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 |
+ |
"average force substraction policy is used\n"); |
36 |
+ |
painCave.isFatal = 0; |
37 |
+ |
simError(); |
38 |
+ |
|
39 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(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 |
+ |
"average force substraction policy is used\n"); |
48 |
+ |
painCave.isFatal = 0; |
49 |
+ |
simError(); |
50 |
+ |
|
51 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(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() |
384 |
|
{ |
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) |
520 |
|
* |
521 |
|
* |
522 |
|
* |
523 |
< |
*/ |
460 |
< |
|
461 |
< |
|
523 |
> |
*/ |
524 |
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
525 |
|
double zsys; |
526 |
+ |
double COM[3]; |
527 |
+ |
double force[3]; |
528 |
|
|
529 |
|
T::calcForce(calcPot, calcStress); |
530 |
|
|
531 |
< |
if (checkZConsState()) |
532 |
< |
zeroOutVel(); |
533 |
< |
|
531 |
> |
if (checkZConsState()){ |
532 |
> |
zeroOutVel(); |
533 |
> |
forcePolicy->update(); |
534 |
> |
} |
535 |
|
zsys = calcZSys(); |
536 |
|
cout << "---------------------------------------------------------------------" <<endl; |
537 |
< |
cout << "current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
538 |
< |
cout << "before calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
539 |
< |
|
537 |
> |
cout << "current time: " << info->getTime() << endl; |
538 |
> |
cout << "center of mass at z: " << zsys << endl; |
539 |
> |
//cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
540 |
> |
cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
541 |
|
|
542 |
+ |
//cout << "before doZConstraintForce, totalForce is " << calcTotalForce() << endl; |
543 |
+ |
|
544 |
|
//do zconstraint force; |
545 |
|
if (haveFixedZMols()) |
546 |
|
this->doZconstraintForce(); |
547 |
< |
|
480 |
< |
|
481 |
< |
|
547 |
> |
|
548 |
|
//use harmonical poteintial to move the molecules to the specified positions |
549 |
|
if (haveMovingZMols()) |
550 |
|
this->doHarmonic(); |
551 |
< |
|
552 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
553 |
< |
cout << "after calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
551 |
> |
|
552 |
> |
//cout << "after doHarmonic, totalForce is " << calcTotalForce() << endl; |
553 |
> |
|
554 |
> |
//write out forces and current positions of z-constraint molecules |
555 |
> |
if(info->getTime() >= curZconsTime){ |
556 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
557 |
> |
zconsMols[i]->getCOM(COM); |
558 |
> |
curZPos[i] = COM[whichDirection]; |
559 |
> |
|
560 |
> |
//if the z-constraint molecule is still moving, just record its force |
561 |
> |
if(states[i] == zcsMoving){ |
562 |
> |
fz[i] = 0; |
563 |
> |
Atom** movingZAtoms; |
564 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
565 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
566 |
> |
movingZAtoms[j]->getFrc(force); |
567 |
> |
fz[i] += force[whichDirection]; |
568 |
> |
} |
569 |
> |
} |
570 |
> |
} |
571 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
572 |
> |
curZconsTime += zconsTime; |
573 |
> |
} |
574 |
> |
|
575 |
> |
//cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
576 |
> |
cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
577 |
|
} |
578 |
+ |
|
579 |
+ |
|
580 |
+ |
/** |
581 |
+ |
* |
582 |
+ |
*/ |
583 |
|
|
584 |
|
template<typename T> double ZConstraint<T>::calcZSys() |
585 |
|
{ |
588 |
|
double totalMass; |
589 |
|
double totalMZ_local; |
590 |
|
double totalMZ; |
497 |
– |
double massOfUncons_local; |
591 |
|
double massOfCurMol; |
592 |
|
double COM[3]; |
593 |
|
|
594 |
|
totalMass_local = 0; |
502 |
– |
totalMass = 0; |
595 |
|
totalMZ_local = 0; |
504 |
– |
totalMZ = 0; |
505 |
– |
massOfUncons_local = 0; |
506 |
– |
|
596 |
|
|
597 |
|
for(int i = 0; i < nMols; i++){ |
598 |
|
massOfCurMol = molecules[i].getTotalMass(); |
600 |
|
|
601 |
|
totalMass_local += massOfCurMol; |
602 |
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
603 |
< |
|
515 |
< |
if(isZConstraintMol(&molecules[i]) == -1){ |
516 |
< |
|
517 |
< |
massOfUncons_local += massOfCurMol; |
518 |
< |
} |
519 |
< |
|
603 |
> |
|
604 |
|
} |
605 |
+ |
|
606 |
|
|
522 |
– |
|
607 |
|
#ifdef IS_MPI |
608 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
609 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
610 |
< |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
611 |
< |
#else |
608 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, |
609 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
610 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
611 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
612 |
> |
#else |
613 |
|
totalMass = totalMass_local; |
614 |
|
totalMZ = totalMZ_local; |
615 |
< |
totalMassOfUncons = massOfUncons_local; |
531 |
< |
#endif |
615 |
> |
#endif |
616 |
|
|
617 |
|
double zsys; |
618 |
|
zsys = totalMZ / totalMass; |
631 |
|
|
632 |
|
/** |
633 |
|
* |
550 |
– |
* |
551 |
– |
* |
634 |
|
*/ |
635 |
|
|
636 |
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
638 |
|
Atom** fixedZAtoms; |
639 |
|
double COMvel[3]; |
640 |
|
double vel[3]; |
641 |
+ |
double zSysCOMVel; |
642 |
|
|
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 |
– |
|
643 |
|
//zero out the velocities of center of mass of fixed z-constrained molecules |
644 |
|
|
645 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
646 |
|
|
647 |
< |
if (states[i] == zcsFixed){ |
647 |
> |
if (states[i] == zcsFixed){ |
648 |
|
|
649 |
< |
zconsMols[i]->getCOMvel(COMvel); |
650 |
< |
cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
649 |
> |
zconsMols[i]->getCOMvel(COMvel); |
650 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
651 |
|
|
652 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
653 |
< |
|
653 |
> |
|
654 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
655 |
|
fixedZAtoms[j]->getVel(vel); |
656 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
657 |
< |
fixedZAtoms[j]->setVel(vel); |
656 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
657 |
> |
fixedZAtoms[j]->setVel(vel); |
658 |
|
} |
659 |
|
|
660 |
< |
zconsMols[i]->getCOMvel(COMvel); |
661 |
< |
cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
660 |
> |
zconsMols[i]->getCOMvel(COMvel); |
661 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
662 |
|
} |
663 |
< |
|
663 |
> |
|
664 |
|
} |
665 |
|
|
666 |
< |
cout << "before resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
667 |
< |
|
666 |
> |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
667 |
> |
|
668 |
> |
zSysCOMVel = calcSysCOMVel(); |
669 |
> |
#ifdef IS_MPI |
670 |
> |
if(worldRank == 0){ |
671 |
> |
#endif |
672 |
> |
cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
673 |
> |
#ifdef IS_MPI |
674 |
> |
} |
675 |
> |
#endif |
676 |
> |
|
677 |
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
678 |
|
double MVzOfMovingMols_local; |
679 |
|
double MVzOfMovingMols; |
692 |
|
if (states[i] == zcsMoving){ |
693 |
|
zconsMols[i]->getCOMvel(COMvel); |
694 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
695 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
695 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
696 |
|
} |
697 |
< |
|
697 |
> |
|
698 |
|
} |
699 |
|
|
700 |
|
#ifndef IS_MPI |
728 |
|
