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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC vs.
Revision 830 by gezelter, Tue Oct 28 16:20:28 2003 UTC

# Line 1 | Line 1
1   #include "Integrator.hpp"
2   #include "simError.h"
3 < #include <cmath>
3 > #include <math.h>
4   template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5 <                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL),
6 <                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
5 >                                    : T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL),
6 >                                      fzOut(NULL), curZconsTime(0), forcePolicy(NULL)
7   {
8  
9    //get properties from SimInfo
# 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 213 | Line 213 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
213  
214        //if user does not specify the zpos for the zconstraint molecule
215        //its initial z coordinate  will be used as default
216 <      for(int i = 0; i < parameters->size(); i++){
216 >      for(int i = 0; i < (int)(parameters->size()); i++){
217  
218          if(!(*parameters)[i].havingZPos){
219   #ifndef IS_MPI
# Line 227 | Line 227 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
227              //query which processor current zconstraint molecule belongs to
228            int *MolToProcMap;
229            int whichNode;
230 <    double initZPos;
230 >          
231            MolToProcMap = mpiSim->getMolToProcMap();
232            whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233          
# Line 244 | Line 244 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
244          
245            }
246  
247 <          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
247 >          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, MPI_COMM_WORLD);        
248   #endif
249              
250            (*parameters)[i].zPos = COM[whichDirection];
# Line 279 | 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;
282 –      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 304 | Line 304 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
304    }
305  
306    //determine the states of z-constraint molecules
307 <  for(int i = 0; i < zconsMols.size(); i++){
307 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
308      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309  
310      zconsMols[i]->getCOM(COM);
# Line 320 | Line 320 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
320    double totalMassOfUncons_local;
321    totalMassOfUncons_local = 0;
322    
323 <  for(int i = 0; i < unconsMols.size(); i++)
323 >  for(int i = 0; i < (int)(unconsMols.size()); i++)
324      totalMassOfUncons_local += unconsMols[i]->getTotalMass();
325      
326   #ifndef IS_MPI
# 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;
336 <  for(int i = 0; i < unconsMols.size(); i++)
336 >  for(int i = 0; i < (int)(unconsMols.size()); i++)
337      nUnconsAtoms_local += unconsMols[i]->getNAtoms();
338      
339   #ifndef IS_MPI
# Line 344 | Line 343 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
343                        MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344   #endif  
345  
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 –  }
356 –
346    forcePolicy->update();
347   }
348  
# Line 405 | 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);
408 –      
397        massOfZConsMols.push_back(molecules[i].getTotalMass());  
398        
399        molecules[i].getCOM(COM);
# Line 420 | Line 408 | template<typename T> void ZConstraint<T>::update()
408    }
409  
410    //determine the states of z-constraint molecules
411 <  for(int i = 0; i < zconsMols.size(); i++){
411 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
412       zconsMols[i]->getCOM(COM);
413        if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
414        states.push_back(zcsFixed);
# Line 452 | Line 440 | template<typename T> void ZConstraint<T>::update()
440        simError();
441      }
442          
443 <    for(int i = 0; i < zconsMols.size(); i++){
443 >    for(int i = 0; i < (int)(zconsMols.size()); i++){
444        indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
445      }
446  
# Line 506 | 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 532 | Line 530 | template<typename T> void ZConstraint<T>::calcForce(in
530  
531    T::calcForce(calcPot, calcStress);
532  
533 <  if (checkZConsState()){
534 <    
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 <    
533 >  if (checkZConsState()){    
534 >    zeroOutVel();    
