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), |
6 |
< |
indexOfZConsMols(NULL) |
5 |
> |
: T(theInfo, the_ff), fz(NULL), curZPos(NULL), |
6 |
> |
indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
7 |
|
{ |
8 |
|
|
9 |
|
//get properties from SimInfo |
11 |
|
ZConsParaData* zConsParaData; |
12 |
|
DoubleData* sampleTime; |
13 |
|
DoubleData* tolerance; |
14 |
+ |
StringData* policy; |
15 |
|
StringData* filename; |
16 |
|
double COM[3]; |
17 |
|
|
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 |
31 |
+ |
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
32 |
+ |
if(!data){ |
33 |
+ |
sprintf( painCave.errMsg, |
34 |
+ |
"ZConstraint Warning: User does not set force substraction policy, " |
35 |
+ |
"PolicyByMass is used\n"); |
36 |
+ |
painCave.isFatal = 0; |
37 |
+ |
simError(); |
38 |
+ |
|
39 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
40 |
+ |
} |
41 |
+ |
else{ |
42 |
+ |
policy = dynamic_cast<StringData*>(data); |
43 |
+ |
|
44 |
+ |
if(!policy){ |
45 |
+ |
sprintf( painCave.errMsg, |
46 |
+ |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
47 |
+ |
"PolicyByMass is used\n"); |
48 |
+ |
painCave.isFatal = 0; |
49 |
+ |
simError(); |
50 |
+ |
|
51 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
52 |
+ |
} |
53 |
+ |
else{ |
54 |
+ |
if(policy->getData() == "BYNUMBER") |
55 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
56 |
+ |
else if(policy->getData() == "BYMASS") |
57 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
58 |
+ |
else{ |
59 |
+ |
sprintf( painCave.errMsg, |
60 |
+ |
"ZConstraint Warning: unknown force substraction policy, " |
61 |
+ |
"average force substraction policy is used\n"); |
62 |
+ |
painCave.isFatal = 0; |
63 |
+ |
simError(); |
64 |
+ |
} |
65 |
+ |
} |
66 |
+ |
} |
67 |
+ |
|
68 |
+ |
|
69 |
|
//retrieve sample time of z-contraint |
70 |
|
data = info->getProperty(ZCONSTIME_ID); |
71 |
|
|
109 |
|
} |
110 |
|
else{ |
111 |
|
|
112 |
< |
filename = dynamic_cast<StringData*>(data); |
112 |
> |
filename = dynamic_cast<StringData*>(data); |
113 |
|
|
114 |
|
if(!filename){ |
115 |
|
|
123 |
|
this->zconsOutput = filename->getData(); |
124 |
|
} |
125 |
|
|
86 |
– |
|
126 |
|
} |
127 |
|
|
128 |
|
//retrieve tolerance for z-constraint molecuels |
152 |
|
} |
153 |
|
|
154 |
|
} |
155 |
< |
|
155 |
> |
|
156 |
|
//retrieve index of z-constraint molecules |
157 |
|
data = info->getProperty(ZCONSPARADATA_ID); |
158 |
|
if(!data) { |
193 |
|
"ZConstraint error: index is out of range\n"); |
194 |
|
painCave.isFatal = 1; |
195 |
|
simError(); |
196 |
< |
} |
196 |
> |
} |
197 |
|
|
198 |
|
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
199 |
|
|
214 |
|
//its initial z coordinate will be used as default |
215 |
|
for(int i = 0; i < parameters->size(); i++){ |
216 |
|
|
217 |
< |
if(!(*parameters)[i].havingZPos){ |
179 |
< |
|
217 |
> |
if(!(*parameters)[i].havingZPos){ |
218 |
|
#ifndef IS_MPI |
219 |
< |
for(int j = 0; j < nMols; j++){ |
220 |
< |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
221 |
< |
molecules[j].getCOM(COM); |
222 |
< |
break; |
185 |
< |
} |
219 |
> |
for(int j = 0; j < nMols; j++){ |
220 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
221 |
> |
molecules[j].getCOM(COM); |
222 |
> |
break; |
223 |
|
} |
224 |
+ |
} |
225 |
|
#else |
226 |
|
//query which processor current zconstraint molecule belongs to |
227 |
< |
int *MolToProcMap; |
228 |
< |
int whichNode; |
229 |
< |
double initZPos; |
230 |
< |
MolToProcMap = mpiSim->getMolToProcMap(); |
231 |
< |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
232 |
< |
|
233 |
< |
//broadcast the zpos of current z-contraint molecule |
234 |
< |
//the node which contain this |
227 |
> |
int *MolToProcMap; |
228 |
> |
int whichNode; |
229 |
> |
double initZPos; |
230 |
> |
MolToProcMap = mpiSim->getMolToProcMap(); |
231 |
> |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
232 |
> |
|
233 |
> |
//broadcast the zpos of current z-contraint molecule |
234 |
> |
//the node which contain this |
235 |
|
|
236 |
< |
if (worldRank == whichNode ){ |
237 |
< |
|
238 |
< |
for(int j = 0; j < nMols; j++) |
239 |
< |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
240 |
< |
molecules[j].getCOM(COM); |
241 |
< |
break; |
242 |
< |
} |
243 |
< |
|
244 |
< |
} |
236 |
> |
if (worldRank == whichNode ){ |
237 |
> |
|
238 |
> |
for(int j = 0; j < nMols; j++) |
239 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
240 |
> |
molecules[j].getCOM(COM); |
241 |
> |
break; |
242 |
> |
} |
243 |
> |
|
244 |
> |
} |
245 |
|
|
246 |
< |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
246 |
> |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
247 |
|
#endif |
248 |
|
|
249 |
< |
(*parameters)[i].zPos = COM[whichDirection]; |
249 |
> |
(*parameters)[i].zPos = COM[whichDirection]; |
250 |
|
|
251 |
< |
sprintf( painCave.errMsg, |
251 |
> |
sprintf( painCave.errMsg, |
252 |
|
"ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
253 |
|
"initial z coornidate will be used \n"); |
254 |
< |
painCave.isFatal = 0; |
255 |
< |
simError(); |
256 |
< |
|
257 |
< |
} |
258 |
< |
} |
259 |
< |
|
254 |
> |
painCave.isFatal = 0; |
255 |
> |
simError(); |
256 |
> |
|
257 |
> |
} |
258 |
> |
} |
259 |
> |
|
260 |
|
}//end if (!zConsParaData) |
261 |
|
}//end if (!data) |
262 |
|
|
276 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
277 |
|
|
278 |
|
zPos.push_back((*parameters)[searchResult].zPos); |
279 |
< |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
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); |
284 |
|
} |
292 |
|
} |
293 |
|
|
294 |
|
fz = new double[zconsMols.size()]; |
295 |
+ |
curZPos = new double[zconsMols.size()]; |
296 |
|
indexOfZConsMols = new int [zconsMols.size()]; |
297 |
|
|
298 |
< |
if(!fz || !indexOfZConsMols){ |
298 |
> |
if(!fz || !curZPos || !indexOfZConsMols){ |
299 |
|
sprintf( painCave.errMsg, |
300 |
|
"Memory allocation failure in class Zconstraint\n"); |
301 |
|
painCave.isFatal = 1; |
306 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
307 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
308 |
|
|
309 |
< |
zconsMols[i]->getCOM(COM); |
309 |
> |
zconsMols[i]->getCOM(COM); |
310 |
|
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
311 |
< |
states.push_back(zcsFixed); |
312 |
< |
else |
313 |
< |
states.push_back(zcsMoving); |
311 |
> |
states.push_back(zcsFixed); |
312 |
> |
else |
313 |
> |
states.push_back(zcsMoving); |
314 |
|
} |
315 |
|
|
316 |
|
#endif |
325 |
|
#ifndef IS_MPI |
326 |
|
totalMassOfUncons = totalMassOfUncons_local; |
327 |
|
#else |
328 |
< |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
328 |
> |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
329 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
330 |
|
#endif |
331 |
|
|
332 |
|
|
339 |
|
#ifndef IS_MPI |
340 |
|
totNumOfUnconsAtoms = nUnconsAtoms_local; |
341 |
|
#else |
342 |
< |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
342 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
343 |
> |
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
|
#endif |
345 |
|
|
346 |
|
// creat zconsWriter |
347 |
< |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
347 |
> |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
348 |
|
|
349 |
|
if(!fzOut){ |
350 |
|
sprintf( painCave.errMsg, |
352 |
|
painCave.isFatal = 1; |
353 |
|
simError(); |
354 |
|
} |
355 |
< |
|
355 |
> |
|
356 |
> |
forcePolicy->update(); |
357 |
|
} |
358 |
|
|
359 |
|
template<typename T> ZConstraint<T>::~ZConstraint() |
360 |
|
{ |
361 |
|
if(fz) |
362 |
|
delete[] fz; |
363 |
+ |
|
364 |
+ |
if(curZPos) |
365 |
+ |
delete[] curZPos; |
366 |
|
|
367 |
|
if(indexOfZConsMols) |
368 |
|
delete[] indexOfZConsMols; |
369 |
|
|
370 |
|
if(fzOut) |
371 |
|
delete fzOut; |
372 |
+ |
|
373 |
+ |
if(forcePolicy) |
374 |
+ |
delete forcePolicy; |
375 |
|
} |
376 |
+ |
|
377 |
+ |
|
378 |
+ |
/** |
379 |
+ |
* |
380 |
+ |
*/ |
381 |
|
|
382 |
|
#ifdef IS_MPI |
383 |
|
template<typename T> void ZConstraint<T>::update() |
403 |
|
|
404 |
|
zconsMols.push_back(&molecules[i]); |
405 |
|
zPos.push_back((*parameters)[index].zPos); |
406 |
< |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
407 |
< |
|
406 |
> |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
407 |
> |
|
408 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
409 |
|
|
410 |
|
molecules[i].getCOM(COM); |
420 |
|
|
421 |
|
//determine the states of z-constraint molecules |
422 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
423 |
< |
zconsMols[i]->getCOM(COM); |
423 |
> |
zconsMols[i]->getCOM(COM); |
424 |
|
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
425 |
< |
states.push_back(zcsFixed); |
426 |
< |
else |
427 |
< |
states.push_back(zcsMoving); |
425 |
> |
states.push_back(zcsFixed); |
426 |
> |
else |
427 |
> |
states.push_back(zcsMoving); |
428 |
|
} |
429 |
|
|
430 |
|
|
432 |
|
// that we want to make the MPI communication simple |
433 |
|
if(fz) |
434 |
|
delete[] fz; |
435 |
+ |
|
436 |
+ |
if(curZPos) |
437 |
+ |
delete[] curZPos; |
438 |
|
|
439 |
|
if(indexOfZConsMols) |
440 |
|
delete[] indexOfZConsMols; |
441 |
|
|
442 |
|
if (zconsMols.size() > 0){ |
443 |
|
fz = new double[zconsMols.size()]; |
444 |
+ |
curZPos = new double[zconsMols.size()]; |
445 |
|
indexOfZConsMols = new int[zconsMols.size()]; |
446 |
|
|
447 |
< |
if(!fz || !indexOfZConsMols){ |
447 |
> |
if(!fz || !curZPos || !indexOfZConsMols){ |
448 |
|
sprintf( painCave.errMsg, |
449 |
|
"Memory allocation failure in class Zconstraint\n"); |
450 |
|
painCave.isFatal = 1; |
458 |
|
} |
459 |
|
else{ |
460 |
|
fz = NULL; |
461 |
+ |
curZPos = NULL; |
462 |
|
indexOfZConsMols = NULL; |
463 |
|
} |
464 |
|
|
465 |
+ |
// |
466 |
+ |
forcePolicy->update(); |
467 |
+ |
|
468 |
|
} |
469 |
|
|
470 |
|
#endif |
471 |
|
|
472 |
< |
/** Function Name: isZConstraintMol |
473 |
< |
** Parameter |
474 |
< |
** Molecule* mol |
475 |
< |
** Return value: |
476 |
< |
** -1, if the molecule is not z-constraint molecule, |
477 |
< |
** other non-negative values, its index in indexOfAllZConsMols vector |
472 |
> |
/** |
473 |
> |
* Function Name: isZConstraintMol |
474 |
> |
* Parameter |
475 |
> |
* Molecule* mol |
476 |
> |
* Return value: |
477 |
> |
* -1, if the molecule is not z-constraint molecule, |
478 |
> |
* other non-negative values, its index in indexOfAllZConsMols vector |
479 |
|
*/ |
480 |
|
|
481 |
|
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
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 |
|
|
525 |
|
*/ |
526 |
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
527 |
|
double zsys; |
528 |
+ |
double COM[3]; |
529 |
+ |
double force[3]; |
530 |
+ |
double zSysCOMVel; |
531 |
|
|
532 |
|
T::calcForce(calcPot, calcStress); |
533 |
|
|
534 |
< |
if (checkZConsState()) |
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 |
+ |
|
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()) |
580 |
|
this->doZconstraintForce(); |
581 |
< |
|
581 |
> |
|
582 |
|
//use harmonical poteintial to move the molecules to the specified positions |
583 |
|
if (haveMovingZMols()) |
584 |
|
this->doHarmonic(); |
585 |
|
|
586 |
< |
//cout << "after doHarmonic, totalForce is " << calcTotalForce() << endl; |
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++){ |
589 |
> |
zconsMols[i]->getCOM(COM); |
590 |
> |
curZPos[i] = COM[whichDirection]; |
591 |
|
|
592 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
593 |
< |
//cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
594 |
< |
cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
592 |
> |
//if the z-constraint molecule is still moving, just record its force |
593 |
> |
if(states[i] == zcsMoving){ |
594 |
> |
fz[i] = 0; |
595 |
> |
Atom** movingZAtoms; |
596 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
597 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
598 |
> |
movingZAtoms[j]->getFrc(force); |
599 |
> |
fz[i] += force[whichDirection]; |
600 |
> |
} |
601 |
> |
} |
602 |
> |
} |
603 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
604 |
> |
curZconsTime += zconsTime; |
605 |
> |
} |
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 |
+ |
/** |
619 |
+ |
* |
620 |
+ |
*/ |
621 |
|
|
622 |
|
template<typename T> double ZConstraint<T>::calcZSys() |
623 |
|
{ |
628 |
|
double totalMZ; |
629 |
|
double massOfCurMol; |
630 |
|
double COM[3]; |
631 |
< |
|
631 |
> |
|
632 |
|
totalMass_local = 0; |
633 |
|
totalMZ_local = 0; |
634 |
|
|
643 |
|
|
644 |
|
|
645 |
|
#ifdef IS_MPI |
646 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
647 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
646 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, |
647 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
648 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
649 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
650 |
|
#else |
651 |
|
totalMass = totalMass_local; |
652 |
|
totalMZ = totalMZ_local; |
669 |
|
|
670 |
|
/** |
671 |
|
* |
540 |
– |
* |
541 |
– |
* |
672 |
|
*/ |
673 |
|
|
674 |
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
676 |
|
Atom** fixedZAtoms; |
677 |
|
double COMvel[3]; |
678 |
|
double vel[3]; |
679 |
+ |
double zSysCOMVel; |
680 |
|
|
681 |
|
//zero out the velocities of center of mass of fixed z-constrained molecules |
682 |
|
|
683 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
684 |
|
|
685 |
< |
if (states[i] == zcsFixed){ |
685 |
> |
if (states[i] == zcsFixed){ |
686 |
|
|
687 |
< |
zconsMols[i]->getCOMvel(COMvel); |
688 |
< |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
687 |
> |
zconsMols[i]->getCOMvel(COMvel); |
688 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
689 |
|
|
690 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
691 |
< |
|
691 |
> |
|
692 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
693 |
|
fixedZAtoms[j]->getVel(vel); |
694 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
695 |
< |
fixedZAtoms[j]->setVel(vel); |
694 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
695 |
> |
fixedZAtoms[j]->setVel(vel); |
696 |
|
} |
697 |
|
|
698 |
< |
zconsMols[i]->getCOMvel(COMvel); |
699 |
< |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
698 |
> |
zconsMols[i]->getCOMvel(COMvel); |
699 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
700 |
|
} |
701 |
< |
|
701 |
> |
|
702 |
|
} |
703 |
|
|
704 |
< |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
705 |
< |
cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl; |
706 |
< |
|
704 |
> |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
705 |
> |
|
706 |
> |
zSysCOMVel = calcSysCOMVel(); |
707 |
> |
#ifdef IS_MPI |
708 |
> |
if(worldRank == 0){ |
709 |
> |
#endif |
710 |
> |
// cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
711 |
> |
#ifdef IS_MPI |
712 |
> |
} |
713 |
> |
#endif |
714 |
> |
|
715 |
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
716 |
|
double MVzOfMovingMols_local; |
717 |
|
double MVzOfMovingMols; |
730 |
|
if (states[i] == zcsMoving){ |
731 |
|
zconsMols[i]->getCOMvel(COMvel); |
732 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
733 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
733 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
734 |
|
} |
735 |
< |
|
735 |
> |
|
736 |
|
} |
737 |
|
|
738 |
|
#ifndef IS_MPI |
766 |
|
if (states[i] ==zcsMoving){ |
767 |
|
|
768 |
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
769 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
769 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
770 |
|
movingZAtoms[j]->getVel(vel); |
771 |
|
vel[whichDirection] -= vzOfMovingMols; |
772 |
< |
movingZAtoms[j]->setVel(vel); |
773 |
< |
} |
774 |
< |
|
772 |
> |
movingZAtoms[j]->setVel(vel); |
773 |
> |
} |
774 |
> |
|
775 |
|
} |
776 |
|
|
777 |
|
} |
778 |
|
|
640 |
– |
cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl; |
779 |
|
|
780 |
+ |
zSysCOMVel = calcSysCOMVel(); |
781 |
+ |
#ifdef IS_MPI |
782 |
+ |
if(worldRank == 0){ |
783 |
+ |
#endif |
784 |
+ |
// cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
785 |
+ |
#ifdef IS_MPI |
786 |
+ |
} |
787 |
+ |
#endif |
788 |
+ |
|
789 |
|
} |
790 |
|
|
791 |
+ |
/** |
792 |
+ |
* |
793 |
+ |
*/ |
794 |
+ |
|
795 |
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
796 |
|
|
797 |
|
Atom** zconsAtoms; |
801 |
|
double COM[3]; |
802 |
|
double force[3]; |
803 |
|
|
804 |
< |
|
654 |
< |
|
655 |
< |
//constrain the molecules which do not reach the specified positions |
804 |
> |
//constrain the molecules which do not reach the specified positions |
805 |
|
|
806 |
|
//Zero Out the force of z-contrained molecules |
807 |
|
totalFZ_local = 0; |
808 |
|
|
809 |
|
//calculate the total z-contrained force of fixed z-contrained molecules |
810 |
< |
cout << "Fixed Molecules" << endl; |
810 |
> |
|
811 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
812 |
< |
|
812 |
> |
|
813 |
|
if (states[i] == zcsFixed){ |
814 |
< |
|
814 |
> |
|
815 |
|
zconsMols[i]->getCOM(COM); |
816 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
817 |
|
|
819 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
820 |
|
zconsAtoms[j]->getFrc(force); |
821 |
|
fz[i] += force[whichDirection]; |
822 |
< |
} |
822 |
> |
} |
823 |
|
totalFZ_local += fz[i]; |
824 |
|
|
825 |
< |
cout << "index: " << indexOfZConsMols[i] |
826 |
< |
<<"\tcurrent zpos: " << COM[whichDirection] |
827 |
< |
<< "\tcurrent fz: " <<fz[i] << endl; |
825 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
826 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
827 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
828 |
|
|
829 |
+ |
|
830 |
|
} |
831 |
< |
|
831 |
> |
|
832 |
|
} |
833 |
< |
|
833 |
> |
|
834 |
> |
//calculate total z-constraint force |
835 |
> |
#ifdef IS_MPI |
836 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
837 |
> |
#else |
838 |
> |
totalFZ = totalFZ_local; |
839 |
> |
#endif |
840 |
> |
|
841 |
> |
|
842 |
|
// apply negative to fixed z-constrained molecues; |
843 |
|
force[0]= 0; |
844 |
|
force[1]= 0; |
847 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
848 |
|
|
849 |
|
if (states[i] == zcsFixed){ |
850 |
< |
|
850 |
> |
|
851 |
|
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
852 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
853 |
|
|
854 |
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
855 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
855 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
856 |
> |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
857 |
|
zconsAtoms[j]->addFrc(force); |
858 |
|
} |
859 |
< |
|
859 |
> |
|
860 |
|
} |
861 |
< |
|
861 |
> |
|
862 |
|
} |
863 |
|
|
864 |
< |
cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
865 |
< |
<< "total force is " << calcTotalForce() << endl; |
707 |
< |
//calculate the number of atoms of moving z-constrained molecules |
708 |
< |
int nMovingZAtoms_local; |
709 |
< |
int nMovingZAtoms; |
710 |
< |
|
711 |
< |
nMovingZAtoms_local = 0; |
712 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
713 |
< |
if(states[i] == zcsMoving) |
714 |
< |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
715 |
< |
|
716 |
< |
#ifdef IS_MPI |
717 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
718 |
< |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
719 |
< |
#else |
720 |
< |
totalFZ = totalFZ_local; |
721 |
< |
nMovingZAtoms = nMovingZAtoms_local; |
722 |
< |
#endif |
864 |
> |
// cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
865 |
> |
// << "total force is " << calcTotalForce() << endl; |
866 |
|
|
867 |
|
force[0]= 0; |
868 |
|
force[1]= 0; |
869 |
|
force[2]= 0; |
727 |
– |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
870 |
|
|
871 |
|
//modify the forces of unconstrained molecules |
730 |
– |
int accessCount = 0; |
872 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
873 |
|
|
874 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
875 |
|
|
876 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
876 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
877 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
878 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
879 |
|
unconsAtoms[j]->addFrc(force); |
880 |
+ |
} |
881 |
|
|
882 |
|
} |
883 |
|
|
884 |
|
//modify the forces of moving z-constrained molecules |
885 |
|
for(int i = 0; i < zconsMols.size(); i++) { |
886 |
|
if (states[i] == zcsMoving){ |
887 |
< |
|
887 |
> |
|
888 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
889 |
|
|
890 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
890 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
891 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
892 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
893 |
|
movingZAtoms[j]->addFrc(force); |
894 |
+ |
} |
895 |
|
} |
896 |
|
} |
750 |
– |
|
751 |
– |
cout << "after substracting z-constraint force from moving molecuels " |
752 |
– |
<< "total force is " << calcTotalForce() << endl; |
897 |
|
|
898 |
< |
} |
898 |
> |
//cout << "after substracting z-constraint force from moving molecuels " |
899 |
> |
// << "total force is " << calcTotalForce() << endl; |
900 |
|
|
756 |
– |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
757 |
– |
double COM[3]; |
758 |
– |
double diff; |
759 |
– |
|
760 |
– |
bool changed; |
761 |
– |
|
762 |
– |
changed = false; |
763 |
– |
|
764 |
– |
for(int i =0; i < zconsMols.size(); i++){ |
765 |
– |
|
766 |
– |
zconsMols[i]->getCOM(COM); |
767 |
– |
diff = fabs(COM[whichDirection] - zPos[i]); |
768 |
– |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
769 |
– |
states[i] = zcsFixed; |
770 |
– |
changed = true; |
771 |
– |
} |
772 |
– |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
773 |
– |
states[i] = zcsMoving; |
774 |
– |
changed = true; |
775 |
– |
} |
776 |
– |
|
777 |
– |
} |
778 |
– |
|
779 |
– |
return changed; |
901 |
|
} |
902 |
|
|
782 |
– |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
783 |
– |
for(int i = 0; i < zconsMols.size(); i++) |
784 |
– |
if (states[i] == zcsFixed) |
785 |
– |
return true; |
786 |
– |
|
787 |
– |
return false; |
788 |
– |
} |
789 |
– |
|
790 |
– |
|
903 |
|
/** |
792 |
– |
* |
793 |
– |
*/ |
794 |
– |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
795 |
– |
for(int i = 0; i < zconsMols.size(); i++) |
796 |
– |
if (states[i] == zcsMoving) |
797 |
– |
return true; |
798 |
– |
|
799 |
– |
return false; |
800 |
– |
|
801 |
– |
} |
802 |
– |
|
803 |
– |
/** |
904 |
|
* |
905 |
|
* |
906 |
|
*/ |
911 |
|
double harmonicF; |
912 |
|
double COM[3]; |
913 |
|
double diff; |
914 |
+ |
double totalFZ_local; |
915 |
|
double totalFZ; |
916 |
< |
|
916 |
> |
|
917 |
|
force[0] = 0; |
918 |
|
force[1] = 0; |
919 |
|
force[2] = 0; |
920 |
|
|
921 |
< |
totalFZ = 0; |
921 |
> |
totalFZ_local = 0; |
922 |
|
|
822 |
– |
cout << "Moving Molecules" << endl; |
923 |
|
for(int i = 0; i < zconsMols.size(); i++) { |
924 |
|
|
925 |
|
if (states[i] == zcsMoving){ |
926 |
|
zconsMols[i]->getCOM(COM); |
927 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
928 |
< |
|
929 |
< |
diff = COM[whichDirection] -zPos[i]; |
930 |
< |
|
927 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
928 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
929 |
> |
|
930 |
> |
diff = COM[whichDirection] -zPos[i]; |
931 |
> |
|
932 |
|
harmonicU = 0.5 * kz[i] * diff * diff; |
933 |
< |
info->lrPot += harmonicU; |
933 |
> |
info->lrPot += harmonicU; |
934 |
|
|
935 |
|
harmonicF = - kz[i] * diff; |
936 |
< |
totalFZ += harmonicF; |
936 |
> |
totalFZ_local += harmonicF; |
937 |
|
|
938 |
< |
// |
939 |
< |
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
839 |
< |
|
938 |
> |
//adjust force |
939 |
> |
|
940 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
941 |
|
|
942 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
942 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
943 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
944 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
945 |
|
movingZAtoms[j]->addFrc(force); |
946 |
+ |
} |
947 |
|
} |
948 |
|
|
949 |
|
} |
950 |
< |
|
950 |
> |
|
951 |
> |
#ifndef IS_MPI |
952 |
> |
totalFZ = totalFZ_local; |
