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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 738 by tim, Tue Sep 2 14:30:12 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 >      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;
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);
397 <
396 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
397 >      
398        massOfZConsMols.push_back(molecules[i].getTotalMass());  
399        
400        molecules[i].getCOM(COM);
# Line 342 | Line 407 | template<typename T> void ZConstraint<T>::update()
407  
408      }
409    }
410 +
411 +  //determine the states of z-constraint molecules
412 +  for(int i = 0; i < zconsMols.size(); i++){
413 +     zconsMols[i]->getCOM(COM);
414 +      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
415 +      states.push_back(zcsFixed);
416 +     else
417 +      states.push_back(zcsMoving);
418 +  }
419 +
420      
421    //The reason to declare fz and indexOfZconsMols as pointer to array is
422    // that we want to make the MPI communication simple
423    if(fz)
424      delete[] fz;
425 +  
426 +  if(curZPos)
427 +    delete[] curZPos;
428      
429    if(indexOfZConsMols)
430      delete[] indexOfZConsMols;
431      
432    if (zconsMols.size() > 0){
433      fz = new double[zconsMols.size()];
434 +   curZPos = new double[zconsMols.size()];
435      indexOfZConsMols =  new int[zconsMols.size()];
436      
437 <    if(!fz || !indexOfZConsMols){
437 >    if(!fz || !curZPos || !indexOfZConsMols){
438        sprintf( painCave.errMsg,
439                 "Memory allocation failure in class Zconstraint\n");
440        painCave.isFatal = 1;
# Line 369 | Line 448 | template<typename T> void ZConstraint<T>::update()
448    }
449    else{
450      fz = NULL;
451 +   curZPos = NULL;
452      indexOfZConsMols = NULL;
453    }
454    
455 +  //
456 +  forcePolicy->update();
457 +  
458   }
459  
460   #endif
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
462 > /**
463 > *  Function Name: isZConstraintMol
464 > *  Parameter
465 > *    Molecule* mol
466 > *  Return value:
467 > *    -1, if the molecule is not z-constraint molecule,
468 > *    other non-negative values, its index in indexOfAllZConsMols vector
469   */
470  
471   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 410 | Line 494 | template<typename T> int ZConstraint<T>::isZConstraint
494    return -1;
495   }
496  
413 – /**
414 – * Description:
415 – *  Reset the z coordinates
416 – */
497   template<typename T> void ZConstraint<T>::integrate(){
498 +
499 +  // creat zconsWriter  
500 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
501    
502 +  if(!fzOut){
503 +    sprintf( painCave.errMsg,
504 +             "Memory allocation failure in class Zconstraint\n");
505 +    painCave.isFatal = 1;
506 +    simError();
507 +  }
508 +  
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 430 | Line 522 | template<typename T> void ZConstraint<T>::integrate(){
522   *
523   *
524   *
525 < */
434 <
435 <
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())
535 <    zeroOutVel();
534 >  if (checkZConsState()){    
535 >    zeroOutVel();    
536 >    forcePolicy->update();
537 >  }  
538 >  
539 >  zsys = calcZSys();
540 >  zSysCOMVel = calcSysCOMVel();
541 > #ifdef IS_MPI
542 >  if(worldRank == 0){
543 > #endif
544 >     //cout << "---------------------------------------------------------------------" <<endl;
545 >     //cout << "current time: " << info->getTime() << endl;
546 >     //cout << "center of mass at z: " << zsys << endl;    
547 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
548  
549 + #ifdef IS_MPI
550 +  }
551 + #endif
552 +
553    //do zconstraint force;
554    if (haveFixedZMols())
555      this->doZconstraintForce();
556 <  
556 >
557    //use harmonical poteintial to move the molecules to the specified positions
558    if (haveMovingZMols())
559 <    //this->doHarmonic();
560 <  
561 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
562 <      
559 >    this->doHarmonic();
560 >
561 >  //write out forces and current positions of z-constraint molecules
562 >  if(info->getTime() >= curZconsTime){    
563 >   for(int i = 0; i < zconsMols.size(); i++){
