156 |
|
simError(); |
157 |
|
} |
158 |
|
|
159 |
< |
maxIndex = (*parameters)[parameters->size()].zconsIndex; |
159 |
> |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
160 |
|
|
161 |
|
#ifndef IS_MPI |
162 |
|
totalNumMol = nMols; |
179 |
|
|
180 |
|
#ifndef IS_MPI |
181 |
|
for(int j = 0; j < nMols; j++){ |
182 |
< |
if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
183 |
< |
molecules[i].getCOM(COM); |
182 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
183 |
> |
molecules[j].getCOM(COM); |
184 |
|
break; |
185 |
|
} |
186 |
|
} |
197 |
|
|
198 |
|
if (worldRank == whichNode ){ |
199 |
|
|
200 |
< |
for(int i = 0; i < nMols; i++) |
201 |
< |
if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
202 |
< |
molecules[i].getCOM(COM); |
200 |
> |
for(int j = 0; j < nMols; j++) |
201 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
202 |
> |
molecules[j].getCOM(COM); |
203 |
|
break; |
204 |
|
} |
205 |
|
|
261 |
|
simError(); |
262 |
|
} |
263 |
|
|
264 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
264 |
> |
//determine the states of z-constraint molecules |
265 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
266 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
267 |
+ |
|
268 |
+ |
zconsMols[i]->getCOM(COM); |
269 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
270 |
+ |
states.push_back(zcsFixed); |
271 |
+ |
else |
272 |
+ |
states.push_back(zcsMoving); |
273 |
+ |
} |
274 |
|
|
275 |
|
#endif |
276 |
+ |
|
277 |
+ |
//get total masss of unconstraint molecules |
278 |
+ |
double totalMassOfUncons_local; |
279 |
+ |
totalMassOfUncons_local = 0; |
280 |
+ |
|
281 |
+ |
for(int i = 0; i < unconsMols.size(); i++) |
282 |
+ |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
283 |
+ |
|
284 |
+ |
#ifndef IS_MPI |
285 |
+ |
totalMassOfUncons = totalMassOfUncons_local; |
286 |
+ |
#else |
287 |
+ |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
288 |
+ |
#endif |
289 |
|
|
290 |
+ |
|
291 |
|
//get total number of unconstrained atoms |
292 |
|
int nUnconsAtoms_local; |
293 |
|
nUnconsAtoms_local = 0; |
298 |
|
totNumOfUnconsAtoms = nUnconsAtoms_local; |
299 |
|
#else |
300 |
|
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
301 |
< |
#endif |
301 |
> |
#endif |
302 |
|
|
303 |
< |
checkZConsState(); |
282 |
< |
|
283 |
< |
// |
303 |
> |
// creat zconsWriter |
304 |
|
fzOut = new ZConsWriter(zconsOutput.c_str()); |
305 |
|
|
306 |
|
if(!fzOut){ |
348 |
|
|
349 |
|
zconsMols.push_back(&molecules[i]); |
350 |
|
zPos.push_back((*parameters)[index].zPos); |
351 |
< |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
352 |
< |
|
351 |
> |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
352 |
> |
|
353 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
354 |
|
|
355 |
|
molecules[i].getCOM(COM); |
362 |
|
|
363 |
|
} |
364 |
|
} |
365 |
+ |
|
366 |
+ |
//determine the states of z-constraint molecules |
367 |
+ |
for(int i = 0; i < zconsMols.size(); i++){ |
368 |
+ |
zconsMols[i]->getCOM(COM); |
369 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
370 |
+ |
states.push_back(zcsFixed); |
371 |
+ |
else |
372 |
+ |
states.push_back(zcsMoving); |
373 |
+ |
} |
374 |
+ |
|
375 |
|
|
376 |
|
//The reason to declare fz and indexOfZconsMols as pointer to array is |
377 |
|
// that we want to make the MPI communication simple |
440 |
|
return -1; |
441 |
|
} |
442 |
|
|
413 |
– |
/** |
414 |
– |
* Description: |
415 |
– |
* Reset the z coordinates |
416 |
– |
*/ |
443 |
|
template<typename T> void ZConstraint<T>::integrate(){ |
444 |
|
|
445 |
|
//zero out the velocities of center of mass of unconstrained molecules |
460 |
|
|
461 |
|
|
462 |
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
463 |
+ |
double zsys; |
464 |
|
|
465 |
|
T::calcForce(calcPot, calcStress); |
466 |
|
|
467 |
|
if (checkZConsState()) |
468 |
< |
zeroOutVel(); |
468 |
> |
zeroOutVel(); |
469 |
> |
|
470 |
> |
zsys = calcZSys(); |
471 |
> |
cout << "---------------------------------------------------------------------" <<endl; |
472 |
> |
cout << "current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
473 |
> |
cout << "before calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
474 |
> |
|
475 |
|
|
476 |
|
//do zconstraint force; |
477 |
|
if (haveFixedZMols()) |
478 |
|
this->doZconstraintForce(); |
479 |
< |
|
479 |
> |
|
480 |
> |
|
481 |
> |
|
482 |
|
//use harmonical poteintial to move the molecules to the specified positions |
483 |
|
if (haveMovingZMols()) |
484 |
< |
//this->doHarmonic(); |
484 |
> |
this->doHarmonic(); |
485 |
|
|
486 |
|
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
487 |
< |
|
487 |
> |
cout << "after calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
488 |
|
} |
489 |
|
|
490 |
|
template<typename T> double ZConstraint<T>::calcZSys() |
556 |
|
Atom** fixedZAtoms; |
557 |
|
double COMvel[3]; |
558 |
|
double vel[3]; |
559 |
< |
|
559 |
> |
|
560 |
> |
double tempMass = 0; |
561 |
> |
double tempMVz =0; |
562 |
> |
double tempVz = 0; |
563 |
> |
for(int i = 0; i < nMols; i++){ |
564 |
> |
molecules[i].getCOMvel(COMvel); |
565 |
> |
tempMass +=molecules[i].getTotalMass(); |
566 |
> |
tempMVz += molecules[i].getTotalMass() * COMvel[whichDirection]; |
567 |
> |
tempVz += COMvel[whichDirection]; |
568 |
> |
} |
569 |
> |
cout << "initial velocity of center of mass is " << tempMVz / tempMass << endl; |
570 |
> |
|
571 |
|
//zero out the velocities of center of mass of fixed z-constrained molecules |
572 |
|
|
573 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
574 |
|
|
575 |
|
if (states[i] == zcsFixed){ |
576 |
|
|
577 |
< |
zconsMols[i]->getCOMvel(COMvel); |
577 |
> |
zconsMols[i]->getCOMvel(COMvel); |
578 |
> |
cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
579 |
> |
|
580 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
581 |
|
|
582 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
583 |
|
fixedZAtoms[j]->getVel(vel); |
584 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
585 |
< |
fixedZAtoms[j]->setVel(vel); |
584 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
585 |
> |
fixedZAtoms[j]->setVel(vel); |
586 |
|
} |
587 |
< |
|
587 |
> |
|
588 |
> |
zconsMols[i]->getCOMvel(COMvel); |
589 |
> |
cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
590 |
|
} |
591 |
|
|
592 |
|
} |
593 |
< |
|
593 |
> |
|
594 |
> |
cout << "before resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
595 |
> |
|
596 |
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
597 |
|
double MVzOfMovingMols_local; |
598 |
|
double MVzOfMovingMols; |
607 |
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
608 |
|
} |
609 |
|
|
610 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
559 |
< |
|
610 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
611 |
|
if (states[i] == zcsMoving){ |
612 |
|
zconsMols[i]->getCOMvel(COMvel); |
613 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
642 |
|
|
643 |
|
//modify the velocities of moving z-constrained molecuels |
644 |
|
Atom** movingZAtoms; |
645 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
645 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
646 |
|
|
647 |
|
if (states[i] ==zcsMoving){ |
648 |
|
|
649 |
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
650 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
650 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
651 |
|
movingZAtoms[j]->getVel(vel); |
652 |
|
vel[whichDirection] -= vzOfMovingMols; |
653 |
< |
movingZAtoms[j]->setVel(vel); |
654 |
< |
} |
653 |
> |
movingZAtoms[j]->setVel(vel); |
654 |
> |
} |
655 |
|
|
656 |
< |
} |
656 |
> |
} |
657 |
|
|
658 |
< |
} |
658 |
> |
} |
659 |
|
|
660 |
+ |
cout << "after resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
661 |
+ |
|
662 |
|
} |
663 |
|
|
664 |
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
669 |
|
double COMvel[3]; |
670 |
|
double COM[3]; |
671 |
|
double force[3]; |
619 |
– |
double zsys; |
672 |
|
|
673 |
|
int nMovingZMols_local; |
674 |
|
int nMovingZMols; |
675 |
|
|
676 |
|
//constrain the molecules which do not reach the specified positions |
625 |
– |
|
626 |
– |
zsys = calcZSys(); |
627 |
– |
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
677 |
|
|
678 |
|
//Zero Out the force of z-contrained molecules |
679 |
|
totalFZ_local = 0; |
702 |
|
|
703 |
|
//calculate the number of atoms of moving z-constrained molecules |
704 |
|
nMovingZMols_local = 0; |
705 |
< |
for(int i = 0; zconsMols.size(); i++){ |
705 |
> |
for(int i = 0; i < zconsMols.size(); i++) |
706 |
|
if(states[i] == zcsMoving) |
707 |
< |
nMovingZMols_local += massOfZConsMols[i]; |
708 |
< |
} |
707 |
> |
nMovingZMols_local += massOfZConsMols[i]; |
708 |
> |
|
709 |
|
#ifdef IS_MPI |
710 |
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
711 |
|
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
