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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 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 456 | Line 520 | template<typename T> void ZConstraint<T>::integrate(){
520   *
521   *
522   *
523 < */
460 <
461 <
523 > */
524   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
525    double zsys;
526 +  double COM[3];
527 +  double force[3];
528  
529    T::calcForce(calcPot, calcStress);
530  
531 <  if (checkZConsState())
532 <  zeroOutVel();
533 <  
531 >  if (checkZConsState()){
532 >    zeroOutVel();
533 >   forcePolicy->update();
534 >  }  
535    zsys = calcZSys();
536    cout << "---------------------------------------------------------------------" <<endl;
537 <  cout << "current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;      
538 <  cout << "before calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
539 <        
537 >  cout << "current time: " << info->getTime() << endl;
538 >  cout << "center of mass at z: " << zsys << endl;    
539 >  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
540 >  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
541  
542 +  //cout <<  "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
543 +
544    //do zconstraint force;
545    if (haveFixedZMols())
546      this->doZconstraintForce();
547 <
480 <
481 <      
547 >    
548    //use harmonical poteintial to move the molecules to the specified positions
549    if (haveMovingZMols())
550      this->doHarmonic();
551 <  
552 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
553 <  cout << "after calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
551 >
552 >  //cout <<  "after doHarmonic, totalForce is " << calcTotalForce() << endl;
553 >
554 >  //write out forces and current positions of z-constraint molecules
555 >  if(info->getTime() >= curZconsTime){    
556 >   for(int i = 0; i < zconsMols.size(); i++){
557 >      zconsMols[i]->getCOM(COM);
558 >    curZPos[i] = COM[whichDirection];
559 >
560 >    //if the z-constraint molecule is still moving, just record its force
561 >    if(states[i] == zcsMoving){
562 >         fz[i] = 0;
563 >      Atom** movingZAtoms;
564 >      movingZAtoms = zconsMols[i]->getMyAtoms();
565 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
566 >           movingZAtoms[j]->getFrc(force);
567 >           fz[i] += force[whichDirection];
568 >      }
569 >     }
570 >   }
571 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
572 >   curZconsTime += zconsTime;
573 >  }
574 >  
575 >  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
576 >  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
577   }
578 +
579 +
580 + /**
581 + *
582 + */
583  
584   template<typename T> double ZConstraint<T>::calcZSys()
585   {
# Line 494 | Line 588 | template<typename T> double ZConstraint<T>::calcZSys()
588    double totalMass;
589    double totalMZ_local;
590    double totalMZ;
497 –  double massOfUncons_local;
591    double massOfCurMol;
592    double COM[3];
593    
594    totalMass_local = 0;
502 –  totalMass = 0;
595    totalMZ_local = 0;
504 –  totalMZ = 0;
505 –  massOfUncons_local = 0;
506 –    
596    
597    for(int i = 0; i < nMols; i++){
598      massOfCurMol = molecules[i].getTotalMass();
# Line 511 | Line 600 | template<typename T> double ZConstraint<T>::calcZSys()
600      
601      totalMass_local += massOfCurMol;
602      totalMZ_local += massOfCurMol * COM[whichDirection];
603 <    
515 <    if(isZConstraintMol(&molecules[i]) == -1){
516 <    
517 <      massOfUncons_local += massOfCurMol;
518 <    }  
519 <    
603 >
604    }
605 +
606    
522 –  
607   #ifdef IS_MPI  
608 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
609 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
610 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
611 < #else
608 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
609 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
610 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
611 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
612 > #else
613    totalMass = totalMass_local;
614    totalMZ = totalMZ_local;
615 <  totalMassOfUncons = massOfUncons_local;
531 < #endif  
615 > #endif  
616  
617    double zsys;
618    zsys = totalMZ / totalMass;
# Line 547 | Line 631 | template<typename T> void ZConstraint<T>::thermalize(
631  
632   /**
633   *
550 – *
551 – *
634   */
635  
636   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 556 | Line 638 | template<typename T> void ZConstraint<T>::zeroOutVel()
638    Atom** fixedZAtoms;  
639    double COMvel[3];
640    double vel[3];
641 +  double zSysCOMVel;
642  
560 –  double tempMass = 0;
561 –  double tempMVz =0;
562 –  double tempVz = 0;
563 –  for(int i = 0; i < nMols; i++){
564 –    molecules[i].getCOMvel(COMvel);
565 –    tempMass +=molecules[i].getTotalMass();  
566 –         tempMVz += molecules[i].getTotalMass() * COMvel[whichDirection];
567 –         tempVz += COMvel[whichDirection];
568 –  }
569 –  cout << "initial velocity of center of mass is " << tempMVz / tempMass << endl;
570 –
643    //zero out the velocities of center of mass of fixed z-constrained molecules
644    
645    for(int i = 0; i < zconsMols.size(); i++){
646  
647 <    if (states[i] == zcsFixed){
647 >    if (states[i] == zcsFixed){
648  
649 <           zconsMols[i]->getCOMvel(COMvel);      
650 <                cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
649 >     zconsMols[i]->getCOMvel(COMvel);      
650 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
651  
652        fixedZAtoms = zconsMols[i]->getMyAtoms();
653 <          
653 >    
654        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
655          fixedZAtoms[j]->getVel(vel);
656 <             vel[whichDirection] -= COMvel[whichDirection];
657 <             fixedZAtoms[j]->setVel(vel);
656 >       vel[whichDirection] -= COMvel[whichDirection];
657 >       fixedZAtoms[j]->setVel(vel);
658        }
659  
660 <                zconsMols[i]->getCOMvel(COMvel);
661 <                cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
660 >    zconsMols[i]->getCOMvel(COMvel);
661 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
662      }
663 <        
663 >  
664    }
665  
666 <        cout << "before resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;    
667 <                  
666 >    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
667 >
668 >  zSysCOMVel = calcSysCOMVel();
669 > #ifdef IS_MPI
670 >  if(worldRank == 0){
671 > #endif
672 >    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
673 > #ifdef IS_MPI
674 >  }
675 > #endif
676 >      
677    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
678    double MVzOfMovingMols_local;
679    double MVzOfMovingMols;
# Line 611 | Line 692 | template<typename T> void ZConstraint<T>::zeroOutVel()
692      if (states[i] == zcsMoving){
693        zconsMols[i]->getCOMvel(COMvel);
694        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
695 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
695 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
696      }
697 <                
697 >    
698    }
699  
700   #ifndef IS_MPI
# Line 647 | Line 728 | template<typename T> void ZConstraint<T>::zeroOutVel()
728      if (states[i] ==zcsMoving){
729    
730        movingZAtoms = zconsMols[i]->getMyAtoms();
731 <           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
731 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
732          movingZAtoms[j]->getVel(vel);
733          vel[whichDirection] -= vzOfMovingMols;
734 <             movingZAtoms[j]->setVel(vel);
735 <          }
736 <          
734 >       movingZAtoms[j]->setVel(vel);
735 >    }
736 >    
737     }
738  
739   }
740  
660 –        cout << "after resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
741  
742 +  zSysCOMVel = calcSysCOMVel();
743 + #ifdef IS_MPI
744 +  if(worldRank == 0){
745 + #endif
746 +    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
747 + #ifdef IS_MPI
748 +  }
749 + #endif
750 +
751   }
752  
753 + /**
754 + *
755 + */
756 +
757   template<typename T> void ZConstraint<T>::doZconstraintForce(){
758  
759    Atom** zconsAtoms;
# Line 670 | Line 763 | template<typename T> void ZConstraint<T>::doZconstrain
763    double COM[3];
764    double force[3];
765  
673 –  int nMovingZMols_local;
674 –  int nMovingZMols;
766  
767 <  //constrain the molecules which do not reach the specified positions  
767 >
768 >  //constrain the molecules which do not reach the specified positions  
769      
770    //Zero Out the force of z-contrained molecules    
771    totalFZ_local = 0;
772  
773    //calculate the total z-contrained force of fixed z-contrained molecules
774 <  cout << "Fixed Molecules" << endl;
774 >
775    for(int i = 0; i < zconsMols.size(); i++){
776 <                
776 >    
777      if (states[i] == zcsFixed){
778 <                
778 >      
779        zconsMols[i]->getCOM(COM);
780        zconsAtoms = zconsMols[i]->getMyAtoms();  
781  
# Line 691 | Line 783 | template<typename T> void ZConstraint<T>::doZconstrain
783        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
784          zconsAtoms[j]->getFrc(force);
785          fz[i] += force[whichDirection];      
786 <      }
786 >      }
787        totalFZ_local += fz[i];
788  
