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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 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 459 | Line 523 | template<typename T> void ZConstraint<T>::calcForce(in
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())
531 >  if (checkZConsState()){
532      zeroOutVel();
533 <  
533 >   forcePolicy->update();
534 >  }  
535    zsys = calcZSys();
536    cout << "---------------------------------------------------------------------" <<endl;
537    cout << "current time: " << info->getTime() << endl;
538 <  cout << "center of mass at z: " << zsys << 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;
542 >  //cout <<  "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
543  
544    //do zconstraint force;
545    if (haveFixedZMols())
# Line 482 | Line 549 | template<typename T> void ZConstraint<T>::calcForce(in
549    if (haveMovingZMols())
550      this->doHarmonic();
551  
552 <  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
552 >  //cout <<  "after doHarmonic, totalForce is " << calcTotalForce() << endl;
553  
554 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
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 498 | Line 590 | template<typename T> double ZConstraint<T>::calcZSys()
590    double totalMZ;
591    double massOfCurMol;
592    double COM[3];
593 <        
593 >  
594    totalMass_local = 0;
595    totalMZ_local = 0;
596    
# Line 513 | Line 605 | template<typename T> double ZConstraint<T>::calcZSys()
605  
606    
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);  
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;
# Line 537 | Line 631 | template<typename T> void ZConstraint<T>::thermalize(
631  
632   /**
633   *
540 – *
541 – *
634   */
635  
636   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 546 | Line 638 | template<typename T> void ZConstraint<T>::zeroOutVel()
638    Atom** fixedZAtoms;  
639    double COMvel[3];
640    double vel[3];
641 +  double zSysCOMVel;
642  
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 moving molecules is " << calcMovingMolsCOMVel() <<endl;      
667 <        cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;  
668 <                  
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 591 | 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 627 | 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  
640 –        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<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 652 | Line 765 | template<typename T> void ZConstraint<T>::doZconstrain
765  
766  
767  
768 <  //constrain the molecules which do not reach the specified positions  
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 670 | 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]
790 <                                <<"\tcurrent zpos: " << COM[whichDirection]
791 <                                << "\tcurrent fz: " <<fz[i] << 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 <        
796 >
797 >  //calculate total z-constraint force
798 > #ifdef IS_MPI
799 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
800 > #else
801 >  totalFZ = totalFZ_local;
802 > #endif
803 >
804 >  
805    // apply negative to fixed z-constrained molecues;
806    force[0]= 0;
807    force[1]= 0;
# Line 689 | 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 <  cout << "after zero out z-constraint force on fixed z-constraint molecuels "
828 <                  << "total force is " << calcTotalForce() << endl;
827 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
828 >  //       << "total force is " << calcTotalForce() << endl;
829 >
830    //calculate the number of atoms of moving z-constrained molecules
831    int nMovingZAtoms_local;
832    int nMovingZAtoms;
833 <        
833 >  
834    nMovingZAtoms_local = 0;
835    for(int i = 0; i < zconsMols.size(); i++)
836      if(states[i] == zcsMoving)
837 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
837 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
838    
839   #ifdef IS_MPI
840 <  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
841 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
840 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
841 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
842   #else
720 –  totalFZ = totalFZ_local;
843    nMovingZAtoms = nMovingZAtoms_local;
844   #endif
845  
846    force[0]= 0;
847    force[1]= 0;
848    force[2]= 0;
727 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
849  
850    //modify the forces of unconstrained molecules
730 –  int accessCount = 0;
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 forces of moving z-constrained molecules
864    for(int i = 0; i < zconsMols.size(); i++) {
865      if (states[i] == zcsMoving){
866 <                
866 >    
867        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
868  
869 <      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
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    }
750 –        
751 –  cout << "after substracting z-constraint force from moving molecuels "
752 –                  << "total force is " << calcTotalForce()  << endl;
876  
877 < }
877 >  //cout << "after substracting z-constraint force from moving molecuels "
878 >  //      << "total force is " << calcTotalForce()  << endl;
879  
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;
880   }
881  
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 –
882   /**
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 – /**
883    *
884    *
885    */
# Line 811 | 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  
822 –  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;
914 <      totalFZ += harmonicF;
914 >      totalFZ_local += harmonicF;
915  
916 <       //
917 <                force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
839 <                
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 <        
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;
851 –  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 + /**
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;
# Line 882 | Line 1061 | template<typename T> double ZConstraint<T>::calcMoving
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 901 | Line 1080 | template<typename T> double ZConstraint<T>::calcMoving
1080    return vzOfMovingMols;
1081   }
1082  
1083 + /**
1084 + *
1085 + */
1086  
1087   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1088   {
1089    double COMvel[3];
1090 <  double tempMVz = 0;
1091 <                
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      molecules[i].getCOMvel(COMvel);
1100 <         tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
1100 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1101    }
1102  
915 –  double massOfZCons_local;
916 –  double massOfZCons;
917 –
1103    massOfZCons_local = 0;
1104 <        
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];  
# Line 951 | Line 1142 | template<typename T> double ZConstraint<T>::calcTotalF
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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