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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 696 by tim, Thu Aug 14 16:16:39 2003 UTC vs.
Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC

# Line 2 | Line 2 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
2   #include "simError.h"
3   #include <cmath>
4   template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5 <                                    : T(theInfo, the_ff), fz(NULL),
6 <                                      indexOfZConsMols(NULL)
5 >                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL),
6 >                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
9    //get properties from SimInfo
# Line 11 | Line 11 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
11    ZConsParaData* zConsParaData;
12    DoubleData* sampleTime;
13    DoubleData* tolerance;
14 +  StringData* policy;
15    StringData* filename;
16    double COM[3];
17  
# Line 26 | Line 27 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
27    double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2;
28    zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox);
29  
30 +  //creat force substraction policy
31 +  data = info->getProperty(ZCONSFORCEPOLICY_ID);
32 +  if(!data){
33 +    sprintf( painCave.errMsg,
34 +               "ZConstraint Warning: User does not set force substraction policy, "
35 +               "PolicyByMass is used\n");
36 +    painCave.isFatal = 0;
37 +    simError();      
38 +
39 +    forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
40 +  }
41 +  else{
42 +    policy = dynamic_cast<StringData*>(data);
43 +    
44 +    if(!policy){
45 +      sprintf( painCave.errMsg,
46 +                 "ZConstraint Error: Convertion from GenericData to StringData failure, "
47 +                 "PolicyByMass is used\n");
48 +      painCave.isFatal = 0;
49 +      simError();      
50 +
51 +      forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
52 +    }
53 +    else{
54 +      if(policy->getData() == "BYNUMBER")
55 +        forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
56 +      else if(policy->getData() == "BYMASS")
57 +        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
58 +      else{
59 +        sprintf( painCave.errMsg,
60 +                  "ZConstraint Warning: unknown force substraction policy, "
61 +                  "PolicyByMass is used\n");
62 +        painCave.isFatal = 0;
63 +        simError();      
64 +        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
65 +      }  
66 +    }
67 +  }
68 +  
69 +  
70    //retrieve sample time of z-contraint
71    data = info->getProperty(ZCONSTIME_ID);
72    
# Line 69 | 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 83 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
124        this->zconsOutput = filename->getData();
125      }
126      
86 –
127    }
128  
129    //retrieve tolerance for z-constraint molecuels
# Line 113 | 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 154 | 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 175 | 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){
179 <
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;
185 <              }
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 238 | 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 <           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 252 | Line 293 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
293    }
294  
295    fz = new double[zconsMols.size()];
296 +  curZPos = new double[zconsMols.size()];
297    indexOfZConsMols = new int [zconsMols.size()];
298  
299 <  if(!fz || !indexOfZConsMols){
299 >  if(!fz || !curZPos || !indexOfZConsMols){
300      sprintf( painCave.errMsg,
301               "Memory allocation failure in class Zconstraint\n");
302      painCave.isFatal = 1;
# Line 265 | 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 284 | 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 297 | 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_DOUBLE,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  
348 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
348 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
349    
350    if(!fzOut){
351      sprintf( painCave.errMsg,
# Line 309 | Line 353 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
353      painCave.isFatal = 1;
354      simError();
355    }
356 <  
356 >
357 >  forcePolicy->update();
358   }
359  
360   template<typename T> ZConstraint<T>::~ZConstraint()
361   {
362    if(fz)
363      delete[] fz;
364 +
365 +  if(curZPos)
366 +    delete[] curZPos;
367    
368    if(indexOfZConsMols)
369      delete[] indexOfZConsMols;
370    
371    if(fzOut)
372      delete fzOut;
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 348 | 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 365 | 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 377 | 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 +  
437 +  if(curZPos)
438 +    delete[] curZPos;
439      
440    if(indexOfZConsMols)
441      delete[] indexOfZConsMols;
442      
443    if (zconsMols.size() > 0){
444      fz = new double[zconsMols.size()];
445 +   curZPos = new double[zconsMols.size()];
446      indexOfZConsMols =  new int[zconsMols.size()];
447      
448 <    if(!fz || !indexOfZConsMols){
448 >    if(!fz || !curZPos || !indexOfZConsMols){
449        sprintf( painCave.errMsg,
450                 "Memory allocation failure in class Zconstraint\n");
451        painCave.isFatal = 1;
# Line 399 | Line 459 | template<typename T> void ZConstraint<T>::update()
459    }
460    else{
461      fz = NULL;
462 +   curZPos = NULL;
463      indexOfZConsMols = NULL;
464    }
465    
466 +  //
467 +  forcePolicy->update();
468 +  
469   }
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 445 | 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 459 | Line 526 | template<typename T> void ZConstraint<T>::calcForce(in
526   */
527   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
528    double zsys;
529 +  double COM[3];
530 +  double force[3];
531 +  double zSysCOMVel;
532  
533    T::calcForce(calcPot, calcStress);
534  
535 <  if (checkZConsState())
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 +
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  
587 <  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
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++){
590 >      zconsMols[i]->getCOM(COM);
591 >    curZPos[i] = COM[whichDirection];
592  
593 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
594 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
595 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
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++){
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;
606 >  }
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 498 | 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 513 | 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 537 | Line 670 | template<typename T> void ZConstraint<T>::thermalize(
670  
671   /**
672   *
540 – *
541 – *
673   */
674  
675   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 546 | 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;      
706 <        cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;  
707 <                  
705 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
706 >
707 >  zSysCOMVel = calcSysCOMVel();
708 > #ifdef IS_MPI
709 >  if(worldRank == 0){
710 > #endif
711 > //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
712 > #ifdef IS_MPI
713 >  }
714 > #endif
715 >      
716    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
717    double MVzOfMovingMols_local;
718    double MVzOfMovingMols;
# Line 591 | 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 627 | 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  
640 –        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
780  
781 +  zSysCOMVel = calcSysCOMVel();
782 + #ifdef IS_MPI
783 +  if(worldRank == 0){
784 + #endif
785 + //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
786 + #ifdef IS_MPI
787 +  }
788 + #endif
789 +
790   }
791  
792 + /**
793 + *
794 + */
795 +
796   template<typename T> void ZConstraint<T>::doZconstraintForce(){
797  
798    Atom** zconsAtoms;
# Line 650 | Line 802 | template<typename T> void ZConstraint<T>::doZconstrain
802    double COM[3];
803    double force[3];
804  
805 <
654 <
655 <  //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 <  cout << "Fixed Molecules" << endl;
811 >
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 670 | 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 <        
834 >
835 >  //calculate total z-constraint force
836 > #ifdef IS_MPI
837 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
838 > #else
839 >  totalFZ = totalFZ_local;
840 > #endif
841 >
842 >  
843    // apply negative to fixed z-constrained molecues;
844    force[0]= 0;
845    force[1]= 0;
# Line 689 | 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;
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;
707 <  //calculate the number of atoms of moving z-constrained molecules
708 <  int nMovingZAtoms_local;
709 <  int nMovingZAtoms;
710 <        
711 <  nMovingZAtoms_local = 0;
712 <  for(int i = 0; i < zconsMols.size(); i++)
713 <    if(states[i] == zcsMoving)
714 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
715 <  
716 < #ifdef IS_MPI
717 <  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