535      forcePolicy->update();
536    }  
537    
# Line 567 | 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 586 | Line 559 | template<typename T> void ZConstraint<T>::calcForce(in
559  
560    //write out forces and current positions of z-constraint molecules
561    if(info->getTime() >= curZconsTime){    
562 <   for(int i = 0; i < zconsMols.size(); i++){
562 >   for(int i = 0; i < (int)(zconsMols.size()); i++){
563        zconsMols[i]->getCOM(COM);
564      curZPos[i] = COM[whichDirection];
565  
# Line 609 | 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
# Line 681 | Line 654 | template<typename T> void ZConstraint<T>::zeroOutVel()
654  
655    //zero out the velocities of center of mass of fixed z-constrained molecules
656    
657 <  for(int i = 0; i < zconsMols.size(); i++){
657 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
658  
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 722 | Line 695 | template<typename T> void ZConstraint<T>::zeroOutVel()
695    MVzOfMovingMols_local = 0;
696    totalMassOfMovingZMols_local = 0;
697  
698 <  for(int i =0; i < unconsMols.size(); i++){
698 >  for(int i =0; i < (int)(unconsMols.size()); i++){
699      unconsMols[i]->getCOMvel(COMvel);
700      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
701    }
702  
703 <  for(int i = 0; i < zconsMols.size(); i++){
703 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
704      if (states[i] == zcsMoving){
705        zconsMols[i]->getCOMvel(COMvel);
706        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
# Line 749 | Line 722 | template<typename T> void ZConstraint<T>::zeroOutVel()
722  
723    //modify the velocites of unconstrained molecules  
724    Atom** unconsAtoms;
725 <  for(int i = 0; i < unconsMols.size(); i++){
725 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
726    
727      unconsAtoms = unconsMols[i]->getMyAtoms();
728      for(int j = 0; j < unconsMols[i]->getNAtoms();j++){
# Line 762 | Line 735 | template<typename T> void ZConstraint<T>::zeroOutVel()
735  
736    //modify the velocities of moving z-constrained molecuels
737    Atom** movingZAtoms;
738 <  for(int i = 0; i < zconsMols.size(); i++){
738 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
739  
740      if (states[i] ==zcsMoving){
741    
# 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 798 | Line 771 | template<typename T> void ZConstraint<T>::doZconstrain
771    Atom** zconsAtoms;
772    double totalFZ;
773    double totalFZ_local;
801 –  double COMvel[3];  
774    double COM[3];
775    double force[3];
776  
# Line 808 | Line 780 | template<typename T> void ZConstraint<T>::doZconstrain
780    totalFZ_local = 0;
781  
782    //calculate the total z-contrained force of fixed z-contrained molecules
783 +  
784 +  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
785 +  //       << "total force is " << calcTotalForce() << endl;
786  
787 <  for(int i = 0; i < zconsMols.size(); i++){
787 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
788      
789      if (states[i] == zcsFixed){
790        
# Line 825 | Line 800 | template<typename T> void ZConstraint<T>::doZconstrain
800  
801        //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
802        //      <<"\tcurrent zpos: " << COM[whichDirection]
803 <      //       << "\tcurrent fz: " <<fz[i] << endl;
803 >      //      << "\tcurrent fz: " <<fz[i] << endl;
804  
805  
806      }
# Line 845 | Line 820 | template<typename T> void ZConstraint<T>::doZconstrain
820    force[1]= 0;
821    force[2]= 0;
822  
823 <  for(int i = 0; i < zconsMols.size(); i++){
823 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
824  
825      if (states[i] == zcsFixed){  
826    
# Line 862 | Line 837 | template<typename T> void ZConstraint<T>::doZconstrain
837    
838    }
839  
840 < //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
841 < //        << "total force is " << calcTotalForce() << endl;
840 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
841 >  //      << "total force is " << calcTotalForce() << endl;
842 >  
843  
844    force[0]= 0;
845    force[1]= 0;
846    force[2]= 0;
847  
848    //modify the forces of unconstrained molecules
849 <  for(int i = 0; i < unconsMols.size(); i++){
849 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
850      
851       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
852      
# Line 883 | Line 859 | template<typename T> void ZConstraint<T>::doZconstrain
859    }      
860  
861   //modify the forces of moving z-constrained molecules
862 <  for(int i = 0; i < zconsMols.size(); i++) {
862 >  for(int i = 0; i < (int)(zconsMols.size()); i++) {
