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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 723 by mmeineke, Tue Aug 26 20:12:51 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, "
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 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 505 | 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 531 | Line 531 | template<typename T> void ZConstraint<T>::calcForce(in
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 <
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 <    
534 >  if (checkZConsState()){    
535 >    zeroOutVel();    
536      forcePolicy->update();
537    }  
538    
# Line 566 | 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 578 | Line 553 | template<typename T> void ZConstraint<T>::calcForce(in
553    //do zconstraint force;
554    if (haveFixedZMols())
555      this->doZconstraintForce();
556 <    
556 >
557    //use harmonical poteintial to move the molecules to the specified positions
558    if (haveMovingZMols())
559      this->doHarmonic();
# Line 608 | 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
615 –
590   }
591  
592  
# 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 802 | Line 776 | template<typename T> void ZConstraint<T>::doZconstrain
776    double COM[3];
777    double force[3];
778  
805 –
806 –
779    //constrain the molecules which do not reach the specified positions  
780      
781    //Zero Out the force of z-contrained molecules    
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 800 | template<typename T> void ZConstraint<T>::doZconstrain
800        }
801        totalFZ_local += fz[i];
802  
803 < //       cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
804 < //              <<"\tcurrent zpos: " << COM[whichDirection]
805 < //              << "\tcurrent fz: " <<fz[i] << endl;
803 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
804 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
805 >      //      << "\tcurrent fz: " <<fz[i] << endl;
806  
807 +
808      }
809      
810    }
# Line 854 | Line 830 | template<typename T> void ZConstraint<T>::doZconstrain
830        zconsAtoms = zconsMols[i]->getMyAtoms();  
831      
832        for(int j =0; j < nAtomOfCurZConsMol; j++) {
833 <      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
834 <        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
833 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
834 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
835          zconsAtoms[j]->addFrc(force);
836        }
837      
# Line 863 | 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  
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 –
846    force[0]= 0;
847    force[1]= 0;
848    force[2]= 0;
# Line 892 | Line 853 | template<typename T> void ZConstraint<T>::doZconstrain
853       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
854      
855       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
856 <       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
857 <       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
856 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
857 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
858         unconsAtoms[j]->addFrc(force);
859       }
860      
# Line 906 | Line 867 | template<typename T> void ZConstraint<T>::doZconstrain
867        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
868  
869        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
870 <        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
871 <        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
870 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
871 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
872          movingZAtoms[j]->addFrc(force);
873        }
874      }
875    }
876 <
877 <  //cout << "after substracting z-constraint force from moving molecuels "
917 <  //      << "total force is " << calcTotalForce()  << endl;
876 > //  cout << "after substracting z-constraint force from moving molecuels "
877 > //        << "total force is " << calcTotalForce()  << endl;
878  
879   }
880  
# Line 944 | Line 904 | template<typename T> void ZConstraint<T>::doHarmonic()
904        zconsMols[i]->getCOM(COM);
905   //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
906   //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
907 +
908 +      diff = COM[whichDirection] -zPos[i];
909      
948 –    diff = COM[whichDirection] -zPos[i];
949 –    
910        harmonicU = 0.5 * kz[i] * diff * diff;  
911 <    info->lrPot += harmonicU;
911 >      info->lrPot += harmonicU;
912  
913        harmonicF =  - kz[i] * diff;
914        totalFZ_local += harmonicF;
# Line 958 | Line 918 | template<typename T> void ZConstraint<T>::doHarmonic()
918        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
919  
920         for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
921 <        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
922 <         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
921 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
922 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
923           movingZAtoms[j]->addFrc(force);
924         }
925      }
# Line 972 | 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 982 | Line 945 | template<typename T> void ZConstraint<T>::doHarmonic()
945       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
946      
947       for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
948 <       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
949 <       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
948 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
949 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
950         unconsAtoms[j]->addFrc(force);    
951       }
952    }  
953 +
954 +  cout << "after substracting harmonic force from moving molecuels "
955 +        << "total force is " << calcTotalForce()  << endl;
956  
957   }
958  
# Line 1023 | Line 989 | template<typename T> bool ZConstraint<T>::checkZConsSt
989   #else
990    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
991   #endif
992 <  
992 >
993    return (changed > 0);
994 +
995   }
996  
997   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
# Line 1046 | Line 1013 | template<typename T> bool ZConstraint<T>::haveFixedZMo
1013    MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1014   #endif
1015  
1016 <  return havingFixed > 0 ? true : false;
1016 >  return (havingFixed > 0);
1017   }
1018  
1019  
# Line 1072 | Line 1039 | template<typename T> bool ZConstraint<T>::haveMovingZM
1039    MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1040   #endif
1041  
1042 <  return havingMoving > 0 ? true : false;
1042 >  return (havingMoving > 0);
1043    
1044   }
1045  
# Line 1203 | Line 1170 | template<typename T> void ZConstraint<T>::PolicyByNumb
1170    nMovingZAtoms = nMovingZAtoms_local;
1171   #endif
1172    totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1206 –
1207 – #ifdef IS_MPI
1208 –  if(worldRank == 0){
1209 – #endif
1210 – //    std::cerr << "\n"
1211 – //            << "*******************************************\n"
1212 – //            << " fiished Policy by numbr()\n"
1213 – //            << "*******************************************\n"
1214 – //            << "\n";
1215 – #ifdef IS_MPI
1216 –  }
1217 – #endif
1173   }
1174  
1175   template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
# Line 1252 | 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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