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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 726 by tim, Tue Aug 26 20:37:30 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 509 | Line 509 | template<typename T> void ZConstraint<T>::integrate(){
509    //zero out the velocities of center of mass of unconstrained molecules
510    //and the velocities of center of mass of every single z-constrained molecueles
511    zeroOutVel();
512 +
513 +  curZconsTime = zconsTime + info->getTime();
514    
515    T::integrate();
516  
# Line 525 | Line 527 | template<typename T> void ZConstraint<T>::calcForce(in
527    double zsys;
528    double COM[3];
529    double force[3];
530 +  double zSysCOMVel;
531  
532    T::calcForce(calcPot, calcStress);
533  
534    if (checkZConsState()){
535 +    
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";
544 + #ifdef IS_MPI
545 +    }
546 + #endif
547      zeroOutVel();
548 <   forcePolicy->update();
548 >
549 > #ifdef IS_MPI
550 >    if(worldRank == 0){
551 > #endif
552 > //       std::cerr << "\n"
553 > //              << "*******************************************\n"
554 > //              << " finished zeroOutVel()\n"
555 > //              << "*******************************************\n"
556 > //              << "\n";
557 > #ifdef IS_MPI
558 >    }
559 > #endif
560 >    
561 >    forcePolicy->update();
562    }  
563 +  
564    zsys = calcZSys();
565 <  cout << "---------------------------------------------------------------------" <<endl;
566 <  cout << "current time: " << info->getTime() << endl;
567 <  cout << "center of mass at z: " << zsys << endl;    
568 <  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
569 <  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
565 >  zSysCOMVel = calcSysCOMVel();
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;
573  
574 <  //cout <<  "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
574 > #ifdef IS_MPI
575 >  }
576 > #endif
577  
578    //do zconstraint force;
579    if (haveFixedZMols())
# Line 549 | Line 583 | template<typename T> void ZConstraint<T>::calcForce(in
583    if (haveMovingZMols())
584      this->doHarmonic();
585  
552 –  //cout <<  "after doHarmonic, totalForce is " << calcTotalForce() << endl;
553 –
586    //write out forces and current positions of z-constraint molecules
587    if(info->getTime() >= curZconsTime){    
588     for(int i = 0; i < zconsMols.size(); i++){
# Line 571 | Line 603 | template<typename T> void ZConstraint<T>::calcForce(in
603      fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
604     curZconsTime += zconsTime;
605    }
606 <  
607 <  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
608 <  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
606 >
607 >  zSysCOMVel = calcSysCOMVel();  
608 > #ifdef IS_MPI
609 >  if(worldRank == 0){
610 > #endif
611 > //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
612 > #ifdef IS_MPI
613 >  }
614 > #endif
615 >
616   }
617  
618  
# Line 669 | Line 708 | template<typename T> void ZConstraint<T>::zeroOutVel()
708   #ifdef IS_MPI
709    if(worldRank == 0){
710   #endif
711 <    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
711 > //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
712   #ifdef IS_MPI
713    }
714   #endif
# Line 743 | Line 782 | template<typename T> void ZConstraint<T>::zeroOutVel()
782   #ifdef IS_MPI
783    if(worldRank == 0){
784   #endif
785 <    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
785 > //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
786   #ifdef IS_MPI
787    }
788   #endif
# Line 786 | Line 825 | template<typename T> void ZConstraint<T>::doZconstrain
825        }
826        totalFZ_local += fz[i];
827  
828 <      cout << "Fixed Molecule --\tindex: " << indexOfZConsMols[i]
829 <             <<"\tcurrent zpos: " << COM[whichDirection]
830 <             << "\tcurrent fz: " <<fz[i] << endl;
828 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
829 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
830 >      //       << "\tcurrent fz: " <<fz[i] << endl;
831  
832 +
833      }
834      
835    }
# Line 815 | Line 855 | template<typename T> void ZConstraint<T>::doZconstrain
855        zconsAtoms = zconsMols[i]->getMyAtoms();  
856      
857        for(int j =0; j < nAtomOfCurZConsMol; j++) {
858 <      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
859 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
858 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
859 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
860          zconsAtoms[j]->addFrc(force);
861        }
862      
# Line 824 | Line 864 | template<typename T> void ZConstraint<T>::doZconstrain
864    
865    }
866  
867 <  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
868 <  //       << "total force is " << calcTotalForce() << endl;
867 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
868 > //        << "total force is " << calcTotalForce() << endl;
869  
870    //calculate the number of atoms of moving z-constrained molecules
871    int nMovingZAtoms_local;
# Line 853 | Line 893 | template<typename T> void ZConstraint<T>::doZconstrain
893       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
894      
895       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
896 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
897 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
896 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
897 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
898         unconsAtoms[j]->addFrc(force);
899       }
900      
# Line 867 | Line 907 | template<typename T> void ZConstraint<T>::doZconstrain
907        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
908  
909        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
910 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
911 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
910 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
911 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
912          movingZAtoms[j]->addFrc(force);
913        }
914      }
# Line 903 | Line 943 | template<typename T> void ZConstraint<T>::doHarmonic()
943  
944      if (states[i] == zcsMoving){
945        zconsMols[i]->getCOM(COM);
946 <      cout << "Moving Molecule --\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
947 <    
948 <    diff = COM[whichDirection] -zPos[i];
946 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
947 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
948 >
949 >      diff = COM[whichDirection] -zPos[i];
950      
951        harmonicU = 0.5 * kz[i] * diff * diff;  
952 <    info->lrPot += harmonicU;
952 >      info->lrPot += harmonicU;
953  
954        harmonicF =  - kz[i] * diff;
955        totalFZ_local += harmonicF;
# Line 918 | Line 959 | template<typename T> void ZConstraint<T>::doHarmonic()
959        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
960  
961         for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
962 <        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
963 <         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
962 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
963 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
964           movingZAtoms[j]->addFrc(force);
965         }
966      }
# Line 942 | Line 983 | template<typename T> void ZConstraint<T>::doHarmonic()
983       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
984      
985       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
986 <       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
987 <       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
986 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
987 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
988         unconsAtoms[j]->addFrc(force);    
989       }
990    }  
# Line 984 | Line 1025 | template<typename T> bool ZConstraint<T>::checkZConsSt
1025    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1026   #endif
1027  
1028 <  return changed > 0 ? true : false;
1028 >  return (changed > 0);
1029 >
1030   }
1031  
1032   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 1006 | Line 1048 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1048    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1049   #endif
1050  
1051 <  return havingFixed > 0 ? true : false;
1051 >  return (havingFixed > 0);
1052   }
1053  
1054  
# Line 1032 | Line 1074 | template<typename T> bool ZConstraint<T>::haveMovingZM
1074    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1075   #endif
1076  
1077 <  return havingMoving > 0 ? true : false;
1077 >  return (havingMoving > 0);
1078    
1079   }
1080  
# Line 1163 | Line 1205 | template<typename T> void ZConstraint<T>::PolicyByNumb
1205    nMovingZAtoms = nMovingZAtoms_local;
1206   #endif
1207    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1208 +
1209 + #ifdef IS_MPI
1210 +  if(worldRank == 0){
1211 + #endif
1212 + //    std::cerr << "\n"
1213 + //            << "*******************************************\n"
1214 + //            << " fiished Policy by numbr()\n"
1215 + //            << "*******************************************\n"
1216 + //            << "\n";
1217 + #ifdef IS_MPI
1218 +  }
1219 + #endif
1220   }
1221  
1222   template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){

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