789 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
789 >      cout << "Fixed Molecule --\tindex: " << indexOfZConsMols[i]
790 >             <<"\tcurrent zpos: " << COM[whichDirection]
791 >             << "\tcurrent fz: " <<fz[i] << endl;
792  
793      }
794 <          
794 >    
795    }
796  
797 <  //calculate the number of atoms of moving z-constrained molecules
704 <  nMovingZMols_local = 0;
705 <  for(int i = 0; i < zconsMols.size(); i++)
706 <    if(states[i] == zcsMoving)
707 <           nMovingZMols_local += massOfZConsMols[i];
708 <  
797 >  //calculate total z-constraint force
798   #ifdef IS_MPI
799    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
711 –  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
800   #else
801    totalFZ = totalFZ_local;
714 –  nMovingZMols = nMovingZMols_local;
802   #endif
803  
804 <  force[0]= 0;
718 <  force[1]= 0;
719 <  force[2]= 0;
720 <  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
721 <
722 <  //modify the forces of unconstrained molecules
723 <  for(int i = 0; i < unconsMols.size(); i++){
724 <    
725 <     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
726 <    
727 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
728 <       unconsAtoms[j]->addFrc(force);
729 <    
730 <  }      
731 <
732 < //modify the forces of moving z-constrained molecules
733 <  for(int i = 0; i < zconsMols.size(); i++) {
734 <   if (states[i] == zcsMoving){
735 <                
736 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
737 <
738 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
739 <       movingZAtoms[j]->addFrc(force);
740 <     }
741 <  }
742 <
804 >  
805    // apply negative to fixed z-constrained molecues;
806    force[0]= 0;
807    force[1]= 0;
# Line 748 | Line 810 | template<typename T> void ZConstraint<T>::doZconstrain
810    for(int i = 0; i < zconsMols.size(); i++){
811  
812      if (states[i] == zcsFixed){  
813 <        
813 >  
814        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
815        zconsAtoms = zconsMols[i]->getMyAtoms();  
816      
817        for(int j =0; j < nAtomOfCurZConsMol; j++) {
818 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
818 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
819 >        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
820          zconsAtoms[j]->addFrc(force);
821        }
822 <                
822 >    
823      }
824 <        
824 >  
825    }
826  
827 < }
827 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
828 >  //       << "total force is " << calcTotalForce() << endl;
829  
830 < template<typename T> bool ZConstraint<T>::checkZConsState(){
831 <  double COM[3];
832 <  double diff;
830 >  //calculate the number of atoms of moving z-constrained molecules
831 >  int nMovingZAtoms_local;
832 >  int nMovingZAtoms;
833    
834 <  bool changed;
834 >  nMovingZAtoms_local = 0;
835 >  for(int i = 0; i < zconsMols.size(); i++)
836 >    if(states[i] == zcsMoving)
837 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
838    
839 <  changed = false;
840 <  
841 <  for(int i =0; i < zconsMols.size(); i++){
839 > #ifdef IS_MPI
840 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
841 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
842 > #else
843 >  nMovingZAtoms = nMovingZAtoms_local;
844 > #endif
845  
846 <    zconsMols[i]->getCOM(COM);
847 <    diff = fabs(COM[whichDirection] - zPos[i]);  
848 <    if (  diff <= zconsTol && states[i] == zcsMoving){
779 <      states[i] = zcsFixed;
780 <        changed = true;
781 <    }
782 <    else if ( diff > zconsTol && states[i] == zcsFixed){
783 <      states[i] = zcsMoving;
784 <        changed = true;  
785 <    }
786 <  
787 <  }
846 >  force[0]= 0;
847 >  force[1]= 0;
848 >  force[2]= 0;
849  
850 <  return changed;
851 < }
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++){          
856 >       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
857 >       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
858 >       unconsAtoms[j]->addFrc(force);
859 >     }
860 >    
861 >  }      
862  
863 < template<typename T> bool ZConstraint<T>::haveFixedZMols(){
864 <  for(int i = 0; i < zconsMols.size(); i++)
865 <    if (states[i] == zcsFixed)
866 <      return true;
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();    
868  
869 <  return false;
870 < }
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  
877 +  //cout << "after substracting z-constraint force from moving molecuels "
878 +  //      << "total force is " << calcTotalForce()  << endl;
879  
801 – /**
802 – *
803 – */
804 – template<typename T> bool ZConstraint<T>::haveMovingZMols(){