718 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
719 < #else
720 <  totalFZ = totalFZ_local;
721 <  nMovingZAtoms = nMovingZAtoms_local;
722 < #endif
865 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
866 > //        << "total force is " << calcTotalForce() << endl;
867  
868    force[0]= 0;
869    force[1]= 0;
870    force[2]= 0;
727 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
871  
872    //modify the forces of unconstrained molecules
730 –  int accessCount = 0;
873    for(int i = 0; i < unconsMols.size(); i++){
874      
875       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
876      
877 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
877 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
878 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
879 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
880         unconsAtoms[j]->addFrc(force);
881 +     }
882      
883    }      
884  
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++)
891 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
892 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
893 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
894          movingZAtoms[j]->addFrc(force);
895 +      }
896      }
897    }
750 –        
751 –  cout << "after substracting z-constraint force from moving molecuels "
752 –                  << "total force is " << calcTotalForce()  << endl;
898  
899 < }
899 >  //cout << "after substracting z-constraint force from moving molecuels "
900 >  //      << "total force is " << calcTotalForce()  << endl;
901  
756 – template<typename T> bool ZConstraint<T>::checkZConsState(){
757 –  double COM[3];
758 –  double diff;
759 –  
760 –  bool changed;
761 –  
762 –  changed = false;
763 –  
764 –  for(int i =0; i < zconsMols.size(); i++){
765 –
766 –    zconsMols[i]->getCOM(COM);
767 –    diff = fabs(COM[whichDirection] - zPos[i]);  
768 –    if (  diff <= zconsTol && states[i] == zcsMoving){
769 –      states[i] = zcsFixed;
770 –        changed = true;
771 –    }
772 –    else if ( diff > zconsTol && states[i] == zcsFixed){
773 –      states[i] = zcsMoving;
774 –        changed = true;  
775 –    }
776 –  
777 –  }
778 –
779 –  return changed;
902   }
903  
782 – template<typename T> bool ZConstraint<T>::haveFixedZMols(){
783 –  for(int i = 0; i < zconsMols.size(); i++)
784 –    if (states[i] == zcsFixed)
785 –      return true;
786 –
787 –  return false;
788 – }
789 –
790 –
904   /**
792 – *
793 – */
794 – template<typename T> bool ZConstraint<T>::haveMovingZMols(){
795 –  for(int i = 0; i < zconsMols.size(); i++)
796 –    if (states[i] == zcsMoving)
797 –      return true;
798 –
799 –  return false;
800 –  
801 – }
802 –
803 – /**
905    *
906    *
907    */
# Line 811 | Line 912 | template<typename T> void ZConstraint<T>::doHarmonic()
912    double harmonicF;
913    double COM[3];
914    double diff;
915 +  double totalFZ_local;
916    double totalFZ;
917 <        
917 >  
918    force[0] = 0;
919    force[1] = 0;
920    force[2] = 0;
921  
922 <  totalFZ = 0;
922 >  totalFZ_local = 0;
923  
822 –  cout << "Moving Molecules" << endl;  
924    for(int i = 0; i < zconsMols.size(); i++) {
925  
926      if (states[i] == zcsMoving){
927        zconsMols[i]->getCOM(COM);
928 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
929 <                
930 <                diff = COM[whichDirection] -zPos[i];
931 <                
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;
934 >      info->lrPot += harmonicU;
935  
936        harmonicF =  - kz[i] * diff;
937 <      totalFZ += harmonicF;
937 >      totalFZ_local += harmonicF;
938  
939 <       //
940 <                force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
839 <                
939 >       //adjust force
940 >    
941        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
942  
943 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
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 <        
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;
851 –  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
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++)          
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 +  
987 +  changed_local = 0;
988 +  
989 +  for(int i =0; i < zconsMols.size(); i++){
990 +
991 +    zconsMols[i]->getCOM(COM);
992 +    diff = fabs(COM[whichDirection] - zPos[i]);  
993 +    if (  diff <= zconsTol && states[i] == zcsMoving){
994 +      states[i] = zcsFixed;
995 +     changed_local = 1;
996 +    }
997 +    else if ( diff > zconsTol && states[i] == zcsFixed){
998 +      states[i] = zcsMoving;
999 +     changed_local = 1;  
1000 +    }
1001 +  
1002 +  }
1003 +
1004 + #ifndef IS_MPI
1005 +  changed =changed_local;
1006 + #else
1007 +  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1008 + #endif
1009 +
1010 +  return (changed > 0);
1011 +
1012 + }
1013 +
1014 + template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1015 +
1016 +  int havingFixed_local;
1017 +  int havingFixed;
1018 +
1019 +  havingFixed_local = 0;
1020 +
1021 +  for(int i = 0; i < zconsMols.size(); i++)
1022 +    if (states[i] == zcsFixed){
1023 +      havingFixed_local = 1;
1024 +    break;
1025 +    }
1026 +
1027 + #ifndef IS_MPI
1028 +  havingFixed = havingFixed_local;
1029 + #else
1030 +  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1031 + #endif
1032 +
1033 +  return (havingFixed > 0);
1034 + }
1035 +
1036 +
1037 + /**
1038 + *
1039 + */
1040 + template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1041 +
1042 +  int havingMoving_local;
1043 +  int havingMoving;
1044 +
1045 +  havingMoving_local = 0;
1046 +
1047 +  for(int i = 0; i < zconsMols.size(); i++)
1048 +    if (states[i] == zcsMoving){
1049 +      havingMoving_local = 1;
1050 +    break;
1051 +    }
1052 +
1053 + #ifndef IS_MPI
1054 +  havingMoving = havingMoving_local;
1055 + #else
1056 +  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1057 + #endif
1058 +
1059 +  return (havingMoving > 0);
1060 +  
1061 + }
1062 +
1063 + /**
1064 + *
1065 + */
1066 +
1067   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1068   {
1069    double MVzOfMovingMols_local;
# Line 882 | 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 901 | 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   {
1113    double COMvel[3];
1114 <  double tempMVz = 0;
1115 <                
1114 >  double tempMVz_local;
1115 >  double tempMVz;
1116 >  double massOfZCons_local;
1117 >  double massOfZCons;
1118 >
1119 >
1120 > tempMVz_local = 0;
1121 >
1122    for(int i =0 ; i < nMols; i++){
1123      molecules[i].getCOMvel(COMvel);
1124 <         tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
1124 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1125    }
1126  
915 –  double massOfZCons_local;
916 –  double massOfZCons;
917 –
1127    massOfZCons_local = 0;
1128 <        
1128 >  
1129    for(int i = 0; i < massOfZConsMols.size(); i++){
1130      massOfZCons_local += massOfZConsMols[i];
1131    }
1132   #ifndef IS_MPI
1133    massOfZCons = massOfZCons_local;
1134 +  tempMVz = tempMVz_local;
1135   #else
1136    MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1137 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1138   #endif
1139  
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 951 | Line 1166 | template<typename T> double ZConstraint<T>::calcTotalF
1166    return totalForce;
1167  
1168   }
1169 +
1170 + /**
1171 + *
1172 + */
1173 +
1174 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1175 +  //calculate the number of atoms of moving z-constrained molecules
1176 +  int nMovingZAtoms_local;
1177 +  int nMovingZAtoms;
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();
1183 +  
1184 + #ifdef IS_MPI
1185 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1186 + #else
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){
1205 +  return totalForce / mol->getNAtoms();
1206 + }
1207 +
1208 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1209 +  return totalForce / totNumOfMovingAtoms;
1210 + }
1211 +
1212 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1213 +    return totalForce / mol->getNAtoms();
1214 + }
1215 +
1216 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1217 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1218 + }
1219 +
1220 + /**
1221 + *
1222 + */
1223 +
1224 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1225 +  //calculate the number of atoms of moving z-constrained molecules
1226 +  double massOfMovingZAtoms_local;
1227 +  double massOfMovingZAtoms;
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();
1233 +  
1234 + #ifdef IS_MPI
1235 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1236 + #else
1237 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1238 + #endif
1239 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1240 + }
1241 +
1242 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1243 +  return totalForce * atom->getMass() / mol->getTotalMass();
1244 + }
1245 +
1246 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1247 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1248 + }
1249 +
1250 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1251 +  return totalForce * atom->getMass() / mol->getTotalMass();
1252 + }
1253 +
1254 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1255 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1256 + }
1257 +

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