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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 682 by tim, Tue Aug 12 17:51:33 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 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), fzOut(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 Subtraction policy
31 +  data = info->getProperty(ZCONSFORCEPOLICY_ID);
32 +  if(!data){
33 +    sprintf( painCave.errMsg,
34 +               "ZConstraint Warning: User does not set force Subtraction policy, "
35 +               "PolicyByMass is used\n");
36 +    painCave.isFatal = 0;
37 +    simError();      
38 +
39 +    forcePolicy = (ForceSubtractionPolicy*) 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 = (ForceSubtractionPolicy*) new PolicyByMass(this);
52 +    }
53 +    else{
54 +      if(policy->getData() == "BYNUMBER")
55 +        forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this);
56 +      else if(policy->getData() == "BYMASS")
57 +        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
58 +      else{
59 +        sprintf( painCave.errMsg,
60 +                  "ZConstraint Warning: unknown force Subtraction policy, "
61 +                  "PolicyByMass is used\n");
62 +        painCave.isFatal = 0;
63 +        simError();      
64 +        forcePolicy = (ForceSubtractionPolicy*) 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()].zconsIndex;
199 >      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
200  
201   #ifndef IS_MPI
202        totalNumMol = nMols;
# 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[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 <                 molecules[i].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 i = 0; i < nMols; i++)
240 <               if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 <                 molecules[i].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        
283 +      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284        molecules[i].getCOM(COM);
285      }
286      else
# 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;
303      simError();
304    }
305  
306 <  for(int i = 0; i < zconsMols.size(); i++)
306 >  //determine the states of z-constraint molecules
307 >  for(int i = 0; i < zconsMols.size(); i++){
308      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309 +
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);
315 +  }
316    
317   #endif
318  
319 +  //get total masss of unconstraint molecules
320 +  double totalMassOfUncons_local;
321 +  totalMassOfUncons_local = 0;
322 +  
323 +  for(int i = 0; i < unconsMols.size(); i++)
324 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
325 +    
326 + #ifndef IS_MPI
327 +  totalMassOfUncons = totalMassOfUncons_local;
328 + #else
329 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
330 +                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331 + #endif
332 +
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
# Line 275 | 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);  
343 < #endif
342 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344 > #endif  
345  
346 <  checkZConsState();
282 <
283 <  //  
284 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
285 <  
286 <  if(!fzOut){
287 <    sprintf( painCave.errMsg,
288 <             "Memory allocation failure in class Zconstraint\n");
289 <    painCave.isFatal = 1;
290 <    simError();
291 <  }
292 <  
346 >  forcePolicy->update();
347   }
348  
349   template<typename T> ZConstraint<T>::~ZConstraint()
350   {
351    if(fz)
352      delete[] fz;
353 +
354 +  if(curZPos)
355 +    delete[] curZPos;
356    
357    if(indexOfZConsMols)
358      delete[] indexOfZConsMols;
359    
360    if(fzOut)
361      delete fzOut;
362 +  
363 +  if(forcePolicy)
364 +    delete forcePolicy;
365   }
366  
367 +
368 + /**
369 + *
370 + */
371 +
372   #ifdef IS_MPI
373   template<typename T> void ZConstraint<T>::update()
374   {
# Line 328 | Line 393 | template<typename T> void ZConstraint<T>::update()
393      
394        zconsMols.push_back(&molecules[i]);      
395        zPos.push_back((*parameters)[index].zPos);
396 <        kz.push_back((*parameters)[index].kRatio * zForceConst);
332 <
396 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
397        massOfZConsMols.push_back(molecules[i].getTotalMass());  
398        
399        molecules[i].getCOM(COM);
# Line 342 | Line 406 | template<typename T> void ZConstraint<T>::update()
406  
407      }
408    }
409 +
410 +  //determine the states of z-constraint molecules
411 +  for(int i = 0; i < zconsMols.size(); i++){
412 +     zconsMols[i]->getCOM(COM);
413 +      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
414 +      states.push_back(zcsFixed);
415 +     else