if (states[i] ==zcsMoving){ |
729 |
|
|
730 |
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
731 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
731 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
732 |
|
movingZAtoms[j]->getVel(vel); |
733 |
|
vel[whichDirection] -= vzOfMovingMols; |
734 |
< |
movingZAtoms[j]->setVel(vel); |
735 |
< |
} |
736 |
< |
|
734 |
> |
movingZAtoms[j]->setVel(vel); |
735 |
> |
} |
736 |
> |
|
737 |
|
} |
738 |
|
|
739 |
|
} |
740 |
|
|
660 |
– |
cout << "after resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
741 |
|
|
742 |
+ |
zSysCOMVel = calcSysCOMVel(); |
743 |
+ |
#ifdef IS_MPI |
744 |
+ |
if(worldRank == 0){ |
745 |
+ |
#endif |
746 |
+ |
cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
747 |
+ |
#ifdef IS_MPI |
748 |
+ |
} |
749 |
+ |
#endif |
750 |
+ |
|
751 |
|
} |
752 |
|
|
753 |
+ |
/** |
754 |
+ |
* |
755 |
+ |
*/ |
756 |
+ |
|
757 |
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
758 |
|
|
759 |
|
Atom** zconsAtoms; |
763 |
|
double COM[3]; |
764 |
|
double force[3]; |
765 |
|
|
673 |
– |
int nMovingZMols_local; |
674 |
– |
int nMovingZMols; |
766 |
|
|
767 |
< |
//constrain the molecules which do not reach the specified positions |
767 |
> |
|
768 |
> |
//constrain the molecules which do not reach the specified positions |
769 |
|
|
770 |
|
//Zero Out the force of z-contrained molecules |
771 |
|
totalFZ_local = 0; |
772 |
|
|
773 |
|
//calculate the total z-contrained force of fixed z-contrained molecules |
774 |
< |
cout << "Fixed Molecules" << endl; |
774 |
> |
|
775 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
776 |
< |
|
776 |
> |
|
777 |
|
if (states[i] == zcsFixed){ |
778 |
< |
|
778 |
> |
|
779 |
|
zconsMols[i]->getCOM(COM); |
780 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
781 |
|
|
783 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
784 |
|
zconsAtoms[j]->getFrc(force); |
785 |
|
fz[i] += force[whichDirection]; |
786 |
< |
} |
786 |
> |
} |
787 |
|
totalFZ_local += fz[i]; |
788 |
|
|
789 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
789 |
> |
cout << "Fixed Molecule --\tindex: " << indexOfZConsMols[i] |
790 |
> |
<<"\tcurrent zpos: " << COM[whichDirection] |
791 |
> |
<< "\tcurrent fz: " <<fz[i] << endl; |
792 |
|
|
793 |
|
} |
794 |
< |
|
794 |
> |
|
795 |
|
} |
796 |
|
|
797 |
< |
//calculate the number of atoms of moving z-constrained molecules |
704 |
< |
nMovingZMols_local = 0; |
705 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
706 |
< |
if(states[i] == zcsMoving) |
707 |
< |
nMovingZMols_local += massOfZConsMols[i]; |
708 |
< |
|
797 |
> |
//calculate total z-constraint force |
798 |
|
#ifdef IS_MPI |
799 |
|
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); |
800 |
|
#else |
801 |
|
totalFZ = totalFZ_local; |
714 |
– |
nMovingZMols = nMovingZMols_local; |
802 |
|
#endif |
803 |
|
|
804 |
< |
force[0]= 0; |
718 |
< |
force[1]= 0; |
719 |
< |
force[2]= 0; |
720 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
721 |
< |
|
722 |
< |
//modify the forces of unconstrained molecules |
723 |
< |
for(int i = 0; i < unconsMols.size(); i++){ |
724 |
< |
|
725 |
< |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
726 |
< |
|
727 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
728 |
< |
unconsAtoms[j]->addFrc(force); |
729 |
< |
|
730 |
< |
} |
731 |
< |
|
732 |
< |
//modify the forces of moving z-constrained molecules |
733 |
< |
for(int i = 0; i < zconsMols.size(); i++) { |
734 |
< |
if (states[i] == zcsMoving){ |
735 |
< |
|
736 |
< |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
737 |
< |
|
738 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
739 |
< |
movingZAtoms[j]->addFrc(force); |
740 |
< |
} |
741 |
< |
} |
742 |
< |
|
804 |
> |
|
805 |
|
// apply negative to fixed z-constrained molecues; |
806 |
|
force[0]= 0; |
807 |
|
force[1]= 0; |
810 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
811 |
|
|
812 |
|
if (states[i] == zcsFixed){ |
813 |
< |
|
813 |
> |
|
814 |
|
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
815 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
816 |
|
|
817 |
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
818 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
818 |
> |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
819 |
> |
//force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
820 |
|
zconsAtoms[j]->addFrc(force); |
821 |
|
} |
822 |
< |
|
822 |
> |
|
823 |
|
} |
824 |
< |
|
824 |
> |
|
825 |
|
} |
826 |
|
|
827 |
< |
} |
827 |
> |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
828 |
> |
// << "total force is " << calcTotalForce() << endl; |
829 |
|
|
830 |
< |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
831 |
< |
double COM[3]; |
832 |
< |
double diff; |
830 |
> |
//calculate the number of atoms of moving z-constrained molecules |
831 |
> |
int nMovingZAtoms_local; |
832 |
> |
int nMovingZAtoms; |
833 |
|
|
834 |
< |
bool changed; |
834 |
> |
nMovingZAtoms_local = 0; |
835 |
> |
for(int i = 0; i < zconsMols.size(); i++) |
836 |
> |
if(states[i] == zcsMoving) |
837 |
> |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
838 |
|
|
839 |
< |
changed = false; |
840 |
< |
|
841 |
< |
for(int i =0; i < zconsMols.size(); i++){ |
839 |
> |
#ifdef IS_MPI |
840 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, |
841 |
> |
MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
842 |
> |
#else |
843 |
> |
nMovingZAtoms = nMovingZAtoms_local; |
844 |
> |
#endif |
845 |
|
|
846 |
< |
zconsMols[i]->getCOM(COM); |
847 |
< |
diff = fabs(COM[whichDirection] - zPos[i]); |
848 |
< |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
779 |
< |
states[i] = zcsFixed; |
780 |
< |
changed = true; |
781 |
< |
} |
782 |
< |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
783 |
< |
states[i] = zcsMoving; |
784 |
< |
changed = true; |
785 |
< |
} |
786 |
< |
|
787 |
< |
} |
846 |
> |
force[0]= 0; |
847 |
> |
force[1]= 0; |
848 |
> |
force[2]= 0; |
849 |
|
|
850 |
< |
return changed; |
851 |
< |
} |
850 |
> |
//modify the forces of unconstrained molecules |
851 |
> |
for(int i = 0; i < unconsMols.size(); i++){ |
852 |
> |
|
853 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
854 |
> |
|
855 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
856 |
> |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
857 |
> |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
858 |
> |
unconsAtoms[j]->addFrc(force); |
859 |
> |
} |
860 |
> |
|
861 |
> |
} |
862 |
|
|
863 |
< |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
864 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
865 |
< |
if (states[i] == zcsFixed) |
866 |
< |
return true; |
863 |
> |
//modify the forces of moving z-constrained molecules |
864 |
> |
for(int i = 0; i < zconsMols.size(); i++) { |
865 |
> |
if (states[i] == zcsMoving){ |
866 |
> |
|
867 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
868 |
|
|
869 |
< |
return false; |
870 |
< |
} |
869 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
870 |
> |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
871 |
> |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
872 |
> |
movingZAtoms[j]->addFrc(force); |
873 |
> |
} |
874 |
> |
} |
875 |
> |
} |
876 |
|
|
877 |
+ |
//cout << "after substracting z-constraint force from moving molecuels " |
878 |
+ |
// << "total force is " << calcTotalForce() << endl; |
879 |
|
|
801 |
– |
/** |
802 |
– |
* |
803 |
– |
*/ |
804 |
– |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
805 |
– |
for(int i = 0; i < zconsMols.size(); i++) |
806 |
– |
if (states[i] == zcsMoving) |
807 |
– |
return true; |
808 |
– |
|
809 |
– |
return false; |
810 |
– |
|
880 |
|
} |
881 |
|
|
882 |
|
/** |
890 |
|
double harmonicF; |
891 |
|
double COM[3]; |
892 |
|
double diff; |
893 |
+ |
double totalFZ_local; |
894 |
|
double totalFZ; |
895 |
< |
|
895 |
> |
|
896 |
|
force[0] = 0; |
897 |
|
force[1] = 0; |
898 |
|
force[2] = 0; |
899 |
|
|
900 |
< |
totalFZ = 0; |
900 |
> |
totalFZ_local = 0; |
901 |
|
|
832 |
– |
cout << "Moving Molecules" << endl; |
902 |
|
for(int i = 0; i < zconsMols.size(); i++) { |
903 |
|
|
904 |
|
if (states[i] == zcsMoving){ |
905 |
|
zconsMols[i]->getCOM(COM); |
906 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
907 |
< |
|
908 |
< |
diff = COM[whichDirection] -zPos[i]; |
909 |
< |
|
906 |
> |
cout << "Moving Molecule --\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
907 |
> |
|
908 |
> |
diff = COM[whichDirection] -zPos[i]; |
909 |
> |
|
910 |
|
harmonicU = 0.5 * kz[i] * diff * diff; |
911 |
< |
info->lrPot += harmonicU; |
911 |
> |
info->lrPot += harmonicU; |
912 |
|
|
913 |
< |
harmonicF = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
914 |
< |
force[whichDirection] = harmonicF; |
915 |
< |
totalFZ += harmonicF; |
916 |
< |
|
913 |
> |
harmonicF = - kz[i] * diff; |
914 |
> |
totalFZ_local += harmonicF; |
915 |
> |
|
916 |
> |
//adjust force |
917 |
> |
|
918 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
919 |
|
|
920 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
920 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
921 |
> |
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
922 |
> |
//force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
923 |
|
movingZAtoms[j]->addFrc(force); |
924 |
+ |
} |
925 |
|
} |
926 |
|
|
927 |
|
} |
928 |
|
|
929 |
+ |
#ifndef IS_MPI |
930 |
+ |
totalFZ = totalFZ_local; |
931 |
+ |
#else |
932 |
+ |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
933 |
+ |
#endif |
934 |
+ |
|
935 |
|
force[0]= 0; |
936 |
|
force[1]= 0; |
937 |
|
force[2]= 0; |
859 |
– |
force[whichDirection] = -totalFZ /totNumOfUnconsAtoms; |
938 |
|
|
939 |
|
//modify the forces of unconstrained molecules |
940 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
941 |
|
|
942 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
943 |
|
|
944 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
944 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
945 |
> |
force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
946 |
> |
//force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
947 |
|
unconsAtoms[j]->addFrc(force); |
948 |
+ |
} |
949 |
|
} |
950 |
|
|
951 |
|
} |
952 |
|
|
953 |
< |
template<typename T> double ZConstraint<T>::calcCOMVel() |
953 |
> |
/** |
954 |
> |
* |
955 |
> |
*/ |
956 |
> |
|
957 |
> |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
958 |
> |
double COM[3]; |
959 |
> |
double diff; |
960 |
> |
|
961 |
> |
int changed_local; |
962 |
> |
int changed; |
963 |
> |
|
964 |
> |
changed_local = 0; |
965 |
> |
|
966 |
> |
for(int i =0; i < zconsMols.size(); i++){ |
967 |
> |
|
968 |
> |
zconsMols[i]->getCOM(COM); |
969 |
> |
diff = fabs(COM[whichDirection] - zPos[i]); |
970 |
> |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
971 |
> |
states[i] = zcsFixed; |
972 |
> |
changed_local = 1; |
973 |
> |
} |
974 |
> |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
975 |
> |
states[i] = zcsMoving; |
976 |
> |
changed_local = 1; |
977 |
> |
} |
978 |
> |
|
979 |
> |
} |
980 |
> |
|
981 |
> |
#ifndef IS_MPI |
982 |
> |
changed =changed_local; |
983 |
> |
#else |
984 |
> |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
985 |
> |
#endif |
986 |
> |
|
987 |
> |
return changed > 0 ? true : false; |
988 |
> |
} |
989 |
> |
|
990 |
> |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
991 |
> |
|
992 |
> |
int havingFixed_local; |
993 |
> |
int havingFixed; |
994 |
> |
|
995 |
> |
havingFixed_local = 0; |
996 |
> |
|
997 |
> |
for(int i = 0; i < zconsMols.size(); i++) |
998 |
> |
if (states[i] == zcsFixed){ |
999 |
> |
havingFixed_local = 1; |
1000 |
> |
break; |
1001 |
> |
} |
1002 |
> |
|
1003 |
> |
#ifndef IS_MPI |
1004 |
> |
havingFixed = havingFixed_local; |
1005 |
> |
#else |
1006 |
> |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1007 |
> |
#endif |
1008 |
> |
|
1009 |
> |
return havingFixed > 0 ? true : false; |
1010 |
> |
} |
1011 |
> |
|
1012 |
> |
|
1013 |
> |
/** |
1014 |
> |
* |
1015 |
> |
*/ |
1016 |
> |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1017 |
> |
|
1018 |
> |
int havingMoving_local; |
1019 |
> |
int havingMoving; |
1020 |
> |
|
1021 |
> |
havingMoving_local = 0; |
1022 |
> |
|
1023 |
> |
for(int i = 0; i < zconsMols.size(); i++) |
1024 |
> |
if (states[i] == zcsMoving){ |
1025 |
> |
havingMoving_local = 1; |
1026 |
> |
break; |
1027 |
> |
} |
1028 |
> |
|
1029 |
> |
#ifndef IS_MPI |
1030 |
> |
havingMoving = havingMoving_local; |
1031 |
> |
#else |
1032 |
> |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1033 |
> |
#endif |
1034 |
> |
|
1035 |
> |
return havingMoving > 0 ? true : false; |
1036 |
> |
|
1037 |
> |
} |
1038 |
> |
|
1039 |
> |
/** |
1040 |
> |
* |
1041 |
> |
*/ |
1042 |
> |
|
1043 |
> |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1044 |
|
{ |
1045 |
|
double MVzOfMovingMols_local; |
1046 |
|
double MVzOfMovingMols; |
1061 |
|
if (states[i] == zcsMoving){ |
1062 |
|
zconsMols[i]->getCOMvel(COMvel); |
1063 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1064 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1064 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1065 |
|
} |
1066 |
< |
|
1066 |
> |
|
1067 |
|
} |
1068 |
|
|
1069 |
|
#ifndef IS_MPI |
1080 |
|
return vzOfMovingMols; |
1081 |
|
} |
1082 |
|
|
1083 |
+ |
/** |
1084 |
+ |
* |
1085 |
+ |
*/ |
1086 |
|
|
1087 |
< |
template<typename T> double ZConstraint<T>::calcCOMVel2() |
1087 |
> |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1088 |
|
{ |
1089 |
|
double COMvel[3]; |
1090 |
< |
double tempMVz = 0; |
1091 |
< |
int index; |
1092 |
< |
|
1090 |
> |
double tempMVz_local; |
1091 |
> |
double tempMVz; |
1092 |
> |
double massOfZCons_local; |
1093 |
> |
double massOfZCons; |
1094 |
> |
|
1095 |
> |
|
1096 |
> |
tempMVz_local = 0; |
1097 |
> |
|
1098 |
|
for(int i =0 ; i < nMols; i++){ |
1099 |
< |
index = isZConstraintMol(&molecules[i]); |
1100 |
< |
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 |
< |
} |
1099 |
> |
molecules[i].getCOMvel(COMvel); |
1100 |
> |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1101 |
|
} |
1102 |
< |
|
1103 |
< |
return tempMVz /totalMassOfUncons; |
1102 |
> |
|
1103 |
> |
massOfZCons_local = 0; |
1104 |
> |
|
1105 |
> |
for(int i = 0; i < massOfZConsMols.size(); i++){ |
1106 |
> |
massOfZCons_local += massOfZConsMols[i]; |
1107 |
> |
} |
1108 |
> |
#ifndef IS_MPI |
1109 |
> |
massOfZCons = massOfZCons_local; |
1110 |
> |
tempMVz = tempMVz_local; |
1111 |
> |
#else |
1112 |
> |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1113 |
> |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1114 |
> |
#endif |
1115 |
> |
|
1116 |
> |
return tempMVz /(totalMassOfUncons + massOfZCons); |
1117 |
|
} |
1118 |
+ |
|
1119 |
+ |
/** |
1120 |
+ |
* |
1121 |
+ |
*/ |
1122 |
+ |
|
1123 |
+ |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1124 |
+ |
|
1125 |
+ |
double force[3]; |
1126 |
+ |
double totalForce_local; |
1127 |
+ |
double totalForce; |
1128 |
+ |
|
1129 |
+ |
totalForce_local = 0; |
1130 |
+ |
|
1131 |
+ |
for(int i = 0; i < nAtoms; i++){ |
1132 |
+ |
atoms[i]->getFrc(force); |
1133 |
+ |
totalForce_local += force[whichDirection]; |
1134 |
+ |
} |
1135 |
+ |
|
1136 |
+ |
#ifndef IS_MPI |
1137 |
+ |
totalForce = totalForce_local; |
1138 |
+ |
#else |
1139 |
+ |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1140 |
+ |
#endif |
1141 |
+ |
|
1142 |
+ |
return totalForce; |
1143 |
+ |
|
1144 |
+ |
} |
1145 |
+ |
|
1146 |
+ |
/** |
1147 |
+ |
* |
1148 |
+ |
*/ |
1149 |
+ |
|
1150 |
+ |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1151 |
+ |
//calculate the number of atoms of moving z-constrained molecules |
1152 |
+ |
int nMovingZAtoms_local; |
1153 |
+ |
int nMovingZAtoms; |
1154 |
+ |
|
1155 |
+ |
nMovingZAtoms_local = 0; |
1156 |
+ |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1157 |
+ |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1158 |
+ |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1159 |
+ |
|
1160 |
+ |
#ifdef IS_MPI |
1161 |
+ |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1162 |
+ |
#else |
1163 |
+ |
nMovingZAtoms = nMovingZAtoms_local; |
1164 |
+ |
#endif |
1165 |
+ |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1166 |
+ |
} |
1167 |
+ |
|
1168 |
+ |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1169 |
+ |
return totalForce / mol->getNAtoms(); |
1170 |
+ |
} |
1171 |
+ |
|
1172 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1173 |
+ |
return totalForce / totNumOfMovingAtoms; |
1174 |
+ |
} |
1175 |
+ |
|
1176 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1177 |
+ |
return totalForce / mol->getNAtoms(); |
1178 |
+ |
} |
1179 |
+ |
|
1180 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1181 |
+ |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1182 |
+ |
} |
1183 |
+ |
|
1184 |
+ |
/** |
1185 |
+ |
* |
1186 |
+ |
*/ |
1187 |
+ |
|
1188 |
+ |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1189 |
+ |
//calculate the number of atoms of moving z-constrained molecules |
1190 |
+ |
double massOfMovingZAtoms_local; |
1191 |
+ |
double massOfMovingZAtoms; |
1192 |
+ |
|
1193 |
+ |
massOfMovingZAtoms_local = 0; |
1194 |
+ |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1195 |
+ |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1196 |
+ |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1197 |
+ |
|
1198 |
+ |
#ifdef IS_MPI |
1199 |
+ |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1200 |
+ |
#else |
1201 |
+ |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1202 |
+ |
#endif |
1203 |
+ |
totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1204 |
+ |
} |
1205 |
+ |
|
1206 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1207 |
+ |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1208 |
+ |
} |
1209 |
+ |
|
1210 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1211 |
+ |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1212 |
+ |
} |
1213 |
+ |
|
1214 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1215 |
+ |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1216 |
+ |
} |
1217 |
+ |
|
1218 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1219 |
+ |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1220 |
+ |
} |
1221 |
+ |
|