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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 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), curZPos(NULL),
5 >                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL), fzOut(NULL),
6                                   indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
# Line 27 | 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
30 >  //creat force Subtraction policy
31    data = info->getProperty(ZCONSFORCEPOLICY_ID);
32    if(!data){
33      sprintf( painCave.errMsg,
34 <               "ZConstraint Warning: User does not set force substraction policy, "
35 <               "average force substraction policy is used\n");
34 >               "ZConstraint Warning: User does not set force Subtraction policy, "
35 >               "PolicyByMass is used\n");
36      painCave.isFatal = 0;
37      simError();      
38  
39 <    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
39 >    forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
40    }
41    else{
42      policy = dynamic_cast<StringData*>(data);
# Line 44 | Line 44 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
44      if(!policy){
45        sprintf( painCave.errMsg,
46                   "ZConstraint Error: Convertion from GenericData to StringData failure, "
47 <                 "average force substraction policy is used\n");
47 >                 "PolicyByMass is used\n");
48        painCave.isFatal = 0;
49        simError();      
50  
51 <      forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
51 >      forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
52      }
53      else{
54        if(policy->getData() == "BYNUMBER")
55 <        forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
55 >        forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this);
56        else if(policy->getData() == "BYMASS")
57 <        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
57 >        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
58        else{
59          sprintf( painCave.errMsg,
60 <                  "ZConstraint Warning: unknown force substraction policy, "
61 <                  "average force substraction policy is used\n");
60 >                  "ZConstraint Warning: unknown force Subtraction policy, "
61 >                  "PolicyByMass is used\n");
62          painCave.isFatal = 0;
63          simError();      
64 +        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
65        }  
66      }
67    }
# Line 249 | Line 250 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
250            (*parameters)[i].zPos = COM[whichDirection];
251  
252            sprintf( painCave.errMsg,
253 <                     "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
253 >                     "ZConstraint warning: Does not specify zpos for z-constraint molecule "
254                       "initial z coornidate will be used \n");
255             painCave.isFatal = 0;
256             simError();  
# Line 276 | Line 277 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
277        massOfZConsMols.push_back(molecules[i].getTotalMass());  
278  
279        zPos.push_back((*parameters)[searchResult].zPos);
280 <      cout << "index: "<< (*parameters)[searchResult].zconsIndex
281 <             <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
281 <      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
280 > //       cout << "index: "<< (*parameters)[searchResult].zconsIndex
281 > //              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
282        
283 +      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284        molecules[i].getCOM(COM);
285      }
286      else
# Line 329 | Line 330 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
330                        MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331   #endif
332  
332 –
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
# Line 343 | Line 343 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
343                        MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344   #endif  
345  
346 –  // creat zconsWriter  
347 –  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348 –  
349 –  if(!fzOut){
350 –    sprintf( painCave.errMsg,
351 –             "Memory allocation failure in class Zconstraint\n");
352 –    painCave.isFatal = 1;
353 –    simError();
354 –  }
355 –
346    forcePolicy->update();
347   }
348  
# Line 404 | Line 394 | template<typename T> void ZConstraint<T>::update()
394        zconsMols.push_back(&molecules[i]);      
395        zPos.push_back((*parameters)[index].zPos);
396        kz.push_back((*parameters)[index].kRatio * zForceConst);
407 –      
397        massOfZConsMols.push_back(molecules[i].getTotalMass());  
398        
399        molecules[i].getCOM(COM);
# Line 505 | Line 494 | template<typename T> void ZConstraint<T>::integrate(){
494   }
495  
496   template<typename T> void ZConstraint<T>::integrate(){
497 +
498 +  // creat zconsWriter  
499 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
500    
501 +  if(!fzOut){
502 +    sprintf( painCave.errMsg,
503 +             "Memory allocation failure in class Zconstraint\n");
504 +    painCave.isFatal = 1;
505 +    simError();
506 +  }
507 +  
508    //zero out the velocities of center of mass of unconstrained molecules
509    //and the velocities of center of mass of every single z-constrained molecueles
510    zeroOutVel();
511 +
512 +  curZconsTime = zconsTime + info->getTime();
513    
514    T::integrate();
515  
# Line 525 | Line 526 | template<typename T> void ZConstraint<T>::calcForce(in
526    double zsys;
527    double COM[3];
528    double force[3];
529 +  double zSysCOMVel;
530  
531    T::calcForce(calcPot, calcStress);
532  
533 <  if (checkZConsState()){
534 <    zeroOutVel();
535 <   forcePolicy->update();
533 >  if (checkZConsState()){    
534 >    zeroOutVel();    
535 >    forcePolicy->update();
536    }  
537 +  
538    zsys = calcZSys();
539 <  cout << "---------------------------------------------------------------------" <<endl;
540 <  cout << "current time: " << info->getTime() << endl;
541 <  cout << "center of mass at z: " << zsys << endl;    
542 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
543 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
539 >  zSysCOMVel = calcSysCOMVel();
540 > #ifdef IS_MPI
541 >  if(worldRank == 0){
542 > #endif
543 >     //cout << "---------------------------------------------------------------------" <<endl;
544 >     //cout << "current time: " << info->getTime() << endl;
545 >     //cout << "center of mass at z: " << zsys << endl;    
546 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
547  
548 <  //cout <<  "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
548 > #ifdef IS_MPI
549 >  }
550 > #endif
551  
552    //do zconstraint force;
553    if (haveFixedZMols())
554      this->doZconstraintForce();
555 <    
555 >
556    //use harmonical poteintial to move the molecules to the specified positions
557    if (haveMovingZMols())
558      this->doHarmonic();
559  
552 –  //cout <<  "after doHarmonic, totalForce is " << calcTotalForce() << endl;
553 –
560    //write out forces and current positions of z-constraint molecules
561    if(info->getTime() >= curZconsTime){    
562     for(int i = 0; i < zconsMols.size(); i++){
# Line 571 | Line 577 | template<typename T> void ZConstraint<T>::calcForce(in
577      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
578     curZconsTime += zconsTime;
579    }
580 <  
581 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
582 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
580 >
581 >  zSysCOMVel = calcSysCOMVel();  
582 > #ifdef IS_MPI
583 >  if(worldRank == 0){
584 > #endif
585 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
586 > #ifdef IS_MPI
587 >  }
588 > #endif
589   }
590  
591  
# Line 647 | Line 659 | template<typename T> void ZConstraint<T>::zeroOutVel()
659      if (states[i] == zcsFixed){
660  
661       zconsMols[i]->getCOMvel(COMvel);      
662 <    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
662 >     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663  
664        fixedZAtoms = zconsMols[i]->getMyAtoms();
665      
# Line 669 | Line 681 | template<typename T> void ZConstraint<T>::zeroOutVel()
681   #ifdef IS_MPI
682    if(worldRank == 0){
683   #endif
684 <    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
684 >     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
685   #ifdef IS_MPI
686    }
687   #endif
# Line 743 | Line 755 | template<typename T> void ZConstraint<T>::zeroOutVel()
755   #ifdef IS_MPI
756    if(worldRank == 0){
757   #endif
758 <    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
758 >     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
759   #ifdef IS_MPI
760    }
761   #endif
# Line 763 | Line 775 | template<typename T> void ZConstraint<T>::doZconstrain
775    double COM[3];
776    double force[3];
777  
766 –
767 –
778    //constrain the molecules which do not reach the specified positions  
779      
780    //Zero Out the force of z-contrained molecules    
781    totalFZ_local = 0;
782  
783    //calculate the total z-contrained force of fixed z-contrained molecules
784 +  
785 +  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
786 +  //       << "total force is " << calcTotalForce() << endl;
787  
788    for(int i = 0; i < zconsMols.size(); i++){
789      
# Line 786 | Line 799 | template<typename T> void ZConstraint<T>::doZconstrain
799        }
800        totalFZ_local += fz[i];
801  
802 <      cout << "Fixed Molecule --\tindex: " << indexOfZConsMols[i]
803 <             <<"\tcurrent zpos: " << COM[whichDirection]
804 <             << "\tcurrent fz: " <<fz[i] << endl;
802 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
803 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
804 >      //      << "\tcurrent fz: " <<fz[i] << endl;
805  
806 +
807      }
808      
809    }
# Line 815 | Line 829 | template<typename T> void ZConstraint<T>::doZconstrain
829        zconsAtoms = zconsMols[i]->getMyAtoms();  
830      
831        for(int j =0; j < nAtomOfCurZConsMol; j++) {
832 <      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
833 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
832 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
833 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
834          zconsAtoms[j]->addFrc(force);
835        }
836      
# Line 825 | Line 839 | template<typename T> void ZConstraint<T>::doZconstrain
839    }
840  
841    //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
842 <  //       << "total force is " << calcTotalForce() << endl;
843 <
830 <  //calculate the number of atoms of moving z-constrained molecules
831 <  int nMovingZAtoms_local;
832 <  int nMovingZAtoms;
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();
838 <  
839 < #ifdef IS_MPI
840 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
841 <                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
842 < #else
843 <  nMovingZAtoms = nMovingZAtoms_local;
844 < #endif
842 >  //      << "total force is " << calcTotalForce() << endl;
843 >  
844  
845    force[0]= 0;
846    force[1]= 0;
# Line 853 | Line 852 | template<typename T> void ZConstraint<T>::doZconstrain
852       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
853      
854       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
855 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
856 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
855 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
856 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
857         unconsAtoms[j]->addFrc(force);
858       }
859      
# Line 867 | Line 866 | template<typename T> void ZConstraint<T>::doZconstrain
866        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
867  
868        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
869 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
870 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
869 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
870 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
871          movingZAtoms[j]->addFrc(force);
872        }
873      }
874    }
875 + //  cout << "after substracting z-constraint force from moving molecuels "
876 + //        << "total force is " << calcTotalForce()  << endl;
877  
877 –  //cout << "after substracting z-constraint force from moving molecuels "
878 –  //      << "total force is " << calcTotalForce()  << endl;
879 –
878   }
879  
880   /**
# Line 903 | Line 901 | template<typename T> void ZConstraint<T>::doHarmonic()
901  
902      if (states[i] == zcsMoving){
903        zconsMols[i]->getCOM(COM);
904 <      cout << "Moving Molecule --\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
904 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
905 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
906 >
907 >      diff = COM[whichDirection] -zPos[i];
908      
908 –    diff = COM[whichDirection] -zPos[i];
909 –    
909        harmonicU = 0.5 * kz[i] * diff * diff;  
910 <    info->lrPot += harmonicU;
910 >      info->lrPot += harmonicU;
911  
912        harmonicF =  - kz[i] * diff;
913        totalFZ_local += harmonicF;
# Line 918 | Line 917 | template<typename T> void ZConstraint<T>::doHarmonic()
917        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
918  
919         for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
920 <        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
921 <         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
920 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
921 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
922           movingZAtoms[j]->addFrc(force);
923         }
924      }
# Line 932 | Line 931 | template<typename T> void ZConstraint<T>::doHarmonic()
931    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
932   #endif
933  
934 +  //cout << "before substracting harmonic force from moving molecuels "
935 +  //      << "total force is " << calcTotalForce()  << endl;
936 +
937    force[0]= 0;
938    force[1]= 0;
939    force[2]= 0;
# Line 942 | Line 944 | template<typename T> void ZConstraint<T>::doHarmonic()
944       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
945      
946       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
947 <       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
948 <       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
947 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
948 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
949         unconsAtoms[j]->addFrc(force);    
950       }
951    }  
952 +
953 +  //cout << "after substracting harmonic force from moving molecuels "
954 +  //      << "total force is " << calcTotalForce()  << endl;
955  
956   }
957  
# Line 984 | Line 989 | template<typename T> bool ZConstraint<T>::checkZConsSt
989    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
990   #endif
991  
992 <  return changed > 0 ? true : false;
992 >  return (changed > 0);
993 >
994   }
995  
996   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 1006 | Line 1012 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1012    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1013   #endif
1014  
1015 <  return havingFixed > 0 ? true : false;
1015 >  return (havingFixed > 0);
1016   }
1017  
1018  
# Line 1032 | Line 1038 | template<typename T> bool ZConstraint<T>::haveMovingZM
1038    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1039   #endif
1040  
1041 <  return havingMoving > 0 ? true : false;
1041 >  return (havingMoving > 0);
1042    
1043   }
1044  
# Line 1200 | Line 1206 | template<typename T> void ZConstraint<T>::PolicyByMass
1206   #else
1207    massOfMovingZAtoms = massOfMovingZAtoms_local;
1208   #endif
1209 <  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1209 >  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1210   }
1211  
1212   template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){

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