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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 736 by tim, Thu Aug 28 21:09:47 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");
61 >                  "PolicyByMass is used\n");
62          painCave.isFatal = 0;
63          simError();      
64 <           }            
65 <         }
64 >        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
65 >      }  
66 >    }
67    }
67 –        
68    
69 <
69 >  
70    //retrieve sample time of z-contraint
71    data = info->getProperty(ZCONSTIME_ID);
72    
# Line 110 | Line 110 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
110    }
111    else{
112  
113 <     filename = dynamic_cast<StringData*>(data);
113 >    filename = dynamic_cast<StringData*>(data);
114      
115      if(!filename){
116  
# Line 124 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
124        this->zconsOutput = filename->getData();
125      }
126      
127 –
127    }
128  
129    //retrieve tolerance for z-constraint molecuels
# Line 154 | Line 153 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
153      }
154  
155    }
156 <        
156 >  
157    //retrieve index of z-constraint molecules
158    data = info->getProperty(ZCONSPARADATA_ID);
159    if(!data) {
# Line 195 | Line 194 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
194                 "ZConstraint error: index is out of range\n");
195          painCave.isFatal = 1;
196          simError();
197 <        }
197 >        }
198  
199        maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
200  
# Line 216 | Line 215 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
215        //its initial z coordinate  will be used as default
216        for(int i = 0; i < parameters->size(); i++){
217  
218 <              if(!(*parameters)[i].havingZPos){
220 <
218 >        if(!(*parameters)[i].havingZPos){
219   #ifndef IS_MPI
220 <            for(int j = 0; j < nMols; j++){
221 <              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 <                 molecules[j].getCOM(COM);
223 <                          break;
226 <              }
220 >          for(int j = 0; j < nMols; j++){
221 >            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 >              molecules[j].getCOM(COM);
223 >        break;
224              }
225 +          }
226   #else
227              //query which processor current zconstraint molecule belongs to
228 <           int *MolToProcMap;
229 <           int whichNode;
230 <                         double initZPos;
231 <           MolToProcMap = mpiSim->getMolToProcMap();
232 <           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233 <                          
234 <           //broadcast the zpos of current z-contraint molecule
235 <           //the node which contain this
228 >          int *MolToProcMap;
229 >          int whichNode;
230 >    double initZPos;
231 >          MolToProcMap = mpiSim->getMolToProcMap();
232 >          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233 >        
234 >          //broadcast the zpos of current z-contraint molecule
235 >          //the node which contain this
236            
237 <           if (worldRank == whichNode ){
238 <                                                
239 <             for(int j = 0; j < nMols; j++)
240 <               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 <                 molecules[j].getCOM(COM);
242 <                                         break;
243 <               }
244 <                                
245 <           }
237 >          if (worldRank == whichNode ){
238 >            
239 >            for(int j = 0; j < nMols; j++)
240 >              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 >                molecules[j].getCOM(COM);
242 >          break;
243 >              }
244 >        
245 >          }
246  
247 <            MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);                          
247 >          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
248   #endif
249              
250 <                 (*parameters)[i].zPos = COM[whichDirection];
250 >          (*parameters)[i].zPos = COM[whichDirection];
251  
252 <            sprintf( painCave.errMsg,
253 <                     "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
252 >          sprintf( painCave.errMsg,
253 >                     "ZConstraint warning: Does not specify zpos for z-constraint molecule "
254                       "initial z coornidate will be used \n");
255 <            painCave.isFatal = 0;
256 <            simError();  
257 <          
258 <              }
259 <            }
260 <                        
255 >           painCave.isFatal = 0;
256 >           simError();  
257 >    
258 >  }
