2 |
|
#include "simError.h" |
3 |
|
#include <cmath> |
4 |
|
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
< |
: T(theInfo, the_ff), fz(NULL), curZPos(NULL), |
5 |
> |
: T(theInfo, the_ff), fz(NULL), curZPos(NULL), fzOut(NULL), |
6 |
|
indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
7 |
|
{ |
8 |
|
|
27 |
|
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
28 |
|
zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
29 |
|
|
30 |
< |
//creat force substraction policy |
30 |
> |
//creat force Subtraction policy |
31 |
|
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
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"); |
34 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
35 |
> |
"PolicyByMass is used\n"); |
36 |
|
painCave.isFatal = 0; |
37 |
|
simError(); |
38 |
|
|
39 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
39 |
> |
forcePolicy = (ForceSubtractionPolicy*) 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 = (ForceSubtractionPolicy*) new PolicyByMass(this); |
52 |
|
} |
53 |
|
else{ |
54 |
|
if(policy->getData() == "BYNUMBER") |
55 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
55 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this); |
56 |
|
else if(policy->getData() == "BYMASS") |
57 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
57 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
58 |
|
else{ |
59 |
|
sprintf( painCave.errMsg, |
60 |
< |
"ZConstraint Warning: unknown force substraction policy, " |
61 |
< |
"average force substraction policy is used\n"); |
60 |
> |
"ZConstraint Warning: unknown force Subtraction policy, " |
61 |
> |
"PolicyByMass is used\n"); |
62 |
|
painCave.isFatal = 0; |
63 |
|
simError(); |
64 |
+ |
forcePolicy = (ForceSubtractionPolicy*) 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; |
281 |
< |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
280 |
> |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 |
> |
// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
282 |
|
|
283 |
+ |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
284 |
|
molecules[i].getCOM(COM); |
285 |
|
} |
286 |
|
else |
329 |
|
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
330 |
|
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 |
|
#endif |
331 |
– |
|
332 |
|
|
333 |
|
//get total number of unconstrained atoms |
334 |
|
int nUnconsAtoms_local; |
343 |
|
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
|
#endif |
345 |
|
|
346 |
– |
// creat zconsWriter |
347 |
– |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
348 |
– |
|
349 |
– |
if(!fzOut){ |
350 |
– |
sprintf( painCave.errMsg, |
351 |
– |
"Memory allocation failure in class Zconstraint\n"); |
352 |
– |
painCave.isFatal = 1; |
353 |
– |
simError(); |
354 |
– |
} |
355 |
– |
|
346 |
|
forcePolicy->update(); |
347 |
|
} |
348 |
|
|
394 |
|
zconsMols.push_back(&molecules[i]); |
395 |
|
zPos.push_back((*parameters)[index].zPos); |
396 |
|
kz.push_back((*parameters)[index].kRatio * zForceConst); |
407 |
– |
|
397 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
398 |
|
|
399 |
|
molecules[i].getCOM(COM); |
494 |
|
} |
495 |
|
|
496 |
|
template<typename T> void ZConstraint<T>::integrate(){ |
497 |
+ |
|
498 |
+ |
// creat zconsWriter |
499 |
+ |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
500 |
|
|
501 |
+ |
if(!fzOut){ |
502 |
+ |
sprintf( painCave.errMsg, |
503 |
+ |
"Memory allocation failure in class Zconstraint\n"); |
504 |
+ |
painCave.isFatal = 1; |
505 |
+ |
simError(); |
506 |
+ |
} |
507 |
+ |
|
508 |
|
//zero out the velocities of center of mass of unconstrained molecules |
509 |
|
//and the velocities of center of mass of every single z-constrained molecueles |
510 |
|
zeroOutVel(); |
511 |
+ |
|
512 |
+ |
curZconsTime = zconsTime + info->getTime(); |
513 |
|
|
514 |
|
T::integrate(); |
515 |
|
|
530 |
|
|
531 |
|
T::calcForce(calcPot, calcStress); |
532 |
|
|
533 |
< |
if (checkZConsState()){ |
534 |
< |
zeroOutVel(); |
535 |
< |
forcePolicy->update(); |
533 |
> |
if (checkZConsState()){ |
534 |
> |
zeroOutVel(); |
535 |
> |
forcePolicy->update(); |
536 |
|
} |
537 |
< |
|
537 |
> |
|
538 |
|
zsys = calcZSys(); |
539 |
|
zSysCOMVel = calcSysCOMVel(); |
540 |
|
#ifdef IS_MPI |
541 |
|
if(worldRank == 0){ |
542 |
|
#endif |
543 |
< |
cout << "---------------------------------------------------------------------" <<endl; |
544 |
< |
cout << "current time: " << info->getTime() << endl; |
545 |
< |
cout << "center of mass at z: " << zsys << endl; |
546 |
< |
cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
543 |
> |
//cout << "---------------------------------------------------------------------" <<endl; |
544 |
> |
//cout << "current time: " << info->getTime() << endl; |
545 |
> |
//cout << "center of mass at z: " << zsys << endl; |
546 |
> |
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
547 |
|
|
548 |
|
#ifdef IS_MPI |
549 |
|
} |
552 |
|
//do zconstraint force; |
553 |
|
if (haveFixedZMols()) |
554 |
|
this->doZconstraintForce(); |
555 |
< |
|
555 |
> |
|
556 |
|
//use harmonical poteintial to move the molecules to the specified positions |
557 |
|
if (haveMovingZMols()) |
558 |
|
this->doHarmonic(); |
582 |
|
#ifdef IS_MPI |
583 |
|
if(worldRank == 0){ |
584 |
|
#endif |
585 |
< |
cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
585 |
> |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
586 |
|
#ifdef IS_MPI |
587 |
|
} |
588 |
|
#endif |
588 |
– |
|
589 |
|
} |
590 |
|
|
591 |
|
|
659 |
|
if (states[i] == zcsFixed){ |
660 |
|
|
661 |
|
zconsMols[i]->getCOMvel(COMvel); |
662 |
< |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
662 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
663 |
|
|
664 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
665 |
|
|
681 |
|
#ifdef IS_MPI |
682 |
|
if(worldRank == 0){ |
683 |
|
#endif |
684 |
< |
cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
684 |
> |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
685 |
|
#ifdef IS_MPI |
686 |
|
} |
687 |
|
#endif |
755 |
|
#ifdef IS_MPI |
756 |
|
if(worldRank == 0){ |
757 |
|
#endif |
758 |
< |
cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
758 |
> |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
759 |
|
#ifdef IS_MPI |
760 |
|
} |
761 |
|
#endif |
775 |
|
double COM[3]; |
776 |
|
double force[3]; |
777 |
|
|
778 |
– |
|
779 |
– |
|
778 |
|
//constrain the molecules which do not reach the specified positions |
779 |
|
|
780 |
|
//Zero Out the force of z-contrained molecules |
781 |
|
totalFZ_local = 0; |
782 |
|
|
783 |
|
//calculate the total z-contrained force of fixed z-contrained molecules |
784 |
+ |
|
785 |
+ |
//cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
786 |
+ |
// << "total force is " << calcTotalForce() << endl; |
787 |
|
|
788 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
789 |
|
|
799 |
|
} |
800 |
|
totalFZ_local += fz[i]; |
801 |
|
|
802 |
< |
cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
803 |
< |
<<"\tcurrent zpos: " << COM[whichDirection] |
804 |
< |
<< "\tcurrent fz: " <<fz[i] << endl; |
802 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
803 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
804 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
805 |
|
|
806 |
+ |
|
807 |
|
} |
808 |
|
|
809 |
|
} |
829 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
830 |
|
|
831 |
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
832 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
833 |
< |
//force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
832 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
833 |
> |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
834 |
|
zconsAtoms[j]->addFrc(force); |
835 |
|
} |
836 |
|
|
839 |
|
} |
840 |
|
|
841 |
|
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
842 |
< |
// << "total force is " << calcTotalForce() << endl; |
842 |
> |
// << "total force is " << calcTotalForce() << endl; |
843 |
> |
|
844 |
|
|
842 |
– |
//calculate the number of atoms of moving z-constrained molecules |
843 |
– |
int nMovingZAtoms_local; |
844 |
– |
int nMovingZAtoms; |
845 |
– |
|
846 |
– |
nMovingZAtoms_local = 0; |
847 |
– |
for(int i = 0; i < zconsMols.size(); i++) |
848 |
– |
if(states[i] == zcsMoving) |
849 |
– |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
850 |
– |
|
851 |
– |
#ifdef IS_MPI |
852 |
– |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, |
853 |
– |
MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
854 |
– |
#else |
855 |
– |
nMovingZAtoms = nMovingZAtoms_local; |
856 |
– |
#endif |
857 |
– |
|
845 |
|
force[0]= 0; |
