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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 711 by mmeineke, Fri Aug 22 20:04:39 2003 UTC vs.
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC

# Line 32 | Line 32 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
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");
35 >               "PolicyByMass is used\n");
36      painCave.isFatal = 0;
37      simError();      
38  
39 <    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
39 >    forcePolicy = (ForceSubstractionPolicy*) 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 = (ForceSubstractionPolicy*) new PolicyByMass(this);
52      }
53      else{
54        if(policy->getData() == "BYNUMBER")
# Line 276 | 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 <      cout << "index: "<< (*parameters)[searchResult].zconsIndex
280 <             <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
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);
# Line 536 | Line 536 | template<typename T> void ZConstraint<T>::calcForce(in
536   #ifdef IS_MPI
537      if(worldRank == 0){
538   #endif
539 <      std::cerr << "\n"
540 <                << "*******************************************\n"
541 <                << " about to call zeroOutVel()\n"
542 <                << "*******************************************\n"
543 <                << "\n";
539 > //       std::cerr << "\n"
540 > //              << "*******************************************\n"
541 > //              << " about to call zeroOutVel()\n"
542 > //              << "*******************************************\n"
543 > //              << "\n";
544   #ifdef IS_MPI
545      }
546   #endif
# Line 549 | Line 549 | template<typename T> void ZConstraint<T>::calcForce(in
549   #ifdef IS_MPI
550      if(worldRank == 0){
551   #endif
552 <      std::cerr << "\n"
553 <                << "*******************************************\n"
554 <                << " finished zeroOutVel()\n"
555 <                << "*******************************************\n"
556 <                << "\n";
552 > //       std::cerr << "\n"
553 > //              << "*******************************************\n"
554 > //              << " finished zeroOutVel()\n"
555 > //              << "*******************************************\n"
556 > //              << "\n";
557   #ifdef IS_MPI
558      }
559   #endif
# Line 566 | Line 566 | template<typename T> void ZConstraint<T>::calcForce(in
566   #ifdef IS_MPI
567    if(worldRank == 0){
568   #endif
569 <    cout << "---------------------------------------------------------------------" <<endl;
570 <    cout << "current time: " << info->getTime() << endl;
571 <    cout << "center of mass at z: " << zsys << endl;    
572 <    cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
569 > //     cout << "---------------------------------------------------------------------" <<endl;
570 > //     cout << "current time: " << info->getTime() << endl;
571 > //     cout << "center of mass at z: " << zsys << endl;    
572 > //     cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
573  
574   #ifdef IS_MPI
575    }
# Line 578 | Line 578 | template<typename T> void ZConstraint<T>::calcForce(in
578    //do zconstraint force;
579    if (haveFixedZMols())
580      this->doZconstraintForce();
581 <    
581 >
582    //use harmonical poteintial to move the molecules to the specified positions
583    if (haveMovingZMols())
584      this->doHarmonic();
# Line 608 | Line 608 | template<typename T> void ZConstraint<T>::calcForce(in
608   #ifdef IS_MPI
609    if(worldRank == 0){
610   #endif
611 <    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
611 > //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
612   #ifdef IS_MPI
613    }
614   #endif
615 –
615   }
616  
617  
# Line 708 | Line 707 | template<typename T> void ZConstraint<T>::zeroOutVel()
707   #ifdef IS_MPI
708    if(worldRank == 0){
709   #endif
710 <    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
710 > //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
711   #ifdef IS_MPI
712    }
713   #endif
# Line 782 | Line 781 | template<typename T> void ZConstraint<T>::zeroOutVel()
781   #ifdef IS_MPI
782    if(worldRank == 0){
783   #endif
784 <    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
784 > //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
785   #ifdef IS_MPI
786    }
787   #endif
# Line 802 | Line 801 | template<typename T> void ZConstraint<T>::doZconstrain
801    double COM[3];
802    double force[3];
803  
805 –
806 –
804    //constrain the molecules which do not reach the specified positions  
805      
806    //Zero Out the force of z-contrained molecules    
# Line 825 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain
822        }
823        totalFZ_local += fz[i];
824  
825 < //       cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
826 < //              <<"\tcurrent zpos: " << COM[whichDirection]
827 < //              << "\tcurrent fz: " <<fz[i] << endl;
825 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
826 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
827 >      //       << "\tcurrent fz: " <<fz[i] << endl;
828  
829 +
830      }
831      
832    }
# Line 854 | Line 852 | template<typename T> void ZConstraint<T>::doZconstrain
852        zconsAtoms = zconsMols[i]->getMyAtoms();  
853      
854        for(int j =0; j < nAtomOfCurZConsMol; j++) {
855 <      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
856 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
855 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
856 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
857          zconsAtoms[j]->addFrc(force);
858        }
859      
# Line 866 | Line 864 | template<typename T> void ZConstraint<T>::doZconstrain
864   //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
865   //        << "total force is " << calcTotalForce() << endl;
866  
869 –  //calculate the number of atoms of moving z-constrained molecules
870 –  int nMovingZAtoms_local;
871 –  int nMovingZAtoms;
872 –  
873 –  nMovingZAtoms_local = 0;
874 –  for(int i = 0; i < zconsMols.size(); i++)
875 –    if(states[i] == zcsMoving)
876 –     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
877 –  
878 – #ifdef IS_MPI
879 –  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
880 –                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
881 – #else
882 –  nMovingZAtoms = nMovingZAtoms_local;
883 – #endif
884 –
867    force[0]= 0;
868    force[1]= 0;
869    force[2]= 0;
# Line 892 | Line 874 | template<typename T> void ZConstraint<T>::doZconstrain
874       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
875      
876       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
877 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
878 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
877 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
878 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
879         unconsAtoms[j]->addFrc(force);
880       }
881      
# Line 906 | Line 888 | template<typename T> void ZConstraint<T>::doZconstrain
888        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
889  
890        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
891 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
892 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
891 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
892 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
893          movingZAtoms[j]->addFrc(force);
894        }
895      }
# Line 942 | Line 924 | template<typename T> void ZConstraint<T>::doHarmonic()
924  
925      if (states[i] == zcsMoving){
926        zconsMols[i]->getCOM(COM);
927 <      cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
928 <           << "\tcurrent zpos: " << COM[whichDirection] << endl;
929 <    
930 <    diff = COM[whichDirection] -zPos[i];
927 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
928 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
929 >
930 >      diff = COM[whichDirection] -zPos[i];
931      
932        harmonicU = 0.5 * kz[i] * diff * diff;  
933 <    info->lrPot += harmonicU;
933 >      info->lrPot += harmonicU;
934  
935        harmonicF =  - kz[i] * diff;
936        totalFZ_local += harmonicF;
# Line 958 | Line 940 | template<typename T> void ZConstraint<T>::doHarmonic()
940        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
941  
942         for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
943 <        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
944 <         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
943 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
944 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
945           movingZAtoms[j]->addFrc(force);
946         }
947      }
# Line 982 | Line 964 | template<typename T> void ZConstraint<T>::doHarmonic()
964       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
965      
966       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
967 <       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
968 <       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
967 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
968 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
969         unconsAtoms[j]->addFrc(force);    
970       }
971    }  
# Line 1023 | Line 1005 | template<typename T> bool ZConstraint<T>::checkZConsSt
1005   #else
1006    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1007   #endif
1008 <  
1008 >
1009    return (changed > 0);
1010 +
1011   }
1012  
1013   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 1046 | Line 1029 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1029    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1030   #endif
1031  
1032 <  return havingFixed > 0 ? true : false;
1032 >  return (havingFixed > 0);
1033   }
1034  
1035  
# Line 1072 | Line 1055 | template<typename T> bool ZConstraint<T>::haveMovingZM
1055    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1056   #endif
1057  
1058 <  return havingMoving > 0 ? true : false;
1058 >  return (havingMoving > 0);
1059    
1060   }
1061  
# Line 1207 | Line 1190 | template<typename T> void ZConstraint<T>::PolicyByNumb
1190   #ifdef IS_MPI
1191    if(worldRank == 0){
1192   #endif
1193 <    std::cerr << "\n"
1194 <              << "*******************************************\n"
1195 <              << " fiished Policy by numbr()\n"
1196 <              << "*******************************************\n"
1197 <              << "\n";
1193 > //    std::cerr << "\n"
1194 > //            << "*******************************************\n"
1195 > //            << " fiished Policy by numbr()\n"
1196 > //            << "*******************************************\n"
1197 > //            << "\n";
1198   #ifdef IS_MPI
1199    }
1200   #endif

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