416 +      states.push_back(zcsMoving);
417 +  }
418 +
419      
420    //The reason to declare fz and indexOfZconsMols as pointer to array is
421    // that we want to make the MPI communication simple
422    if(fz)
423      delete[] fz;
424 +  
425 +  if(curZPos)
426 +    delete[] curZPos;
427      
428    if(indexOfZConsMols)
429      delete[] indexOfZConsMols;
430      
431    if (zconsMols.size() > 0){
432      fz = new double[zconsMols.size()];
433 +   curZPos = new double[zconsMols.size()];
434      indexOfZConsMols =  new int[zconsMols.size()];
435      
436 <    if(!fz || !indexOfZConsMols){
436 >    if(!fz || !curZPos || !indexOfZConsMols){
437        sprintf( painCave.errMsg,
438                 "Memory allocation failure in class Zconstraint\n");
439        painCave.isFatal = 1;
# Line 369 | Line 447 | template<typename T> void ZConstraint<T>::update()
447    }
448    else{
449      fz = NULL;
450 +   curZPos = NULL;
451      indexOfZConsMols = NULL;
452    }
453    
454 +  //
455 +  forcePolicy->update();
456 +  
457   }
458  
459   #endif
460  
461 < /**  Function Name: isZConstraintMol
462 < **  Parameter
463 < **    Molecule* mol
464 < **  Return value:
465 < **    -1, if the molecule is not z-constraint molecule,
466 < **    other non-negative values, its index in indexOfAllZConsMols vector
461 > /**
462 > *  Function Name: isZConstraintMol
463 > *  Parameter
464 > *    Molecule* mol
465 > *  Return value:
466 > *    -1, if the molecule is not z-constraint molecule,
467 > *    other non-negative values, its index in indexOfAllZConsMols vector
468   */
469  
470   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 410 | Line 493 | template<typename T> int ZConstraint<T>::isZConstraint
493    return -1;
494   }
495  
413 – /**
414 – * Description:
415 – *  Reset the z coordinates
416 – */
496   template<typename T> void ZConstraint<T>::integrate(){
497 +
498 +  // creat zconsWriter  
499 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
500    
501 +  if(!fzOut){
502 +    sprintf( painCave.errMsg,
503 +             "Memory allocation failure in class Zconstraint\n");
504 +    painCave.isFatal = 1;
505 +    simError();
506 +  }
507 +  
508    //zero out the velocities of center of mass of unconstrained molecules
509    //and the velocities of center of mass of every single z-constrained molecueles
510    zeroOutVel();
511 +
512 +  curZconsTime = zconsTime + info->getTime();
513    
514    T::integrate();
515  
# Line 430 | Line 521 | template<typename T> void ZConstraint<T>::integrate(){
521   *
522   *
523   *
524 < */
434 <
435 <
524 > */
525   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
526 +  double zsys;
527 +  double COM[3];
528 +  double force[3];
529 +  double zSysCOMVel;
530  
531    T::calcForce(calcPot, calcStress);
532  
533 <  if (checkZConsState())
534 <    zeroOutVel();
533 >  if (checkZConsState()){    
534 >    zeroOutVel();    
535 >    forcePolicy->update();
536 >  }  
537 >  
538 >  zsys = calcZSys();
539 >  zSysCOMVel = calcSysCOMVel();
540 > #ifdef IS_MPI
541 >  if(worldRank == 0){
542 > #endif
543 >     //cout << "---------------------------------------------------------------------" <<endl;
544 >     //cout << "current time: " << info->getTime() << endl;
545 >     //cout << "center of mass at z: " << zsys << endl;    
546 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
547  
548 + #ifdef IS_MPI
549 +  }
550 + #endif
551 +
552    //do zconstraint force;
553    if (haveFixedZMols())
554      this->doZconstraintForce();
555 <  
555 >
556    //use harmonical poteintial to move the molecules to the specified positions
557    if (haveMovingZMols())
558 <    //this->doHarmonic();
559 <  
560 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
561 <      
558 >    this->doHarmonic();
559 >
560 >  //write out forces and current positions of z-constraint molecules
561 >  if(info->getTime() >= curZconsTime){    
562 >   for(int i = 0; i < zconsMols.size(); i++){
563 >      zconsMols[i]->getCOM(COM);
564 >    curZPos[i] = COM[whichDirection];
565 >
566 >    //if the z-constraint molecule is still moving, just record its force
567 >    if(states[i] == zcsMoving){
568 >         fz[i] = 0;
569 >      Atom** movingZAtoms;
570 >      movingZAtoms = zconsMols[i]->getMyAtoms();
571 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
572 >           movingZAtoms[j]->getFrc(force);
573 >           fz[i] += force[whichDirection];
574 >      }
575 >     }
576 >   }
577 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
578 >   curZconsTime += zconsTime;
579 >  }
580 >
581 >  zSysCOMVel = calcSysCOMVel();  
582 > #ifdef IS_MPI
583 >  if(worldRank == 0){
584 > #endif
585 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
586 > #ifdef IS_MPI
587 >  }
588 > #endif
589   }
590 +
591 +
592 + /**
593 + *
594 + */
595  
596   template<typename T> double ZConstraint<T>::calcZSys()
597   {
# Line 459 | Line 600 | template<typename T> double ZConstraint<T>::calcZSys()
600    double totalMass;
601    double totalMZ_local;
602    double totalMZ;
462 –  double massOfUncons_local;
603    double massOfCurMol;
604    double COM[3];
605    
606    totalMass_local = 0;
467 –  totalMass = 0;
607    totalMZ_local = 0;
469 –  totalMZ = 0;
470 –  massOfUncons_local = 0;
471 –    
608    
609    for(int i = 0; i < nMols; i++){
610      massOfCurMol = molecules[i].getTotalMass();
# Line 476 | Line 612 | template<typename T> double ZConstraint<T>::calcZSys()
612      
613      totalMass_local += massOfCurMol;
614      totalMZ_local += massOfCurMol * COM[whichDirection];
615 <    
480 <    if(isZConstraintMol(&molecules[i]) == -1){
481 <    
482 <      massOfUncons_local += massOfCurMol;
483 <    }  
484 <    
615 >
616    }
617 +
618    
487 –  
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);  
622 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
623 < #else
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;
627 <  totalMassOfUncons = massOfUncons_local;
496 < #endif  
627 > #endif  
628  
629    double zsys;
630    zsys = totalMZ / totalMass;
# Line 512 | Line 643 | template<typename T> void ZConstraint<T>::thermalize(
643  
644   /**
645   *
515 – *
516 – *
646   */
647  
648   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 521 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel()
650    Atom** fixedZAtoms;  
651    double COMvel[3];
652    double vel[3];
653 <  
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);      
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 <          
671 >
672 >    zconsMols[i]->getCOMvel(COMvel);
673 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
674      }
541 –        
542 –  }
675    
676 +  }
677 +
678 +    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
679 +
680 +  zSysCOMVel = calcSysCOMVel();
681 + #ifdef IS_MPI
682 +  if(worldRank == 0){
683 + #endif
684 +     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
685 + #ifdef IS_MPI
686 +  }
687 + #endif
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 555 | Line 700 | template<typename T> void ZConstraint<T>::zeroOutVel()
700      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
701    }
702  
703 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
559 <
703 >  for(int i = 0; i < zconsMols.size(); i++){
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 591 | Line 735 | template<typename T> void ZConstraint<T>::zeroOutVel()
735  
736    //modify the velocities of moving z-constrained molecuels
737    Atom** movingZAtoms;
738 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
738 >  for(int i = 0; i < zconsMols.size(); i++){
739  
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);
603 <        }
604 <          
746 >       movingZAtoms[j]->setVel(vel);
747      }
748 +    
749 +   }
750  
751 + }
752 +
753 +
754 +  zSysCOMVel = calcSysCOMVel();
755 + #ifdef IS_MPI
756 +  if(worldRank == 0){
757 + #endif
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 616 | Line 774 | template<typename T> void ZConstraint<T>::doZconstrain
774    double COMvel[3];  
775    double COM[3];
776    double force[3];
619 –  double zsys;
777  
778 <  int nMovingZMols_local;
622 <  int nMovingZMols;
623 <
624 <  //constrain the molecules which do not reach the specified positions  
625 <
626 <   zsys = calcZSys();
627 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
778 >  //constrain the molecules which do not reach the specified positions  
779      
780    //Zero Out the force of z-contrained molecules    
781    totalFZ_local = 0;
782  
783    //calculate the total z-contrained force of fixed z-contrained molecules
784 <  cout << "Fixed Molecules" << endl;
784 >  
785 >  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
786 >  //       << "total force is " << calcTotalForce() << endl;
787 >
788    for(int i = 0; i < zconsMols.size(); i++){
789 <                
789 >    
790      if (states[i] == zcsFixed){
791 <                
791 >      
792        zconsMols[i]->getCOM(COM);
793        zconsAtoms = zconsMols[i]->getMyAtoms();  
794  
# Line 642 | Line 796 | template<typename T> void ZConstraint<T>::doZconstrain
796        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
797          zconsAtoms[j]->getFrc(force);
798          fz[i] += force[whichDirection];      
799 <      }
799 >      }
800        totalFZ_local += fz[i];
801  
802 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
802 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
803 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
804 >      //      << "\tcurrent fz: " <<fz[i] << endl;
805  
806 +
807      }
808 <          
808 >    
809    }
810  
811 <  //calculate the number of atoms of moving z-constrained molecules
655 <  nMovingZMols_local = 0;
656 <  for(int i = 0; zconsMols.size(); i++){
657 <    if(states[i] == zcsMoving)
658 <        nMovingZMols_local += massOfZConsMols[i];
659 <  }
811 >  //calculate total z-constraint force
812   #ifdef IS_MPI
813    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
662 –  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
814   #else
815    totalFZ = totalFZ_local;
665 –  nMovingZMols = nMovingZMols_local;
816   #endif
817  
818 +  
819 +  // apply negative to fixed z-constrained molecues;
820    force[0]= 0;
821    force[1]= 0;
822    force[2]= 0;
671 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
823  
824 <  //modify the velocites of unconstrained molecules
824 >  for(int i = 0; i < zconsMols.size(); i++){
825 >
826 >    if (states[i] == zcsFixed){  
827 >  
828 >      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
829 >      zconsAtoms = zconsMols[i]->getMyAtoms();  
830 >    
831 >      for(int j =0; j < nAtomOfCurZConsMol; j++) {
832 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
833 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
834 >        zconsAtoms[j]->addFrc(force);
835 >      }
836 >    
837 >    }
838 >  
839 >  }
840 >
841 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
842 >  //      << "total force is " << calcTotalForce() << endl;
843 >  
844 >
845 >  force[0]= 0;
846 >  force[1]= 0;
847 >  force[2]= 0;
848 >
849 >  //modify the forces of unconstrained molecules
850    for(int i = 0; i < unconsMols.size(); i++){
851      
852       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
853      
854 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
854 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
855 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
856 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
857         unconsAtoms[j]->addFrc(force);
858 +     }
859      
860    }      
861  
862 < //modify the velocities of moving z-constrained molecules
862 > //modify the forces of moving z-constrained molecules
863    for(int i = 0; i < zconsMols.size(); i++) {
864 <   if (states[i] == zcsMoving){
865 <                
866 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
864 >    if (states[i] == zcsMoving){
865 >    
866 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
867  
868 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
869 <       movingZAtoms[j]->addFrc(force);
870 <     }
868 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
869 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
870 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
871 >        movingZAtoms[j]->addFrc(force);
872 >      }
873 >    }
874    }
875 + //  cout << "after substracting z-constraint force from moving molecuels "
876 + //        << "total force is " << calcTotalForce()  << endl;
877  
878 <  // apply negative to fixed z-constrained molecues;
878 > }
879 >
880 > /**
881 >  *
882 >  *
883 >  */
884 >
885 > template<typename T> void ZConstraint<T>::doHarmonic(){
886 >  double force[3];
887 >  double harmonicU;
888 >  double harmonicF;
889 >  double COM[3];
890 >  double diff;
891 >  double totalFZ_local;
892 >  double totalFZ;
893 >  
894 >  force[0] = 0;
895 >  force[1] = 0;
896 >  force[2] = 0;
897 >
898 >  totalFZ_local = 0;
899 >
900 >  for(int i = 0; i < zconsMols.size(); i++) {
901 >
902 >    if (states[i] == zcsMoving){
903 >      zconsMols[i]->getCOM(COM);
904 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
905 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
906 >
907 >      diff = COM[whichDirection] -zPos[i];
908 >    
909 >      harmonicU = 0.5 * kz[i] * diff * diff;  
910 >      info->lrPot += harmonicU;
911 >
912 >      harmonicF =  - kz[i] * diff;
913 >      totalFZ_local += harmonicF;
914 >
915 >       //adjust force
916 >    
917 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
918 >
919 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
920 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
921 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
922 >         movingZAtoms[j]->addFrc(force);
923 >       }
924 >    }
925 >
926 >  }
927 >
928 > #ifndef IS_MPI
929 >  totalFZ = totalFZ_local;
930 > #else
931 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
932 > #endif
933 >
934 >  //cout << "before substracting harmonic force from moving molecuels "
935 >  //      << "total force is " << calcTotalForce()  << endl;
936 >
937    force[0]= 0;
938    force[1]= 0;
939    force[2]= 0;
940  
941 <  for(int i = 0; i < zconsMols.size(); i++){
941 >  //modify the forces of unconstrained molecules