846 |
|
force[1]= 0; |
847 |
|
force[2]= 0; |
852 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
853 |
|
|
854 |
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
855 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
856 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
855 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
856 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
857 |
|
unconsAtoms[j]->addFrc(force); |
858 |
|
} |
859 |
|
|
866 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
867 |
|
|
868 |
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
869 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
870 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
869 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
870 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
871 |
|
movingZAtoms[j]->addFrc(force); |
872 |
|
} |
873 |
|
} |
874 |
|
} |
875 |
+ |
// cout << "after substracting z-constraint force from moving molecuels " |
876 |
+ |
// << "total force is " << calcTotalForce() << endl; |
877 |
|
|
889 |
– |
//cout << "after substracting z-constraint force from moving molecuels " |
890 |
– |
// << "total force is " << calcTotalForce() << endl; |
891 |
– |
|
878 |
|
} |
879 |
|
|
880 |
|
/** |
901 |
|
|
902 |
|
if (states[i] == zcsMoving){ |
903 |
|
zconsMols[i]->getCOM(COM); |
904 |
< |
cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
904 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
905 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
906 |
> |
|
907 |
> |
diff = COM[whichDirection] -zPos[i]; |
908 |
|
|
920 |
– |
diff = COM[whichDirection] -zPos[i]; |
921 |
– |
|
909 |
|
harmonicU = 0.5 * kz[i] * diff * diff; |
910 |
< |
info->lrPot += harmonicU; |
910 |
> |
info->lrPot += harmonicU; |
911 |
|
|
912 |
|
harmonicF = - kz[i] * diff; |
913 |
|
totalFZ_local += harmonicF; |
917 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
918 |
|
|
919 |
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
920 |
< |
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
921 |
< |
//force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
920 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
921 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
922 |
|
movingZAtoms[j]->addFrc(force); |
923 |
|
} |
924 |
|
} |
931 |
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
932 |
|
#endif |
933 |
|
|
934 |
+ |
//cout << "before substracting harmonic force from moving molecuels " |
935 |
+ |
// << "total force is " << calcTotalForce() << endl; |
936 |
+ |
|
937 |
|
force[0]= 0; |
938 |
|
force[1]= 0; |
939 |
|
force[2]= 0; |
944 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
945 |
|
|
946 |
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
947 |
< |
force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
948 |
< |
//force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
947 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
948 |
> |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
949 |
|
unconsAtoms[j]->addFrc(force); |
950 |
|
} |
951 |
|
} |
952 |
|
|
953 |
+ |
//cout << "after substracting harmonic force from moving molecuels " |
954 |
+ |
// << "total force is " << calcTotalForce() << endl; |
955 |
+ |
|
956 |
|
} |
957 |
|
|
958 |
|
/** |
989 |
|
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
990 |
|
#endif |
991 |
|
|
992 |
< |
return changed > 0 ? true : false; |
992 |
> |
return (changed > 0); |
993 |
> |
|
994 |
|
} |
995 |
|
|
996 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1012 |
|
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1013 |
|
#endif |
1014 |
|
|
1015 |
< |
return havingFixed > 0 ? true : false; |
1015 |
> |
return (havingFixed > 0); |
1016 |
|
} |
1017 |
|
|
1018 |
|
|
1038 |
|
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1039 |
|
#endif |
1040 |
|
|
1041 |
< |
return havingMoving > 0 ? true : false; |
1041 |
> |
return (havingMoving > 0); |
1042 |
|
|
1043 |
|
} |
1044 |
|
|
1206 |
|
#else |
1207 |
|
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1208 |
|
#endif |
1209 |
< |
totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1209 |
> |
totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons; |
1210 |
|
} |
1211 |
|
|
1212 |
|
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |