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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 711 by mmeineke, Fri Aug 22 20:04:39 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 +               "average force substraction policy is used\n");
36 +    painCave.isFatal = 0;
37 +    simError();      
38 +
39 +    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(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 +                 "average force substraction policy 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{
59 +        sprintf( painCave.errMsg,
60 +                  "ZConstraint Warning: unknown force substraction policy, "
61 +                  "average force substraction policy is used\n");
62 +        painCave.isFatal = 0;
63 +        simError();      
64 +      }  
65 +    }
66 +  }
67 +  
68 +  
69    //retrieve sample time of z-contraint
70    data = info->getProperty(ZCONSTIME_ID);
71    
# Line 69 | Line 109 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
109    }
110    else{
111  
112 <     filename = dynamic_cast<StringData*>(data);
112 >    filename = dynamic_cast<StringData*>(data);
113      
114      if(!filename){
115  
# Line 83 | Line 123 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
123        this->zconsOutput = filename->getData();
124      }
125      
86 –
126    }
127  
128    //retrieve tolerance for z-constraint molecuels
# Line 113 | Line 152 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
152      }
153  
154    }
155 <        
155 >  
156    //retrieve index of z-constraint molecules
157    data = info->getProperty(ZCONSPARADATA_ID);
158    if(!data) {
# Line 154 | Line 193 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
193                 "ZConstraint error: index is out of range\n");
194          painCave.isFatal = 1;
195          simError();
196 <        }
196 >        }
197  
198        maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
199  
# Line 175 | Line 214 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
214        //its initial z coordinate  will be used as default
215        for(int i = 0; i < parameters->size(); i++){
216  
217 <              if(!(*parameters)[i].havingZPos){
179 <
217 >        if(!(*parameters)[i].havingZPos){
218   #ifndef IS_MPI
219 <            for(int j = 0; j < nMols; j++){
220 <              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 <                 molecules[j].getCOM(COM);
222 <                          break;
185 <              }
219 >          for(int j = 0; j < nMols; j++){
220 >            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 >              molecules[j].getCOM(COM);
222 >        break;
223              }
224 +          }
225   #else
226              //query which processor current zconstraint molecule belongs to
227 <           int *MolToProcMap;
228 <           int whichNode;
229 <                         double initZPos;
230 <           MolToProcMap = mpiSim->getMolToProcMap();
231 <           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
232 <                          
233 <           //broadcast the zpos of current z-contraint molecule
234 <           //the node which contain this
227 >          int *MolToProcMap;
228 >          int whichNode;
229 >    double initZPos;
230 >          MolToProcMap = mpiSim->getMolToProcMap();
231 >          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
232 >        
233 >          //broadcast the zpos of current z-contraint molecule
234 >          //the node which contain this
235            
236 <           if (worldRank == whichNode ){
237 <                                                
238 <             for(int j = 0; j < nMols; j++)
239 <               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 <                 molecules[j].getCOM(COM);
241 <                                         break;
242 <               }
243 <                                
244 <           }
236 >          if (worldRank == whichNode ){
237 >            
238 >            for(int j = 0; j < nMols; j++)
239 >              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 >                molecules[j].getCOM(COM);
241 >          break;
242 >              }
243 >        
244 >          }
245  
246 <            MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);                          
246 >          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
247   #endif
248              
249 <                 (*parameters)[i].zPos = COM[whichDirection];
249 >          (*parameters)[i].zPos = COM[whichDirection];
250  
251 <            sprintf( painCave.errMsg,
251 >          sprintf( painCave.errMsg,
252                       "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
253                       "initial z coornidate will be used \n");
254 <            painCave.isFatal = 0;
255 <            simError();  
256 <          
257 <              }
258 <            }
259 <                        
254 >           painCave.isFatal = 0;
255 >           simError();  
256 >    
257 >  }
258 >      }
259 >      
260      }//end if (!zConsParaData)
261    }//end  if (!data)
262              
# Line 238 | Line 276 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
276        massOfZConsMols.push_back(molecules[i].getTotalMass());  
277  
278        zPos.push_back((*parameters)[searchResult].zPos);
279 <           kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
279 >      cout << "index: "<< (*parameters)[searchResult].zconsIndex
280 >             <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
281 >      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
282        
283        molecules[i].getCOM(COM);
284      }
# Line 252 | Line 292 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
292    }
293  
294    fz = new double[zconsMols.size()];
295 +  curZPos = new double[zconsMols.size()];
296    indexOfZConsMols = new int [zconsMols.size()];
297  
298 <  if(!fz || !indexOfZConsMols){
298 >  if(!fz || !curZPos || !indexOfZConsMols){
299      sprintf( painCave.errMsg,
300               "Memory allocation failure in class Zconstraint\n");
301      painCave.isFatal = 1;
# Line 265 | Line 306 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
306    for(int i = 0; i < zconsMols.size(); i++){
307      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
308  
309 <         zconsMols[i]->getCOM(COM);
309 >    zconsMols[i]->getCOM(COM);
310      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
311 <                states.push_back(zcsFixed);
312 <         else
313 <                states.push_back(zcsMoving);
311 >      states.push_back(zcsFixed);
312 >    else
313 >      states.push_back(zcsMoving);
314    }
315    
316   #endif
# Line 284 | Line 325 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
325   #ifndef IS_MPI
326    totalMassOfUncons = totalMassOfUncons_local;
327   #else
328 <  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
328 >  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
329 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
330   #endif
331  
332  
# Line 297 | Line 339 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
339   #ifndef IS_MPI
340    totNumOfUnconsAtoms = nUnconsAtoms_local;
341   #else
342 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
342 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344   #endif  
345  
346    // creat zconsWriter  
347 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
347 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348    
349    if(!fzOut){
350      sprintf( painCave.errMsg,
# Line 309 | Line 352 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
352      painCave.isFatal = 1;
353      simError();
354    }
355 <  
355 >
356 >  forcePolicy->update();
357   }
358  
359   template<typename T> ZConstraint<T>::~ZConstraint()
360   {
361    if(fz)
362      delete[] fz;
363 +
364 +  if(curZPos)
365 +    delete[] curZPos;
366    
367    if(indexOfZConsMols)
368      delete[] indexOfZConsMols;
369    
370    if(fzOut)
371      delete fzOut;
372 +  
373 +  if(forcePolicy)
374 +    delete forcePolicy;
375   }
376  
377 +
378 + /**
379 + *
380 + */
381 +
382   #ifdef IS_MPI
383   template<typename T> void ZConstraint<T>::update()
384   {
# Line 348 | Line 403 | template<typename T> void ZConstraint<T>::update()
403      
404        zconsMols.push_back(&molecules[i]);      
405        zPos.push_back((*parameters)[index].zPos);
406 <        kz.push_back((*parameters)[index].kRatio * zForceConst);
407 <                        
406 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
407 >      
408        massOfZConsMols.push_back(molecules[i].getTotalMass());  
409        
410        molecules[i].getCOM(COM);
# Line 365 | Line 420 | template<typename T> void ZConstraint<T>::update()
420  
421    //determine the states of z-constraint molecules
422    for(int i = 0; i < zconsMols.size(); i++){
423 <           zconsMols[i]->getCOM(COM);
423 >     zconsMols[i]->getCOM(COM);
424        if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
425 <                  states.push_back(zcsFixed);
426 <           else
427 <                  states.push_back(zcsMoving);
425 >      states.push_back(zcsFixed);
426 >     else
427 >      states.push_back(zcsMoving);
428    }
429  
430      
# Line 377 | Line 432 | template<typename T> void ZConstraint<T>::update()
432    // that we want to make the MPI communication simple
433    if(fz)
434      delete[] fz;
435 +  
436 +  if(curZPos)
437 +    delete[] curZPos;
438      
439    if(indexOfZConsMols)
440      delete[] indexOfZConsMols;
441      
442    if (zconsMols.size() > 0){
443      fz = new double[zconsMols.size()];
444 +   curZPos = new double[zconsMols.size()];
445      indexOfZConsMols =  new int[zconsMols.size()];
446      
447 <    if(!fz || !indexOfZConsMols){
447 >    if(!fz || !curZPos || !indexOfZConsMols){
448        sprintf( painCave.errMsg,
449                 "Memory allocation failure in class Zconstraint\n");
450        painCave.isFatal = 1;
# Line 399 | Line 458 | template<typename T> void ZConstraint<T>::update()
458    }
459    else{
460      fz = NULL;
461 +   curZPos = NULL;
462      indexOfZConsMols = NULL;
463    }
464    
465 +  //
466 +  forcePolicy->update();
467 +  
468   }
469  
470   #endif
471  
472 < /**  Function Name: isZConstraintMol
473 < **  Parameter
474 < **    Molecule* mol
475 < **  Return value:
476 < **    -1, if the molecule is not z-constraint molecule,
477 < **    other non-negative values, its index in indexOfAllZConsMols vector
472 > /**
473 > *  Function Name: isZConstraintMol
474 > *  Parameter
475 > *    Molecule* mol
476 > *  Return value:
477 > *    -1, if the molecule is not z-constraint molecule,
478 > *    other non-negative values, its index in indexOfAllZConsMols vector
479   */
480  
481   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 445 | Line 509 | template<typename T> void ZConstraint<T>::integrate(){
509    //zero out the velocities of center of mass of unconstrained molecules
510    //and the velocities of center of mass of every single z-constrained molecueles
511    zeroOutVel();
512 +
513 +  curZconsTime = zconsTime + info->getTime();
514    
515    T::integrate();
516  
# Line 459 | Line 525 | template<typename T> void ZConstraint<T>::calcForce(in
525   */
526   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
527    double zsys;
528 +  double COM[3];
529 +  double force[3];
530 +  double zSysCOMVel;
531  
532    T::calcForce(calcPot, calcStress);
533  
534 <  if (checkZConsState())
534 >  if (checkZConsState()){
535 >    
536 > #ifdef IS_MPI
537 >    if(worldRank == 0){
538 > #endif
539 >      std::cerr << "\n"
540 >                << "*******************************************\n"
541 >                << " about to call zeroOutVel()\n"
542 >                << "*******************************************\n"
543 >                << "\n";
544 > #ifdef IS_MPI
545 >    }
546 > #endif
547      zeroOutVel();
548 +
549 + #ifdef IS_MPI
550 +    if(worldRank == 0){
551 + #endif
552 +      std::cerr << "\n"
553 +                << "*******************************************\n"
554 +                << " finished zeroOutVel()\n"
555 +                << "*******************************************\n"
556 +                << "\n";
557 + #ifdef IS_MPI
558 +    }
559 + #endif
560 +    
561 +    forcePolicy->update();
562 +  }  
563    
564    zsys = calcZSys();
565 <  cout << "---------------------------------------------------------------------" <<endl;
566 <  cout << "current time: " << info->getTime() << endl;
567 <  cout << "center of mass at z: " << zsys << endl;      
568 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
569 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
565 >  zSysCOMVel = calcSysCOMVel();
566 > #ifdef IS_MPI
567 >  if(worldRank == 0){
568 > #endif
569 >    cout << "---------------------------------------------------------------------" <<endl;
570 >    cout << "current time: " << info->getTime() << endl;
571 >    cout << "center of mass at z: " << zsys << endl;    
572 >    cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
573  
574 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
574 > #ifdef IS_MPI
575 >  }
576 > #endif
577  
578    //do zconstraint force;
579    if (haveFixedZMols())
# Line 482 | Line 583 | template<typename T> void ZConstraint<T>::calcForce(in
583    if (haveMovingZMols())
584      this->doHarmonic();
585  
586 <  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
586 >  //write out forces and current positions of z-constraint molecules
587 >  if(info->getTime() >= curZconsTime){    
588 >   for(int i = 0; i < zconsMols.size(); i++){
589 >      zconsMols[i]->getCOM(COM);
590 >    curZPos[i] = COM[whichDirection];
591  
592 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
593 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
594 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
592 >    //if the z-constraint molecule is still moving, just record its force
593 >    if(states[i] == zcsMoving){
594 >         fz[i] = 0;
595 >      Atom** movingZAtoms;
596 >      movingZAtoms = zconsMols[i]->getMyAtoms();
597 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
598 >           movingZAtoms[j]->getFrc(force);
599 >           fz[i] += force[whichDirection];
600 >      }
601 >     }
602 >   }
603 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
604 >   curZconsTime += zconsTime;
605 >  }
606 >
607 >  zSysCOMVel = calcSysCOMVel();  
608 > #ifdef IS_MPI
609 >  if(worldRank == 0){
610 > #endif
611 >    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
612 > #ifdef IS_MPI
613 >  }
614 > #endif
615 >
616   }
617 +
618 +
619 + /**
620 + *
621 + */
622  
623   template<typename T> double ZConstraint<T>::calcZSys()
624   {
# Line 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 652 | Line 804 | template<typename T> void ZConstraint<T>::doZconstrain
804  
805  
806  
807 <  //constrain the molecules which do not reach the specified positions  
807 >  //constrain the molecules which do not reach the specified positions  
808      
809    //Zero Out the force of z-contrained molecules    
810    totalFZ_local = 0;
811  
812    //calculate the total z-contrained force of fixed z-contrained molecules
813 <  cout << "Fixed Molecules" << endl;
813 >
814    for(int i = 0; i < zconsMols.size(); i++){
815 <                
815 >    
816      if (states[i] == zcsFixed){
817 <                
817 >      
818        zconsMols[i]->getCOM(COM);
819        zconsAtoms = zconsMols[i]->getMyAtoms();  
820  
# Line 670 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain
822        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
823          zconsAtoms[j]->getFrc(force);
824          fz[i] += force[whichDirection];      
825 <      }
825 >      }
826        totalFZ_local += fz[i];
827  
828 <      cout << "index: " << indexOfZConsMols[i]
829 <                                <<"\tcurrent zpos: " << COM[whichDirection]
830 <                                << "\tcurrent fz: " <<fz[i] << endl;
828 > //       cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
829 > //              <<"\tcurrent zpos: " << COM[whichDirection]
830 > //              << "\tcurrent fz: " <<fz[i] << endl;
831  
832      }
833 <          
833 >    
834    }
835 <        
835 >
836 >  //calculate total z-constraint force
837 > #ifdef IS_MPI
838 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
839 > #else
840 >  totalFZ = totalFZ_local;
841 > #endif
842 >
843 >  
844    // apply negative to fixed z-constrained molecues;
845    force[0]= 0;
846    force[1]= 0;
# Line 689 | Line 849 | template<typename T> void ZConstraint<T>::doZconstrain
849    for(int i = 0; i < zconsMols.size(); i++){
850  
851      if (states[i] == zcsFixed){  
852 <        
852 >  
853        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
854        zconsAtoms = zconsMols[i]->getMyAtoms();  
855      
856        for(int j =0; j < nAtomOfCurZConsMol; j++) {
857 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
857 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
858 >        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
859          zconsAtoms[j]->addFrc(force);
860        }
861 <                
861 >    
862      }
863 <        
863 >  
864    }
865  
866 <  cout << "after zero out z-constraint force on fixed z-constraint molecuels "
867 <                  << "total force is " << calcTotalForce() << endl;
866 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
867 > //        << "total force is " << calcTotalForce() << endl;
868 >
869    //calculate the number of atoms of moving z-constrained molecules
870    int nMovingZAtoms_local;
871    int nMovingZAtoms;
872 <        
872 >  
873    nMovingZAtoms_local = 0;
874    for(int i = 0; i < zconsMols.size(); i++)
875      if(states[i] == zcsMoving)
876 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
876 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
877    
878   #ifdef IS_MPI
879 <  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
880 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
879 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
880 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
881   #else
720 –  totalFZ = totalFZ_local;
882    nMovingZAtoms = nMovingZAtoms_local;
883   #endif
884  
885    force[0]= 0;
886    force[1]= 0;
887    force[2]= 0;
727 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
888  
889    //modify the forces of unconstrained molecules
730 –  int accessCount = 0;
890    for(int i = 0; i < unconsMols.size(); i++){
891      
892       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
893      
894 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
894 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
895 >       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
896 >       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
897         unconsAtoms[j]->addFrc(force);
898 +     }
899      
900    }      
901  
902   //modify the forces of moving z-constrained molecules
903    for(int i = 0; i < zconsMols.size(); i++) {
904      if (states[i] == zcsMoving){
905 <                
905 >    
906        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
907  
908 <      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
908 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
909 >        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
910 >        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
911          movingZAtoms[j]->addFrc(force);
912 +      }
913      }
914    }
750 –        
751 –  cout << "after substracting z-constraint force from moving molecuels "
752 –                  << "total force is " << calcTotalForce()  << endl;
