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") |
276 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
277 |
|
|
278 |
|
zPos.push_back((*parameters)[searchResult].zPos); |
279 |
< |
cout << "index: "<< (*parameters)[searchResult].zconsIndex |
280 |
< |
<<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
279 |
> |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
280 |
> |
// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
281 |
|
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
282 |
|
|
283 |
|
molecules[i].getCOM(COM); |
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"; |
539 |
> |
// std::cerr << "\n" |
540 |
> |
// << "*******************************************\n" |
541 |
> |
// << " about to call zeroOutVel()\n" |
542 |
> |
// << "*******************************************\n" |
543 |
> |
// << "\n"; |
544 |
|
#ifdef IS_MPI |
545 |
|
} |
546 |
|
#endif |
549 |
|
#ifdef IS_MPI |
550 |
|
if(worldRank == 0){ |
551 |
|
#endif |
552 |
< |
std::cerr << "\n" |
553 |
< |
<< "*******************************************\n" |
554 |
< |
<< " finished zeroOutVel()\n" |
555 |
< |
<< "*******************************************\n" |
556 |
< |
<< "\n"; |
552 |
> |
// std::cerr << "\n" |
553 |
> |
// << "*******************************************\n" |
554 |
> |
// << " finished zeroOutVel()\n" |
555 |
> |
// << "*******************************************\n" |
556 |
> |
// << "\n"; |
557 |
|
#ifdef IS_MPI |
558 |
|
} |
559 |
|
#endif |
566 |
|
#ifdef IS_MPI |
567 |
|
if(worldRank == 0){ |
568 |
|
#endif |
569 |
< |
cout << "---------------------------------------------------------------------" <<endl; |
570 |
< |
cout << "current time: " << info->getTime() << endl; |
571 |
< |
cout << "center of mass at z: " << zsys << endl; |
572 |
< |
cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
569 |
> |
// cout << "---------------------------------------------------------------------" <<endl; |
570 |
> |
// cout << "current time: " << info->getTime() << endl; |
571 |
> |
// cout << "center of mass at z: " << zsys << endl; |
572 |
> |
// cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
573 |
|
|
574 |
|
#ifdef IS_MPI |
575 |
|
} |
608 |
|
#ifdef IS_MPI |
609 |
|
if(worldRank == 0){ |
610 |
|
#endif |
611 |
< |
cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
611 |
> |
// cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
612 |
|
#ifdef IS_MPI |
613 |
|
} |
614 |
|
#endif |
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 |
825 |
|
} |
826 |
|
totalFZ_local += fz[i]; |
827 |
|
|
828 |
< |
// cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
829 |
< |
// <<"\tcurrent zpos: " << COM[whichDirection] |
830 |
< |
// << "\tcurrent fz: " <<fz[i] << endl; |
828 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
829 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
830 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
831 |
|
|
832 |
+ |
|
833 |
|
} |
834 |
|
|
835 |
|
} |
855 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
856 |
|
|
857 |
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
858 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
859 |
< |
//force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
858 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
859 |
> |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
860 |
|
zconsAtoms[j]->addFrc(force); |
861 |
|
} |
862 |
|
|
893 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
894 |
|
|
895 |
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
896 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
897 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
896 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
897 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
898 |
|
unconsAtoms[j]->addFrc(force); |
899 |
|
} |
900 |
|
|
907 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
908 |
|
|
909 |
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
910 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
911 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
910 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
911 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
912 |
|
movingZAtoms[j]->addFrc(force); |
913 |
|
} |
914 |
|
} |
943 |
|
|
944 |
|
if (states[i] == zcsMoving){ |
945 |
|
zconsMols[i]->getCOM(COM); |
946 |
< |
cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
947 |
< |
<< "\tcurrent zpos: " << COM[whichDirection] << endl; |
946 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
947 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
948 |
> |
|
949 |
> |
diff = COM[whichDirection] -zPos[i]; |
950 |
|
|
948 |
– |
diff = COM[whichDirection] -zPos[i]; |
949 |
– |
|
951 |
|
harmonicU = 0.5 * kz[i] * diff * diff; |
952 |
< |
info->lrPot += harmonicU; |
952 |
> |
info->lrPot += harmonicU; |
953 |
|
|
954 |
|
harmonicF = - kz[i] * diff; |
955 |
|
totalFZ_local += harmonicF; |
959 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
960 |
|
|
961 |
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
962 |
< |
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
963 |
< |
//force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
962 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
963 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
964 |
|
movingZAtoms[j]->addFrc(force); |
965 |
|
} |
966 |
|
} |
983 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
984 |
|
|
985 |
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
986 |
< |
force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
987 |
< |
//force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
986 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
987 |
> |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
988 |
|
unconsAtoms[j]->addFrc(force); |
989 |
|
} |
990 |
|
} |
1024 |
|
#else |
1025 |
|
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1026 |
|
#endif |
1027 |
< |
|
1027 |
> |
|
1028 |
|
return (changed > 0); |
1029 |
+ |
|
1030 |
|
} |
1031 |
|
|
1032 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1048 |
|
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1049 |
|
#endif |
1050 |
|
|
1051 |
< |
return havingFixed > 0 ? true : false; |
1051 |
> |
return (havingFixed > 0); |
1052 |
|
} |
1053 |
|
|
1054 |
|
|
1074 |
|
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1075 |
|
#endif |
1076 |
|
|
1077 |
< |
return havingMoving > 0 ? true : false; |
1077 |
> |
return (havingMoving > 0); |
1078 |
|
|
1079 |
|
} |
1080 |
|
|
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"; |
1212 |
> |
// std::cerr << "\n" |
1213 |
> |
// << "*******************************************\n" |
1214 |
> |
// << " fiished Policy by numbr()\n" |
1215 |
> |
// << "*******************************************\n" |
1216 |
> |
// << "\n"; |
1217 |
|
#ifdef IS_MPI |
1218 |
|
} |
1219 |
|
#endif |