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"); |
35 |
> |
"PolicyByMass is used\n"); |
36 |
|
painCave.isFatal = 0; |
37 |
|
simError(); |
38 |
|
|
39 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
39 |
> |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
40 |
|
} |
41 |
|
else{ |
42 |
|
policy = dynamic_cast<StringData*>(data); |
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 = (ForceSubstractionPolicy*) new PolicyByMass(this); |
52 |
|
} |
53 |
|
else{ |
54 |
|
if(policy->getData() == "BYNUMBER") |
58 |
|
else{ |
59 |
|
sprintf( painCave.errMsg, |
60 |
|
"ZConstraint Warning: unknown force substraction policy, " |
61 |
< |
"average force substraction policy is used\n"); |
61 |
> |
"PolicyByMass is used\n"); |
62 |
|
painCave.isFatal = 0; |
63 |
|
simError(); |
64 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
65 |
|
} |
66 |
|
} |
67 |
|
} |
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(); |
277 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
278 |
|
|
279 |
|
zPos.push_back((*parameters)[searchResult].zPos); |
280 |
< |
cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 |
< |
<<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
280 |
> |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 |
> |
// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
282 |
|
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
283 |
|
|
284 |
|
molecules[i].getCOM(COM); |
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"; |
540 |
> |
// std::cerr << "\n" |
541 |
> |
// << "*******************************************\n" |
542 |
> |
// << " about to call zeroOutVel()\n" |
543 |
> |
// << "*******************************************\n" |
544 |
> |
// << "\n"; |
545 |
|
#ifdef IS_MPI |
546 |
|
} |
547 |
|
#endif |
550 |
|
#ifdef IS_MPI |
551 |
|
if(worldRank == 0){ |
552 |
|
#endif |
553 |
< |
std::cerr << "\n" |
554 |
< |
<< "*******************************************\n" |
555 |
< |
<< " finished zeroOutVel()\n" |
556 |
< |
<< "*******************************************\n" |
557 |
< |
<< "\n"; |
553 |
> |
// std::cerr << "\n" |
554 |
> |
// << "*******************************************\n" |
555 |
> |
// << " finished zeroOutVel()\n" |
556 |
> |
// << "*******************************************\n" |
557 |
> |
// << "\n"; |
558 |
|
#ifdef IS_MPI |
559 |
|
} |
560 |
|
#endif |
567 |
|
#ifdef IS_MPI |
568 |
|
if(worldRank == 0){ |
569 |
|
#endif |
570 |
< |
cout << "---------------------------------------------------------------------" <<endl; |
571 |
< |
cout << "current time: " << info->getTime() << endl; |
572 |
< |
cout << "center of mass at z: " << zsys << endl; |
573 |
< |
cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
570 |
> |
// cout << "---------------------------------------------------------------------" <<endl; |
571 |
> |
// cout << "current time: " << info->getTime() << endl; |
572 |
> |
// cout << "center of mass at z: " << zsys << endl; |
573 |
> |
// cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
574 |
|
|
575 |
|
#ifdef IS_MPI |
576 |
|
} |
579 |
|
//do zconstraint force; |
580 |
|
if (haveFixedZMols()) |
581 |
|
this->doZconstraintForce(); |
582 |
< |
|
582 |
> |
|
583 |
|
//use harmonical poteintial to move the molecules to the specified positions |
584 |
|
if (haveMovingZMols()) |
585 |
|
this->doHarmonic(); |
609 |
|
#ifdef IS_MPI |
610 |
|
if(worldRank == 0){ |
611 |
|
#endif |
612 |
< |
cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
612 |
> |
// cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
613 |
|
#ifdef IS_MPI |
614 |
|
} |
615 |
|
#endif |
615 |
– |
|
616 |
|
} |
617 |
|
|
618 |
|
|
708 |
|
#ifdef IS_MPI |
709 |
|
if(worldRank == 0){ |
710 |
|
#endif |
711 |
< |
cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
711 |
> |
// cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
712 |
|
#ifdef IS_MPI |
713 |
|
} |
714 |
|
#endif |
782 |
|
#ifdef IS_MPI |
783 |
|
if(worldRank == 0){ |
784 |
|
#endif |
785 |
< |
cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
785 |
> |
// cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
786 |
|
#ifdef IS_MPI |
787 |
|
} |
788 |
|
#endif |
802 |
|
double COM[3]; |
803 |
|
double force[3]; |
804 |
|
|
805 |
– |
|
806 |
– |
|
805 |
|
//constrain the molecules which do not reach the specified positions |
806 |
|
|
807 |
|
//Zero Out the force of z-contrained molecules |
823 |
|
} |
824 |
|
totalFZ_local += fz[i]; |
825 |
|
|
826 |
< |
// cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
827 |
< |
// <<"\tcurrent zpos: " << COM[whichDirection] |
828 |
< |
// << "\tcurrent fz: " <<fz[i] << endl; |
826 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
827 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
828 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
829 |
|
|
830 |
+ |
|
831 |
|
} |
832 |
|
|
833 |
|
} |
853 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
854 |
|
|
855 |
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
856 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
857 |
< |
//force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
856 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
857 |
> |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
858 |
|
zconsAtoms[j]->addFrc(force); |
859 |
|
} |
860 |
|
|
865 |
|
// cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
866 |
|
// << "total force is " << calcTotalForce() << endl; |
867 |
|
|
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 |
– |
|
868 |
|
force[0]= 0; |
869 |
|
force[1]= 0; |
870 |
|
force[2]= 0; |
875 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
876 |
|
|
877 |
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
878 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
879 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
878 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
879 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
880 |
|
unconsAtoms[j]->addFrc(force); |
881 |
|
} |
882 |
|
|
889 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
890 |
|
|
891 |
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
892 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
893 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
892 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
893 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
894 |
|
movingZAtoms[j]->addFrc(force); |
895 |
|
} |
896 |
|
} |
925 |
|
|
926 |
|
if (states[i] == zcsMoving){ |
927 |
|
zconsMols[i]->getCOM(COM); |
928 |
< |
cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
929 |
< |
<< "\tcurrent zpos: " << COM[whichDirection] << endl; |
930 |
< |
|
931 |
< |
diff = COM[whichDirection] -zPos[i]; |
928 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
929 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
930 |
> |
|
931 |
> |
diff = COM[whichDirection] -zPos[i]; |
932 |
|
|
933 |
|
harmonicU = 0.5 * kz[i] * diff * diff; |
934 |
< |
info->lrPot += harmonicU; |
934 |
> |
info->lrPot += harmonicU; |
935 |
|
|
936 |
|
harmonicF = - kz[i] * diff; |
937 |
|
totalFZ_local += harmonicF; |
941 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
942 |
|
|
943 |
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
944 |
< |
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
945 |
< |
//force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
944 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
945 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
946 |
|
movingZAtoms[j]->addFrc(force); |
947 |
|
} |
948 |
|
} |
965 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
966 |
|
|
967 |
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
968 |
< |
force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
969 |
< |
//force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
968 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
969 |
> |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
970 |
|
unconsAtoms[j]->addFrc(force); |
971 |
|
} |
972 |
|
} |
1006 |
|
#else |
1007 |
|
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1008 |
|
#endif |
1009 |
< |
|
1009 |
> |
|
1010 |
|
return (changed > 0); |
1011 |
+ |
|
1012 |
|
} |
1013 |
|
|
1014 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1030 |
|
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1031 |
|
#endif |
1032 |
|
|
1033 |
< |
return havingFixed > 0 ? true : false; |
1033 |
> |
return (havingFixed > 0); |
1034 |
|
} |
1035 |
|
|
1036 |
|
|
1056 |
|
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1057 |
|
#endif |
1058 |
|
|
1059 |
< |
return havingMoving > 0 ? true : false; |
1059 |
> |
return (havingMoving > 0); |
1060 |
|
|
1061 |
|
} |
1062 |
|
|
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"; |
1194 |
> |
// std::cerr << "\n" |
1195 |
> |
// << "*******************************************\n" |
1196 |
> |
// << " fiished Policy by numbr()\n" |
1197 |
> |
// << "*******************************************\n" |
1198 |
> |
// << "\n"; |
1199 |
|
#ifdef IS_MPI |
1200 |
|
} |
1201 |
|
#endif |