805 –  for(int i = 0; i < zconsMols.size(); i++)
806 –    if (states[i] == zcsMoving)
807 –      return true;
808 –
809 –  return false;
810 –  
880   }
881  
882   /**
# Line 821 | Line 890 | template<typename T> void ZConstraint<T>::doHarmonic()
890    double harmonicF;
891    double COM[3];
892    double diff;
893 +  double totalFZ_local;
894    double totalFZ;
895 <        
895 >  
896    force[0] = 0;
897    force[1] = 0;
898    force[2] = 0;
899  
900 <  totalFZ = 0;
900 >  totalFZ_local = 0;
901  
832 –  cout << "Moving Molecules" << endl;  
902    for(int i = 0; i < zconsMols.size(); i++) {
903  
904      if (states[i] == zcsMoving){
905        zconsMols[i]->getCOM(COM);
906 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
907 <                
908 <                diff = COM[whichDirection] -zPos[i];
909 <                
906 >      cout << "Moving Molecule --\tindex: " << indexOfZConsMols[i] <<"\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;
911 >    info->lrPot += harmonicU;
912  
913 <      harmonicF =  - kz[i] * diff / zconsMols[i]->getNAtoms();
914 <                force[whichDirection] = harmonicF;
915 <      totalFZ += harmonicF;
916 <                
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++)          
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    force[0]= 0;
936    force[1]= 0;
937    force[2]= 0;
859 –  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
938  
939    //modify the forces of unconstrained molecules
940    for(int i = 0; i < unconsMols.size(); i++){
941      
942       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
943      
944 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
944 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
945 >       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
946 >       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
947         unconsAtoms[j]->addFrc(force);    
948 +     }
949    }  
950  
951   }
952  
953 < template<typename T> double ZConstraint<T>::calcCOMVel()
953 > /**
954 > *
955 > */
956 >
957 > template<typename T> bool ZConstraint<T>::checkZConsState(){
958 >  double COM[3];
959 >  double diff;
960 >  
961 >  int changed_local;
962 >  int changed;
963 >  
964 >  changed_local = 0;
965 >  
966 >  for(int i =0; i < zconsMols.size(); i++){
967 >
968 >    zconsMols[i]->getCOM(COM);
969 >    diff = fabs(COM[whichDirection] - zPos[i]);  
970 >    if (  diff <= zconsTol && states[i] == zcsMoving){
971 >      states[i] = zcsFixed;
972 >     changed_local = 1;
973 >    }
974 >    else if ( diff > zconsTol && states[i] == zcsFixed){
975 >      states[i] = zcsMoving;
976 >     changed_local = 1;  
977 >    }
978 >  
979 >  }
980 >
981 > #ifndef IS_MPI
982 >  changed =changed_local;
983 > #else
984 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
985 > #endif
986 >
987 >  return changed > 0 ? true : false;
988 > }
989 >
990 > template<typename T> bool ZConstraint<T>::haveFixedZMols(){
991 >
992 >  int havingFixed_local;
993 >  int havingFixed;
994 >
995 >  havingFixed_local = 0;
996 >
997 >  for(int i = 0; i < zconsMols.size(); i++)
998 >    if (states[i] == zcsFixed){
999 >      havingFixed_local = 1;
1000 >    break;
1001 >    }
1002 >
1003 > #ifndef IS_MPI
1004 >  havingFixed = havingFixed_local;
1005 > #else
1006 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1007 > #endif
1008 >
1009 >  return havingFixed > 0 ? true : false;
1010 > }
1011 >
1012 >
1013 > /**
1014 > *
1015 > */
1016 > template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1017 >
1018 >  int havingMoving_local;
1019 >  int havingMoving;
1020 >
1021 >  havingMoving_local = 0;
1022 >
1023 >  for(int i = 0; i < zconsMols.size(); i++)
1024 >    if (states[i] == zcsMoving){
1025 >      havingMoving_local = 1;
1026 >    break;
1027 >    }
1028 >
1029 > #ifndef IS_MPI
1030 >  havingMoving = havingMoving_local;
1031 > #else
1032 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1033 > #endif
1034 >
1035 >  return havingMoving > 0 ? true : false;
1036 >  
1037 > }
1038 >
1039 > /**
1040 > *
1041 > */
1042 >
1043 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1044   {
1045    double MVzOfMovingMols_local;
1046    double MVzOfMovingMols;
# Line 890 | Line 1061 | template<typename T> double ZConstraint<T>::calcCOMVel
1061      if (states[i] == zcsMoving){
1062        zconsMols[i]->getCOMvel(COMvel);
1063        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1064 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1064 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1065      }
1066 <                
1066 >    
1067    }
1068  
1069   #ifndef IS_MPI
# Line 909 | Line 1080 | template<typename T> double ZConstraint<T>::calcCOMVel
1080    return vzOfMovingMols;
1081   }
1082  
1083 + /**
1084 + *
1085 + */
1086  
1087 < template<typename T> double ZConstraint<T>::calcCOMVel2()
1087 > template<typename T> double ZConstraint<T>::calcSysCOMVel()
1088   {
1089    double COMvel[3];
1090 <  double tempMVz = 0;
1091 <  int index;
1092 <                
1090 >  double tempMVz_local;
1091 >  double tempMVz;
1092 >  double massOfZCons_local;
1093 >  double massOfZCons;
1094 >
1095 >
1096 > tempMVz_local = 0;
1097 >
1098    for(int i =0 ; i < nMols; i++){
1099 <         index = isZConstraintMol(&molecules[i]);
1100 <    if( index == -1){
922 <       molecules[i].getCOMvel(COMvel);
923 <            tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
924 <    }
925 <         else if(states[i] == zcsMoving){
926 <       zconsMols[index]->getCOMvel(COMvel);
927 <            tempMVz += massOfZConsMols[index]*COMvel[whichDirection];    
928 <         }
1099 >    molecules[i].getCOMvel(COMvel);
1100 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1101    }
1102 <        
1103 <  return tempMVz /totalMassOfUncons;
1102 >
1103 >  massOfZCons_local = 0;
1104 >  
1105 >  for(int i = 0; i < massOfZConsMols.size(); i++){
1106 >    massOfZCons_local += massOfZConsMols[i];
1107 >  }
1108 > #ifndef IS_MPI
1109 >  massOfZCons = massOfZCons_local;
1110 >  tempMVz = tempMVz_local;
1111 > #else
1112 >  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1113 >  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114 > #endif
1115 >
1116 >  return tempMVz /(totalMassOfUncons + massOfZCons);
1117   }
1118 +
1119 + /**
1120 + *
1121 + */
1122 +
1123 + template<typename T> double ZConstraint<T>::calcTotalForce(){
1124 +
1125 +  double force[3];  
1126 +  double totalForce_local;
1127 +  double totalForce;
1128 +
1129 +  totalForce_local = 0;
1130 +
1131 +  for(int i = 0; i < nAtoms; i++){
1132 +    atoms[i]->getFrc(force);
1133 +    totalForce_local += force[whichDirection];
1134 +  }
1135 +
1136 + #ifndef IS_MPI
1137 +  totalForce = totalForce_local;
1138 + #else
1139 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1140 + #endif
1141 +
1142 +  return totalForce;
1143 +
1144 + }
1145 +
1146 + /**
1147 + *
1148 + */
1149 +
1150 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1151 +  //calculate the number of atoms of moving z-constrained molecules
1152 +  int nMovingZAtoms_local;
1153 +  int nMovingZAtoms;
1154 +  
1155 +  nMovingZAtoms_local = 0;
1156 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1157 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1158 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1159 +  
1160 + #ifdef IS_MPI
1161 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1162 + #else
1163 +  nMovingZAtoms = nMovingZAtoms_local;
1164 + #endif
1165 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1166 + }
1167 +
1168 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1169 +  return totalForce / mol->getNAtoms();
1170 + }
1171 +
1172 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1173 +  return totalForce / totNumOfMovingAtoms;
1174 + }
1175 +
1176 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1177 +    return totalForce / mol->getNAtoms();
1178 + }
1179 +
1180 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1181 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1182 + }
1183 +
1184 + /**
1185 + *
1186 + */
1187 +
1188 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1189 +  //calculate the number of atoms of moving z-constrained molecules
1190 +  double massOfMovingZAtoms_local;
1191 +  double massOfMovingZAtoms;
1192 +  
1193 +  massOfMovingZAtoms_local = 0;
1194 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1195 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1196 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1197 +  
1198 + #ifdef IS_MPI
1199 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1200 + #else
1201 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1202 + #endif
1203 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1204 + }
1205 +
1206 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1207 +  return totalForce * atom->getMass() / mol->getTotalMass();
1208 + }
1209 +
1210 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1211 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1212 + }
1213 +
1214 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1215 +  return totalForce * atom->getMass() / mol->getTotalMass();
1216 + }
1217 +
1218 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1219 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1220 + }
1221 +

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