1128    for(int i = 0; i < massOfZConsMols.size(); i++){
1129      massOfZCons_local += massOfZConsMols[i];
1130    }
# Line 1102 | Line 1139 | template<typename T> double ZConstraint<T>::calcTotalF
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 1133 | Line 1174 | template<typename T> void ZConstraint<T>::PolicyByNumb
1174    //calculate the number of atoms of moving z-constrained molecules
1175    int nMovingZAtoms_local;
1176    int nMovingZAtoms;
1177 <        
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();
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);
# Line 1145 | Line 1186 | template<typename T> void ZConstraint<T>::PolicyByNumb
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){
1203 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1204    return totalForce / mol->getNAtoms();
1205   }
1206  
# Line 1171 | Line 1224 | template<typename T> void ZConstraint<T>::PolicyByMass
1224    //calculate the number of atoms of moving z-constrained molecules
1225    double massOfMovingZAtoms_local;
1226    double massOfMovingZAtoms;
1227 <        
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();
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);

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