564 >      zconsMols[i]->getCOM(COM);
565 >    curZPos[i] = COM[whichDirection];
566 >
567 >    //if the z-constraint molecule is still moving, just record its force
568 >    if(states[i] == zcsMoving){
569 >         fz[i] = 0;
570 >      Atom** movingZAtoms;
571 >      movingZAtoms = zconsMols[i]->getMyAtoms();
572 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
573 >           movingZAtoms[j]->getFrc(force);
574 >           fz[i] += force[whichDirection];
575 >      }
576 >     }
577 >   }
578 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
579 >   curZconsTime += zconsTime;
580 >  }
581 >
582 >  zSysCOMVel = calcSysCOMVel();  
583 > #ifdef IS_MPI
584 >  if(worldRank == 0){
585 > #endif
586 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
587 > #ifdef IS_MPI
588 >  }
589 > #endif
590   }
591 +
592 +
593 + /**
594 + *
595 + */
596  
597   template<typename T> double ZConstraint<T>::calcZSys()
598   {
# Line 459 | Line 601 | template<typename T> double ZConstraint<T>::calcZSys()
601    double totalMass;
602    double totalMZ_local;
603    double totalMZ;
462 –  double massOfUncons_local;
604    double massOfCurMol;
605    double COM[3];
606    
607    totalMass_local = 0;
467 –  totalMass = 0;
608    totalMZ_local = 0;
469 –  totalMZ = 0;
470 –  massOfUncons_local = 0;
471 –    
609    
610    for(int i = 0; i < nMols; i++){
611      massOfCurMol = molecules[i].getTotalMass();
# Line 476 | Line 613 | template<typename T> double ZConstraint<T>::calcZSys()
613      
614      totalMass_local += massOfCurMol;
615      totalMZ_local += massOfCurMol * COM[whichDirection];
616 <    
480 <    if(isZConstraintMol(&molecules[i]) == -1){
481 <    
482 <      massOfUncons_local += massOfCurMol;
483 <    }  
484 <    
616 >
617    }
618 +
619    
487 –  
620   #ifdef IS_MPI  
621 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
622 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
623 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
624 < #else
621 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
622 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
623 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
624 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
625 > #else
626    totalMass = totalMass_local;
627    totalMZ = totalMZ_local;
628 <  totalMassOfUncons = massOfUncons_local;
496 < #endif  
628 > #endif  
629  
630    double zsys;
631    zsys = totalMZ / totalMass;
# Line 512 | Line 644 | template<typename T> void ZConstraint<T>::thermalize(
644  
645   /**
646   *
515 – *
516 – *
647   */
648  
649   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 521 | Line 651 | template<typename T> void ZConstraint<T>::zeroOutVel()
651    Atom** fixedZAtoms;  
652    double COMvel[3];
653    double vel[3];
654 <  
654 >  double zSysCOMVel;
655 >
656    //zero out the velocities of center of mass of fixed z-constrained molecules
657    
658    for(int i = 0; i < zconsMols.size(); i++){
659  
660 <    if (states[i] == zcsFixed){
660 >    if (states[i] == zcsFixed){
661  
662 <        zconsMols[i]->getCOMvel(COMvel);      
662 >     zconsMols[i]->getCOMvel(COMvel);      
663 >     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
664 >
665        fixedZAtoms = zconsMols[i]->getMyAtoms();
666 <          
666 >    
667        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
668          fixedZAtoms[j]->getVel(vel);
669 <          vel[whichDirection] -= COMvel[whichDirection];
670 <          fixedZAtoms[j]->setVel(vel);
669 >       vel[whichDirection] -= COMvel[whichDirection];
670 >       fixedZAtoms[j]->setVel(vel);
671        }
672 <          
672 >
673 >    zconsMols[i]->getCOMvel(COMvel);
674 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
675      }
541 –        
542 –  }
676    
677 +  }
678 +
679 +    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
680 +
681 +  zSysCOMVel = calcSysCOMVel();
682 + #ifdef IS_MPI
683 +  if(worldRank == 0){
684 + #endif
685 +     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
686 + #ifdef IS_MPI
687 +  }
688 + #endif
689 +      
690    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
691    double MVzOfMovingMols_local;
692    double MVzOfMovingMols;
# Line 555 | Line 701 | template<typename T> void ZConstraint<T>::zeroOutVel()
701      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
702    }
703  
704 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
559 <
704 >  for(int i = 0; i < zconsMols.size(); i++){
705      if (states[i] == zcsMoving){
706        zconsMols[i]->getCOMvel(COMvel);
707        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
708 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
708 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
709      }
710 <                
710 >    
711    }
712  
713   #ifndef IS_MPI
# Line 591 | Line 736 | template<typename T> void ZConstraint<T>::zeroOutVel()
736  
737    //modify the velocities of moving z-constrained molecuels
738    Atom** movingZAtoms;
739 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
739 >  for(int i = 0; i < zconsMols.size(); i++){
740  
741      if (states[i] ==zcsMoving){
742    
743        movingZAtoms = zconsMols[i]->getMyAtoms();
744 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
744 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
745          movingZAtoms[j]->getVel(vel);
746          vel[whichDirection] -= vzOfMovingMols;
747 <          movingZAtoms[j]->setVel(vel);
603 <        }
604 <          
747 >       movingZAtoms[j]->setVel(vel);
748      }
749 +    
750 +   }
751  
752 + }
753 +
754 +
755 +  zSysCOMVel = calcSysCOMVel();
756 + #ifdef IS_MPI
757 +  if(worldRank == 0){
758 + #endif
759 +     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
760 + #ifdef IS_MPI
761    }
762 + #endif
763  
764   }
765  
766 + /**
767 + *
768 + */
769 +
770   template<typename T> void ZConstraint<T>::doZconstraintForce(){
771  
772    Atom** zconsAtoms;
# Line 616 | Line 775 | template<typename T> void ZConstraint<T>::doZconstrain
775    double COMvel[3];  
776    double COM[3];
777    double force[3];
619 –  double zsys;
778  
779 <  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;  
779 >  //constrain the molecules which do not reach the specified positions  
780      
781    //Zero Out the force of z-contrained molecules    
782    totalFZ_local = 0;
783  
784    //calculate the total z-contrained force of fixed z-contrained molecules
785 <  cout << "Fixed Molecules" << endl;
785 >  
786 >  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
787 >  //       << "total force is " << calcTotalForce() << endl;
788 >
789    for(int i = 0; i < zconsMols.size(); i++){
790 <                
790 >    
791      if (states[i] == zcsFixed){
792 <                
792 >      
793        zconsMols[i]->getCOM(COM);
794        zconsAtoms = zconsMols[i]->getMyAtoms();  
795  
# Line 642 | Line 797 | template<typename T> void ZConstraint<T>::doZconstrain
797        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
798          zconsAtoms[j]->getFrc(force);
799          fz[i] += force[whichDirection];      
800 <      }
800 >      }
801        totalFZ_local += fz[i];
802  
803 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
803 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
804 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
805 >      //      << "\tcurrent fz: " <<fz[i] << endl;
806  
807 +
808      }
809 <          
809 >    
810    }
811  
812 <  //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 <  }
812 >  //calculate total z-constraint force
813   #ifdef IS_MPI
814    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);
815   #else
816    totalFZ = totalFZ_local;
665 –  nMovingZMols = nMovingZMols_local;
817   #endif
818  
819 +  
820 +  // apply negative to fixed z-constrained molecues;
821    force[0]= 0;
822    force[1]= 0;
823    force[2]= 0;
671 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
824  
825 <  //modify the velocites of unconstrained molecules
825 >  for(int i = 0; i < zconsMols.size(); i++){
826 >
827 >    if (states[i] == zcsFixed){  
828 >  
829 >      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
830 >      zconsAtoms = zconsMols[i]->getMyAtoms();  
831 >    
832 >      for(int j =0; j < nAtomOfCurZConsMol; j++) {
833 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
834 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
835 >        zconsAtoms[j]->addFrc(force);
836 >      }