942 >  for(int i = 0; i < unconsMols.size(); i++){
943 >    
944 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
945 >    
946 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
947 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
948 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
949 >       unconsAtoms[j]->addFrc(force);    
950 >     }
951 >  }  
952  
953 <    if (states[i] == zcsFixed){  
954 <        
703 <      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
704 <      zconsAtoms = zconsMols[i]->getMyAtoms();  
705 <    
706 <      for(int j =0; j < nAtomOfCurZConsMol; j++) {
707 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
708 <        zconsAtoms[j]->addFrc(force);
709 <      }
710 <                
711 <    }
712 <        
713 <  }
953 >  //cout << "after substracting harmonic force from moving molecuels "
954 >  //      << "total force is " << calcTotalForce()  << endl;
955  
956   }
957  
958 + /**
959 + *
960 + */
961 +
962   template<typename T> bool ZConstraint<T>::checkZConsState(){
963    double COM[3];
964    double diff;
965    
966 <  bool changed;
966 >  int changed_local;
967 >  int changed;
968    
969 <  changed = false;
969 >  changed_local = 0;
970    
971    for(int i =0; i < zconsMols.size(); i++){
972  
# Line 728 | Line 974 | template<typename T> bool ZConstraint<T>::checkZConsSt
974      diff = fabs(COM[whichDirection] - zPos[i]);  
975      if (  diff <= zconsTol && states[i] == zcsMoving){
976        states[i] = zcsFixed;
977 <        changed = true;
977 >     changed_local = 1;
978      }
979      else if ( diff > zconsTol && states[i] == zcsFixed){
980        states[i] = zcsMoving;
981 <        changed = true;  
981 >     changed_local = 1;  
982      }
983    
984    }
985  
986 <  return changed;
986 > #ifndef IS_MPI
987 >  changed =changed_local;
988 > #else
989 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
990 > #endif
991 >
992 >  return (changed > 0);
993 >
994   }
995  
996   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
997 +
998 +  int havingFixed_local;
999 +  int havingFixed;
1000 +
1001 +  havingFixed_local = 0;
1002 +
1003    for(int i = 0; i < zconsMols.size(); i++)
1004 <    if (states[i] == zcsFixed)
1005 <      return true;
1004 >    if (states[i] == zcsFixed){
1005 >      havingFixed_local = 1;
1006 >    break;
1007 >    }
1008  
1009 <  return false;
1009 > #ifndef IS_MPI
1010 >  havingFixed = havingFixed_local;
1011 > #else
1012 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1013 > #endif
1014 >
1015 >  return (havingFixed > 0);
1016   }
1017  
1018  
# Line 753 | Line 1020 | template<typename T> bool ZConstraint<T>::haveMovingZM
1020   *
1021   */
1022   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1023 +
1024 +  int havingMoving_local;
1025 +  int havingMoving;
1026 +
1027 +  havingMoving_local = 0;
1028 +
1029    for(int i = 0; i < zconsMols.size(); i++)
1030 <    if (states[i] == zcsMoving)
1031 <      return true;
1030 >    if (states[i] == zcsMoving){
1031 >      havingMoving_local = 1;
1032 >    break;
1033 >    }
1034  
1035 <  return false;
1035 > #ifndef IS_MPI
1036 >  havingMoving = havingMoving_local;
1037 > #else
1038 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1039 > #endif
1040 >
1041 >  return (havingMoving > 0);
1042    
1043   }
1044  
1045   /**
1046 <  *
1047 <  *
767 <  */
1046 > *
1047 > */
1048  
1049 < template<typename T> void ZConstraint<T>::doHarmonic(){
1050 <  double force[3];
1051 <  double harmonicU;
1052 <  double COM[3];
1053 <  double diff;
1054 <        
1055 <  force[0] = 0;
1056 <  force[1] = 0;
1057 <  force[2] = 0;
1049 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1050 > {
1051 >  double MVzOfMovingMols_local;
1052 >  double MVzOfMovingMols;
1053 >  double totalMassOfMovingZMols_local;
1054 >  double totalMassOfMovingZMols;
1055 >  double COMvel[3];
1056 >      
1057 >  MVzOfMovingMols_local = 0;
1058 >  totalMassOfMovingZMols_local = 0;
1059  
1060 <  cout << "Moving Molecules" << endl;  
1061 <  for(int i = 0; i < zconsMols.size(); i++) {
1060 >  for(int i =0; i < unconsMols.size(); i++){
1061 >    unconsMols[i]->getCOMvel(COMvel);
1062 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1063 >  }
1064  
1065 +  for(int i = 0; i < zconsMols.size(); i++){
1066 +
1067      if (states[i] == zcsMoving){
1068 <      zconsMols[i]->getCOM(COM):
1069 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
1070 <                
1071 <                diff = COM[whichDirection] -zPos[i];
1072 <                
1073 <      harmonicU = 0.5 * kz[i] * diff * diff;  
789 <                info->ltPot += harmonicU;
1068 >      zconsMols[i]->getCOMvel(COMvel);
1069 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1070 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1071 >    }
1072 >    
1073 >  }
1074  
1075 <                force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms();
1076 <                
1077 <      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
1075 > #ifndef IS_MPI
1076 >  MVzOfMovingMols = MVzOfMovingMols_local;
1077 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1078 > #else
1079 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1080 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1081 > #endif
1082  
1083 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
1084 <         movingZAtoms[j]->addFrc(force);
797 <    }
1083 >  double vzOfMovingMols;
1084 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1085  
1086 +  return vzOfMovingMols;
1087 + }
1088 +
1089 + /**
1090 + *
1091 + */
1092 +
1093 + template<typename T> double ZConstraint<T>::calcSysCOMVel()
1094 + {
1095 +  double COMvel[3];
1096 +  double tempMVz_local;
1097 +  double tempMVz;
1098 +  double massOfZCons_local;
1099 +  double massOfZCons;
1100 +
1101 +
1102 + tempMVz_local = 0;
1103 +
1104 +  for(int i =0 ; i < nMols; i++){
1105 +    molecules[i].getCOMvel(COMvel);
1106 +   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1107    }
1108  
1109 +  massOfZCons_local = 0;
1110 +  
1111 +  for(int i = 0; i < massOfZConsMols.size(); i++){
1112 +    massOfZCons_local += massOfZConsMols[i];
1113 +  }
1114 + #ifndef IS_MPI
1115 +  massOfZCons = massOfZCons_local;
1116 +  tempMVz = tempMVz_local;
1117 + #else
1118 +  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1119 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1120 + #endif
1121 +
1122 +  return tempMVz /(totalMassOfUncons + massOfZCons);
1123   }
1124 +
1125 + /**
1126 + *
1127 + */
1128 +
1129 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1130 +
1131 +  double force[3];  
1132 +  double totalForce_local;
1133 +  double totalForce;
1134 +
1135 +  totalForce_local = 0;
1136 +
1137 +  for(int i = 0; i < nAtoms; i++){
1138 +    atoms[i]->getFrc(force);
1139 +    totalForce_local += force[whichDirection];
1140 +  }
1141 +
1142 + #ifndef IS_MPI
1143 +  totalForce = totalForce_local;
1144 + #else
1145 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1146 + #endif
1147 +
1148 +  return totalForce;
1149 +
1150 + }
1151 +
1152 + /**
1153 + *
1154 + */
1155 +
1156 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1157 +  //calculate the number of atoms of moving z-constrained molecules
1158 +  int nMovingZAtoms_local;
1159 +  int nMovingZAtoms;
1160 +  
1161 +  nMovingZAtoms_local = 0;
1162 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1163 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1164 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1165 +  
1166 + #ifdef IS_MPI
1167 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1168 + #else
1169 +  nMovingZAtoms = nMovingZAtoms_local;
1170 + #endif
1171 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1172 + }
1173 +
1174 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1175 +  return totalForce / mol->getNAtoms();
1176 + }
1177 +
1178 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1179 +  return totalForce / totNumOfMovingAtoms;
1180 + }
1181 +
1182 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1183 +    return totalForce / mol->getNAtoms();
1184 + }
1185 +
1186 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1187 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1188 + }
1189 +
1190 + /**
1191 + *
1192 + */
1193 +
1194 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1195 +  //calculate the number of atoms of moving z-constrained molecules
1196 +  double massOfMovingZAtoms_local;
1197 +  double massOfMovingZAtoms;
1198 +  
1199 +  massOfMovingZAtoms_local = 0;
1200 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1201 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1202 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1203 +  
1204 + #ifdef IS_MPI
1205 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1206 + #else
1207 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1208 + #endif
1209 +  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1210 + }
1211 +
1212 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1213 +  return totalForce * atom->getMass() / mol->getTotalMass();
1214 + }
1215 +
1216 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1217 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1218 + }
1219 +
1220 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1221 +  return totalForce * atom->getMass() / mol->getTotalMass();
1222 + }
1223 +
1224 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1225 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1226 + }
1227 +

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