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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 702 by tim, Wed Aug 20 14:50:32 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 +  double zSysCOMVel;
529  
530    T::calcForce(calcPot, calcStress);
531  
532 <  if (checkZConsState())
532 >  if (checkZConsState()){
533      zeroOutVel();
534 <  
534 >   forcePolicy->update();
535 >  }  
536 >
537    zsys = calcZSys();
538 <  cout << "---------------------------------------------------------------------" <<endl;
539 <  cout << "current time: " << info->getTime() << endl;
540 <  cout << "center of mass at z: " << zsys << endl;      
541 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
542 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
538 >  zSysCOMVel = calcSysCOMVel();
539 > #ifdef IS_MPI
540 >  if(worldRank == 0){
541 > #endif
542 >    cout << "---------------------------------------------------------------------" <<endl;
543 >    cout << "current time: " << info->getTime() << endl;
544 >    cout << "center of mass at z: " << zsys << endl;    
545 >    cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
546  
547 <  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
547 > #ifdef IS_MPI
548 >  }
549 > #endif
550  
551    //do zconstraint force;
552    if (haveFixedZMols())
# Line 482 | Line 556 | template<typename T> void ZConstraint<T>::calcForce(in
556    if (haveMovingZMols())
557      this->doHarmonic();
558  
559 <  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
559 >  //write out forces and current positions of z-constraint molecules
560 >  if(info->getTime() >= curZconsTime){    
561 >   for(int i = 0; i < zconsMols.size(); i++){
562 >      zconsMols[i]->getCOM(COM);
563 >    curZPos[i] = COM[whichDirection];
564  
565 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
566 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
567 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
565 >    //if the z-constraint molecule is still moving, just record its force
566 >    if(states[i] == zcsMoving){
567 >         fz[i] = 0;
568 >      Atom** movingZAtoms;
569 >      movingZAtoms = zconsMols[i]->getMyAtoms();
570 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
571 >           movingZAtoms[j]->getFrc(force);
572 >           fz[i] += force[whichDirection];
573 >      }
574 >     }
575 >   }
576 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
577 >   curZconsTime += zconsTime;
578 >  }
579 >
580 >  zSysCOMVel = calcSysCOMVel();  
581 > #ifdef IS_MPI
582 >  if(worldRank == 0){
583 > #endif
584 >    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
585 > #ifdef IS_MPI
586 >  }
587 > #endif
588 >
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++){
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 591 | Line 704 | template<typename T> void ZConstraint<T>::zeroOutVel()
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 627 | Line 740 | template<typename T> void ZConstraint<T>::zeroOutVel()
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;
# Line 652 | Line 777 | template<typename T> void ZConstraint<T>::doZconstrain
777  
778  
779  
780 <  //constrain the molecules which do not reach the specified positions  
780 >  //constrain the molecules which do not reach the specified positions  
781      
782    //Zero Out the force of z-contrained molecules    
783    totalFZ_local = 0;
784  
785    //calculate the total z-contrained force of fixed z-contrained molecules
786 <  cout << "Fixed Molecules" << endl;
786 >
787    for(int i = 0; i < zconsMols.size(); i++){
788 <                
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 <          
806 >    
807    }
808 <        
808 >
809 >  //calculate total z-constraint force
810 > #ifdef IS_MPI
811 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
812 > #else
813 >  totalFZ = totalFZ_local;
814 > #endif
815 >
816 >  
817    // apply negative to fixed z-constrained molecues;
818    force[0]= 0;
819    force[1]= 0;
# Line 689 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain
822    for(int i = 0; i < zconsMols.size(); i++){
823  
824      if (states[i] == zcsFixed){  
825 <        
825 >  
826        int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
827        zconsAtoms = zconsMols[i]->getMyAtoms();  
828      
829        for(int j =0; j < nAtomOfCurZConsMol; j++) {
830 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
830 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
831 >        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
832          zconsAtoms[j]->addFrc(force);
833        }
834 <                
834 >    
835      }
836 <        
836 >  
837    }
838  
839 <  cout << "after zero out z-constraint force on fixed z-constraint molecuels "
840 <                  << "total force is " << calcTotalForce() << endl;
839 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
840 >  //       << "total force is " << calcTotalForce() << endl;
841 >
842    //calculate the number of atoms of moving z-constrained molecules
843    int nMovingZAtoms_local;
844    int nMovingZAtoms;
845 <        
845 >  
846    nMovingZAtoms_local = 0;
847    for(int i = 0; i < zconsMols.size(); i++)
848      if(states[i] == zcsMoving)
849 <           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
849 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
850    
851   #ifdef IS_MPI
852 <  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
853 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
852 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