953 |
> |
#else |
954 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
955 |
> |
#endif |
956 |
> |
|
957 |
|
force[0]= 0; |
958 |
|
force[1]= 0; |
959 |
|
force[2]= 0; |
851 |
– |
force[whichDirection] = -totalFZ /totNumOfUnconsAtoms; |
960 |
|
|
961 |
|
//modify the forces of unconstrained molecules |
962 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
963 |
|
|
964 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
965 |
|
|
966 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
966 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
967 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
968 |
> |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
969 |
|
unconsAtoms[j]->addFrc(force); |
970 |
+ |
} |
971 |
|
} |
972 |
+ |
|
973 |
+ |
} |
974 |
+ |
|
975 |
+ |
/** |
976 |
+ |
* |
977 |
+ |
*/ |
978 |
+ |
|
979 |
+ |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
980 |
+ |
double COM[3]; |
981 |
+ |
double diff; |
982 |
+ |
|
983 |
+ |
int changed_local; |
984 |
+ |
int changed; |
985 |
+ |
|
986 |
+ |
changed_local = 0; |
987 |
+ |
|
988 |
+ |
for(int i =0; i < zconsMols.size(); i++){ |
989 |
+ |
|
990 |
+ |
zconsMols[i]->getCOM(COM); |
991 |
+ |
diff = fabs(COM[whichDirection] - zPos[i]); |
992 |
+ |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
993 |
+ |
states[i] = zcsFixed; |
994 |
+ |
changed_local = 1; |
995 |
+ |
} |
996 |
+ |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
997 |
+ |
states[i] = zcsMoving; |
998 |
+ |
changed_local = 1; |
999 |
+ |
} |
1000 |
+ |
|
1001 |
+ |
} |
1002 |
+ |
|
1003 |
+ |
#ifndef IS_MPI |
1004 |
+ |
changed =changed_local; |
1005 |
+ |
#else |
1006 |
+ |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1007 |
+ |
#endif |
1008 |
|
|
1009 |
+ |
return (changed > 0); |
1010 |
+ |
|
1011 |
|
} |
1012 |
|
|
1013 |
+ |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1014 |
+ |
|
1015 |
+ |
int havingFixed_local; |
1016 |
+ |
int havingFixed; |
1017 |
+ |
|
1018 |
+ |
havingFixed_local = 0; |
1019 |
+ |
|
1020 |
+ |
for(int i = 0; i < zconsMols.size(); i++) |
1021 |
+ |
if (states[i] == zcsFixed){ |
1022 |
+ |
havingFixed_local = 1; |
1023 |
+ |
break; |
1024 |
+ |
} |
1025 |
+ |
|
1026 |
+ |
#ifndef IS_MPI |
1027 |
+ |
havingFixed = havingFixed_local; |
1028 |
+ |
#else |
1029 |
+ |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1030 |
+ |
#endif |
1031 |
+ |
|
1032 |
+ |
return (havingFixed > 0); |
1033 |
+ |
} |
1034 |
+ |
|
1035 |
+ |
|
1036 |
+ |
/** |
1037 |
+ |
* |
1038 |
+ |
*/ |
1039 |
+ |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1040 |
+ |
|
1041 |
+ |
int havingMoving_local; |
1042 |
+ |
int havingMoving; |
1043 |
+ |
|
1044 |
+ |
havingMoving_local = 0; |
1045 |
+ |
|
1046 |
+ |
for(int i = 0; i < zconsMols.size(); i++) |
1047 |
+ |
if (states[i] == zcsMoving){ |
1048 |
+ |
havingMoving_local = 1; |
1049 |
+ |
break; |
1050 |
+ |
} |
1051 |
+ |
|
1052 |
+ |
#ifndef IS_MPI |
1053 |
+ |
havingMoving = havingMoving_local; |
1054 |
+ |
#else |
1055 |
+ |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1056 |
+ |
#endif |
1057 |
+ |
|
1058 |
+ |
return (havingMoving > 0); |
1059 |
+ |
|
1060 |
+ |
} |
1061 |
+ |
|
1062 |
+ |
/** |
1063 |
+ |
* |
1064 |
+ |
*/ |
1065 |
+ |
|
1066 |
|
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1067 |
|
{ |
1068 |
|
double MVzOfMovingMols_local; |
1084 |
|
if (states[i] == zcsMoving){ |
1085 |
|
zconsMols[i]->getCOMvel(COMvel); |
1086 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1087 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1087 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1088 |
|
} |
1089 |
< |
|
1089 |
> |
|
1090 |
|
} |
1091 |
|
|
1092 |
|
#ifndef IS_MPI |
1103 |
|
return vzOfMovingMols; |
1104 |
|
} |
1105 |
|
|
1106 |
+ |
/** |
1107 |
+ |
* |
1108 |
+ |
*/ |
1109 |
|
|
1110 |
|
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1111 |
|
{ |
1112 |
|
double COMvel[3]; |
1113 |
< |
double tempMVz = 0; |
1114 |
< |
|
1113 |
> |
double tempMVz_local; |
1114 |
> |
double tempMVz; |
