ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 682 by tim, Tue Aug 12 17:51:33 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()].zconsIndex;
198 >      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
199  
200   #ifndef IS_MPI
201        totalNumMol = nMols;
# 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[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 <                 molecules[i].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 i = 0; i < nMols; i++)
239 <               if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 <                 molecules[i].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;
302      simError();
303    }
304  
305 <  for(int i = 0; i < zconsMols.size(); i++)
305 >  //determine the states of z-constraint molecules
306 >  for(int i = 0; i < zconsMols.size(); i++){
307      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
308 +
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);
314 +  }
315    
316   #endif
317  
318 +  //get total masss of unconstraint molecules
319 +  double totalMassOfUncons_local;
320 +  totalMassOfUncons_local = 0;
321 +  
322 +  for(int i = 0; i < unconsMols.size(); i++)
323 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
324 +    
325 + #ifndef IS_MPI
326 +  totalMassOfUncons = totalMassOfUncons_local;
327 + #else
328 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
329 +                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
330 + #endif
331 +
332 +
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
# Line 275 | Line 339 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
339   #ifndef IS_MPI
340    totNumOfUnconsAtoms = nUnconsAtoms_local;
341   #else
342 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
343 < #endif
342 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344 > #endif  
345  
346 <  checkZConsState();
347 <
283 <  //  
284 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
346 >  // creat zconsWriter  
347 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348    
349    if(!fzOut){
350      sprintf( painCave.errMsg,
# Line 289 | 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 328 | 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 342 | Line 417 | template<typename T> void ZConstraint<T>::update()
417  
418      }
419    }
420 +
421 +  //determine the states of z-constraint molecules
422 +  for(int i = 0; i < zconsMols.size(); i++){
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);
428 +  }
429 +
430      
431    //The reason to declare fz and indexOfZconsMols as pointer to array is
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 369 | 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 410 | Line 504 | template<typename T> int ZConstraint<T>::isZConstraint
504    return -1;
505   }
506  
413 – /**
414 – * Description:
415 – *  Reset the z coordinates
416 – */
507   template<typename T> void ZConstraint<T>::integrate(){
508    
509    //zero out the velocities of center of mass of unconstrained molecules
# Line 430 | Line 520 | template<typename T> void ZConstraint<T>::integrate(){
520   *
521   *
522   *
523 < */
434 <
435 <
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 +   forcePolicy->update();
535 +  }  
536  
537 +  zsys = calcZSys();
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 + #ifdef IS_MPI
548 +  }
549 + #endif
550 +
551    //do zconstraint force;
552    if (haveFixedZMols())
553      this->doZconstraintForce();
554 <  
554 >    
555    //use harmonical poteintial to move the molecules to the specified positions
556    if (haveMovingZMols())
557 <    //this->doHarmonic();
558 <  
559 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
560 <      
557 >    this->doHarmonic();
558 >
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 >    //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 459 | Line 600 | template<typename T> double ZConstraint<T>::calcZSys()
600    double totalMass;
601    double totalMZ_local;
602    double totalMZ;
462 –  double massOfUncons_local;
603    double massOfCurMol;
604    double COM[3];
605    
606    totalMass_local = 0;
467 –  totalMass = 0;
607    totalMZ_local = 0;
469 –  totalMZ = 0;
470 –  massOfUncons_local = 0;
471 –    
608    
609    for(int i = 0; i < nMols; i++){
610      massOfCurMol = molecules[i].getTotalMass();
# Line 476 | Line 612 | template<typename T> double ZConstraint<T>::calcZSys()
612      
613      totalMass_local += massOfCurMol;
614      totalMZ_local += massOfCurMol * COM[whichDirection];
615 <    
480 <    if(isZConstraintMol(&molecules[i]) == -1){
481 <    
482 <      massOfUncons_local += massOfCurMol;
483 <    }  
484 <    
615 >
616    }
617 +
618    
487 –  
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);  
622 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
623 < #else
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;
627 <  totalMassOfUncons = massOfUncons_local;
496 < #endif  
627 > #endif  
628  
629    double zsys;
630    zsys = totalMZ / totalMass;
# Line 512 | Line 643 | template<typename T> void ZConstraint<T>::thermalize(
643  
644   /**
645   *
515 – *
516 – *
646   */
647  
648   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 521 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel()
650    Atom** fixedZAtoms;  
651    double COMvel[3];
652    double vel[3];
653 <  
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);      
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 <    }
673 <        
674 <  }
671 >
672 >    zconsMols[i]->getCOMvel(COMvel);
673 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
674 >    }
675    
676 +  }
677 +
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 555 | Line 700 | template<typename T> void ZConstraint<T>::zeroOutVel()
700      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
701    }
702  
703 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
559 <
703 >  for(int i = 0; i < 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 591 | 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[i]->getNAtoms(); i++){
738 >  for(int i = 0; i < 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);
603 <        }
604 <          
746 >       movingZAtoms[j]->setVel(vel);
747      }
748 +    
749 +   }
750  
751 + }
752 +
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 616 | Line 774 | template<typename T> void ZConstraint<T>::doZconstrain
774    double COMvel[3];  
775    double COM[3];
776    double force[3];
619 –  double zsys;
777  
621 –  int nMovingZMols_local;
622 –  int nMovingZMols;
778  
624 –  //constrain the molecules which do not reach the specified positions  
779  
780 <   zsys = calcZSys();
627 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
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 642 | 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] <<"\tcurrent zpos: " << COM[whichDirection] << 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  
809 <  //calculate the number of atoms of moving z-constrained molecules
655 <  nMovingZMols_local = 0;
656 <  for(int i = 0; zconsMols.size(); i++){
657 <    if(states[i] == zcsMoving)
658 <        nMovingZMols_local += massOfZConsMols[i];
659 <  }
809 >  //calculate total z-constraint force
810   #ifdef IS_MPI
811    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
662 –  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
812   #else
813    totalFZ = totalFZ_local;
665 –  nMovingZMols = nMovingZMols_local;
814   #endif
815  
816 <  force[0]= 0;
669 <  force[1]= 0;
670 <  force[2]= 0;
671 <  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
672 <
673 <  //modify the velocites of unconstrained molecules
674 <  for(int i = 0; i < unconsMols.size(); i++){
675 <    
676 <     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
677 <    
678 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
679 <       unconsAtoms[j]->addFrc(force);
680 <    
681 <  }      
682 <
683 < //modify the velocities of moving z-constrained molecules
684 <  for(int i = 0; i < zconsMols.size(); i++) {
685 <   if (states[i] == zcsMoving){
686 <                
687 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
688 <
689 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
690 <       movingZAtoms[j]->addFrc(force);
691 <     }
692 <  }
693 <
816 >  
817    // apply negative to fixed z-constrained molecues;
818    force[0]= 0;
819    force[1]= 0;
# Line 699 | 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;
841 +
842 +  //calculate the number of atoms of moving z-constrained molecules
843 +  int nMovingZAtoms_local;
844 +  int nMovingZAtoms;
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();
850 +  
851 + #ifdef IS_MPI
852 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
853 +                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
854 + #else
855 +  nMovingZAtoms = nMovingZAtoms_local;
856 + #endif
857 +
858 +  force[0]= 0;
859 +  force[1]= 0;
860 +  force[2]= 0;
861 +
862 +  //modify the forces of unconstrained molecules
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++){          
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 +    
879 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
880 +
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 +  }
888 +
889 +  //cout << "after substracting z-constraint force from moving molecuels "
890 +  //      << "total force is " << calcTotalForce()  << endl;
891 +
892   }
893  
894 + /**
895 +  *
896 +  *
897 +  */
898 +
899 + template<typename T> void ZConstraint<T>::doHarmonic(){
900 +  double force[3];
901 +  double harmonicU;
902 +  double harmonicF;
903 +  double COM[3];
904 +  double diff;
905 +  double totalFZ_local;
906 +  double totalFZ;
907 +  
908 +  force[0] = 0;
909 +  force[1] = 0;
910 +  force[2] = 0;
911 +
912 +  totalFZ_local = 0;
913 +
914 +  for(int i = 0; i < zconsMols.size(); i++) {
915 +
916 +    if (states[i] == zcsMoving){
917 +      zconsMols[i]->getCOM(COM);
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;
924 +
925 +      harmonicF =  - kz[i] * diff;
926 +      totalFZ_local += harmonicF;
927 +
928 +       //adjust force
929 +    
930 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
931 +
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 +
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;
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++){          
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 <  bool changed;
973 >  int changed_local;
974 >  int changed;
975    
976 <  changed = false;
976 >  changed_local = 0;
977    
978    for(int i =0; i < zconsMols.size(); i++){
979  
# Line 728 | Line 981 | template<typename T> bool ZConstraint<T>::checkZConsSt
981      diff = fabs(COM[whichDirection] - zPos[i]);  
982      if (  diff <= zconsTol && states[i] == zcsMoving){
983        states[i] = zcsFixed;
984 <        changed = true;
984 >     changed_local = 1;
985      }
986      else if ( diff > zconsTol && states[i] == zcsFixed){
987        states[i] = zcsMoving;
988 <        changed = true;  
988 >     changed_local = 1;  
989      }
990    
991    }
992  
993 <  return changed;
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 <      return true;
1010 >    if (states[i] == zcsFixed){
1011 >      havingFixed_local = 1;
1012 >    break;
1013 >    }
1014  
1015 <  return false;
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  
# Line 753 | Line 1026 | template<typename T> bool ZConstraint<T>::haveMovingZM
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 <      return true;
1036 >    if (states[i] == zcsMoving){
1037 >      havingMoving_local = 1;
1038 >    break;
1039 >    }
1040  
1041 <  return false;
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 <  *
767 <  */
1052 > *
1053 > */
1054  
1055 < template<typename T> void ZConstraint<T>::doHarmonic(){
1056 <  double force[3];
1057 <  double harmonicU;
1058 <  double COM[3];
1059 <  double diff;
1060 <        
1061 <  force[0] = 0;
1062 <  force[1] = 0;
1063 <  force[2] = 0;
1055 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1056 > {
1057 >  double MVzOfMovingMols_local;
1058 >  double MVzOfMovingMols;
1059 >  double totalMassOfMovingZMols_local;
1060 >  double totalMassOfMovingZMols;
1061 >  double COMvel[3];
1062 >      
1063 >  MVzOfMovingMols_local = 0;
1064 >  totalMassOfMovingZMols_local = 0;
1065  
1066 <  cout << "Moving Molecules" << endl;  
1067 <  for(int i = 0; i < zconsMols.size(); i++) {
1066 >  for(int i =0; i < unconsMols.size(); i++){
1067 >    unconsMols[i]->getCOMvel(COMvel);
1068 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1069 >  }
1070  
1071 +  for(int i = 0; i < zconsMols.size(); i++){
1072 +
1073      if (states[i] == zcsMoving){
1074 <      zconsMols[i]->getCOM(COM):
1075 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
1076 <                
1077 <                diff = COM[whichDirection] -zPos[i];
1078 <                
1079 <      harmonicU = 0.5 * kz[i] * diff * diff;  
789 <                info->ltPot += harmonicU;
1074 >      zconsMols[i]->getCOMvel(COMvel);
1075 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1076 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1077 >    }
1078 >    
1079 >  }
1080  
1081 <                force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms();
1082 <                
1083 <      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
1081 > #ifndef IS_MPI
1082 >  MVzOfMovingMols = MVzOfMovingMols_local;
1083 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1084 > #else
1085 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1086 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1087 > #endif
1088  
1089 <       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
1090 <         movingZAtoms[j]->addFrc(force);
797 <    }
1089 >  double vzOfMovingMols;
1090 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1091  
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_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_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1113    }
1114  
1115 +  massOfZCons_local = 0;
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];  
1138 +  double totalForce_local;
1139 +  double totalForce;
1140 +
1141 +  totalForce_local = 0;
1142 +
1143 +  for(int i = 0; i < nAtoms; i++){
1144 +    atoms[i]->getFrc(force);
1145 +    totalForce_local += force[whichDirection];
1146 +  }
1147 +
1148 + #ifndef IS_MPI
1149 +  totalForce = totalForce_local;
1150 + #else
1151 +  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1152 + #endif
1153 +
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 +

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines