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root/group/trunk/OOPSE-1.0/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE-1.0/libmdtools/ZConstraint.cpp (file contents):
Revision 1334 by gezelter, Fri Jul 16 18:58:03 2004 UTC vs.
Revision 1353 by tim, Mon Jul 19 21:25:21 2004 UTC

# Line 476 | Line 476 | template<typename T> void ZConstraint<T>::update(){
476    if(usingSMD)
477    prevCantPos = cantPos;
478  
479 –  //
479    forcePolicy->update();
480   }
481  
# Line 535 | Line 534 | template<typename T> void ZConstraint<T>::integrate(){
534    T::integrate();
535   }
536  
538 –
539 – /**
540 – *
541 – *
542 – *
543 – *
544 – */
537   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
538    double zsys;
539    double COM[3];
# Line 565 | Line 557 | template<typename T> void ZConstraint<T>::calcForce(in
557   #ifdef IS_MPI
558    if (worldRank == 0){
559   #endif
568 –    //cout << "---------------------------------------------------------------------" <<endl;
569 –    //cout << "current time: " << info->getTime() << endl;
570 –    //cout << "center of mass at z: " << zsys << endl;    
571 –    //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
560  
561   #ifdef IS_MPI
562    }
# Line 613 | Line 601 | template<typename T> void ZConstraint<T>::calcForce(in
601   #ifdef IS_MPI
602    if (worldRank == 0){
603   #endif
616 –    //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
604   #ifdef IS_MPI
605    }
606   #endif
607   }
608  
609  
623 – /**
624 – *
625 – */
626 –
610   template<typename T> double ZConstraint<T>::calcZSys(){
611    //calculate reference z coordinate for z-constraint molecules
612    double totalMass_local;
# Line 660 | Line 643 | template<typename T> double ZConstraint<T>::calcZSys()
643    return zsys;
644   }
645  
663 – /**
664 – *
665 – */
646   template<typename T> void ZConstraint<T>::thermalize(void){
647    T::thermalize();
648    zeroOutVel();
649   }
650  
671 – /**
672 – *
673 – */
674 –
651   template<typename T> void ZConstraint<T>::zeroOutVel(){
652    Atom** fixedZAtoms;  
653    double COMvel[3];
# Line 694 | Line 670 | template<typename T> void ZConstraint<T>::zeroOutVel()
670        }
671  
672        zconsMols[i]->getCOMvel(COMvel);
697 –      //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
673      }
674    }
675  
701 –  //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
702 –
676    zSysCOMVel = calcSysCOMVel();
677   #ifdef IS_MPI
678    if (worldRank == 0){
679   #endif
707 –    //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
680   #ifdef IS_MPI
681    }
682   #endif
# Line 774 | Line 746 | template<typename T> void ZConstraint<T>::zeroOutVel()
746   #ifdef IS_MPI
747    if (worldRank == 0){
748   #endif
777 –    //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
749   #ifdef IS_MPI
750    }
751   #endif
752   }
753  
783 – /**
784 – *
785 – */
754  
755   template<typename T> void ZConstraint<T>::doZconstraintForce(){
756    Atom** zconsAtoms;
# Line 798 | Line 766 | template<typename T> void ZConstraint<T>::doZconstrain
766  
767    //calculate the total z-contrained force of fixed z-contrained molecules
768  
801 –  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
802 –  //       << "total force is " << calcTotalForce() << endl;
803 –
769    for (int i = 0; i < (int) (zconsMols.size()); i++){
770      if (states[i] == zcsFixed){
771        zconsMols[i]->getCOM(COM);
# Line 813 | Line 778 | template<typename T> void ZConstraint<T>::doZconstrain
778        }
779        totalFZ_local += fz[i];
780  
816 –      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
817 –      //      <<"\tcurrent zpos: " << COM[whichDirection]
818 –      //      << "\tcurrent fz: " <<fz[i] << endl;
781      }
782    }
783  
# Line 847 | Line 809 | template<typename T> void ZConstraint<T>::doZconstrain
809      }
810    }
811  
850 –  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
851 –  //      << "total force is " << calcTotalForce() << endl;
852 –
853 –
812    force[0] = 0;
813    force[1] = 0;
814    force[2] = 0;
# Line 880 | Line 838 | template<typename T> void ZConstraint<T>::doZconstrain
838        }
839      }
840    }
883 –  //  cout << "after substracting z-constraint force from moving molecuels "
884 –  //        << "total force is " << calcTotalForce()  << endl;
841   }
842  
887 – /**
888 –  *
889 –  *
890 –  */
843  
844   template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){
845    double force[3];
# Line 907 | Line 859 | template<typename T> void ZConstraint<T>::doHarmonic(v
859    for (int i = 0; i < (int) (zconsMols.size()); i++){
860      if (states[i] == zcsMoving){
861        zconsMols[i]->getCOM(COM);
910 –      //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
911 –      //     << "\tcurrent zpos: " << COM[whichDirection] << endl;
862  
863        diff = COM[whichDirection] - resPos[i];
864  
# Line 923 | Line 873 | template<typename T> void ZConstraint<T>::doHarmonic(v
873        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
874  
875        for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
926 –        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
876          force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],
877                                                                 movingZAtoms[j],
878                                                                 harmonicF);
# Line 938 | Line 887 | template<typename T> void ZConstraint<T>::doHarmonic(v
887    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
888   #endif
889  
941 –  //cout << "before substracting harmonic force from moving molecuels "
942 –  //      << "total force is " << calcTotalForce()  << endl;
943 –
890    force[0] = 0;
891    force[1] = 0;
892    force[2] = 0;
# Line 957 | Line 903 | template<typename T> void ZConstraint<T>::doHarmonic(v
903      }
904    }  
905  
960 –  //cout << "after substracting harmonic force from moving molecuels "
961 –  //      << "total force is " << calcTotalForce()  << endl;
906   }
907  
964 – /**
965 – *
966 – */
967 –
908   template<typename T> bool ZConstraint<T>::checkZConsState(){
909    double COM[3];
910    double diff;
# Line 1031 | Line 971 | template<typename T> bool ZConstraint<T>::haveFixedZMo
971   }
972  
973  
1034 – /**
1035 – *
1036 – */
974   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
975    int havingMoving_local;
976    int havingMoving;
# Line 1056 | Line 993 | template<typename T> bool ZConstraint<T>::haveMovingZM
993    return (havingMoving > 0);
994   }
995  
1059 – /**
1060 – *
1061 – */
996  
997   template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){
998    double MVzOfMovingMols_local;
# Line 1100 | Line 1034 | template<typename T> double ZConstraint<T>::calcMoving
1034    return vzOfMovingMols;
1035   }
1036  
1103 – /**
1104 – *
1105 – */
1106 –
1037   template<typename T> double ZConstraint<T>::calcSysCOMVel(){
1038    double COMvel[3];
1039    double tempMVz_local;
# Line 1136 | Line 1066 | template<typename T> double ZConstraint<T>::calcSysCOM
1066    return tempMVz / (totalMassOfUncons + massOfZCons);
1067   }
1068  
1139 – /**
1140 – *
1141 – */
1142 –
1069   template<typename T> double ZConstraint<T>::calcTotalForce(){
1070    double force[3];  
1071    double totalForce_local;
# Line 1162 | Line 1088 | template<typename T> double ZConstraint<T>::calcTotalF
1088    return totalForce;
1089   }
1090  
1165 – /**
1166 – *
1167 – */
1168 –
1091   template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1092    //calculate the number of atoms of moving z-constrained molecules
1093    int nMovingZAtoms_local;
# Line 1208 | Line 1130 | template<typename T> double ZConstraint<T>::PolicyByNu
1130    return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1131   }
1132  
1211 – /**
1212 – *
1213 – */
1133  
1134   template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1135    //calculate the number of atoms of moving z-constrained molecules

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