863      if (states[i] == zcsMoving){
864      
865        Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
# Line 895 | Line 871 | template<typename T> void ZConstraint<T>::doZconstrain
871        }
872      }
873    }
874 + //  cout << "after substracting z-constraint force from moving molecuels "
875 + //        << "total force is " << calcTotalForce()  << endl;
876  
899 –  //cout << "after substracting z-constraint force from moving molecuels "
900 –  //      << "total force is " << calcTotalForce()  << endl;
901 –
877   }
878  
879   /**
# Line 921 | Line 896 | template<typename T> void ZConstraint<T>::doHarmonic()
896  
897    totalFZ_local = 0;
898  
899 <  for(int i = 0; i < zconsMols.size(); i++) {
899 >  for(int i = 0; i < (int)(zconsMols.size()); i++) {
900  
901      if (states[i] == zcsMoving){
902        zconsMols[i]->getCOM(COM);
# Line 955 | Line 930 | template<typename T> void ZConstraint<T>::doHarmonic()
930    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
931   #endif
932  
933 +  //cout << "before substracting harmonic force from moving molecuels "
934 +  //      << "total force is " << calcTotalForce()  << endl;
935 +
936    force[0]= 0;
937    force[1]= 0;
938    force[2]= 0;
939  
940    //modify the forces of unconstrained molecules
941 <  for(int i = 0; i < unconsMols.size(); i++){
941 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
942      
943       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
944      
# Line 971 | Line 949 | template<typename T> void ZConstraint<T>::doHarmonic()
949       }
950    }  
951  
952 +  //cout << "after substracting harmonic force from moving molecuels "
953 +  //      << "total force is " << calcTotalForce()  << endl;
954 +
955   }
956  
957   /**
# Line 986 | Line 967 | template<typename T> bool ZConstraint<T>::checkZConsSt
967    
968    changed_local = 0;
969    
970 <  for(int i =0; i < zconsMols.size(); i++){
970 >  for(int i =0; i < (int)(zconsMols.size()); i++){
971  
972      zconsMols[i]->getCOM(COM);
973      diff = fabs(COM[whichDirection] - zPos[i]);  
# Line 1018 | Line 999 | template<typename T> bool ZConstraint<T>::haveFixedZMo
999  
1000    havingFixed_local = 0;
1001  
1002 <  for(int i = 0; i < zconsMols.size(); i++)
1002 >  for(int i = 0; i < (int)(zconsMols.size()); i++)
1003      if (states[i] == zcsFixed){
1004        havingFixed_local = 1;
1005      break;
# Line 1044 | Line 1025 | template<typename T> bool ZConstraint<T>::haveMovingZM
1025  
1026    havingMoving_local = 0;
1027  
1028 <  for(int i = 0; i < zconsMols.size(); i++)
1028 >  for(int i = 0; i < (int)(zconsMols.size()); i++)
1029      if (states[i] == zcsMoving){
1030        havingMoving_local = 1;
1031      break;
# Line 1126 | Line 1107 | template<typename T> double ZConstraint<T>::calcSysCOM
1107  
1108    massOfZCons_local = 0;
1109    
1110 <  for(int i = 0; i < massOfZConsMols.size(); i++){
1110 >  for(int i = 0; i < (int)(massOfZConsMols.size()); i++){
1111      massOfZCons_local += massOfZConsMols[i];
1112    }
1113   #ifndef IS_MPI
# Line 1177 | Line 1158 | template<typename T> void ZConstraint<T>::PolicyByNumb
1158    int nMovingZAtoms;
1159    
1160    nMovingZAtoms_local = 0;
1161 <  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1161 >  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1162      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1163       nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1164    
# Line 1187 | Line 1168 | template<typename T> void ZConstraint<T>::PolicyByNumb
1168    nMovingZAtoms = nMovingZAtoms_local;
1169   #endif
1170    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
1171   }
1172  
1173   template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
# Line 1227 | Line 1196 | template<typename T> void ZConstraint<T>::PolicyByMass
1196    double massOfMovingZAtoms;
1197    
1198    massOfMovingZAtoms_local = 0;
1199 <  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1199 >  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1200      if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1201       massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1202    
# Line 1236 | Line 1205 | template<typename T> void ZConstraint<T>::PolicyByMass
1205   #else
1206    massOfMovingZAtoms = massOfMovingZAtoms_local;
1207   #endif
1208 <  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1208 >  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1209   }
1210  
1211   template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){

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