719 |
|
force[2]= 0; |
720 |
|
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
721 |
|
|
722 |
< |
//modify the velocites of unconstrained molecules |
722 |
> |
//modify the forces of unconstrained molecules |
723 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
724 |
|
|
725 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
729 |
|
|
730 |
|
} |
731 |
|
|
732 |
< |
//modify the velocities of moving z-constrained molecules |
732 |
> |
//modify the forces of moving z-constrained molecules |
733 |
|
for(int i = 0; i < zconsMols.size(); i++) { |
734 |
|
if (states[i] == zcsMoving){ |
735 |
|
|
818 |
|
template<typename T> void ZConstraint<T>::doHarmonic(){ |
819 |
|
double force[3]; |
820 |
|
double harmonicU; |
821 |
+ |
double harmonicF; |
822 |
|
double COM[3]; |
823 |
|
double diff; |
824 |
+ |
double totalFZ; |
825 |
|
|
826 |
|
force[0] = 0; |
827 |
|
force[1] = 0; |
828 |
|
force[2] = 0; |
829 |
|
|
830 |
+ |
totalFZ = 0; |
831 |
+ |
|
832 |
|
cout << "Moving Molecules" << endl; |
833 |
|
for(int i = 0; i < zconsMols.size(); i++) { |
834 |
|
|
835 |
|
if (states[i] == zcsMoving){ |
836 |
< |
zconsMols[i]->getCOM(COM): |
836 |
> |
zconsMols[i]->getCOM(COM); |
837 |
|
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
838 |
|
|
839 |
|
diff = COM[whichDirection] -zPos[i]; |
840 |
|
|
841 |
|
harmonicU = 0.5 * kz[i] * diff * diff; |
842 |
< |
info->ltPot += harmonicU; |
842 |
> |
info->lrPot += harmonicU; |
843 |
|
|
844 |
< |
force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
844 |
> |
harmonicF = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
845 |
> |
force[whichDirection] = harmonicF; |
846 |
> |
totalFZ += harmonicF; |
847 |
|
|
848 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
849 |
|
|
853 |
|
|
854 |
|
} |
855 |
|
|
856 |
+ |
force[0]= 0; |
857 |
+ |
force[1]= 0; |
858 |
+ |
force[2]= 0; |
859 |
+ |
force[whichDirection] = -totalFZ /totNumOfUnconsAtoms; |
860 |
+ |
|
861 |
+ |
//modify the forces of unconstrained molecules |
862 |
+ |
for(int i = 0; i < unconsMols.size(); i++){ |
863 |
+ |
|
864 |
+ |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
865 |
+ |
|
866 |
+ |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
867 |
+ |
unconsAtoms[j]->addFrc(force); |
868 |
+ |
} |
869 |
+ |
|
870 |
|
} |
871 |
+ |
|
872 |
+ |
template<typename T> double ZConstraint<T>::calcCOMVel() |
873 |
+ |
{ |
874 |
+ |
double MVzOfMovingMols_local; |
875 |
+ |
double MVzOfMovingMols; |
876 |
+ |
double totalMassOfMovingZMols_local; |
877 |
+ |
double totalMassOfMovingZMols; |
878 |
+ |
double COMvel[3]; |
879 |
+ |
|
880 |
+ |
MVzOfMovingMols_local = 0; |
881 |
+ |
totalMassOfMovingZMols_local = 0; |
882 |
+ |
|
883 |
+ |
for(int i =0; i < unconsMols.size(); i++){ |
884 |
+ |
unconsMols[i]->getCOMvel(COMvel); |
885 |
+ |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
886 |
+ |
} |
887 |
+ |
|
888 |
+ |
for(int i = 0; i < zconsMols.size(); i++){ |
889 |
+ |
|
890 |
+ |
if (states[i] == zcsMoving){ |
891 |
+ |
zconsMols[i]->getCOMvel(COMvel); |
892 |
+ |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
893 |
+ |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
894 |
+ |
} |
895 |
+ |
|
896 |
+ |
} |
897 |
+ |
|
898 |
+ |
#ifndef IS_MPI |
899 |
+ |
MVzOfMovingMols = MVzOfMovingMols_local; |
900 |
+ |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
901 |
+ |
#else |
902 |
+ |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
903 |
+ |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
904 |
+ |
#endif |
905 |
+ |
|
906 |
+ |
double vzOfMovingMols; |
907 |
+ |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
908 |
+ |
|
909 |
+ |
return vzOfMovingMols; |
910 |
+ |
} |
911 |
+ |
|
912 |
+ |
|
913 |
+ |
template<typename T> double ZConstraint<T>::calcCOMVel2() |
914 |
+ |
{ |
915 |
+ |
double COMvel[3]; |
916 |
+ |
double tempMVz = 0; |
917 |
+ |
int index; |
918 |
+ |
|
919 |
+ |
for(int i =0 ; i < nMols; i++){ |
920 |
+ |
index = isZConstraintMol(&molecules[i]); |
921 |
+ |
if( index == -1){ |
922 |
+ |
molecules[i].getCOMvel(COMvel); |
923 |
+ |
tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection]; |
924 |
+ |
} |
925 |
+ |
else if(states[i] == zcsMoving){ |
926 |
+ |
zconsMols[index]->getCOMvel(COMvel); |
927 |
+ |
tempMVz += massOfZConsMols[index]*COMvel[whichDirection]; |
928 |
+ |
} |
929 |
+ |
} |
930 |
+ |
|
931 |
+ |
return tempMVz /totalMassOfUncons; |
932 |
+ |
} |