1115 |
> |
double massOfZCons_local; |
1116 |
> |
double massOfZCons; |
1117 |
> |
|
1118 |
> |
|
1119 |
> |
tempMVz_local = 0; |
1120 |
> |
|
1121 |
|
for(int i =0 ; i < nMols; i++){ |
1122 |
|
molecules[i].getCOMvel(COMvel); |
1123 |
< |
tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1123 |
> |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1124 |
|
} |
1125 |
|
|
915 |
– |
double massOfZCons_local; |
916 |
– |
double massOfZCons; |
917 |
– |
|
1126 |
|
massOfZCons_local = 0; |
1127 |
< |
|
1127 |
> |
|
1128 |
|
for(int i = 0; i < massOfZConsMols.size(); i++){ |
1129 |
|
massOfZCons_local += massOfZConsMols[i]; |
1130 |
|
} |
1131 |
|
#ifndef IS_MPI |
1132 |
|
massOfZCons = massOfZCons_local; |
1133 |
+ |
tempMVz = tempMVz_local; |
1134 |
|
#else |
1135 |
|
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1136 |
+ |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1137 |
|
#endif |
1138 |
|
|
1139 |
|
return tempMVz /(totalMassOfUncons + massOfZCons); |
1140 |
|
} |
1141 |
|
|
1142 |
+ |
/** |
1143 |
+ |
* |
1144 |
+ |
*/ |
1145 |
+ |
|
1146 |
|
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1147 |
|
|
1148 |
|
double force[3]; |
1165 |
|
return totalForce; |
1166 |
|
|
1167 |
|
} |
1168 |
+ |
|
1169 |
+ |
/** |
1170 |
+ |
* |
1171 |
+ |
*/ |
1172 |
+ |
|
1173 |
+ |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1174 |
+ |
//calculate the number of atoms of moving z-constrained molecules |
1175 |
+ |
int nMovingZAtoms_local; |
1176 |
+ |
int nMovingZAtoms; |
1177 |
+ |
|
1178 |
+ |
nMovingZAtoms_local = 0; |
1179 |
+ |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1180 |
+ |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1181 |
+ |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1182 |
+ |
|
1183 |
+ |
#ifdef IS_MPI |
1184 |
+ |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1185 |
+ |
#else |
1186 |
+ |
nMovingZAtoms = nMovingZAtoms_local; |
1187 |
+ |
#endif |
1188 |
+ |
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 |
1201 |
+ |
} |
1202 |
+ |
|
1203 |
+ |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1204 |
+ |
return totalForce / mol->getNAtoms(); |
1205 |
+ |
} |
1206 |
+ |
|
1207 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1208 |
+ |
return totalForce / totNumOfMovingAtoms; |
1209 |
+ |
} |
1210 |
+ |
|
1211 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1212 |
+ |
return totalForce / mol->getNAtoms(); |
1213 |
+ |
} |
1214 |
+ |
|
1215 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1216 |
+ |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1217 |
+ |
} |
1218 |
+ |
|
1219 |
+ |
/** |
1220 |
+ |
* |
1221 |
+ |
*/ |
1222 |
+ |
|
1223 |
+ |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1224 |
+ |
//calculate the number of atoms of moving z-constrained molecules |
1225 |
+ |
double massOfMovingZAtoms_local; |
1226 |
+ |
double massOfMovingZAtoms; |
1227 |
+ |
|
1228 |
+ |
massOfMovingZAtoms_local = 0; |
1229 |
+ |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1230 |
+ |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1231 |
+ |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1232 |
+ |
|
1233 |
+ |
#ifdef IS_MPI |
1234 |
+ |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1235 |
+ |
#else |
1236 |
+ |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1237 |
+ |
#endif |
1238 |
+ |
totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1239 |
+ |
} |
1240 |
+ |
|
1241 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1242 |
+ |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1243 |
+ |
} |
1244 |
+ |
|
1245 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1246 |
+ |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1247 |
+ |
} |
1248 |
+ |
|
1249 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1250 |
+ |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1251 |
+ |
} |
1252 |
+ |
|
1253 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1254 |
+ |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1255 |
+ |
} |
1256 |
+ |
|