837 >    
838 >    }
839 >  
840 >  }
841 >
842 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
843 >  //      << "total force is " << calcTotalForce() << endl;
844 >  
845 >
846 >  force[0]= 0;
847 >  force[1]= 0;
848 >  force[2]= 0;
849 >
850 >  //modify the forces of unconstrained molecules
851    for(int i = 0; i < unconsMols.size(); i++){
852      
853       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
854      
855 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
855 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
856 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
857 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
858         unconsAtoms[j]->addFrc(force);
859 +     }
860      
861    }      
862  
863 < //modify the velocities of moving z-constrained molecules
863 > //modify the forces of moving z-constrained molecules
864    for(int i = 0; i < zconsMols.size(); i++) {
865 <   if (states[i] == zcsMoving){
866 <                
867 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
865 >    if (states[i] == zcsMoving){
866 >    
867 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
868  
869 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
870 <       movingZAtoms[j]->addFrc(force);
871 <     }
869 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
870 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
871 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
872 >        movingZAtoms[j]->addFrc(force);
873 >      }
874 >    }
875    }
876 + //  cout << "after substracting z-constraint force from moving molecuels "
877 + //        << "total force is " << calcTotalForce()  << endl;
878  
879 <  // apply negative to fixed z-constrained molecues;
879 > }
880 >
881 > /**
882 >  *
883 >  *
884 >  */
885 >
886 > template<typename T> void ZConstraint<T>::doHarmonic(){
887 >  double force[3];
888 >  double harmonicU;
889 >  double harmonicF;
890 >  double COM[3];
891 >  double diff;
892 >  double totalFZ_local;
893 >  double totalFZ;
894 >  
895 >  force[0] = 0;
896 >  force[1] = 0;
897 >  force[2] = 0;
898 >
899 >  totalFZ_local = 0;
900 >
901 >  for(int i = 0; i < zconsMols.size(); i++) {
902 >
903 >    if (states[i] == zcsMoving){
904 >      zconsMols[i]->getCOM(COM);
905 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
906 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
907 >
908 >      diff = COM[whichDirection] -zPos[i];
909 >    
910 >      harmonicU = 0.5 * kz[i] * diff * diff;  
911 >      info->lrPot += harmonicU;
912 >
913 >      harmonicF =  - kz[i] * diff;
914 >      totalFZ_local += harmonicF;
915 >
916 >       //adjust force
917 >    
918 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
919 >
920 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
921 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
922 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
923 >         movingZAtoms[j]->addFrc(force);
924 >       }
925 >    }
926 >
927 >  }
928 >
929 > #ifndef IS_MPI
930 >  totalFZ = totalFZ_local;
931 > #else
932 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
933 > #endif
934 >
935 >  cout << "before substracting harmonic force from moving molecuels "
936 >        << "total force is " << calcTotalForce()  << endl;
937 >
938    force[0]= 0;
939    force[1]= 0;
940    force[2]= 0;
941  
942 <  for(int i = 0; i < zconsMols.size(); i++){
942 >  //modify the forces of unconstrained molecules
943 >  for(int i = 0; i < unconsMols.size(); i++){
944 >    
945 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
946 >    
947 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
948 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
949 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
950 >       unconsAtoms[j]->addFrc(force);    
951 >     }
952 >  }  
953  
954 <    if (states[i] == zcsFixed){  
955 <        
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 <  }
954 >  cout << "after substracting harmonic force from moving molecuels "
955 >        << "total force is " << calcTotalForce()  << endl;
956  
957   }
958  
959 + /**
960 + *
961 + */
962 +
963   template<typename T> bool ZConstraint<T>::checkZConsState(){
964    double COM[3];
965    double diff;
966    
