# | Line 2 | Line 2 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
---|---|---|
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 | |
# | Line 11 | Line 11 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
11 | ZConsParaData* zConsParaData; | |
12 | DoubleData* sampleTime; | |
13 | DoubleData* tolerance; | |
14 | + | StringData* policy; |
15 | StringData* filename; | |
16 | double COM[3]; | |
17 | ||
# | Line 26 | Line 27 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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 | ||
# | Line 69 | Line 109 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
109 | } | |
110 | else{ | |
111 | ||
112 | < | filename = dynamic_cast<StringData*>(data); |
112 | > | filename = dynamic_cast<StringData*>(data); |
113 | ||
114 | if(!filename){ | |
115 | ||
# | Line 83 | Line 123 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
123 | this->zconsOutput = filename->getData(); | |
124 | } | |
125 | ||
86 | – | |
126 | } | |
127 | ||
128 | //retrieve tolerance for z-constraint molecuels | |
# | Line 113 | Line 152 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
152 | } | |
153 | ||
154 | } | |
155 | < | |
155 | > | |
156 | //retrieve index of z-constraint molecules | |
157 | data = info->getProperty(ZCONSPARADATA_ID); | |
158 | if(!data) { | |
# | Line 154 | Line 193 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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 | ||
# | Line 175 | Line 214 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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 | ||
# | Line 238 | Line 276 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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 | } | |
# | Line 252 | Line 292 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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; | |
# | Line 265 | Line 306 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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 | |
# | Line 284 | Line 325 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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 | ||
# | Line 297 | Line 339 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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, | |
# | Line 309 | Line 352 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
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 | { | |
# | Line 348 | Line 403 | 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); | |
# | Line 365 | Line 420 | template<typename T> void ZConstraint<T>::update() | |
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 | ||
# | Line 377 | Line 432 | template<typename T> void ZConstraint<T>::update() | |
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; | |
# | Line 399 | Line 458 | template<typename T> void ZConstraint<T>::update() | |
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) | |
# | Line 445 | Line 509 | template<typename T> void ZConstraint<T>::integrate(){ | |
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 | ||
# | Line 456 | Line 522 | template<typename T> void ZConstraint<T>::integrate(){ | |
522 | * | |
523 | * | |
524 | * | |
525 | < | */ |
460 | < | |
461 | < | |
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()) |
535 | < | zeroOutVel(); |
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() <<"\tcenter of mass at z: " << zsys << endl; |
567 | < | cout << "before calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
568 | < | |
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 | + | #ifdef IS_MPI |
575 | + | } |
576 | + | #endif |
577 | + | |
578 | //do zconstraint force; | |
579 | if (haveFixedZMols()) | |
580 | this->doZconstraintForce(); | |
581 | < | |
480 | < | |
481 | < | |
581 | > | |
582 | //use harmonical poteintial to move the molecules to the specified positions | |
583 | if (haveMovingZMols()) | |
584 | this->doHarmonic(); | |
585 | < | |
586 | < | fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
587 | < | cout << "after calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
585 | > | |
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 | > | //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 | ||
623 | template<typename T> double ZConstraint<T>::calcZSys() | |
624 | { | |
# | Line 494 | Line 627 | template<typename T> double ZConstraint<T>::calcZSys() | |
627 | double totalMass; | |
628 | double totalMZ_local; | |
629 | double totalMZ; | |
497 | – | double massOfUncons_local; |
630 | double massOfCurMol; | |
631 | double COM[3]; | |
632 | ||
633 | totalMass_local = 0; | |
502 | – | totalMass = 0; |
634 | totalMZ_local = 0; | |
504 | – | totalMZ = 0; |
505 | – | massOfUncons_local = 0; |
506 | – | |
635 | ||
636 | for(int i = 0; i < nMols; i++){ | |
637 | massOfCurMol = molecules[i].getTotalMass(); | |
# | Line 511 | Line 639 | template<typename T> double ZConstraint<T>::calcZSys() | |
639 | ||
640 | totalMass_local += massOfCurMol; | |
641 | totalMZ_local += massOfCurMol * COM[whichDirection]; | |
642 | < | |
515 | < | if(isZConstraintMol(&molecules[i]) == -1){ |
516 | < | |
517 | < | massOfUncons_local += massOfCurMol; |
518 | < | } |
519 | < | |
642 | > | |
643 | } | |
644 | + | |
645 | ||
522 | – | |
646 | #ifdef IS_MPI | |
647 | < | MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
648 | < | MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
649 | < | MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
650 | < | #else |
647 | > | MPI_Allreduce(&totalMass_local, &totalMass, 1, |
648 | > | MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
649 | > | MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
650 | > | MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
651 | > | #else |
652 | totalMass = totalMass_local; | |
653 | totalMZ = totalMZ_local; | |
654 | < | totalMassOfUncons = massOfUncons_local; |
531 | < | #endif |
654 | > | #endif |
655 | ||
656 | double zsys; | |
657 | zsys = totalMZ / totalMass; | |
# | Line 547 | Line 670 | template<typename T> void ZConstraint<T>::thermalize( | |
670 | ||
671 | /** | |
672 | * | |
550 | – | * |
551 | – | * |
673 | */ | |
674 | ||
675 | template<typename T> void ZConstraint<T>::zeroOutVel(){ | |
# | Line 556 | Line 677 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
677 | Atom** fixedZAtoms; | |
678 | double COMvel[3]; | |
679 | double vel[3]; | |
680 | + | double zSysCOMVel; |
681 | ||
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 | – | |
682 | //zero out the velocities of center of mass of fixed z-constrained molecules | |
683 | ||
684 | for(int i = 0; i < zconsMols.size(); i++){ | |
685 | ||
686 | < | if (states[i] == zcsFixed){ |
686 | > | if (states[i] == zcsFixed){ |
687 | ||
688 | < | zconsMols[i]->getCOMvel(COMvel); |
689 | < | cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
688 | > | zconsMols[i]->getCOMvel(COMvel); |
689 | > | //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
690 | ||
691 | fixedZAtoms = zconsMols[i]->getMyAtoms(); | |
692 | < | |
692 | > | |
693 | for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ | |
694 | fixedZAtoms[j]->getVel(vel); | |
695 | < | vel[whichDirection] -= COMvel[whichDirection]; |
696 | < | fixedZAtoms[j]->setVel(vel); |
695 | > | vel[whichDirection] -= COMvel[whichDirection]; |
696 | > | fixedZAtoms[j]->setVel(vel); |
697 | } | |
698 | ||
699 | < | zconsMols[i]->getCOMvel(COMvel); |
700 | < | cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
699 | > | zconsMols[i]->getCOMvel(COMvel); |
700 | > | //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
701 | } | |
702 | < | |
702 | > | |
703 | } | |
704 | ||
705 | < | cout << "before resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
706 | < | |
705 | > | //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
706 | > | |
707 | > | zSysCOMVel = calcSysCOMVel(); |
708 | > | #ifdef IS_MPI |
709 | > | if(worldRank == 0){ |
710 | > | #endif |
711 | > | // cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
712 | > | #ifdef IS_MPI |
713 | > | } |
714 | > | #endif |
715 | > | |
716 | // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules | |
717 | double MVzOfMovingMols_local; | |
718 | double MVzOfMovingMols; | |
# | Line 611 | Line 731 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
731 | if (states[i] == zcsMoving){ | |
732 | zconsMols[i]->getCOMvel(COMvel); | |
733 | MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; | |
734 | < | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
734 | > | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
735 | } | |
736 | < | |
736 | > | |
737 | } | |
738 | ||
739 | #ifndef IS_MPI | |
# | Line 647 | Line 767 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
767 | if (states[i] ==zcsMoving){ | |
768 | ||
769 | movingZAtoms = zconsMols[i]->getMyAtoms(); | |
770 | < | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
770 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