853 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
854   #else
720 –  totalFZ = totalFZ_local;
855    nMovingZAtoms = nMovingZAtoms_local;
856   #endif
857  
858    force[0]= 0;
859    force[1]= 0;
860    force[2]= 0;
727 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
861  
862    //modify the forces of unconstrained molecules
730 –  int accessCount = 0;
863    for(int i = 0; i < unconsMols.size(); i++){
864      
865       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
866      
867 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
867 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
868 >       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
869 >       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
870         unconsAtoms[j]->addFrc(force);
871 +     }
872      
873    }      
874  
875   //modify the forces of moving z-constrained molecules
876    for(int i = 0; i < zconsMols.size(); i++) {
877      if (states[i] == zcsMoving){
878 <                
878 >    
879        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
880  
881 <      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
881 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
882 >        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
883 >        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
884          movingZAtoms[j]->addFrc(force);
885 +      }
886      }
887    }
750 –        
751 –  cout << "after substracting z-constraint force from moving molecuels "
752 –                  << "total force is " << calcTotalForce()  << endl;
888  
889 < }
889 >  //cout << "after substracting z-constraint force from moving molecuels "
890 >  //      << "total force is " << calcTotalForce()  << endl;
891  
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;
892   }
893  
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 –
894   /**
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 – /**
895    *
896    *
897    */
# Line 811 | Line 902 | template<typename T> void ZConstraint<T>::doHarmonic()
902    double harmonicF;
903    double COM[3];
904    double diff;
905 +  double totalFZ_local;
906    double totalFZ;
907 <        
907 >  
908    force[0] = 0;
909    force[1] = 0;
910    force[2] = 0;
911  
912 <  totalFZ = 0;
912 >  totalFZ_local = 0;
913  
822 –  cout << "Moving Molecules" << endl;  
914    for(int i = 0; i < zconsMols.size(); i++) {
915  
916      if (states[i] == zcsMoving){
917        zconsMols[i]->getCOM(COM);
918 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
919 <                
920 <                diff = COM[whichDirection] -zPos[i];
921 <                
918 >      cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
919 >    
920 >    diff = COM[whichDirection] -zPos[i];
921 >    
922        harmonicU = 0.5 * kz[i] * diff * diff;  
923 <                info->lrPot += harmonicU;
923 >    info->lrPot += harmonicU;
924  
925        harmonicF =  - kz[i] * diff;
926 <      totalFZ += harmonicF;
926 >      totalFZ_local += harmonicF;
927  
928 <       //
929 <                force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
839 <                
928 >       //adjust force
929 >    
930        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
931  
932 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
932 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
933 >        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
934 >         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
935           movingZAtoms[j]->addFrc(force);
936 +       }
937      }
938  
939    }
940 <        
940 >
941 > #ifndef IS_MPI
942 >  totalFZ = totalFZ_local;
943 > #else
944 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
945 > #endif
946 >
947    force[0]= 0;
948    force[1]= 0;
949    force[2]= 0;
851 –  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
950  
951    //modify the forces of unconstrained molecules
952    for(int i = 0; i < unconsMols.size(); i++){
953      
954       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
955      
956 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
956 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
957 >       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
958 >       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
959         unconsAtoms[j]->addFrc(force);    
960 +     }
961    }  
962  
963   }
964  
965 + /**
966 + *
967 + */
968 +
969 + template<typename T> bool ZConstraint<T>::checkZConsState(){
970 +  double COM[3];
971 +  double diff;
972 +  
973 +  int changed_local;
974 +  int changed;
975 +  
976 +  changed_local = 0;
977 +  
978 +  for(int i =0; i < zconsMols.size(); i++){
979 +
980 +    zconsMols[i]->getCOM(COM);
981 +    diff = fabs(COM[whichDirection] - zPos[i]);  
982 +    if (  diff <= zconsTol && states[i] == zcsMoving){
983 +      states[i] = zcsFixed;
984 +     changed_local = 1;
985 +    }
986 +    else if ( diff > zconsTol && states[i] == zcsFixed){
987 +      states[i] = zcsMoving;
988 +     changed_local = 1;  
989 +    }
990 +  
991 +  }
992 +
993 + #ifndef IS_MPI
994 +  changed =changed_local;
995 + #else
996 +  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
997 + #endif
998 +
999 +  return changed > 0 ? true : false;
1000 + }
1001 +
1002 + template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1003 +
1004 +  int havingFixed_local;
1005 +  int havingFixed;
1006 +
1007 +  havingFixed_local = 0;
1008 +
1009 +  for(int i = 0; i < zconsMols.size(); i++)
1010 +    if (states[i] == zcsFixed){
1011 +      havingFixed_local = 1;