967 <  bool changed;
967 >  int changed_local;
968 >  int changed;
969    
970 <  changed = false;
970 >  changed_local = 0;
971    
972    for(int i =0; i < zconsMols.size(); i++){
973  
# Line 728 | Line 975 | template<typename T> bool ZConstraint<T>::checkZConsSt
975      diff = fabs(COM[whichDirection] - zPos[i]);  
976      if (  diff <= zconsTol && states[i] == zcsMoving){
977        states[i] = zcsFixed;
978 <        changed = true;
978 >     changed_local = 1;
979      }
980      else if ( diff > zconsTol && states[i] == zcsFixed){
981        states[i] = zcsMoving;
982 <        changed = true;  
982 >     changed_local = 1;  
983      }
984    
985    }
986  
987 <  return changed;
987 > #ifndef IS_MPI
988 >  changed =changed_local;
989 > #else
990 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
991 > #endif
992 >
993 >  return (changed > 0);
994 >
995   }
996  
997   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
998 +
999 +  int havingFixed_local;
1000 +  int havingFixed;
1001 +
1002 +  havingFixed_local = 0;
1003 +
1004    for(int i = 0; i < zconsMols.size(); i++)
1005 <    if (states[i] == zcsFixed)
1006 <      return true;
1005 >    if (states[i] == zcsFixed){
1006 >      havingFixed_local = 1;
1007 >    break;
1008 >    }
1009  
1010 <  return false;
1010 > #ifndef IS_MPI
1011 >  havingFixed = havingFixed_local;
1012 > #else
1013 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1014 > #endif
1015 >
1016 >  return (havingFixed > 0);
1017   }
1018  
1019  
# Line 753 | Line 1021 | template<typename T> bool ZConstraint<T>::haveMovingZM
1021   *
1022   */
1023   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1024 +
1025 +  int havingMoving_local;
1026 +  int havingMoving;
1027 +
1028 +  havingMoving_local = 0;
1029 +
1030    for(int i = 0; i < zconsMols.size(); i++)
1031 <    if (states[i] == zcsMoving)
1032 <      return true;
1031 >    if (states[i] == zcsMoving){
1032 >      havingMoving_local = 1;
1033 >    break;
1034 >    }
1035  
1036 <  return false;
1036 > #ifndef IS_MPI
1037 >  havingMoving = havingMoving_local;
1038 > #else
1039 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1040 > #endif
1041 >
1042 >  return (havingMoving > 0);
1043    
1044   }
1045  
1046   /**
1047 <  *
1048 <  *
767 <  */
1047 > *
1048 > */
1049  
1050 < template<typename T> void ZConstraint<T>::doHarmonic(){
1051 <  double force[3];
1052 <  double harmonicU;
1053 <  double COM[3];
1054 <  double diff;
1055 <        
1056 <  force[0] = 0;
1057 <  force[1] = 0;
1058 <  force[2] = 0;
1050 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1051 > {
1052 >  double MVzOfMovingMols_local;
1053 >  double MVzOfMovingMols;
1054 >  double totalMassOfMovingZMols_local;
1055 >  double totalMassOfMovingZMols;
1056 >  double COMvel[3];
1057 >      
1058 >  MVzOfMovingMols_local = 0;
1059 >  totalMassOfMovingZMols_local = 0;
1060  
1061 <  cout << "Moving Molecules" << endl;  
1062 <  for(int i = 0; i < zconsMols.size(); i++) {
1061 >  for(int i =0; i < unconsMols.size(); i++){
1062 >    unconsMols[i]->getCOMvel(COMvel);
1063 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1064 >  }
1065  
1066 +  for(int i = 0; i < zconsMols.size(); i++){
1067 +
1068      if (states[i] == zcsMoving){
1069 <      zconsMols[i]->getCOM(COM):
1070 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
1071 <                
1072 <                diff = COM[whichDirection] -zPos[i];
1073 <                
1074 <      harmonicU = 0.5 * kz[i] * diff * diff;  
789 <                info->ltPot += harmonicU;
1069 >      zconsMols[i]->getCOMvel(COMvel);
1070 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1071 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1072 >    }
1073 >    
1074 >  }
1075  
1076 <                force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms();
1077 <                
1078 <      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
1076 > #ifndef IS_MPI
1077 >  MVzOfMovingMols = MVzOfMovingMols_local;
1078 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1079 > #else
1080 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1081 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1082 > #endif
1083  
1084 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
