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); |
509 |
|
//zero out the velocities of center of mass of unconstrained molecules |
510 |
|
//and the velocities of center of mass of every single z-constrained molecueles |
511 |
|
zeroOutVel(); |
512 |
+ |
|
513 |
+ |
curZconsTime = zconsTime + info->getTime(); |
514 |
|
|
515 |
|
T::integrate(); |
516 |
|
|
527 |
|
double zsys; |
528 |
|
double COM[3]; |
529 |
|
double force[3]; |
530 |
+ |
double zSysCOMVel; |
531 |
|
|
532 |
|
T::calcForce(calcPot, calcStress); |
533 |
|
|
534 |
|
if (checkZConsState()){ |
535 |
+ |
|
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 |
< |
forcePolicy->update(); |
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 |
> |
|
561 |
> |
forcePolicy->update(); |
562 |
|
} |
563 |
+ |
|
564 |
|
zsys = calcZSys(); |
565 |
< |
cout << "---------------------------------------------------------------------" <<endl; |
566 |
< |
cout << "current time: " << info->getTime() << endl; |
567 |
< |
cout << "center of mass at z: " << zsys << endl; |
568 |
< |
//cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
569 |
< |
cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
565 |
> |
zSysCOMVel = calcSysCOMVel(); |
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; |
573 |
|
|
574 |
< |
//cout << "before doZConstraintForce, totalForce is " << calcTotalForce() << endl; |
574 |
> |
#ifdef IS_MPI |
575 |
> |
} |
576 |
> |
#endif |
577 |
|
|
578 |
|
//do zconstraint force; |
579 |
|
if (haveFixedZMols()) |
583 |
|
if (haveMovingZMols()) |
584 |
|
this->doHarmonic(); |
585 |
|
|
552 |
– |
//cout << "after doHarmonic, totalForce is " << calcTotalForce() << endl; |
553 |
– |
|
586 |
|
//write out forces and current positions of z-constraint molecules |
587 |
|
if(info->getTime() >= curZconsTime){ |
588 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
603 |
|
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
604 |
|
curZconsTime += zconsTime; |
605 |
|
} |
606 |
< |
|
607 |
< |
//cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
608 |
< |
cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
606 |
> |
|
607 |
> |
zSysCOMVel = calcSysCOMVel(); |
608 |
> |
#ifdef IS_MPI |
609 |
> |
if(worldRank == 0){ |
610 |
> |
#endif |
611 |
> |
// cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
612 |
> |
#ifdef IS_MPI |
613 |
> |
} |
614 |
> |
#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 |
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 |
|
|
863 |
|
|
864 |
|
} |
865 |
|
|
866 |
< |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
867 |
< |
// << "total force is " << calcTotalForce() << endl; |
866 |
> |
// cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
867 |
> |
// << "total force is " << calcTotalForce() << endl; |
868 |
|
|
869 |
|
//calculate the number of atoms of moving z-constrained molecules |
870 |
|
int nMovingZAtoms_local; |
942 |
|
|
943 |
|
if (states[i] == zcsMoving){ |
944 |
|
zconsMols[i]->getCOM(COM); |
945 |
< |
cout << "Moving Molecule --\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
945 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
946 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
947 |
|
|
948 |
|
diff = COM[whichDirection] -zPos[i]; |
949 |
|
|
1023 |
|
#else |
1024 |
|
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1025 |
|
#endif |
1026 |
< |
|
1027 |
< |
return changed > 0 ? true : false; |
1026 |
> |
|
1027 |
> |
return (changed > 0); |
1028 |
|
} |
1029 |
|
|
1030 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1203 |
|
nMovingZAtoms = nMovingZAtoms_local; |
1204 |
|
#endif |
1205 |
|
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1206 |
+ |
|
1207 |
+ |
#ifdef IS_MPI |
1208 |
+ |
if(worldRank == 0){ |
1209 |
+ |
#endif |
1210 |
+ |
// std::cerr << "\n" |
1211 |
+ |
// << "*******************************************\n" |
1212 |
+ |
// << " fiished Policy by numbr()\n" |
1213 |
+ |
// << "*******************************************\n" |
1214 |
+ |
// << "\n"; |
1215 |
+ |
#ifdef IS_MPI |
1216 |
+ |
} |
1217 |
+ |
#endif |
1218 |
|
} |
1219 |
|
|
1220 |
|
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |