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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 702 by tim, Wed Aug 20 14:50:32 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 40 | Line 40 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
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");
# Line 49 | Line 49 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
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{
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 519 | Line 525 | template<typename T> void ZConstraint<T>::calcForce(in
525    double zsys;
526    double COM[3];
527    double force[3];
528 +  double zSysCOMVel;
529  
530    T::calcForce(calcPot, calcStress);
531  
532    if (checkZConsState()){
533      zeroOutVel();
534 <         forcePolicy->update();
534 >   forcePolicy->update();
535    }  
536 +
537    zsys = calcZSys();
538 <  cout << "---------------------------------------------------------------------" <<endl;
539 <  cout << "current time: " << info->getTime() << endl;
540 <  cout << "center of mass at z: " << zsys << endl;      
541 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
542 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
538 >  zSysCOMVel = calcSysCOMVel();
539 > #ifdef IS_MPI
540 >  if(worldRank == 0){
541 > #endif
542 >    cout << "---------------------------------------------------------------------" <<endl;
543 >    cout << "current time: " << info->getTime() << endl;
544 >    cout << "center of mass at z: " << zsys << endl;    
545 >    cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
546  
547 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
547 > #ifdef IS_MPI
548 >  }
549 > #endif
550  
551    //do zconstraint force;
552    if (haveFixedZMols())
# Line 543 | Line 556 | template<typename T> void ZConstraint<T>::calcForce(in
556    if (haveMovingZMols())
557      this->doHarmonic();
558  
546 –  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 –
559    //write out forces and current positions of z-constraint molecules
560 <  if(info->getTime() >= curZconsTime){          
561 <         for(int i = 0; i < zconsMols.size(); i++){
560 >  if(info->getTime() >= curZconsTime){    
561 >   for(int i = 0; i < zconsMols.size(); i++){
562        zconsMols[i]->getCOM(COM);
563 <                curZPos[i] = COM[whichDirection];
563 >    curZPos[i] = COM[whichDirection];
564  
565 <                //if the z-constraint molecule is still moving, just record its force
566 <                if(states[i] == zcsMoving){
565 >    //if the z-constraint molecule is still moving, just record its force
566 >    if(states[i] == zcsMoving){
567           fz[i] = 0;
568 <                  Atom** movingZAtoms;
569 <                  movingZAtoms = zconsMols[i]->getMyAtoms();
570 <                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
568 >      Atom** movingZAtoms;
569 >      movingZAtoms = zconsMols[i]->getMyAtoms();
570 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
571             movingZAtoms[j]->getFrc(force);
572             fz[i] += force[whichDirection];
573 <                  }
574 <           }
575 <         }
573 >      }
574 >     }
575 >   }
576      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
577 <         curZconsTime += zconsTime;
577 >   curZconsTime += zconsTime;
578    }
579 <        
580 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
581 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
579 >
580 >  zSysCOMVel = calcSysCOMVel();  
581 > #ifdef IS_MPI
582 >  if(worldRank == 0){
583 > #endif
584 >    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
585 > #ifdef IS_MPI
586 >  }
587 > #endif
588 >
589   }
590 +
591 +
592 + /**
593 + *
594 + */
595  
596   template<typename T> double ZConstraint<T>::calcZSys()
597   {
# Line 579 | Line 602 | template<typename T> double ZConstraint<T>::calcZSys()
602    double totalMZ;
603    double massOfCurMol;
604    double COM[3];
605 <        
605 >  
606    totalMass_local = 0;
607    totalMZ_local = 0;
608    
# Line 594 | Line 617 | template<typename T> double ZConstraint<T>::calcZSys()
617  
618    
619   #ifdef IS_MPI  
620 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
621 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
620 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
621 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
622 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
623 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
624   #else
625    totalMass = totalMass_local;
626    totalMZ = totalMZ_local;
# Line 618 | Line 643 | template<typename T> void ZConstraint<T>::thermalize(
643  
644   /**
645   *
621 – *
622 – *
646   */
647  
648   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 627 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel()
