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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 696 by tim, Thu Aug 14 16:16:39 2003 UTC vs.
Revision 830 by gezelter, Tue Oct 28 16:20:28 2003 UTC

# Line 1 | Line 1
1   #include "Integrator.hpp"
2   #include "simError.h"
3 < #include <cmath>
3 > #include <math.h>
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), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL),
6 >                                      fzOut(NULL), curZconsTime(0), forcePolicy(NULL)
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() - 1].zconsIndex;
200  
# Line 173 | Line 213 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
213  
214        //if user does not specify the zpos for the zconstraint molecule
215        //its initial z coordinate  will be used as default
216 <      for(int i = 0; i < parameters->size(); i++){
216 >      for(int i = 0; i < (int)(parameters->size()); i++){
217  
218 <              if(!(*parameters)[i].havingZPos){
179 <
218 >        if(!(*parameters)[i].havingZPos){
219   #ifndef IS_MPI
220 <            for(int j = 0; j < nMols; j++){
221 <              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 <                 molecules[j].getCOM(COM);
223 <                          break;
185 <              }
220 >          for(int j = 0; j < nMols; j++){
221 >            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 >              molecules[j].getCOM(COM);
223 >        break;
224              }
225 +          }
226   #else
227              //query which processor current zconstraint molecule belongs to
228 <           int *MolToProcMap;
229 <           int whichNode;
230 <                         double initZPos;
231 <           MolToProcMap = mpiSim->getMolToProcMap();
232 <           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233 <                          
234 <           //broadcast the zpos of current z-contraint molecule
235 <           //the node which contain this
228 >          int *MolToProcMap;
229 >          int whichNode;
230 >          
231 >          MolToProcMap = mpiSim->getMolToProcMap();
232 >          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233 >        
234 >          //broadcast the zpos of current z-contraint molecule
235 >          //the node which contain this
236            
237 <           if (worldRank == whichNode ){
238 <                                                
239 <             for(int j = 0; j < nMols; j++)
240 <               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 <                 molecules[j].getCOM(COM);
242 <                                         break;
243 <               }
244 <                                
245 <           }
237 >          if (worldRank == whichNode ){
238 >            
239 >            for(int j = 0; j < nMols; j++)
240 >              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 >                molecules[j].getCOM(COM);
242 >          break;
243 >              }
244 >        
245 >          }
246  
247 <            MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);                          
247 >          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, 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;
# Line 262 | Line 304 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
304    }
305  
306    //determine the states of z-constraint molecules
307 <  for(int i = 0; i < zconsMols.size(); i++){
307 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
308      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309  
310 <         zconsMols[i]->getCOM(COM);
310 >    zconsMols[i]->getCOM(COM);
311      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
312 <                states.push_back(zcsFixed);
313 <         else
314 <                states.push_back(zcsMoving);
312 >      states.push_back(zcsFixed);
313 >    else
314 >      states.push_back(zcsMoving);
315    }
316    
317   #endif
# Line 278 | Line 320 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
320    double totalMassOfUncons_local;
321    totalMassOfUncons_local = 0;
322    
323 <  for(int i = 0; i < unconsMols.size(); i++)
323 >  for(int i = 0; i < (int)(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, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
329 >  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
330 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331   #endif
332  
290 –
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
336 <  for(int i = 0; i < unconsMols.size(); i++)
336 >  for(int i = 0; i < (int)(unconsMols.size()); i++)
337      nUnconsAtoms_local += unconsMols[i]->getNAtoms();
338      
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  
304 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
305 <  
306 <  if(!fzOut){
307 <    sprintf( painCave.errMsg,
308 <             "Memory allocation failure in class Zconstraint\n");
309 <    painCave.isFatal = 1;
310 <    simError();
311 <  }
312 <  
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 348 | 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);
352 <                        
396 >      kz.push_back((*parameters)[index].kRatio * zForceConst);
397        massOfZConsMols.push_back(molecules[i].getTotalMass());  
398        
399        molecules[i].getCOM(COM);
# Line 364 | Line 408 | template<typename T> void ZConstraint<T>::update()
408    }
409  
410    //determine the states of z-constraint molecules
411 <  for(int i = 0; i < zconsMols.size(); i++){
412 <           zconsMols[i]->getCOM(COM);
411 >  for(int i = 0; i < (int)(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);
414 >      states.push_back(zcsFixed);
415 >     else
416 >      states.push_back(zcsMoving);
417    }
418  
419      
# Line 377 | Line 421 | template<typename T> void ZConstraint<T>::update()
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;
440        simError();
441      }
442          
443 <    for(int i = 0; i < zconsMols.size(); i++){
443 >    for(int i = 0; i < (int)(zconsMols.size()); i++){
444        indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
445      }
446  
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 441 | Line 494 | template<typename T> void ZConstraint<T>::integrate(){
494   }
495  
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 459 | Line 524 | template<typename T> void ZConstraint<T>::calcForce(in
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 <  cout << "---------------------------------------------------------------------" <<endl;
540 <  cout << "current time: " << info->getTime() << endl;
541 <  cout << "center of mass at z: " << zsys << endl;      
542 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
543 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
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 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
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 <  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
560 >  //write out forces and current positions of z-constraint molecules
561 >  if(info->getTime() >= curZconsTime){    
562 >   for(int i = 0; i < (int)(zconsMols.size()); i++){
563 >      zconsMols[i]->getCOM(COM);
564 >    curZPos[i] = COM[whichDirection];
565  
566 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
567 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
568 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
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 498 | Line 602 | template<typename T> double ZConstraint<T>::calcZSys()
602    double totalMZ;
603    double massOfCurMol;
604    double COM[3];
605 <        
605 >  
606    totalMass_local = 0;
607    totalMZ_local = 0;
608    
# Line 513 | Line 617 | template<typename T> double ZConstraint<T>::calcZSys()
617  
618    
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);  
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;
# Line 537 | Line 643 | template<typename T> void ZConstraint<T>::thermalize(
643  
644   /**
645   *
540 – *
541 – *
646   */
647  
648   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 546 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel()
650    Atom** fixedZAtoms;  
651    double COMvel[3];
652    double vel[3];
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++){
657 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
658  
659 <    if (states[i] == zcsFixed){
659 >    if (states[i] == zcsFixed){
660  
661 <           zconsMols[i]->getCOMvel(COMvel);      
662 <                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
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  
672 <                zconsMols[i]->getCOMvel(COMvel);
673 <                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
672 >    zconsMols[i]->getCOMvel(COMvel);
673 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
674      }
675 <        
675 >  
676    }
677  
678 <        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
679 <        cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;  
680 <                  
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 582 | Line 695 | template<typename T> void ZConstraint<T>::zeroOutVel()
695    MVzOfMovingMols_local = 0;
696    totalMassOfMovingZMols_local = 0;
697  
698 <  for(int i =0; i < unconsMols.size(); i++){
698 >  for(int i =0; i < (int)(unconsMols.size()); i++){
699      unconsMols[i]->getCOMvel(COMvel);
700      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
701    }
702  
703 <  for(int i = 0; i < zconsMols.size(); i++){
703 >  for(int i = 0; i < (int)(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 609 | Line 722 | template<typename T> void ZConstraint<T>::zeroOutVel()
722  
723    //modify the velocites of unconstrained molecules  
724    Atom** unconsAtoms;
725 <  for(int i = 0; i < unconsMols.size(); i++){
725 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
726    
727      unconsAtoms = unconsMols[i]->getMyAtoms();
728      for(int j = 0; j < unconsMols[i]->getNAtoms();j++){
# Line 622 | 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.size(); i++){
738 >  for(int i = 0; i < (int)(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);
747 <          }
748 <          
746 >       movingZAtoms[j]->setVel(vel);
747 >    }
748 >    
749     }
750  
751   }
752  
640 –        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
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;
772    double totalFZ;
773    double totalFZ_local;
649 –  double COMvel[3];  
774    double COM[3];
