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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 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), fzOut(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 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 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 333 | Line 333 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
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 408 | 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 440 | 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 559 | 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 654 | 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  
# Line 695 | 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 722 | 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 735 | 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 771 | Line 771 | template<typename T> void ZConstraint<T>::doZconstrain
771    Atom** zconsAtoms;
772    double totalFZ;
773    double totalFZ_local;
774 –  double COMvel[3];  
774    double COM[3];
775    double force[3];
776  
# Line 785 | Line 784 | template<typename T> void ZConstraint<T>::doZconstrain
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 821 | 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 847 | Line 846 | template<typename T> void ZConstraint<T>::doZconstrain
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 860 | 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 897 | 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 939 | Line 938 | template<typename T> void ZConstraint<T>::doHarmonic()
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 968 | 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 1000 | 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 1026 | 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 1108 | 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 1159 | 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 1197 | 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    

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