2 |
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#include "simError.h" |
3 |
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#include <cmath> |
4 |
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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 |
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indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
7 |
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{ |
8 |
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|
27 |
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double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
28 |
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zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
29 |
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|
30 |
< |
//creat force substraction policy |
30 |
> |
//creat force Subtraction policy |
31 |
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data = info->getProperty(ZCONSFORCEPOLICY_ID); |
32 |
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if(!data){ |
33 |
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sprintf( painCave.errMsg, |
34 |
< |
"ZConstraint Warning: User does not set force substraction policy, " |
34 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
35 |
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"PolicyByMass is used\n"); |
36 |
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painCave.isFatal = 0; |
37 |
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simError(); |
38 |
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|
39 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
39 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
40 |
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} |
41 |
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else{ |
42 |
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policy = dynamic_cast<StringData*>(data); |
48 |
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painCave.isFatal = 0; |
49 |
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simError(); |
50 |
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|
51 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
51 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
52 |
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} |
53 |
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else{ |
54 |
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if(policy->getData() == "BYNUMBER") |
55 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
55 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this); |
56 |
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else if(policy->getData() == "BYMASS") |
57 |
< |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
57 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
58 |
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else{ |
59 |
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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 |
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painCave.isFatal = 0; |
63 |
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simError(); |
64 |
+ |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
65 |
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} |
66 |
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} |
67 |
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} |
250 |
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(*parameters)[i].zPos = COM[whichDirection]; |
251 |
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|
252 |
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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 |
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"initial z coornidate will be used \n"); |
255 |
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painCave.isFatal = 0; |
256 |
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simError(); |
279 |
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zPos.push_back((*parameters)[searchResult].zPos); |
280 |
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// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 |
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// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
281 |
– |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
282 |
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|
283 |
+ |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
284 |
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molecules[i].getCOM(COM); |
285 |
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} |
286 |
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else |
330 |
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MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 |
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#endif |
332 |
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|
332 |
– |
|
333 |
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//get total number of unconstrained atoms |
334 |
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int nUnconsAtoms_local; |
335 |
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nUnconsAtoms_local = 0; |
342 |
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MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
343 |
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MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
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#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 |
– |
} |
345 |
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|
346 |
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forcePolicy->update(); |
347 |
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} |
394 |
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zconsMols.push_back(&molecules[i]); |
395 |
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zPos.push_back((*parameters)[index].zPos); |
396 |
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kz.push_back((*parameters)[index].kRatio * zForceConst); |
407 |
– |
|
397 |
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massOfZConsMols.push_back(molecules[i].getTotalMass()); |
398 |
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|
399 |
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molecules[i].getCOM(COM); |
494 |
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} |
495 |
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|
496 |
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template<typename T> void ZConstraint<T>::integrate(){ |
497 |
+ |
|
498 |
+ |
// creat zconsWriter |
499 |
+ |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
500 |
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|
501 |
+ |
if(!fzOut){ |
502 |
+ |
sprintf( painCave.errMsg, |
503 |
+ |
"Memory allocation failure in class Zconstraint\n"); |
504 |
+ |
painCave.isFatal = 1; |
505 |
+ |
simError(); |
506 |
+ |
} |
507 |
+ |
|
508 |
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//zero out the velocities of center of mass of unconstrained molecules |
509 |
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//and the velocities of center of mass of every single z-constrained molecueles |
510 |
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zeroOutVel(); |
530 |
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|
531 |
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T::calcForce(calcPot, calcStress); |
532 |
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|
533 |
< |
if (checkZConsState()){ |
534 |
< |
|
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 |
< |
|
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 |
< |
|
533 |
> |
if (checkZConsState()){ |
534 |
> |
zeroOutVel(); |
535 |
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forcePolicy->update(); |
536 |
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} |
537 |
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|
540 |
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#ifdef IS_MPI |
541 |
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if(worldRank == 0){ |
542 |
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#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 |
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|
548 |
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#ifdef IS_MPI |
549 |
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} |
582 |
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#ifdef IS_MPI |
583 |
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if(worldRank == 0){ |
584 |
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#endif |
585 |
< |
// cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
585 |
> |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
586 |
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#ifdef IS_MPI |
587 |
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} |
588 |
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#endif |
659 |
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if (states[i] == zcsFixed){ |
660 |
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|
661 |
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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 |
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|
664 |
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fixedZAtoms = zconsMols[i]->getMyAtoms(); |
665 |
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|
681 |
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#ifdef IS_MPI |
682 |
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if(worldRank == 0){ |
683 |
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#endif |
684 |
< |
// cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
684 |
> |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
685 |
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#ifdef IS_MPI |
686 |
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} |
687 |
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#endif |
755 |
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#ifdef IS_MPI |
756 |
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if(worldRank == 0){ |
757 |
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#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 |
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#ifdef IS_MPI |
760 |
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} |
761 |
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#endif |
781 |
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totalFZ_local = 0; |
782 |
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|
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 |
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|
788 |
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for(int i = 0; i < zconsMols.size(); i++){ |
789 |
|
|
801 |
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|
802 |
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//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
803 |
|
// <<"\tcurrent zpos: " << COM[whichDirection] |
804 |
< |
// << "\tcurrent fz: " <<fz[i] << endl; |
804 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
805 |
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|
806 |
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|
807 |
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} |
838 |
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|
839 |
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} |
840 |
|
|
841 |
< |
// cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
842 |
< |
// << "total force is " << calcTotalForce() << endl; |
841 |
> |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
842 |
> |
// << "total force is " << calcTotalForce() << endl; |
843 |
> |
|
844 |
|
|
845 |
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force[0]= 0; |
846 |
|
force[1]= 0; |
872 |
|
} |
873 |
|
} |
874 |
|
} |
875 |
+ |
// cout << "after substracting z-constraint force from moving molecuels " |
876 |
+ |
// << "total force is " << calcTotalForce() << endl; |
877 |
|
|
898 |
– |
//cout << "after substracting z-constraint force from moving molecuels " |
899 |
– |
// << "total force is " << calcTotalForce() << endl; |
900 |
– |
|
878 |
|
} |
879 |
|
|
880 |
|
/** |
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; |
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 |
|
|
1169 |
|
nMovingZAtoms = nMovingZAtoms_local; |
1170 |
|
#endif |
1171 |
|
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1189 |
– |
|
1190 |
– |
#ifdef IS_MPI |
1191 |
– |
if(worldRank == 0){ |
1192 |
– |
#endif |
1193 |
– |
// std::cerr << "\n" |
1194 |
– |
// << "*******************************************\n" |
1195 |
– |
// << " fiished Policy by numbr()\n" |
1196 |
– |
// << "*******************************************\n" |
1197 |
– |
// << "\n"; |
1198 |
– |
#ifdef IS_MPI |
1199 |
– |
} |
1200 |
– |
#endif |
1172 |
|
} |
1173 |
|
|
1174 |
|
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
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){ |