775    double force[3];
776  
777 <
654 <
655 <  //constrain the molecules which do not reach the specified positions  
777 >  //constrain the molecules which do not reach the specified positions  
778      
779    //Zero Out the force of z-contrained molecules    
780    totalFZ_local = 0;
781  
782    //calculate the total z-contrained force of fixed z-contrained molecules
783 <  cout << "Fixed Molecules" << endl;
784 <  for(int i = 0; i < zconsMols.size(); i++){
785 <                
783 >  
784 >  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
785 >  //       << "total force is " << calcTotalForce() << endl;
786 >
787 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
788 >    
789      if (states[i] == zcsFixed){
790 <                
790 >      
791        zconsMols[i]->getCOM(COM);
792        zconsAtoms = zconsMols[i]->getMyAtoms();  
793  
# Line 670 | Line 795 | template<typename T> void ZConstraint<T>::doZconstrain
795        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
796          zconsAtoms[j]->getFrc(force);
797          fz[i] += force[whichDirection];      
798 <      }
798 >      }
799        totalFZ_local += fz[i];
800  
801 <      cout << "index: " << indexOfZConsMols[i]
802 <                                <<"\tcurrent zpos: " << COM[whichDirection]
803 <                                << "\tcurrent fz: " <<fz[i] << endl;
801 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
802 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
803 >      //      << "\tcurrent fz: " <<fz[i] << endl;
804  
805 <    }
806 <          
805 >
806 >    }
807 >    
808    }
809 <        
809 >
810 >  //calculate total z-constraint force
811 > #ifdef IS_MPI
812 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
813 > #else
814 >  totalFZ = totalFZ_local;
815 > #endif
816 >
817 >  
818    // apply negative to fixed z-constrained molecues;
819    force[0]= 0;
820    force[1]= 0;
821    force[2]= 0;
822  
823 <  for(int i = 0; i < zconsMols.size(); i++){
823 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
824  
825      if (states[i] == zcsFixed){  
826 <        
826 >  
827        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
828        zconsAtoms = zconsMols[i]->getMyAtoms();  
829      
830        for(int j =0; j < nAtomOfCurZConsMol; j++) {
831 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
831 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
832 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
833          zconsAtoms[j]->addFrc(force);
834        }
835 <                
835 >    
836      }
837 <        
837 >  
838    }
839  
840 <  cout << "after zero out z-constraint force on fixed z-constraint molecuels "
841 <                  << "total force is " << calcTotalForce() << endl;
842 <  //calculate the number of atoms of moving z-constrained molecules
708 <  int nMovingZAtoms_local;
709 <  int nMovingZAtoms;
710 <        
711 <  nMovingZAtoms_local = 0;
712 <  for(int i = 0; i < zconsMols.size(); i++)
713 <    if(states[i] == zcsMoving)
714 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
715 <  
716 < #ifdef IS_MPI
717 <  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
718 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
719 < #else
720 <  totalFZ = totalFZ_local;
721 <  nMovingZAtoms = nMovingZAtoms_local;
722 < #endif
840 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
841 >  //      << "total force is " << calcTotalForce() << endl;
842 >  
843  
844    force[0]= 0;
845    force[1]= 0;
846    force[2]= 0;
727 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
847  
848    //modify the forces of unconstrained molecules
849 <  int accessCount = 0;
731 <  for(int i = 0; i < unconsMols.size(); i++){
849 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
850      
851       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
852      
853 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
853 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
854 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
855 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
856         unconsAtoms[j]->addFrc(force);
857 +     }
858      
859    }      
860  
861   //modify the forces of moving z-constrained molecules
862 <  for(int i = 0; i < zconsMols.size(); i++) {
862 >  for(int i = 0; i < (int)(zconsMols.size()); i++) {
863      if (states[i] == zcsMoving){
864 <                
864 >    
865        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
866  
867 <      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
867 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
868 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
869 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
870          movingZAtoms[j]->addFrc(force);
871 +      }
872      }
873    }
874 <        
875 <  cout << "after substracting z-constraint force from moving molecuels "
752 <                  << "total force is " << calcTotalForce()  << endl;
874 > //  cout << "after substracting z-constraint force from moving molecuels "
875 > //        << "total force is " << calcTotalForce()  << endl;
876  
877   }
878  
756 – template<typename T> bool ZConstraint<T>::checkZConsState(){
757 –  double COM[3];
758 –  double diff;
759 –  
760 –  bool changed;
761 –  
762 –  changed = false;
763 –  
764 –  for(int i =0; i < zconsMols.size(); i++){
765 –
766 –    zconsMols[i]->getCOM(COM);
767 –    diff = fabs(COM[whichDirection] - zPos[i]);  
768 –    if (  diff <= zconsTol && states[i] == zcsMoving){
769 –      states[i] = zcsFixed;
770 –        changed = true;
771 –    }
772 –    else if ( diff > zconsTol && states[i] == zcsFixed){
773 –      states[i] = zcsMoving;
774 –        changed = true;  
775 –    }
776 –  
777 –  }
778 –
779 –  return changed;
780 – }
781 –
782 – template<typename T> bool ZConstraint<T>::haveFixedZMols(){
783 –  for(int i = 0; i < zconsMols.size(); i++)
784 –    if (states[i] == zcsFixed)
785 –      return true;
786 –
787 –  return false;
788 – }
789 –
790 –
879   /**
792 – *
793 – */
794 – template<typename T> bool ZConstraint<T>::haveMovingZMols(){
795 –  for(int i = 0; i < zconsMols.size(); i++)
796 –    if (states[i] == zcsMoving)
797 –      return true;
798 –
799 –  return false;
800 –  
801 – }
802 –
803 – /**
880    *
881    *
882    */
# Line 811 | Line 887 | template<typename T> void ZConstraint<T>::doHarmonic()
887    double harmonicF;
888    double COM[3];
889    double diff;
890 +  double totalFZ_local;
891    double totalFZ;
892 <        
892 >  
893    force[0] = 0;
894    force[1] = 0;
895    force[2] = 0;
896  
897 <  totalFZ = 0;
897 >  totalFZ_local = 0;
898  
899 <  cout << "Moving Molecules" << endl;  
823 <  for(int i = 0; i < zconsMols.size(); i++) {
899 >  for(int i = 0; i < (int)(zconsMols.size()); i++) {
900  
901      if (states[i] == zcsMoving){
902        zconsMols[i]->getCOM(COM);
903 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
904 <                
905 <                diff = COM[whichDirection] -zPos[i];
906 <                
903 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
904 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
905 >
906 >      diff = COM[whichDirection] -zPos[i];
907 >    
908        harmonicU = 0.5 * kz[i] * diff * diff;  
909 <                info->lrPot += harmonicU;
909 >      info->lrPot += harmonicU;
910  
911        harmonicF =  - kz[i] * diff;
912 <      totalFZ += harmonicF;
912 >      totalFZ_local += harmonicF;
913  
914 <       //
915 <                force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
839 <                
914 >       //adjust force
915 >    
916        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
917  
918 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
918 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
919 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
920 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
921           movingZAtoms[j]->addFrc(force);
922 +       }
923      }
924  
925    }
926 <        
926 >
927 > #ifndef IS_MPI
928 >  totalFZ = totalFZ_local;
929 > #else
930 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
931 > #endif
932 >
933 >  //cout << "before substracting harmonic force from moving molecuels "
934 >  //      << "total force is " << calcTotalForce()  << endl;
935 >
936    force[0]= 0;
937    force[1]= 0;
938    force[2]= 0;
851 –  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
939  
940    //modify the forces of unconstrained molecules
941 <  for(int i = 0; i < unconsMols.size(); i++){
941 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
942      
943       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
944      
945 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
945 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
946 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
947 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
948         unconsAtoms[j]->addFrc(force);    
949 +     }
950    }  
951 +
952 +  //cout << "after substracting harmonic force from moving molecuels "
953 +  //      << "total force is " << calcTotalForce()  << endl;
954 +
955 + }
956 +
957 + /**
958 + *
959 + */
960 +
961 + template<typename T> bool ZConstraint<T>::checkZConsState(){
962 +  double COM[3];
963 +  double diff;
964 +  
965 +  int changed_local;
966 +  int changed;
967 +  
968 +  changed_local = 0;
969 +  
970 +  for(int i =0; i < (int)(zconsMols.size()); i++){
971 +
972 +    zconsMols[i]->getCOM(COM);
973 +    diff = fabs(COM[whichDirection] - zPos[i]);  
974 +    if (  diff <= zconsTol && states[i] == zcsMoving){
975 +      states[i] = zcsFixed;
976 +     changed_local = 1;
977 +    }
978 +    else if ( diff > zconsTol && states[i] == zcsFixed){
979 +      states[i] = zcsMoving;
980 +     changed_local = 1;  
981 +    }
982 +  
983 +  }
984  
985 + #ifndef IS_MPI
986 +  changed =changed_local;
987 + #else
988 +  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
989 + #endif
990 +
991 +  return (changed > 0);
992 +
993   }
994  
995 + template<typename T> bool ZConstraint<T>::haveFixedZMols(){
996 +
997 +  int havingFixed_local;
998 +  int havingFixed;
999 +
1000 +  havingFixed_local = 0;
1001 +
1002 +  for(int i = 0; i < (int)(zconsMols.size()); i++)
1003 +    if (states[i] == zcsFixed){
1004 +      havingFixed_local = 1;
1005 +    break;
1006 +    }
1007 +
1008 + #ifndef IS_MPI
1009 +  havingFixed = havingFixed_local;
1010 + #else
1011 +  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1012 + #endif
1013 +
1014 +  return (havingFixed > 0);
1015 + }
1016 +
1017 +
1018 + /**
1019 + *
1020 + */
1021 + template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1022 +
1023 +  int havingMoving_local;
1024 +  int havingMoving;
1025 +
1026 +  havingMoving_local = 0;
1027 +
1028 +  for(int i = 0; i < (int)(zconsMols.size()); i++)
1029 +    if (states[i] == zcsMoving){
1030 +      havingMoving_local = 1;
1031 +    break;
1032 +    }
1033 +
1034 + #ifndef IS_MPI
1035 +  havingMoving = havingMoving_local;
1036 + #else
1037 +  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1038 + #endif
1039 +
1040 +  return (havingMoving > 0);
1041 +  
1042 + }
1043 +
1044 + /**
1045 + *
1046 + */
1047 +
1048   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1049   {
1050    double MVzOfMovingMols_local;
# Line 882 | Line 1066 | template<typename T> double ZConstraint<T>::calcMoving
1066      if (states[i] == zcsMoving){
1067        zconsMols[i]->getCOMvel(COMvel);
1068        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1069 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1069 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1070      }
1071 <                
1071 >    
1072    }
1073  
1074   #ifndef IS_MPI
# Line 901 | Line 1085 | template<typename T> double ZConstraint<T>::calcMoving
1085    return vzOfMovingMols;
1086   }
1087  
1088 + /**
1089 + *
1090 + */
1091  
1092   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1093   {
1094    double COMvel[3];
1095 <  double tempMVz = 0;
1096 <                
1095 >  double tempMVz_local;
1096 >  double tempMVz;
1097 >  double massOfZCons_local;
1098 >  double massOfZCons;
1099 >
1100 >
1101 > tempMVz_local = 0;
1102 >
1103    for(int i =0 ; i < nMols; i++){
1104      molecules[i].getCOMvel(COMvel);
1105 <         tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
1105 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1106    }
1107  
915 –  double massOfZCons_local;
916 –  double massOfZCons;
917 –
1108    massOfZCons_local = 0;
1109 <        
1110 <  for(int i = 0; i < massOfZConsMols.size(); i++){
1109 >  
1110 >  for(int i = 0; i < (int)(massOfZConsMols.size()); i++){
1111      massOfZCons_local += massOfZConsMols[i];
1112    }
1113   #ifndef IS_MPI
1114    massOfZCons = massOfZCons_local;
1115 +  tempMVz = tempMVz_local;
1116   #else
1117    MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1118 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1119   #endif
1120  
1121    return tempMVz /(totalMassOfUncons + massOfZCons);
1122   }
1123  
1124 + /**
1125 + *
1126 + */
1127 +
1128   template<typename T> double ZConstraint<T>::calcTotalForce(){
1129  
1130    double force[3];  
# Line 951 | Line 1147 | template<typename T> double ZConstraint<T>::calcTotalF
1147    return totalForce;
1148  
1149   }
1150 +
1151 + /**
1152 + *
1153 + */
1154 +
1155 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1156 +  //calculate the number of atoms of moving z-constrained molecules
1157 +  int nMovingZAtoms_local;
1158 +  int nMovingZAtoms;
1159 +  
1160 +  nMovingZAtoms_local = 0;
1161 +  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1162 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1163 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1164 +  
1165 + #ifdef IS_MPI
1166 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1167 + #else
1168 +  nMovingZAtoms = nMovingZAtoms_local;
1169 + #endif
1170 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1171 + }
1172 +
1173 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1174 +  return totalForce / mol->getNAtoms();
1175 + }
1176 +
1177 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1178 +  return totalForce / totNumOfMovingAtoms;
1179 + }
1180 +
1181 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1182 +    return totalForce / mol->getNAtoms();
1183 + }
1184 +
1185 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1186 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1187 + }
1188 +
1189 + /**
1190 + *
1191 + */
1192 +
1193 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1194 +  //calculate the number of atoms of moving z-constrained molecules
1195 +  double massOfMovingZAtoms_local;
1196 +  double massOfMovingZAtoms;
1197 +  
1198 +  massOfMovingZAtoms_local = 0;
1199 +  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1200 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1201 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1202 +  
1203 + #ifdef IS_MPI
1204 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1205 + #else
1206 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1207 + #endif
1208 +  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1209 + }
1210 +
1211 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1212 +  return totalForce * atom->getMass() / mol->getTotalMass();
1213 + }
1214 +
1215 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1216 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1217 + }
1218 +
1219 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1220 +  return totalForce * atom->getMass() / mol->getTotalMass();
1221 + }
1222 +
1223 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1224 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1225 + }
1226 +

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