259 >      }
260 >      
261      }//end if (!zConsParaData)
262    }//end  if (!data)
263              
# Line 279 | Line 277 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
277        massOfZConsMols.push_back(molecules[i].getTotalMass());  
278  
279        zPos.push_back((*parameters)[searchResult].zPos);
280 <                cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
281 <           kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
280 > //       cout << "index: "<< (*parameters)[searchResult].zconsIndex
281 > //              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
282 >      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
283        
284        molecules[i].getCOM(COM);
285      }
# Line 308 | Line 307 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
307    for(int i = 0; i < zconsMols.size(); i++){
308      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309  
310 <         zconsMols[i]->getCOM(COM);
310 >    zconsMols[i]->getCOM(COM);
311      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
312 <                states.push_back(zcsFixed);
313 <         else
314 <                states.push_back(zcsMoving);
312 >      states.push_back(zcsFixed);
313 >    else
314 >      states.push_back(zcsMoving);
315    }
316    
317   #endif
# Line 327 | Line 326 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
326   #ifndef IS_MPI
327    totalMassOfUncons = totalMassOfUncons_local;
328   #else
329 <  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
329 >  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
330 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331   #endif
332  
333  
# Line 340 | Line 340 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
340   #ifndef IS_MPI
341    totNumOfUnconsAtoms = nUnconsAtoms_local;
342   #else
343 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
343 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
344 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
345   #endif  
346  
347    // creat zconsWriter  
# Line 369 | Line 370 | template<typename T> ZConstraint<T>::~ZConstraint()
370    
371    if(fzOut)
372      delete fzOut;
373 <        
373 >  
374    if(forcePolicy)
375      delete forcePolicy;
376   }
377  
378 +
379 + /**
380 + *
381 + */
382 +
383   #ifdef IS_MPI
384   template<typename T> void ZConstraint<T>::update()
385   {
# Line 398 | Line 404 | template<typename T> void ZConstraint<T>::update()
404      
405        zconsMols.push_back(&molecules[i]);      
406        zPos.push_back((*parameters)[index].zPos);
407 <        kz.push_back((*parameters)[index].kRatio * zForceConst);
408 <                        
407 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
408 >      
409        massOfZConsMols.push_back(molecules[i].getTotalMass());  
410        
411        molecules[i].getCOM(COM);
# Line 415 | Line 421 | template<typename T> void ZConstraint<T>::update()
421  
422    //determine the states of z-constraint molecules
423    for(int i = 0; i < zconsMols.size(); i++){
424 <           zconsMols[i]->getCOM(COM);
424 >     zconsMols[i]->getCOM(COM);
425        if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
426 <                  states.push_back(zcsFixed);
427 <           else
428 <                  states.push_back(zcsMoving);
426 >      states.push_back(zcsFixed);
427 >     else
428 >      states.push_back(zcsMoving);
429    }
430  
431      
# Line 427 | Line 433 | template<typename T> void ZConstraint<T>::update()
433    // that we want to make the MPI communication simple
434    if(fz)
435      delete[] fz;
436 <        
436 >  
437    if(curZPos)
438      delete[] curZPos;
439      
# Line 436 | Line 442 | template<typename T> void ZConstraint<T>::update()
442      
443    if (zconsMols.size() > 0){
444      fz = new double[zconsMols.size()];
445 <         curZPos = new double[zconsMols.size()];
445 >   curZPos = new double[zconsMols.size()];
446      indexOfZConsMols =  new int[zconsMols.size()];
447      
448      if(!fz || !curZPos || !indexOfZConsMols){
# Line 453 | Line 459 | template<typename T> void ZConstraint<T>::update()
459    }
460    else{
461      fz = NULL;
462 <         curZPos = NULL;
462 >   curZPos = NULL;
463      indexOfZConsMols = NULL;
464    }
465 <        
465 >  
466    //
467    forcePolicy->update();
468    
# Line 464 | Line 470 | template<typename T> void ZConstraint<T>::update()
470  
471   #endif
472  
473 < /**  Function Name: isZConstraintMol
474 < **  Parameter
475 < **    Molecule* mol
476 < **  Return value:
477 < **    -1, if the molecule is not z-constraint molecule,
478 < **    other non-negative values, its index in indexOfAllZConsMols vector
473 > /**
474 > *  Function Name: isZConstraintMol
475 > *  Parameter
476 > *    Molecule* mol
477 > *  Return value:
478 > *    -1, if the molecule is not z-constraint molecule,
479 > *    other non-negative values, its index in indexOfAllZConsMols vector
480   */
481  
482   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 503 | Line 510 | template<typename T> void ZConstraint<T>::integrate(){
510    //zero out the velocities of center of mass of unconstrained molecules
511    //and the velocities of center of mass of every single z-constrained molecueles
512    zeroOutVel();
513 +
514 +  curZconsTime = zconsTime + info->getTime();
515    
516    T::integrate();
517  
# Line 519 | Line 528 | template<typename T> void ZConstraint<T>::calcForce(in
528    double zsys;
529    double COM[3];
530    double force[3];
531 +  double zSysCOMVel;
532  
533    T::calcForce(calcPot, calcStress);
534  
535    if (checkZConsState()){
536 +    
537 + #ifdef IS_MPI
538 +    if(worldRank == 0){
539 + #endif
540 + //       std::cerr << "\n"
541 + //              << "*******************************************\n"
542 + //              << " about to call zeroOutVel()\n"
543 + //              << "*******************************************\n"
544 + //              << "\n";
545 + #ifdef IS_MPI
546 +    }
547 + #endif
548      zeroOutVel();
549 <         forcePolicy->update();
549 >
550 > #ifdef IS_MPI
551 >    if(worldRank == 0){
552 > #endif
553 > //       std::cerr << "\n"
554 > //              << "*******************************************\n"
555 > //              << " finished zeroOutVel()\n"
556 > //              << "*******************************************\n"
557 > //              << "\n";
558 > #ifdef IS_MPI
559 >    }
560 > #endif
561 >    
562 >    forcePolicy->update();
563    }  
564 +  
565    zsys = calcZSys();
566 <  cout << "---------------------------------------------------------------------" <<endl;
567 <  cout << "current time: " << info->getTime() << endl;
568 <  cout << "center of mass at z: " << zsys << endl;      
569 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
570 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
566 >  zSysCOMVel = calcSysCOMVel();
567 > #ifdef IS_MPI
568 >  if(worldRank == 0){
569 > #endif
570 > //     cout << "---------------------------------------------------------------------" <<endl;
571 > //     cout << "current time: " << info->getTime() << endl;
572 > //     cout << "center of mass at z: " << zsys << endl;    
573 > //     cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
574  
575 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
575 > #ifdef IS_MPI
576 >  }
577 > #endif
578  
579    //do zconstraint force;
580    if (haveFixedZMols())
581      this->doZconstraintForce();
582 <    
582 >
583    //use harmonical poteintial to move the molecules to the specified positions
584    if (haveMovingZMols())
585      this->doHarmonic();
586  
546 –  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 –
587    //write out forces and current positions of z-constraint molecules
588 <  if(info->getTime() >= curZconsTime){          
589 <         for(int i = 0; i < zconsMols.size(); i++){
588 >  if(info->getTime() >= curZconsTime){    
589 >   for(int i = 0; i < zconsMols.size(); i++){
590        zconsMols[i]->getCOM(COM);
591 <                curZPos[i] = COM[whichDirection];
591 >    curZPos[i] = COM[whichDirection];
592  
593 <                //if the z-constraint molecule is still moving, just record its force
594 <                if(states[i] == zcsMoving){
593 >    //if the z-constraint molecule is still moving, just record its force
594 >    if(states[i] == zcsMoving){
595           fz[i] = 0;
596 <                  Atom** movingZAtoms;
597 <                  movingZAtoms = zconsMols[i]->getMyAtoms();
598 <                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
596 >      Atom** movingZAtoms;
597 >      movingZAtoms = zconsMols[i]->getMyAtoms();
598 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
599             movingZAtoms[j]->getFrc(force);
600             fz[i] += force[whichDirection];
601 <                  }
602 <           }
603 <         }
604 <    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
605 <         curZconsTime += zconsTime;
601 >      }
602 >     }
603 >   }
604 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
605 >   curZconsTime += zconsTime;
606    }
607 <        
608 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
609 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
607 >
608 >  zSysCOMVel = calcSysCOMVel();  
609 > #ifdef IS_MPI
610 >  if(worldRank == 0){
611 > #endif
612 > //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
613 > #ifdef IS_MPI
614 >  }
615 > #endif
616   }
617 +
618 +
619 + /**
620 + *
621 + */
622  
623   template<typename T> double ZConstraint<T>::calcZSys()
624   {
# Line 579 | Line 629 | template<typename T> double ZConstraint<T>::calcZSys()
629    double totalMZ;
630    double massOfCurMol;
631    double COM[3];
632 <        
632 >  
633    totalMass_local = 0;
634    totalMZ_local = 0;
635    
# Line 594 | Line 644 | template<typename T> double ZConstraint<T>::calcZSys()
644  
645    
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);  
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;
# Line 618 | Line 670 | template<typename T> void ZConstraint<T>::thermalize(
670  
671   /**
672   *
621 – *
622 – *
673   */
674  
675   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 627 | Line 677 | template<typename T> void ZConstraint<T>::zeroOutVel()
677    Atom** fixedZAtoms;  
678    double COMvel[3];
679    double vel[3];
680 +  double zSysCOMVel;
681  
682    //zero out the velocities of center of mass of fixed z-constrained molecules
683    
684    for(int i = 0; i < zconsMols.size(); i++){
685  
686 <    if (states[i] == zcsFixed){
686 >    if (states[i] == zcsFixed){
687  
688 <           zconsMols[i]->getCOMvel(COMvel);      
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 moving molecules is " << calcMovingMolsCOMVel() <<endl;      
705 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
706  
707 +  zSysCOMVel = calcSysCOMVel();
708   #ifdef IS_MPI
709 <  if (worldRank == 0){
709 >  if(worldRank == 0){
710   #endif
711 <    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
711 > //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
712   #ifdef IS_MPI
713    }
714   #endif
715 <                  
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 679 | 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 715 | 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  
780 +
781 +  zSysCOMVel = calcSysCOMVel();
782   #ifdef IS_MPI
783 <  if (worldRank == 0){
783 >  if(worldRank == 0){
784   #endif
785 <        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
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 744 | Line 802 | template<typename T> void ZConstraint<T>::doZconstrain
802    double COM[3];
803    double force[3];
804  
805 <
748 <
749 <  //constrain the molecules which do not reach the specified positions  
805 >  //constrain the molecules which do not reach the specified positions  
806      
807    //Zero Out the force of z-contrained molecules    
808    totalFZ_local = 0;
809  
810    //calculate the total z-contrained force of fixed z-contrained molecules
811  
756 – #ifdef IS_MPI
757 –  if (worldRank == 0){
758 – #endif
759 –    cout << "Fixed Molecules" << endl;
760 – #ifdef IS_MPI
761 –  }
762 – #endif
763 –
812    for(int i = 0; i < zconsMols.size(); i++){
813 <                
813 >    
814      if (states[i] == zcsFixed){
815 <                
815 >      
816        zconsMols[i]->getCOM(COM);
817        zconsAtoms = zconsMols[i]->getMyAtoms();  
818  
# Line 772 | Line 820 | template<typename T> void ZConstraint<T>::doZconstrain
820        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
821          zconsAtoms[j]->getFrc(force);
822          fz[i] += force[whichDirection];      
823 <      }
823 >      }
824        totalFZ_local += fz[i];
825  
826 <      cout << "index: " << indexOfZConsMols[i]
827 <                                <<"\tcurrent zpos: " << COM[whichDirection]
828 <                                << "\tcurrent fz: " <<fz[i] << endl;
826 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
827 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
828 >      //       << "\tcurrent fz: " <<fz[i] << endl;
829  
830 +
831      }
832 <          
832 >    
833    }
834  
835    //calculate total z-constraint force
# Line 790 | Line 839 | template<typename T> void ZConstraint<T>::doZconstrain
839    totalFZ = totalFZ_local;
840   #endif
841  
842 <        
842 >  
843    // apply negative to fixed z-constrained molecues;
844    force[0]= 0;
845    force[1]= 0;
# Line 799 | Line 848 | template<typename T> void ZConstraint<T>::doZconstrain
848    for(int i = 0; i < zconsMols.size(); i++){
849  
850      if (states[i] == zcsFixed){  
851 <        
851 >  
852        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
853        zconsAtoms = zconsMols[i]->getMyAtoms();  
854      
855        for(int j =0; j < nAtomOfCurZConsMol; j++) {
856 <                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
857 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
856 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
857 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
858          zconsAtoms[j]->addFrc(force);
859        }
860 <                
860 >    
861      }
862 <        
862 >  
863    }
864  
865 <  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
866 <  //               << "total force is " << calcTotalForce() << endl;
865 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
866 > //        << "total force is " << calcTotalForce() << endl;
867  
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 –
868    force[0]= 0;
869    force[1]= 0;
870    force[2]= 0;
# Line 841 | Line 875 | template<typename T> void ZConstraint<T>::doZconstrain
875       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
876      
877       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
878 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
879 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
878 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
879 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
880         unconsAtoms[j]->addFrc(force);
881       }
882      
# Line 851 | Line 885 | template<typename T> void ZConstraint<T>::doZconstrain
885   //modify the forces of moving z-constrained molecules
886    for(int i = 0; i < zconsMols.size(); i++) {
887      if (states[i] == zcsMoving){
888 <                
888 >    
889        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
890  
891        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
892 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
893 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
892 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
893 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
894          movingZAtoms[j]->addFrc(force);
895        }
896      }
897    }
898  
899    //cout << "after substracting z-constraint force from moving molecuels "
900 <  //              << "total force is " << calcTotalForce()  << endl;
900 >  //      << "total force is " << calcTotalForce()  << endl;
901 >
902 > }
903 >
904 > /**
905 >  *
906 >  *
907 >  */
908 >
909 > template<typename T> void ZConstraint<T>::doHarmonic(){
910 >  double force[3];
911 >  double harmonicU;
912 >  double harmonicF;
913 >  double COM[3];
914 >  double diff;
915 >  double totalFZ_local;
916 >  double totalFZ;
917 >  
918 >  force[0] = 0;
919 >  force[1] = 0;
920 >  force[2] = 0;
921 >
922 >  totalFZ_local = 0;
923 >
924 >  for(int i = 0; i < zconsMols.size(); i++) {
925 >
926 >    if (states[i] == zcsMoving){
927 >      zconsMols[i]->getCOM(COM);
928 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
929 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
930 >
931 >      diff = COM[whichDirection] -zPos[i];
932 >    
933 >      harmonicU = 0.5 * kz[i] * diff * diff;  
934 >      info->lrPot += harmonicU;
935 >
936 >      harmonicF =  - kz[i] * diff;
937 >      totalFZ_local += harmonicF;
938 >
939 >       //adjust force
940 >    
941 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
942 >
943 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
944 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
945 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
946 >         movingZAtoms[j]->addFrc(force);
947 >       }
948 >    }
949 >
950 >  }
951 >
952 > #ifndef IS_MPI
953 >  totalFZ = totalFZ_local;
954 > #else
955 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
956 > #endif
957 >
958 >  force[0]= 0;
959 >  force[1]= 0;
960 >  force[2]= 0;
961 >
962 >  //modify the forces of unconstrained molecules
963 >  for(int i = 0; i < unconsMols.size(); i++){
964 >    
965 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
966 >    
967 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
968 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
969 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
970 >       unconsAtoms[j]->addFrc(force);    
971 >     }
972 >  }  
973  
974   }
975  
976 + /**
977 + *
978 + */
979 +
980   template<typename T> bool ZConstraint<T>::checkZConsState(){
981    double COM[3];
982    double diff;
983    
984    int changed_local;
985    int changed;
986 <        
986 >  
987    changed_local = 0;
988    
989    for(int i =0; i < zconsMols.size(); i++){
# Line 882 | Line 992 | template<typename T> bool ZConstraint<T>::checkZConsSt
992      diff = fabs(COM[whichDirection] - zPos[i]);  
993      if (  diff <= zconsTol && states[i] == zcsMoving){
994        states[i] = zcsFixed;
995 <           changed_local = 1;
995 >     changed_local = 1;
996      }
997      else if ( diff > zconsTol && states[i] == zcsFixed){
998        states[i] = zcsMoving;
999 <           changed_local = 1;    
999 >     changed_local = 1;  
1000      }
1001    
1002    }
# Line 897 | Line 1007 | template<typename T> bool ZConstraint<T>::checkZConsSt
1007    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1008   #endif
1009  
1010 <  return changed > 0 ? true : false;
1010 >  return (changed > 0);
1011 >
1012   }
1013  
1014   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 910 | Line 1021 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1021    for(int i = 0; i < zconsMols.size(); i++)