771 | movingZAtoms[j]->getVel(vel); | |
772 | vel[whichDirection] -= vzOfMovingMols; | |
773 | < | movingZAtoms[j]->setVel(vel); |
774 | < | } |
775 | < | |
773 | > | movingZAtoms[j]->setVel(vel); |
774 | > | } |
775 | > | |
776 | } | |
777 | ||
778 | } | |
779 | ||
660 | – | cout << "after resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; |
780 | ||
781 | + | zSysCOMVel = calcSysCOMVel(); |
782 | + | #ifdef IS_MPI |
783 | + | if(worldRank == 0){ |
784 | + | #endif |
785 | + | // cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
786 | + | #ifdef IS_MPI |
787 | + | } |
788 | + | #endif |
789 | + | |
790 | } | |
791 | ||
792 | + | /** |
793 | + | * |
794 | + | */ |
795 | + | |
796 | template<typename T> void ZConstraint<T>::doZconstraintForce(){ | |
797 | ||
798 | Atom** zconsAtoms; | |
# | Line 670 | Line 802 | template<typename T> void ZConstraint<T>::doZconstrain | |
802 | double COM[3]; | |
803 | double force[3]; | |
804 | ||
673 | – | int nMovingZMols_local; |
674 | – | int nMovingZMols; |
805 | ||
806 | < | //constrain the molecules which do not reach the specified positions |
806 | > | |
807 | > | //constrain the molecules which do not reach the specified positions |
808 | ||
809 | //Zero Out the force of z-contrained molecules | |
810 | totalFZ_local = 0; | |
811 | ||
812 | //calculate the total z-contrained force of fixed z-contrained molecules | |
813 | < | cout << "Fixed Molecules" << endl; |
813 | > | |
814 | for(int i = 0; i < zconsMols.size(); i++){ | |
815 | < | |
815 | > | |
816 | if (states[i] == zcsFixed){ | |
817 | < | |
817 | > | |
818 | zconsMols[i]->getCOM(COM); | |
819 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
820 | ||
# | Line 691 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain | |
822 | for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { | |
823 | zconsAtoms[j]->getFrc(force); | |
824 | fz[i] += force[whichDirection]; | |
825 | < | } |
825 | > | } |
826 | totalFZ_local += fz[i]; | |
827 | ||
828 | < | cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
828 | > | //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
829 | > | // <<"\tcurrent zpos: " << COM[whichDirection] |
830 | > | // << "\tcurrent fz: " <<fz[i] << endl; |
831 | ||
832 | + | |
833 | } | |
834 | < | |
834 | > | |
835 | } | |
836 | ||
837 | < | //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 | < | |
837 | > | //calculate total z-constraint force |
838 | #ifdef IS_MPI | |
839 | 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); |
840 | #else | |
841 | totalFZ = totalFZ_local; | |
714 | – | nMovingZMols = nMovingZMols_local; |
842 | #endif | |
843 | ||
844 | < | 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 | < | |
844 | > | |
845 | // apply negative to fixed z-constrained molecues; | |
846 | force[0]= 0; | |
847 | force[1]= 0; | |
# | Line 748 | Line 850 | template<typename T> void ZConstraint<T>::doZconstrain | |
850 | for(int i = 0; i < zconsMols.size(); i++){ | |
851 | ||
852 | if (states[i] == zcsFixed){ | |
853 | < | |
853 | > | |
854 | int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); | |
855 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
856 | ||
857 | for(int j =0; j < nAtomOfCurZConsMol; j++) { | |
858 | < | force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
858 | > | //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
859 | > | force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
860 | zconsAtoms[j]->addFrc(force); | |
861 | } | |
862 | < | |
862 | > | |
863 | } | |
864 | < | |
864 | > | |
865 | } | |
866 | ||
867 | < | } |
867 | > | // cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
868 | > | // << "total force is " << calcTotalForce() << endl; |
869 | ||
870 | < | template<typename T> bool ZConstraint<T>::checkZConsState(){ |
871 | < | double COM[3]; |
872 | < | double diff; |
870 | > | //calculate the number of atoms of moving z-constrained molecules |
871 | > | int nMovingZAtoms_local; |
872 | > | int nMovingZAtoms; |
873 | ||
874 | < | bool changed; |
874 | > | nMovingZAtoms_local = 0; |
875 | > | for(int i = 0; i < zconsMols.size(); i++) |
876 | > | if(states[i] == zcsMoving) |
877 | > | nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
878 | ||
879 | < | changed = false; |
880 | < | |
881 | < | for(int i =0; i < zconsMols.size(); i++){ |
879 | > | #ifdef IS_MPI |
880 | > | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, |
