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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 726 by tim, Tue Aug 26 20:37:30 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 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, "
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 278 | Line 279 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
279        zPos.push_back((*parameters)[searchResult].zPos);
280   //       cout << "index: "<< (*parameters)[searchResult].zconsIndex
281   //              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
281 –      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
282        
283 +      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284        molecules[i].getCOM(COM);
285      }
286      else
# 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 342 | 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  
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 –  }
345  
346    forcePolicy->update();
347   }
# Line 404 | Line 394 | template<typename T> void ZConstraint<T>::update()
394        zconsMols.push_back(&molecules[i]);      
395        zPos.push_back((*parameters)[index].zPos);
396        kz.push_back((*parameters)[index].kRatio * zForceConst);
407 –      
397        massOfZConsMols.push_back(molecules[i].getTotalMass());  
398        
399        molecules[i].getCOM(COM);
# Line 505 | Line 494 | template<typename T> void ZConstraint<T>::integrate(){
494   }
495  
496   template<typename T> void ZConstraint<T>::integrate(){
497 +
498 +  // creat zconsWriter  
499 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
500    
501 +  if(!fzOut){
502 +    sprintf( painCave.errMsg,
503 +             "Memory allocation failure in class Zconstraint\n");
504 +    painCave.isFatal = 1;
505 +    simError();
506 +  }
507 +  
508    //zero out the velocities of center of mass of unconstrained molecules
509    //and the velocities of center of mass of every single z-constrained molecueles
510    zeroOutVel();
# Line 531 | Line 530 | template<typename T> void ZConstraint<T>::calcForce(in
530  
531    T::calcForce(calcPot, calcStress);
532  
533 <  if (checkZConsState()){
534 <    
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 <    
533 >  if (checkZConsState()){    
534 >    zeroOutVel();    
535      forcePolicy->update();
536    }  
537    
# Line 566 | Line 540 | template<typename T> void ZConstraint<T>::calcForce(in
540   #ifdef IS_MPI
541    if(worldRank == 0){
542   #endif
543 < //     cout << "---------------------------------------------------------------------" <<endl;
544 < //     cout << "current time: " << info->getTime() << endl;
545 < //     cout << "center of mass at z: " << zsys << endl;    
546 < //     cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
543 >     //cout << "---------------------------------------------------------------------" <<endl;
544 >     //cout << "current time: " << info->getTime() << endl;
545 >     //cout << "center of mass at z: " << zsys << endl;    
546 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
547  
548   #ifdef IS_MPI
549    }
# Line 578 | Line 552 | template<typename T> void ZConstraint<T>::calcForce(in
552    //do zconstraint force;
553    if (haveFixedZMols())
554      this->doZconstraintForce();
555 <    
555 >
556    //use harmonical poteintial to move the molecules to the specified positions
557    if (haveMovingZMols())
558      this->doHarmonic();
# Line 608 | Line 582 | template<typename T> void ZConstraint<T>::calcForce(in
582   #ifdef IS_MPI
583    if(worldRank == 0){
584   #endif
585 < //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
585 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
586   #ifdef IS_MPI
587    }
588   #endif
615 –
589   }
590  
591  
# Line 686 | Line 659 | template<typename T> void ZConstraint<T>::zeroOutVel()
659      if (states[i] == zcsFixed){
660  
661       zconsMols[i]->getCOMvel(COMvel);      
662 <    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
662 >     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663  
664        fixedZAtoms = zconsMols[i]->getMyAtoms();
665      
# Line 708 | Line 681 | template<typename T> void ZConstraint<T>::zeroOutVel()
681   #ifdef IS_MPI
682    if(worldRank == 0){
683   #endif
684 < //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
684 >     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
685   #ifdef IS_MPI
686    }
687   #endif
# Line 782 | Line 755 | template<typename T> void ZConstraint<T>::zeroOutVel()
755   #ifdef IS_MPI
756    if(worldRank == 0){
757   #endif
758 < //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
758 >     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
759   #ifdef IS_MPI
760    }
761   #endif
# Line 802 | Line 775 | template<typename T> void ZConstraint<T>::doZconstrain
775    double COM[3];
776    double force[3];
777  
805 –
806 –
778    //constrain the molecules which do not reach the specified positions  
779      
780    //Zero Out the force of z-contrained molecules    
781    totalFZ_local = 0;
782  
783    //calculate the total z-contrained force of fixed z-contrained molecules
784 +  
785 +  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
786 +  //       << "total force is " << calcTotalForce() << endl;
787  
788    for(int i = 0; i < zconsMols.size(); i++){
789      
# Line 827 | Line 801 | template<typename T> void ZConstraint<T>::doZconstrain
801  
802        //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
803        //      <<"\tcurrent zpos: " << COM[whichDirection]
804 <      //       << "\tcurrent fz: " <<fz[i] << endl;
804 >      //      << "\tcurrent fz: " <<fz[i] << endl;
805  
806  
807      }
# Line 864 | Line 838 | template<typename T> void ZConstraint<T>::doZconstrain
838    
839    }
840  
841 < //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
842 < //        << "total force is " << calcTotalForce() << endl;
843 <
870 <  //calculate the number of atoms of moving z-constrained molecules
871 <  int nMovingZAtoms_local;
872 <  int nMovingZAtoms;
873 <  
874 <  nMovingZAtoms_local = 0;
875 <  for(int i = 0; i < zconsMols.size(); i++)
876 <    if(states[i] == zcsMoving)
877 <     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
878 <  
879 < #ifdef IS_MPI
880 <  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
881 <                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
882 < #else
883 <  nMovingZAtoms = nMovingZAtoms_local;
884 < #endif
841 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
842 >  //      << "total force is " << calcTotalForce() << endl;
843 >  
844  
845    force[0]= 0;
846    force[1]= 0;
# Line 913 | Line 872 | template<typename T> void ZConstraint<T>::doZconstrain
872        }
873      }
874    }
875 + //  cout << "after substracting z-constraint force from moving molecuels "
876 + //        << "total force is " << calcTotalForce()  << endl;
877  
917 –  //cout << "after substracting z-constraint force from moving molecuels "
918 –  //      << "total force is " << calcTotalForce()  << endl;
919 –
878   }
879  
880   /**
# Line 973 | Line 931 | template<typename T> void ZConstraint<T>::doHarmonic()
931    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
932   #endif
933  
934 +  //cout << "before substracting harmonic force from moving molecuels "
935 +  //      << "total force is " << calcTotalForce()  << endl;
936 +
937    force[0]= 0;
938    force[1]= 0;
939    force[2]= 0;
# Line 989 | Line 950 | template<typename T> void ZConstraint<T>::doHarmonic()
950       }
951    }  
952  
953 +  //cout << "after substracting harmonic force from moving molecuels "
954 +  //      << "total force is " << calcTotalForce()  << endl;
955 +
956   }
957  
958   /**
# Line 1205 | Line 1169 | template<typename T> void ZConstraint<T>::PolicyByNumb
1169    nMovingZAtoms = nMovingZAtoms_local;
1170   #endif
1171    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
1172   }
1173  
1174   template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
# Line 1254 | Line 1206 | template<typename T> void ZConstraint<T>::PolicyByMass
1206   #else
1207    massOfMovingZAtoms = massOfMovingZAtoms_local;
1208   #endif
1209 <  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1209 >  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1210   }
1211  
1212   template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){

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