1012 +    break;
1013 +    }
1014 +
1015 + #ifndef IS_MPI
1016 +  havingFixed = havingFixed_local;
1017 + #else
1018 +  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1019 + #endif
1020 +
1021 +  return havingFixed > 0 ? true : false;
1022 + }
1023 +
1024 +
1025 + /**
1026 + *
1027 + */
1028 + template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1029 +
1030 +  int havingMoving_local;
1031 +  int havingMoving;
1032 +
1033 +  havingMoving_local = 0;
1034 +
1035 +  for(int i = 0; i < zconsMols.size(); i++)
1036 +    if (states[i] == zcsMoving){
1037 +      havingMoving_local = 1;
1038 +    break;
1039 +    }
1040 +
1041 + #ifndef IS_MPI
1042 +  havingMoving = havingMoving_local;
1043 + #else
1044 +  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1045 + #endif
1046 +
1047 +  return havingMoving > 0 ? true : false;
1048 +  
1049 + }
1050 +
1051 + /**
1052 + *
1053 + */
1054 +
1055   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1056   {
1057    double MVzOfMovingMols_local;
# Line 882 | Line 1073 | template<typename T> double ZConstraint<T>::calcMoving
1073      if (states[i] == zcsMoving){
1074        zconsMols[i]->getCOMvel(COMvel);
1075        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1076 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1076 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1077      }
1078 <                
1078 >    
1079    }
1080  
1081   #ifndef IS_MPI
# Line 901 | Line 1092 | template<typename T> double ZConstraint<T>::calcMoving
1092    return vzOfMovingMols;
1093   }
1094  
1095 + /**
1096 + *
1097 + */
1098  
1099   template<typename T> double ZConstraint<T>::calcSysCOMVel()
1100   {
1101    double COMvel[3];
1102 <  double tempMVz = 0;
1103 <                
1102 >  double tempMVz_local;
1103 >  double tempMVz;
1104 >  double massOfZCons_local;
1105 >  double massOfZCons;
1106 >
1107 >
1108 > tempMVz_local = 0;
1109 >
1110    for(int i =0 ; i < nMols; i++){
1111      molecules[i].getCOMvel(COMvel);
1112 <         tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
1112 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1113    }
1114  
915 –  double massOfZCons_local;
916 –  double massOfZCons;
917 –
1115    massOfZCons_local = 0;
1116 <        
1116 >  
1117    for(int i = 0; i < massOfZConsMols.size(); i++){
1118      massOfZCons_local += massOfZConsMols[i];
1119    }
1120   #ifndef IS_MPI
1121    massOfZCons = massOfZCons_local;
1122 +  tempMVz = tempMVz_local;
1123   #else
1124    MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1125 +  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1126   #endif
1127  
1128    return tempMVz /(totalMassOfUncons + massOfZCons);
1129   }
1130  
1131 + /**
1132 + *
1133 + */
1134 +
1135   template<typename T> double ZConstraint<T>::calcTotalForce(){
1136  
1137    double force[3];  
# Line 951 | Line 1154 | template<typename T> double ZConstraint<T>::calcTotalF
1154    return totalForce;
1155  
1156   }
1157 +
1158 + /**
1159 + *
1160 + */
1161 +
1162 + template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1163 +  //calculate the number of atoms of moving z-constrained molecules
1164 +  int nMovingZAtoms_local;
1165 +  int nMovingZAtoms;
1166 +  
1167 +  nMovingZAtoms_local = 0;
1168 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1169 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1170 +     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1171 +  
1172 + #ifdef IS_MPI
1173 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1174 + #else
1175 +  nMovingZAtoms = nMovingZAtoms_local;
1176 + #endif
1177 +  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1178 + }
1179 +
1180 + template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1181 +  return totalForce / mol->getNAtoms();
1182 + }
1183 +
1184 + template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1185 +  return totalForce / totNumOfMovingAtoms;
1186 + }
1187 +
1188 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1189 +    return totalForce / mol->getNAtoms();
1190 + }
1191 +
1192 + template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1193 +  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1194 + }
1195 +
1196 + /**
1197 + *
1198 + */
1199 +
1200 + template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1201 +  //calculate the number of atoms of moving z-constrained molecules
1202 +  double massOfMovingZAtoms_local;
1203 +  double massOfMovingZAtoms;
1204 +  
1205 +  massOfMovingZAtoms_local = 0;
1206 +  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1207 +    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1208 +     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1209 +  
1210 + #ifdef IS_MPI
1211 +  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1212 + #else
1213 +  massOfMovingZAtoms = massOfMovingZAtoms_local;
1214 + #endif
1215 +  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1216 + }
1217 +
1218 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1219 +  return totalForce * atom->getMass() / mol->getTotalMass();
1220 + }
1221 +
1222 + template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1223 +    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1224 + }
1225 +
1226 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1227 +  return totalForce * atom->getMass() / mol->getTotalMass();
1228 + }
1229 +
1230 + template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1231 +    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1232 + }
1233 +

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