881 | > | MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
882 | > | #else |
883 | > | nMovingZAtoms = nMovingZAtoms_local; |
884 | > | #endif |
885 | ||
886 | < | zconsMols[i]->getCOM(COM); |
887 | < | diff = fabs(COM[whichDirection] - zPos[i]); |
888 | < | 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 | < | } |
886 | > | force[0]= 0; |
887 | > | force[1]= 0; |
888 | > | force[2]= 0; |
889 | ||
890 | < | return changed; |
891 | < | } |
890 | > | //modify the forces of unconstrained molecules |
891 | > | for(int i = 0; i < unconsMols.size(); i++){ |
892 | > | |
893 | > | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
894 | > | |
895 | > | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
896 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
897 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
898 | > | unconsAtoms[j]->addFrc(force); |
899 | > | } |
900 | > | |
901 | > | } |
902 | ||
903 | < | template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
904 | < | for(int i = 0; i < zconsMols.size(); i++) |
905 | < | if (states[i] == zcsFixed) |
906 | < | return true; |
903 | > | //modify the forces of moving z-constrained molecules |
904 | > | for(int i = 0; i < zconsMols.size(); i++) { |
905 | > | if (states[i] == zcsMoving){ |
906 | > | |
907 | > | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
908 | ||
909 | < | return false; |
910 | < | } |
909 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
910 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
911 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
912 | > | movingZAtoms[j]->addFrc(force); |
913 | > | } |
914 | > | } |
915 | > | } |
916 | ||
917 | + | //cout << "after substracting z-constraint force from moving molecuels " |
918 | + | // << "total force is " << calcTotalForce() << endl; |
919 | ||
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 | – | |
920 | } | |
921 | ||
922 | /** | |
# | Line 821 | Line 930 | template<typename T> void ZConstraint<T>::doHarmonic() | |
930 | double harmonicF; | |
931 | double COM[3]; | |
932 | double diff; | |
933 | + | double totalFZ_local; |
934 | double totalFZ; | |
935 | < | |
935 | > | |
936 | force[0] = 0; | |
937 | force[1] = 0; | |
938 | force[2] = 0; | |
939 | ||
940 | < | totalFZ = 0; |
940 | > | totalFZ_local = 0; |
941 | ||
832 | – | cout << "Moving Molecules" << endl; |
942 | for(int i = 0; i < zconsMols.size(); i++) { | |
943 | ||
944 | if (states[i] == zcsMoving){ | |
945 | zconsMols[i]->getCOM(COM); | |
946 | < | cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
947 | < | |
948 | < | diff = COM[whichDirection] -zPos[i]; |
949 | < | |
946 | > | // cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
947 | > | // << "\tcurrent zpos: " << COM[whichDirection] << endl; |
948 | > | |
949 | > | diff = COM[whichDirection] -zPos[i]; |
950 | > | |
951 | harmonicU = 0.5 * kz[i] * diff * diff; | |
952 | < | info->lrPot += harmonicU; |
952 | > | info->lrPot += harmonicU; |
953 | ||
954 | < | harmonicF = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
955 | < | force[whichDirection] = harmonicF; |
956 | < | totalFZ += harmonicF; |
957 | < | |
954 | > | harmonicF = - kz[i] * diff; |
955 | > | totalFZ_local += harmonicF; |
956 | > | |
957 | > | //adjust force |
958 | > | |
959 | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); | |
960 | ||
961 | < | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
961 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
962 | > | //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
963 | > | force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
964 | movingZAtoms[j]->addFrc(force); | |
965 | + | } |
966 | } | |
967 | ||
968 | } | |
969 | ||
970 | + | #ifndef IS_MPI |
971 | + | totalFZ = totalFZ_local; |
972 | + | #else |
973 | + | MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
974 | + | #endif |
975 | + | |
976 | force[0]= 0; | |
977 | force[1]= 0; | |
978 | force[2]= 0; | |
859 | – | force[whichDirection] = -totalFZ /totNumOfUnconsAtoms; |
979 | ||
980 | //modify the forces of unconstrained molecules | |
981 | for(int i = 0; i < unconsMols.size(); i++){ | |
982 | ||
983 | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); | |
984 | ||
985 | < | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
985 | > | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
986 | > | //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
987 | > | force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