650    Atom** fixedZAtoms;  
651    double COMvel[3];
652    double vel[3];
653 +  double zSysCOMVel;
654  
655    //zero out the velocities of center of mass of fixed z-constrained molecules
656    
657    for(int i = 0; i < zconsMols.size(); i++){
658  
659 <    if (states[i] == zcsFixed){
659 >    if (states[i] == zcsFixed){
660  
661 <           zconsMols[i]->getCOMvel(COMvel);      
662 <                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
661 >     zconsMols[i]->getCOMvel(COMvel);      
662 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663  
664        fixedZAtoms = zconsMols[i]->getMyAtoms();
665 <          
665 >    
666        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
667          fixedZAtoms[j]->getVel(vel);
668 <             vel[whichDirection] -= COMvel[whichDirection];
669 <             fixedZAtoms[j]->setVel(vel);
668 >       vel[whichDirection] -= COMvel[whichDirection];
669 >       fixedZAtoms[j]->setVel(vel);
670        }
671  
672 <                zconsMols[i]->getCOMvel(COMvel);
673 <                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
672 >    zconsMols[i]->getCOMvel(COMvel);
673 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
674      }
675 <        
675 >  
676    }
677  
678 <        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
678 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
679  
680 +  zSysCOMVel = calcSysCOMVel();
681   #ifdef IS_MPI
682 <  if (worldRank == 0){
682 >  if(worldRank == 0){
683   #endif
684 <    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
684 >    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
685   #ifdef IS_MPI
686    }
687   #endif
688 <                  
688 >      
689    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
690    double MVzOfMovingMols_local;
691    double MVzOfMovingMols;
# Line 679 | Line 704 | template<typename T> void ZConstraint<T>::zeroOutVel()
704      if (states[i] == zcsMoving){
705        zconsMols[i]->getCOMvel(COMvel);
706        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
707 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
707 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
708      }
709 <                
709 >    
710    }
711  
712   #ifndef IS_MPI
# Line 715 | Line 740 | template<typename T> void ZConstraint<T>::zeroOutVel()
740      if (states[i] ==zcsMoving){
741    
742        movingZAtoms = zconsMols[i]->getMyAtoms();
743 <           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
743 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
744          movingZAtoms[j]->getVel(vel);
745          vel[whichDirection] -= vzOfMovingMols;
746 <             movingZAtoms[j]->setVel(vel);
747 <          }
748 <          
746 >       movingZAtoms[j]->setVel(vel);
747 >    }
748 >    
749     }
750  
751   }
752  
753 +
754 +  zSysCOMVel = calcSysCOMVel();
755   #ifdef IS_MPI
756 <  if (worldRank == 0){
756 >  if(worldRank == 0){
757   #endif
758 <        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
758 >    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
759   #ifdef IS_MPI
760    }
761   #endif
762  
763   }
764  
765 + /**
766 + *
767 + */
768 +
769   template<typename T> void ZConstraint<T>::doZconstraintForce(){
770  
771    Atom** zconsAtoms;
# Line 746 | Line 777 | template<typename T> void ZConstraint<T>::doZconstrain
777  
778  
779  
780 <  //constrain the molecules which do not reach the specified positions  
780 >  //constrain the molecules which do not reach the specified positions  
781      
782    //Zero Out the force of z-contrained molecules    
783    totalFZ_local = 0;
784  
785    //calculate the total z-contrained force of fixed z-contrained molecules
786  
756 – #ifdef IS_MPI
757 –  if (worldRank == 0){
758 – #endif
759 –    cout << "Fixed Molecules" << endl;
760 – #ifdef IS_MPI
761 –  }
762 – #endif
763 –
787    for(int i = 0; i < zconsMols.size(); i++){
788 <                
788 >    
789      if (states[i] == zcsFixed){
790 <                
790 >      
791        zconsMols[i]->getCOM(COM);
792        zconsAtoms = zconsMols[i]->getMyAtoms();  
793  
# Line 772 | Line 795 | template<typename T> void ZConstraint<T>::doZconstrain
795        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
796          zconsAtoms[j]->getFrc(force);
797          fz[i] += force[whichDirection];      
798 <      }
798 >      }
799        totalFZ_local += fz[i];
800  
801 <      cout << "index: " << indexOfZConsMols[i]
802 <                                <<"\tcurrent zpos: " << COM[whichDirection]
803 <                                << "\tcurrent fz: " <<fz[i] << endl;
801 >      cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
802 >             <<"\tcurrent zpos: " << COM[whichDirection]
803 >             << "\tcurrent fz: " <<fz[i] << endl;
804  
805      }
806 <          
806 >    
807    }
808  
809    //calculate total z-constraint force
# Line 790 | Line 813 | template<typename T> void ZConstraint<T>::doZconstrain
813    totalFZ = totalFZ_local;
814   #endif
815  
816 <        
816 >  
817    // apply negative to fixed z-constrained molecues;
818    force[0]= 0;
819    force[1]= 0;
# Line 799 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain
822    for(int i = 0; i < zconsMols.size(); i++){
823  
824      if (states[i] == zcsFixed){  
825 <        
825 >  
826        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
827        zconsAtoms = zconsMols[i]->getMyAtoms();  
828      
829        for(int j =0; j < nAtomOfCurZConsMol; j++) {
830 <                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
830 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
831          //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
832          zconsAtoms[j]->addFrc(force);
833        }
834 <                
834 >    
835      }
836 <        
836 >  
837    }
838  
839    //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
840 <  //               << "total force is " << calcTotalForce() << endl;
840 >  //       << "total force is " << calcTotalForce() << endl;
841  
842    //calculate the number of atoms of moving z-constrained molecules
843    int nMovingZAtoms_local;
844    int nMovingZAtoms;
845 <        
845 >  
846    nMovingZAtoms_local = 0;
847    for(int i = 0; i < zconsMols.size(); i++)
848      if(states[i] == zcsMoving)
849 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
849 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
850    
851   #ifdef IS_MPI
852 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
852 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
853 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
854   #else
855    nMovingZAtoms = nMovingZAtoms_local;
856   #endif
# Line 851 | Line 875 | template<typename T> void ZConstraint<T>::doZconstrain
875   //modify the forces of moving z-constrained molecules
876    for(int i = 0; i < zconsMols.size(); i++) {
877      if (states[i] == zcsMoving){
878 <                
878 >    
879        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
880  
881        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
# Line 863 | Line 887 | template<typename T> void ZConstraint<T>::doZconstrain
887    }
888  
889    //cout << "after substracting z-constraint force from moving molecuels "
890 <  //              << "total force is " << calcTotalForce()  << endl;
890 >  //      << "total force is " << calcTotalForce()  << endl;
891  
892   }
893  
894 + /**
895 +  *
896 +  *
897 +  */
898 +
899 + template<typename T> void ZConstraint<T>::doHarmonic(){
900 +  double force[3];
901 +  double harmonicU;
902 +  double harmonicF;
903 +  double COM[3];
904 +  double diff;
905 +  double totalFZ_local;
906 +  double totalFZ;
907 +  
908 +  force[0] = 0;
909 +  force[1] = 0;
910 +  force[2] = 0;
911 +
912 +  totalFZ_local = 0;
913 +
914 +  for(int i = 0; i < zconsMols.size(); i++) {
915 +
916 +    if (states[i] == zcsMoving){
917 +      zconsMols[i]->getCOM(COM);
918 +      cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
919 +    
920 +    diff = COM[whichDirection] -zPos[i];
921 +    
922 +      harmonicU = 0.5 * kz[i] * diff * diff;  
923 +    info->lrPot += harmonicU;
924 +
925 +      harmonicF =  - kz[i] * diff;
926 +      totalFZ_local += harmonicF;
927 +
928 +       //adjust force
929 +    
930 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
931 +
932 +       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
933 +        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
934 +         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
935 +         movingZAtoms[j]->addFrc(force);
936 +       }
937 +    }
938 +
939 +  }
940 +
941 + #ifndef IS_MPI
942 +  totalFZ = totalFZ_local;
943 + #else
944 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
945 + #endif
946 +
947 +  force[0]= 0;
948 +  force[1]= 0;
949 +  force[2]= 0;
950 +
951 +  //modify the forces of unconstrained molecules
952 +  for(int i = 0; i < unconsMols.size(); i++){
953 +    
954 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
955 +    
956 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
957 +       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
958 +       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
959 +       unconsAtoms[j]->addFrc(force);    
960 +     }
961 +  }  
962 +
963 + }
964 +
965 + /**
966 + *
967 + */
968 +
969   template<typename T> bool ZConstraint<T>::checkZConsState(){
970    double COM[3];
971    double diff;
972    
973    int changed_local;
974    int changed;
975 <        
975 >  
976    changed_local = 0;
977    
978    for(int i =0; i < zconsMols.size(); i++){
# Line 882 | Line 981 | template<typename T> bool ZConstraint<T>::checkZConsSt
981      diff = fabs(COM[whichDirection] - zPos[i]);  
982      if (  diff <= zconsTol && states[i] == zcsMoving){
983        states[i] = zcsFixed;
984 <           changed_local = 1;
984 >     changed_local = 1;
985      }
986      else if ( diff > zconsTol && states[i] == zcsFixed){
987        states[i] = zcsMoving;
988 <           changed_local = 1;    
988 >     changed_local = 1;  
989      }
990    
991    }
# Line 910 | Line 1009 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1009    for(int i = 0; i < zconsMols.size(); i++)
1010      if (states[i] == zcsFixed){
1011        havingFixed_local = 1;
1012 <                break;
1012 >    break;
1013      }
1014  
1015   #ifndef IS_MPI
# Line 936 | Line 1035 | template<typename T> bool ZConstraint<T>::haveMovingZM
1035    for(int i = 0; i < zconsMols.size(); i++)
1036      if (states[i] == zcsMoving){
1037        havingMoving_local = 1;
1038 <                break;
1038 >    break;
1039      }
1040  
1041   #ifndef IS_MPI
# Line 950 | Line 1049 | template<typename T> bool ZConstraint<T>::haveMovingZM
1049   }
1050  
1051   /**
1052 <  *
1053 <  *
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();    
1052 > *
1053 > */
1054  
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 –    }
1005 –
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 –
1055   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1056   {
1057    double MVzOfMovingMols_local;
# Line 1050 | Line 1073 | template<typename T> double ZConstraint<T>::calcMoving
1073      if (states[i] == zcsMoving){
1074        zconsMols[i]->getCOMvel(COMvel);
1075        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1076 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1076 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1077      }
1078 <                
1078 >    
1079    }
1080  
1081   #ifndef IS_MPI
# Line 1069 | Line 1092 | template<typename T> double ZConstraint<T>::calcMoving
1092    return vzOfMovingMols;
1093   }
1094  
1095 + /**
1096 + *
1097 + */
1098  
1099   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1100   {
# Line 1083 | Line 1109 | template<typename T> double ZConstraint<T>::calcSysCOM
1109  
1110    for(int i =0 ; i < nMols; i++){
1111      molecules[i].getCOMvel(COMvel);
1112 <         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1112 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1113    }
1114  
1115    massOfZCons_local = 0;
1116 <        
1116 >  
1117    for(int i = 0; i < massOfZConsMols.size(); i++){
1118      massOfZCons_local += massOfZConsMols[i];
1119    }
# Line 1102 | Line 1128 | template<typename T> double ZConstraint<T>::calcTotalF
1128    return tempMVz /(totalMassOfUncons + massOfZCons);
1129   }
1130  
1131 + /**
1132 + *
1133 + */
1134 +
1135   template<typename T> double ZConstraint<T>::calcTotalForce(){
1136  
1137    double force[3];  
# Line 1133 | Line 1163 | template<typename T> void ZConstraint<T>::PolicyByNumb
1163    //calculate the number of atoms of moving z-constrained molecules
1164    int nMovingZAtoms_local;
1165    int nMovingZAtoms;
1166 <        
1166 >  
1167    nMovingZAtoms_local = 0;
1168    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1169      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1170 <           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1170 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1171    
1172   #ifdef IS_MPI
1173    MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
# Line 1147 | Line 1177 | template<typename T> double ZConstraint<T>::PolicyByNu
1177    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1178   }
1179  
1180 < template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1180 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1181    return totalForce / mol->getNAtoms();
1182   }
1183  
# Line 1171 | Line 1201 | template<typename T> void ZConstraint<T>::PolicyByMass
1201    //calculate the number of atoms of moving z-constrained molecules
1202    double massOfMovingZAtoms_local;
1203    double massOfMovingZAtoms;
1204 <        
1204 >  
1205    massOfMovingZAtoms_local = 0;
1206    for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1207      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1208 <           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1208 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1209    
1210   #ifdef IS_MPI
1211    MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);

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