915  
916 < }
916 >  //cout << "after substracting z-constraint force from moving molecuels "
917 >  //      << "total force is " << calcTotalForce()  << endl;
918  
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;
919   }
920  
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 –
921   /**
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 – /**
922    *
923    *
924    */
# Line 811 | Line 929 | template<typename T> void ZConstraint<T>::doHarmonic()
929    double harmonicF;
930    double COM[3];
931    double diff;
932 +  double totalFZ_local;
933    double totalFZ;
934 <        
934 >  
935    force[0] = 0;
936    force[1] = 0;
937    force[2] = 0;
938  
939 <  totalFZ = 0;
939 >  totalFZ_local = 0;
940  
822 –  cout << "Moving Molecules" << endl;  
941    for(int i = 0; i < zconsMols.size(); i++) {
942  
943      if (states[i] == zcsMoving){
944        zconsMols[i]->getCOM(COM);
945 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
946 <                
947 <                diff = COM[whichDirection] -zPos[i];
948 <                
945 >      cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
946 >           << "\tcurrent zpos: " << COM[whichDirection] << endl;
947 >    
948 >    diff = COM[whichDirection] -zPos[i];
949 >    
950        harmonicU = 0.5 * kz[i] * diff * diff;  
951 <                info->lrPot += harmonicU;
951 >    info->lrPot += harmonicU;
952  
953        harmonicF =  - kz[i] * diff;
954 <      totalFZ += harmonicF;
954 >      totalFZ_local += harmonicF;
955  
956 <       //
957 <                force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
839 <                
956 >       //adjust force
957 >    
958        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
959  
960 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
960 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
961 >        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
962 >         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
963           movingZAtoms[j]->addFrc(force);
964 +       }
965      }
966  
967    }
968 <        
968 >
969 > #ifndef IS_MPI
970 >  totalFZ = totalFZ_local;
971 > #else
972 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
973 > #endif
974 >
975    force[0]= 0;
976    force[1]= 0;
977    force[2]= 0;
851 –  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
978  
979    //modify the forces of unconstrained molecules
980    for(int i = 0; i < unconsMols.size(); i++){
981      
982       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
983      
984 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
984 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
985 >       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
986 >       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
987         unconsAtoms[j]->addFrc(force);    
988 +     }
989    }  
990  
991   }
992  
993 + /**
994 + *
995 + */
996 +
997 + template<typename T> bool ZConstraint<T>::checkZConsState(){
998 +  double COM[3];
999 +  double diff;
1000 +  
1001 +  int changed_local;
1002 +  int changed;
1003 +  
1004 +  changed_local = 0;
1005 +  
1006 +  for(int i =0; i < zconsMols.size(); i++){
1007 +
1008 +    zconsMols[i]->getCOM(COM);
1009 +    diff = fabs(COM[whichDirection] - zPos[i]);  
1010 +    if (  diff <= zconsTol && states[i] == zcsMoving){
1011 +      states[i] = zcsFixed;
1012 +     changed_local = 1;
1013 +    }
1014 +    else if ( diff > zconsTol && states[i] == zcsFixed){
1015 +      states[i] = zcsMoving;
1016 +     changed_local = 1;  
1017 +    }
1018 +  
1019 +  }
1020 +
1021 + #ifndef IS_MPI
1022 +  changed =changed_local;
1023 + #else
1024 +  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1025 + #endif
1026 +  
1027 +  return (changed > 0);
1028 + }
1029 +
1030 + template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1031 +
1032 +  int havingFixed_local;
1033 +  int havingFixed;
1034 +
1035 +  havingFixed_local = 0;
1036 +
1037 +  for(int i = 0; i < zconsMols.size(); i++)
1038 +    if (states[i] == zcsFixed){
1039 +      havingFixed_local = 1;
1040 +    break;
1041 +    }
1042 +
1043 + #ifndef IS_MPI
1044 +  havingFixed = havingFixed_local;
1045 + #else
1046 +  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1047 + #endif
1048 +
1049 +  return havingFixed > 0 ? true : false;
1050 + }
1051 +
1052 +
1053 + /**
1054 + *
1055 + */
1056 + template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1057 +
1058 +  int havingMoving_local;
1059 +  int havingMoving;
1060 +
1061 +  havingMoving_local = 0;
1062 +
1063 +  for(int i = 0; i < zconsMols.size(); i++)
1064 +    if (states[i] == zcsMoving){
1065 +      havingMoving_local = 1;
1066 +    break;
1067 +    }
1068 +
1069 + #ifndef IS_MPI
1070 +  havingMoving = havingMoving_local;
1071 + #else
1072 +  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1073 + #endif
1074 +
1075 +  return havingMoving > 0 ? true : false;
1076 +  
1077 + }
1078 +
1079 + /**
1080 + *
1081 + */
1082 +
1083   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1084   {
1085    double MVzOfMovingMols_local;
# Line 882 | Line 1101 | template<typename T> double ZConstraint<T>::calcMoving
1101      if (states[i] == zcsMoving){
1102        zconsMols[i]->getCOMvel(COMvel);
1103        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1104 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1104 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1105      }
1106 <                
1106 >    
1107    }
1108  
1109   #ifndef IS_MPI
# Line 901 | Line 1120 | template<typename T> double ZConstraint<T>::calcMoving
1120    return vzOfMovingMols;
1121   }
1122  
1123 + /**
1124 + *
1125 + */
1126  
1127   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1128   {
1129    double COMvel[3];
1130 <  double tempMVz = 0;
1131 <                
1130 >  double tempMVz_local;
1131 >  double tempMVz;
1132 >  double massOfZCons_local;
1133 >  double massOfZCons;
1134 >
1135 >
1136 > tempMVz_local = 0;
1137 >
1138    for(int i =0 ; i < nMols; i++){
1139      molecules[i].getCOMvel(COMvel);
1140 <         tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
1140 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1141    }
1142  
915 –  double massOfZCons_local;
916 –  double massOfZCons;
917 –
1143    massOfZCons_local = 0;
1144 <        
1144 >  
1145    for(int i = 0; i < massOfZConsMols.size(); i++){
1146      massOfZCons_local += massOfZConsMols[i];
1147    }
1148   #ifndef IS_MPI
1149    massOfZCons = massOfZCons_local;
1150 +  tempMVz = tempMVz_local;
1151   #else
1152    MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1153 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1154   #endif
1155  
1156    return tempMVz /(totalMassOfUncons + massOfZCons);
1157   }
1158  
1159 + /**
1160 + *
1161 + */
1162 +
1163   template<typename T> double ZConstraint<T>::calcTotalForce(){
1164  
1165    double force[3];  
# Line 951 | Line 1182 | template<typename T> double ZConstraint<T>::calcTotalF
1182    return totalForce;
1183  
1184   }
1185 +
1186 + /**
1187 + *
1188 + */
1189 +
1190 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1191 +  //calculate the number of atoms of moving z-constrained molecules
1192 +  int nMovingZAtoms_local;
1193 +  int nMovingZAtoms;
1194 +  
1195 +  nMovingZAtoms_local = 0;
1196 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1197 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1198 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1199 +  
1200 + #ifdef IS_MPI
1201 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1202 + #else
1203 +  nMovingZAtoms = nMovingZAtoms_local;
1204 + #endif
1205 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1206 +
1207 + #ifdef IS_MPI
1208 +  if(worldRank == 0){
1209 + #endif
1210 +    std::cerr << "\n"
1211 +              << "*******************************************\n"
1212 +              << " fiished Policy by numbr()\n"
1213 +              << "*******************************************\n"
1214 +              << "\n";
1215 + #ifdef IS_MPI
1216 +  }
1217 + #endif
1218 + }
1219 +
1220 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1221 +  return totalForce / mol->getNAtoms();
1222 + }
1223 +
1224 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1225 +  return totalForce / totNumOfMovingAtoms;
1226 + }
1227 +
1228 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1229 +    return totalForce / mol->getNAtoms();
1230 + }
1231 +
1232 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1233 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1234 + }
1235 +
1236 + /**
1237 + *
1238 + */
1239 +
1240 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1241 +  //calculate the number of atoms of moving z-constrained molecules
1242 +  double massOfMovingZAtoms_local;
1243 +  double massOfMovingZAtoms;
1244 +  
1245 +  massOfMovingZAtoms_local = 0;
1246 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1247 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1248 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1249 +  
1250 + #ifdef IS_MPI
1251 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1252 + #else
1253 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1254 + #endif
1255 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1256 + }
1257 +
1258 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1259 +  return totalForce * atom->getMass() / mol->getTotalMass();
1260 + }
1261 +
1262 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1263 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1264 + }
1265 +
1266 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1267 +  return totalForce * atom->getMass() / mol->getTotalMass();
1268 + }
1269 +
1270 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1271 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1272 + }
1273 +

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