988 | unconsAtoms[j]->addFrc(force); | |
989 | + | } |
990 | } | |
991 | ||
992 | } | |
993 | ||
994 | < | template<typename T> double ZConstraint<T>::calcCOMVel() |
994 | > | /** |
995 | > | * |
996 | > | */ |
997 | > | |
998 | > | template<typename T> bool ZConstraint<T>::checkZConsState(){ |
999 | > | double COM[3]; |
1000 | > | double diff; |
1001 | > | |
1002 | > | int changed_local; |
1003 | > | int changed; |
1004 | > | |
1005 | > | changed_local = 0; |
1006 | > | |
1007 | > | for(int i =0; i < zconsMols.size(); i++){ |
1008 | > | |
1009 | > | zconsMols[i]->getCOM(COM); |
1010 | > | diff = fabs(COM[whichDirection] - zPos[i]); |
1011 | > | if ( diff <= zconsTol && states[i] == zcsMoving){ |
1012 | > | states[i] = zcsFixed; |
1013 | > | changed_local = 1; |
1014 | > | } |
1015 | > | else if ( diff > zconsTol && states[i] == zcsFixed){ |
1016 | > | states[i] = zcsMoving; |
1017 | > | changed_local = 1; |
1018 | > | } |
1019 | > | |
1020 | > | } |
1021 | > | |
1022 | > | #ifndef IS_MPI |
1023 | > | changed =changed_local; |
1024 | > | #else |
1025 | > | MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1026 | > | #endif |
1027 | > | |
1028 | > | return (changed > 0); |
1029 | > | |
1030 | > | } |
1031 | > | |
1032 | > | template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1033 | > | |
1034 | > | int havingFixed_local; |
1035 | > | int havingFixed; |
1036 | > | |
1037 | > | havingFixed_local = 0; |
1038 | > | |
1039 | > | for(int i = 0; i < zconsMols.size(); i++) |
1040 | > | if (states[i] == zcsFixed){ |
1041 | > | havingFixed_local = 1; |
1042 | > | break; |
1043 | > | } |
1044 | > | |
1045 | > | #ifndef IS_MPI |
1046 | > | havingFixed = havingFixed_local; |
1047 | > | #else |
1048 | > | MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1049 | > | #endif |
1050 | > | |
1051 | > | return (havingFixed > 0); |
1052 | > | } |
1053 | > | |
1054 | > | |
1055 | > | /** |
1056 | > | * |
1057 | > | */ |
1058 | > | template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1059 | > | |
1060 | > | int havingMoving_local; |
1061 | > | int havingMoving; |
1062 | > | |
1063 | > | havingMoving_local = 0; |
1064 | > | |
1065 | > | for(int i = 0; i < zconsMols.size(); i++) |
1066 | > | if (states[i] == zcsMoving){ |
1067 | > | havingMoving_local = 1; |
1068 | > | break; |
1069 | > | } |
1070 | > | |
1071 | > | #ifndef IS_MPI |
1072 | > | havingMoving = havingMoving_local; |
1073 | > | #else |
1074 | > | MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1075 | > | #endif |
1076 | > | |
1077 | > | return (havingMoving > 0); |
1078 | > | |
1079 | > | } |
1080 | > | |
1081 | > | /** |
1082 | > | * |
1083 | > | */ |
1084 | > | |
1085 | > | template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1086 | { | |
1087 | double MVzOfMovingMols_local; | |
1088 | double MVzOfMovingMols; | |
# | Line 890 | Line 1103 | template<typename T> double ZConstraint<T>::calcCOMVel | |
1103 | if (states[i] == zcsMoving){ | |
1104 | zconsMols[i]->getCOMvel(COMvel); | |
1105 | MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; | |
1106 | < | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1106 | > | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1107 | } | |
1108 | < | |
1108 | > | |
1109 | } | |
1110 | ||
1111 | #ifndef IS_MPI | |
# | Line 909 | Line 1122 | template<typename T> double ZConstraint<T>::calcCOMVel | |
1122 | return vzOfMovingMols; | |
1123 | } | |
1124 | ||
1125 | + | /** |
1126 | + | * |
1127 | + | */ |
1128 | ||
1129 | < | template<typename T> double ZConstraint<T>::calcCOMVel2() |
1129 | > | template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1130 | { | |
1131 | double COMvel[3]; | |
1132 | < | double tempMVz = 0; |
1133 | < | int index; |
1134 | < | |
1132 | > | double tempMVz_local; |
1133 | > | double tempMVz; |
1134 | > | double massOfZCons_local; |
1135 | > | double massOfZCons; |
1136 | > | |
1137 | > | |
1138 | > | tempMVz_local = 0; |
1139 | > | |
1140 | for(int i =0 ; i < nMols; i++){ | |
1141 | < | index = isZConstraintMol(&molecules[i]); |
1142 | < | 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 | < | } |
1141 | > | molecules[i].getCOMvel(COMvel); |
1142 | > | tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1143 | } | |
1144 | < | |
1145 | < | return tempMVz /totalMassOfUncons; |
1144 | > | |
1145 | > | massOfZCons_local = 0; |
1146 | > | |
1147 | > | for(int i = 0; i < massOfZConsMols.size(); i++){ |
1148 | > | massOfZCons_local += massOfZConsMols[i]; |