1085 <         movingZAtoms[j]->addFrc(force);
797 <    }
1084 >  double vzOfMovingMols;
1085 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1086  
1087 +  return vzOfMovingMols;
1088 + }
1089 +
1090 + /**
1091 + *
1092 + */
1093 +
1094 + template<typename T> double ZConstraint<T>::calcSysCOMVel()
1095 + {
1096 +  double COMvel[3];
1097 +  double tempMVz_local;
1098 +  double tempMVz;
1099 +  double massOfZCons_local;
1100 +  double massOfZCons;
1101 +
1102 +
1103 + tempMVz_local = 0;
1104 +
1105 +  for(int i =0 ; i < nMols; i++){
1106 +    molecules[i].getCOMvel(COMvel);
1107 +   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1108    }
1109  
1110 +  massOfZCons_local = 0;
1111 +  
1112 +  for(int i = 0; i < massOfZConsMols.size(); i++){
1113 +    massOfZCons_local += massOfZConsMols[i];
1114 +  }
1115 + #ifndef IS_MPI
1116 +  massOfZCons = massOfZCons_local;
1117 +  tempMVz = tempMVz_local;
1118 + #else
1119 +  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1120 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1121 + #endif
1122 +
1123 +  return tempMVz /(totalMassOfUncons + massOfZCons);
1124   }
1125 +
1126 + /**
1127 + *
1128 + */
1129 +
1130 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1131 +
1132 +  double force[3];  
1133 +  double totalForce_local;
1134 +  double totalForce;
1135 +
1136 +  totalForce_local = 0;
1137 +
1138 +  for(int i = 0; i < nAtoms; i++){
1139 +    atoms[i]->getFrc(force);
1140 +    totalForce_local += force[whichDirection];
1141 +  }
1142 +
1143 + #ifndef IS_MPI
1144 +  totalForce = totalForce_local;
1145 + #else
1146 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1147 + #endif
1148 +
1149 +  return totalForce;
1150 +
1151 + }
1152 +
1153 + /**
1154 + *
1155 + */
1156 +
1157 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1158 +  //calculate the number of atoms of moving z-constrained molecules
1159 +  int nMovingZAtoms_local;
1160 +  int nMovingZAtoms;
1161 +  
1162 +  nMovingZAtoms_local = 0;
1163 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1164 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1165 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1166 +  
1167 + #ifdef IS_MPI
1168 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1169 + #else
1170 +  nMovingZAtoms = nMovingZAtoms_local;
1171 + #endif
1172 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1173 + }
1174 +
1175 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1176 +  return totalForce / mol->getNAtoms();
1177 + }
1178 +
1179 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1180 +  return totalForce / totNumOfMovingAtoms;
1181 + }
1182 +
1183 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1184 +    return totalForce / mol->getNAtoms();
1185 + }
1186 +
1187 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1188 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1189 + }
1190 +
1191 + /**
1192 + *
1193 + */
1194 +
1195 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1196 +  //calculate the number of atoms of moving z-constrained molecules
1197 +  double massOfMovingZAtoms_local;
1198 +  double massOfMovingZAtoms;
1199 +  
1200 +  massOfMovingZAtoms_local = 0;
1201 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1202 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1203 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1204 +  
1205 + #ifdef IS_MPI
1206 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1207 + #else
1208 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1209 + #endif
1210 +  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1211 + }
1212 +
1213 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1214 +  return totalForce * atom->getMass() / mol->getTotalMass();
1215 + }
1216 +
1217 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1218 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1219 + }
1220 +
1221 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1222 +  return totalForce * atom->getMass() / mol->getTotalMass();
1223 + }
1224 +
1225 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1226 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1227 + }
1228 +

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