1022      if (states[i] == zcsFixed){
1023        havingFixed_local = 1;
1024 <                break;
1024 >    break;
1025      }
1026  
1027   #ifndef IS_MPI
# Line 919 | Line 1030 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1030    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1031   #endif
1032  
1033 <  return havingFixed > 0 ? true : false;
1033 >  return (havingFixed > 0);
1034   }
1035  
1036  
# Line 936 | Line 1047 | template<typename T> bool ZConstraint<T>::haveMovingZM
1047    for(int i = 0; i < zconsMols.size(); i++)
1048      if (states[i] == zcsMoving){
1049        havingMoving_local = 1;
1050 <                break;
1050 >    break;
1051      }
1052  
1053   #ifndef IS_MPI
# Line 945 | Line 1056 | template<typename T> bool ZConstraint<T>::haveMovingZM
1056    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1057   #endif
1058  
1059 <  return havingMoving > 0 ? true : false;
1059 >  return (havingMoving > 0);
1060    
1061   }
1062  
1063   /**
1064 <  *
1065 <  *
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 <    }
1064 > *
1065 > */
1066  
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 –
1067   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1068   {
1069    double MVzOfMovingMols_local;
# Line 1050 | Line 1085 | template<typename T> double ZConstraint<T>::calcMoving
1085      if (states[i] == zcsMoving){
1086        zconsMols[i]->getCOMvel(COMvel);
1087        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1088 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1088 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1089      }
1090 <                
1090 >    
1091    }
1092  
1093   #ifndef IS_MPI
# Line 1069 | Line 1104 | template<typename T> double ZConstraint<T>::calcMoving
1104    return vzOfMovingMols;
1105   }
1106  
1107 + /**
1108 + *
1109 + */
1110  
1111   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1112   {
# Line 1083 | Line 1121 | template<typename T> double ZConstraint<T>::calcSysCOM
1121  
1122    for(int i =0 ; i < nMols; i++){
1123      molecules[i].getCOMvel(COMvel);
1124 <         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1124 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1125    }
1126  
1127    massOfZCons_local = 0;
1128 <        
1128 >  
1129    for(int i = 0; i < massOfZConsMols.size(); i++){
1130      massOfZCons_local += massOfZConsMols[i];
1131    }
# Line 1102 | Line 1140 | template<typename T> double ZConstraint<T>::calcTotalF
1140    return tempMVz /(totalMassOfUncons + massOfZCons);
1141   }
1142  
1143 + /**
1144 + *
1145 + */
1146 +
1147   template<typename T> double ZConstraint<T>::calcTotalForce(){
1148  
1149    double force[3];  
# Line 1133 | Line 1175 | template<typename T> void ZConstraint<T>::PolicyByNumb
1175    //calculate the number of atoms of moving z-constrained molecules
1176    int nMovingZAtoms_local;
1177    int nMovingZAtoms;
1178 <        
1178 >  
1179    nMovingZAtoms_local = 0;
1180    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1181      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1182 <           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1182 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1183    
1184   #ifdef IS_MPI
1185    MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 1145 | Line 1187 | template<typename T> void ZConstraint<T>::PolicyByNumb
1187    nMovingZAtoms = nMovingZAtoms_local;
1188   #endif
1189    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1190 +
1191 + #ifdef IS_MPI
1192 +  if(worldRank == 0){
1193 + #endif
1194 + //    std::cerr << "\n"
1195 + //            << "*******************************************\n"
1196 + //            << " fiished Policy by numbr()\n"
1197 + //            << "*******************************************\n"
1198 + //            << "\n";
1199 + #ifdef IS_MPI
1200 +  }
1201 + #endif
1202   }
1203  
1204 < template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1204 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1205    return totalForce / mol->getNAtoms();
1206   }
1207  
# Line 1171 | Line 1225 | template<typename T> void ZConstraint<T>::PolicyByMass
1225    //calculate the number of atoms of moving z-constrained molecules
1226    double massOfMovingZAtoms_local;
1227    double massOfMovingZAtoms;
1228 <        
1228 >  
1229    massOfMovingZAtoms_local = 0;
1230    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1231      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1232 <           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1232 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1233    
1234   #ifdef IS_MPI
1235    MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);

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