1149 | > | } |
1150 | > | #ifndef IS_MPI |
1151 | > | massOfZCons = massOfZCons_local; |
1152 | > | tempMVz = tempMVz_local; |
1153 | > | #else |
1154 | > | MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1155 | > | MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1156 | > | #endif |
1157 | > | |
1158 | > | return tempMVz /(totalMassOfUncons + massOfZCons); |
1159 | } | |
1160 | + | |
1161 | + | /** |
1162 | + | * |
1163 | + | */ |
1164 | + | |
1165 | + | template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1166 | + | |
1167 | + | double force[3]; |
1168 | + | double totalForce_local; |
1169 | + | double totalForce; |
1170 | + | |
1171 | + | totalForce_local = 0; |
1172 | + | |
1173 | + | for(int i = 0; i < nAtoms; i++){ |
1174 | + | atoms[i]->getFrc(force); |
1175 | + | totalForce_local += force[whichDirection]; |
1176 | + | } |
1177 | + | |
1178 | + | #ifndef IS_MPI |
1179 | + | totalForce = totalForce_local; |
1180 | + | #else |
1181 | + | MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1182 | + | #endif |
1183 | + | |
1184 | + | return totalForce; |
1185 | + | |
1186 | + | } |
1187 | + | |
1188 | + | /** |
1189 | + | * |
1190 | + | */ |
1191 | + | |
1192 | + | template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1193 | + | //calculate the number of atoms of moving z-constrained molecules |
1194 | + | int nMovingZAtoms_local; |
1195 | + | int nMovingZAtoms; |
1196 | + | |
1197 | + | nMovingZAtoms_local = 0; |
1198 | + | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1199 | + | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1200 | + | nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1201 | + | |
1202 | + | #ifdef IS_MPI |
1203 | + | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1204 | + | #else |
1205 | + | nMovingZAtoms = nMovingZAtoms_local; |
1206 | + | #endif |
1207 | + | totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1208 | + | |
1209 | + | #ifdef IS_MPI |
1210 | + | if(worldRank == 0){ |
1211 | + | #endif |
1212 | + | // std::cerr << "\n" |
1213 | + | // << "*******************************************\n" |
1214 | + | // << " fiished Policy by numbr()\n" |
1215 | + | // << "*******************************************\n" |
1216 | + | // << "\n"; |
1217 | + | #ifdef IS_MPI |
1218 | + | } |
1219 | + | #endif |
1220 | + | } |
1221 | + | |
1222 | + | template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1223 | + | return totalForce / mol->getNAtoms(); |
1224 | + | } |
1225 | + | |
1226 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1227 | + | return totalForce / totNumOfMovingAtoms; |
1228 | + | } |
1229 | + | |
1230 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1231 | + | return totalForce / mol->getNAtoms(); |
1232 | + | } |
1233 | + | |
1234 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1235 | + | return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1236 | + | } |
1237 | + | |
1238 | + | /** |
1239 | + | * |
1240 | + | */ |
1241 | + | |
1242 | + | template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1243 | + | //calculate the number of atoms of moving z-constrained molecules |
1244 | + | double massOfMovingZAtoms_local; |
1245 | + | double massOfMovingZAtoms; |
1246 | + | |
1247 | + | massOfMovingZAtoms_local = 0; |
1248 | + | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1249 | + | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1250 | + | massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1251 | + | |
1252 | + | #ifdef IS_MPI |
1253 | + | MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1254 | + | #else |
1255 | + | massOfMovingZAtoms = massOfMovingZAtoms_local; |
1256 | + | #endif |
1257 | + | totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1258 | + | } |
1259 | + | |
1260 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1261 | + | return totalForce * atom->getMass() / mol->getTotalMass(); |
1262 | + | } |
1263 | + | |
1264 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1265 | + | return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1266 | + | } |
1267 | + | |
1268 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1269 | + | return totalForce * atom->getMass() / mol->getTotalMass(); |
1270 | + | } |
1271 | + | |
1272 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1273 | + | return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1274 | + | } |
1275 | + |
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