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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 737 by tim, Thu Aug 28 21:09:47 2003 UTC vs.
Revision 738 by tim, Tue Sep 2 14:30:12 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, "
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 PolicyByMass(this);
39 >    forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
40    }
41    else{
42      policy = dynamic_cast<StringData*>(data);
# Line 48 | Line 48 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
48        painCave.isFatal = 0;
49        simError();      
50  
51 <      forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(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, "
60 >                  "ZConstraint Warning: unknown force Subtraction policy, "
61                    "PolicyByMass is used\n");
62          painCave.isFatal = 0;
63          simError();      
64 <        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
64 >        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
65        }  
66      }
67    }
# Line 330 | Line 330 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
330                        MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331   #endif
332  
333 –
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
# Line 343 | Line 342 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
342    MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343                        MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344   #endif  
346 –
347 –  // creat zconsWriter  
348 –  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
349 –  
350 –  if(!fzOut){
351 –    sprintf( painCave.errMsg,
352 –             "Memory allocation failure in class Zconstraint\n");
353 –    painCave.isFatal = 1;
354 –    simError();
355 –  }
345  
346    forcePolicy->update();
347   }
# Line 506 | Line 495 | template<typename T> void ZConstraint<T>::integrate(){
495   }
496  
497   template<typename T> void ZConstraint<T>::integrate(){
498 +
499 +  // creat zconsWriter  
500 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
501    
502 +  if(!fzOut){
503 +    sprintf( painCave.errMsg,
504 +             "Memory allocation failure in class Zconstraint\n");
505 +    painCave.isFatal = 1;
506 +    simError();
507 +  }
508 +  
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();
# Line 532 | Line 531 | template<typename T> void ZConstraint<T>::calcForce(in
531  
532    T::calcForce(calcPot, calcStress);
533  
534 <  if (checkZConsState()){
535 <    
537 < #ifdef IS_MPI
538 <    if(worldRank == 0){
539 < #endif
540 < //       std::cerr << "\n"
541 < //              << "*******************************************\n"
542 < //              << " about to call zeroOutVel()\n"
543 < //              << "*******************************************\n"
544 < //              << "\n";
545 < #ifdef IS_MPI
546 <    }
547 < #endif
548 <    zeroOutVel();
549 <
550 < #ifdef IS_MPI
551 <    if(worldRank == 0){
552 < #endif
553 < //       std::cerr << "\n"
554 < //              << "*******************************************\n"
555 < //              << " finished zeroOutVel()\n"
556 < //              << "*******************************************\n"
557 < //              << "\n";
558 < #ifdef IS_MPI
559 <    }
560 < #endif
561 <    
534 >  if (checkZConsState()){    
535 >    zeroOutVel();    
536      forcePolicy->update();
537    }  
538    
# Line 567 | Line 541 | template<typename T> void ZConstraint<T>::calcForce(in
541   #ifdef IS_MPI
542    if(worldRank == 0){
543   #endif
544 < //     cout << "---------------------------------------------------------------------" <<endl;
545 < //     cout << "current time: " << info->getTime() << endl;
546 < //     cout << "center of mass at z: " << zsys << endl;    
547 < //     cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
544 >     //cout << "---------------------------------------------------------------------" <<endl;
545 >     //cout << "current time: " << info->getTime() << endl;
546 >     //cout << "center of mass at z: " << zsys << endl;    
547 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
548  
549   #ifdef IS_MPI
550    }
# Line 609 | Line 583 | template<typename T> void ZConstraint<T>::calcForce(in
583   #ifdef IS_MPI
584    if(worldRank == 0){
585   #endif
586 < //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
586 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
587   #ifdef IS_MPI
588    }
589   #endif
# Line 686 | Line 660 | template<typename T> void ZConstraint<T>::zeroOutVel()
660      if (states[i] == zcsFixed){
661  
662       zconsMols[i]->getCOMvel(COMvel);      
663 <    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663 >     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
664  
665        fixedZAtoms = zconsMols[i]->getMyAtoms();
666      
# Line 708 | Line 682 | template<typename T> void ZConstraint<T>::zeroOutVel()
682   #ifdef IS_MPI
683    if(worldRank == 0){
684   #endif
685 < //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
685 >     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
686   #ifdef IS_MPI
687    }
688   #endif
# Line 782 | Line 756 | template<typename T> void ZConstraint<T>::zeroOutVel()
756   #ifdef IS_MPI
757    if(worldRank == 0){
758   #endif
759 < //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
759 >     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
760   #ifdef IS_MPI
761    }
762   #endif
# Line 808 | Line 782 | template<typename T> void ZConstraint<T>::doZconstrain
782    totalFZ_local = 0;
783  
784    //calculate the total z-contrained force of fixed z-contrained molecules
785 +  
786 +  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
787 +  //       << "total force is " << calcTotalForce() << endl;
788  
789    for(int i = 0; i < zconsMols.size(); i++){
790      
# Line 825 | Line 802 | template<typename T> void ZConstraint<T>::doZconstrain
802  
803        //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
804        //      <<"\tcurrent zpos: " << COM[whichDirection]
805 <      //       << "\tcurrent fz: " <<fz[i] << endl;
805 >      //      << "\tcurrent fz: " <<fz[i] << endl;
806  
807  
808      }
# Line 862 | Line 839 | template<typename T> void ZConstraint<T>::doZconstrain
839    
840    }
841  
842 < //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
843 < //        << "total force is " << calcTotalForce() << endl;
842 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
843 >  //      << "total force is " << calcTotalForce() << endl;
844 >  
845  
846    force[0]= 0;
847    force[1]= 0;
# Line 895 | Line 873 | template<typename T> void ZConstraint<T>::doZconstrain
873        }
874      }
875    }
876 + //  cout << "after substracting z-constraint force from moving molecuels "
877 + //        << "total force is " << calcTotalForce()  << endl;
878  
899 –  //cout << "after substracting z-constraint force from moving molecuels "
900 –  //      << "total force is " << calcTotalForce()  << endl;
901 –
879   }
880  
881   /**
# Line 955 | Line 932 | template<typename T> void ZConstraint<T>::doHarmonic()
932    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
933   #endif
934  
935 +  cout << "before substracting harmonic force from moving molecuels "
936 +        << "total force is " << calcTotalForce()  << endl;
937 +
938    force[0]= 0;
939    force[1]= 0;
940    force[2]= 0;
# Line 971 | Line 951 | template<typename T> void ZConstraint<T>::doHarmonic()
951       }
952    }  
953  
954 +  cout << "after substracting harmonic force from moving molecuels "
955 +        << "total force is " << calcTotalForce()  << endl;
956 +
957   }
958  
959   /**
# Line 1187 | Line 1170 | template<typename T> void ZConstraint<T>::PolicyByNumb
1170    nMovingZAtoms = nMovingZAtoms_local;
1171   #endif
1172    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1190 –
1191 – #ifdef IS_MPI
1192 –  if(worldRank == 0){
1193 – #endif
1194 – //    std::cerr << "\n"
1195 – //            << "*******************************************\n"
1196 – //            << " fiished Policy by numbr()\n"
1197 – //            << "*******************************************\n"
1198 – //            << "\n";
1199 – #ifdef IS_MPI
1200 –  }
1201 – #endif
1173   }
1174  
1175   template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
# Line 1236 | Line 1207 | template<typename T> void ZConstraint<T>::PolicyByMass
1207   #else
1208    massOfMovingZAtoms = massOfMovingZAtoms_local;
1209   #endif
1210 <  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1210 >  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1211   }
1212  
1213   template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){

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