# | 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 | + | "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 | ||
# | 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()].zconsIndex; |
198 | > | maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
199 | ||
200 | #ifndef IS_MPI | |
201 | totalNumMol = nMols; | |
# | 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[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
221 | < | molecules[i].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 i = 0; i < nMols; i++) |
239 | < | if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
240 | < | molecules[i].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; | |
302 | simError(); | |
303 | } | |
304 | ||
305 | < | for(int i = 0; i < zconsMols.size(); i++) |
305 | > | //determine the states of z-constraint molecules |
306 | > | for(int i = 0; i < zconsMols.size(); i++){ |
307 | indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); | |
308 | + | |
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); |
314 | + | } |
315 | ||
316 | #endif | |
317 | ||
318 | + | //get total masss of unconstraint molecules |
319 | + | double totalMassOfUncons_local; |
320 | + | totalMassOfUncons_local = 0; |
321 | + | |
322 | + | for(int i = 0; i < unconsMols.size(); i++) |
323 | + | totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
324 | + | |
325 | + | #ifndef IS_MPI |
326 | + | totalMassOfUncons = totalMassOfUncons_local; |
327 | + | #else |
328 | + | MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
329 | + | MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
330 | + | #endif |
331 | + | |
332 | + | |
333 | //get total number of unconstrained atoms | |
334 | int nUnconsAtoms_local; | |
335 | nUnconsAtoms_local = 0; | |
# | Line 275 | 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); |
343 | < | #endif |
342 | > | MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
343 | > | MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 | > | #endif |
345 | ||
346 | < | checkZConsState(); |
347 | < | |
283 | < | // |
284 | < | fzOut = new ZConsWriter(zconsOutput.c_str()); |
346 | > | // creat zconsWriter |
347 | > | fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
348 | ||
349 | if(!fzOut){ | |
350 | sprintf( painCave.errMsg, | |
# | Line 289 | 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 328 | 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 342 | Line 417 | template<typename T> void ZConstraint<T>::update() | |
417 | ||
418 | } | |
419 | } | |
420 | + | |
421 | + | //determine the states of z-constraint molecules |
422 | + | for(int i = 0; i < zconsMols.size(); i++){ |
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); |
428 | + | } |
429 | + | |
430 | ||
431 | //The reason to declare fz and indexOfZconsMols as pointer to array is | |
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 369 | 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 410 | Line 504 | template<typename T> int ZConstraint<T>::isZConstraint | |
504 | return -1; | |
505 | } | |
506 | ||
413 | – | /** |
414 | – | * Description: |
415 | – | * Reset the z coordinates |
416 | – | */ |
507 | template<typename T> void ZConstraint<T>::integrate(){ | |
508 | ||
509 | //zero out the velocities of center of mass of unconstrained molecules | |
# | Line 430 | Line 520 | template<typename T> void ZConstraint<T>::integrate(){ | |
520 | * | |
521 | * | |
522 | * | |
523 | < | */ |
434 | < | |
435 | < | |
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 | + | double zSysCOMVel; |
529 | ||
530 | T::calcForce(calcPot, calcStress); | |
531 | ||
532 | < | if (checkZConsState()) |
532 | > | if (checkZConsState()){ |
533 | zeroOutVel(); | |
534 | + | forcePolicy->update(); |
535 | + | } |
536 | ||
537 | + | zsys = calcZSys(); |
538 | + | zSysCOMVel = calcSysCOMVel(); |
539 | + | #ifdef IS_MPI |
540 | + | if(worldRank == 0){ |
541 | + | #endif |
542 | + | cout << "---------------------------------------------------------------------" <<endl; |
543 | + | cout << "current time: " << info->getTime() << endl; |
544 | + | cout << "center of mass at z: " << zsys << endl; |
545 | + | cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
546 | + | |
547 | + | #ifdef IS_MPI |
548 | + | } |
549 | + | #endif |
550 | + | |
551 | //do zconstraint force; | |
552 | if (haveFixedZMols()) | |
553 | this->doZconstraintForce(); | |
554 | < | |
554 | > | |
555 | //use harmonical poteintial to move the molecules to the specified positions | |
556 | if (haveMovingZMols()) | |
557 | < | //this->doHarmonic(); |
558 | < | |
559 | < | fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
560 | < | |
557 | > | this->doHarmonic(); |
558 | > | |
559 | > | //write out forces and current positions of z-constraint molecules |
560 | > | if(info->getTime() >= curZconsTime){ |
561 | > | for(int i = 0; i < zconsMols.size(); i++){ |
562 | > | zconsMols[i]->getCOM(COM); |
563 | > | curZPos[i] = COM[whichDirection]; |
564 | > | |
565 | > | //if the z-constraint molecule is still moving, just record its force |
566 | > | if(states[i] == zcsMoving){ |
567 | > | fz[i] = 0; |
568 | > | Atom** movingZAtoms; |
569 | > | movingZAtoms = zconsMols[i]->getMyAtoms(); |
570 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
571 | > | movingZAtoms[j]->getFrc(force); |
572 | > | fz[i] += force[whichDirection]; |
573 | > | } |
574 | > | } |
575 | > | } |
576 | > | fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
577 | > | curZconsTime += zconsTime; |
578 | > | } |
579 | > | |
580 | > | zSysCOMVel = calcSysCOMVel(); |
581 | > | #ifdef IS_MPI |
582 | > | if(worldRank == 0){ |
583 | > | #endif |
584 | > | cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
585 | > | #ifdef IS_MPI |
586 | > | } |
587 | > | #endif |
588 | > | |
589 | } | |
590 | + | |
591 | + | |
592 | + | /** |
593 | + | * |
594 | + | */ |
595 | ||
596 | template<typename T> double ZConstraint<T>::calcZSys() | |
597 | { | |
# | Line 459 | Line 600 | template<typename T> double ZConstraint<T>::calcZSys() | |
600 | double totalMass; | |
601 | double totalMZ_local; | |
602 | double totalMZ; | |
462 | – | double massOfUncons_local; |
603 | double massOfCurMol; | |
604 | double COM[3]; | |
605 | ||
606 | totalMass_local = 0; | |
467 | – | totalMass = 0; |
607 | totalMZ_local = 0; | |
469 | – | totalMZ = 0; |
470 | – | massOfUncons_local = 0; |
471 | – | |
608 | ||
609 | for(int i = 0; i < nMols; i++){ | |
610 | massOfCurMol = molecules[i].getTotalMass(); | |
# | Line 476 | Line 612 | template<typename T> double ZConstraint<T>::calcZSys() | |
612 | ||
613 | totalMass_local += massOfCurMol; | |
614 | totalMZ_local += massOfCurMol * COM[whichDirection]; | |
615 | < | |
480 | < | if(isZConstraintMol(&molecules[i]) == -1){ |
481 | < | |
482 | < | massOfUncons_local += massOfCurMol; |
483 | < | } |
484 | < | |
615 | > | |
616 | } | |
617 | + | |
618 | ||
487 | – | |
619 | #ifdef IS_MPI | |
620 | < | MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
621 | < | MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
622 | < | MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
623 | < | #else |
620 | > | MPI_Allreduce(&totalMass_local, &totalMass, 1, |
621 | > | MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
622 | > | MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
623 | > | MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
624 | > | #else |
625 | totalMass = totalMass_local; | |
626 | totalMZ = totalMZ_local; | |
627 | < | totalMassOfUncons = massOfUncons_local; |
496 | < | #endif |
627 | > | #endif |
628 | ||
629 | double zsys; | |
630 | zsys = totalMZ / totalMass; | |
# | Line 512 | Line 643 | template<typename T> void ZConstraint<T>::thermalize( | |
643 | ||
644 | /** | |
645 | * | |
515 | – | * |
516 | – | * |
646 | */ | |
647 | ||
648 | template<typename T> void ZConstraint<T>::zeroOutVel(){ | |
# | Line 521 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
650 | Atom** fixedZAtoms; | |
651 | double COMvel[3]; | |
652 | double vel[3]; | |
653 | < | |
653 | > | double zSysCOMVel; |
654 | > | |
655 | //zero out the velocities of center of mass of fixed z-constrained molecules | |
656 | ||
657 | for(int i = 0; i < zconsMols.size(); i++){ | |
658 | ||
659 | < | if (states[i] == zcsFixed){ |
659 | > | if (states[i] == zcsFixed){ |
660 | ||
661 | < | zconsMols[i]->getCOMvel(COMvel); |
661 | > | zconsMols[i]->getCOMvel(COMvel); |
662 | > | //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
663 | > | |
664 | fixedZAtoms = zconsMols[i]->getMyAtoms(); | |
665 | < | |
665 | > | |
666 | for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ | |
667 | fixedZAtoms[j]->getVel(vel); | |
668 | < | vel[whichDirection] -= COMvel[whichDirection]; |
669 | < | fixedZAtoms[j]->setVel(vel); |
668 | > | vel[whichDirection] -= COMvel[whichDirection]; |
669 | > | fixedZAtoms[j]->setVel(vel); |
670 | } | |
671 | < | |
672 | < | } |
673 | < | |
674 | < | } |
671 | > | |
672 | > | zconsMols[i]->getCOMvel(COMvel); |
673 | > | //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
674 | > | } |
675 | ||
676 | + | } |
677 | + | |
678 | + | //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
679 | + | |
680 | + | zSysCOMVel = calcSysCOMVel(); |
681 | + | #ifdef IS_MPI |
682 | + | if(worldRank == 0){ |
683 | + | #endif |
684 | + | cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
685 | + | #ifdef IS_MPI |
686 | + | } |
687 | + | #endif |
688 | + | |
689 | // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules | |
690 | double MVzOfMovingMols_local; | |
691 | double MVzOfMovingMols; | |
# | Line 555 | Line 700 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
700 | MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; | |
701 | } | |
702 | ||
703 | < | for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
559 | < | |
703 | > | for(int i = 0; i < zconsMols.size(); i++){ |
704 | if (states[i] == zcsMoving){ | |
705 | zconsMols[i]->getCOMvel(COMvel); | |
706 | MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; | |
707 | < | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
707 | > | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
708 | } | |
709 | < | |
709 | > | |
710 | } | |
711 | ||
712 | #ifndef IS_MPI | |
# | Line 591 | Line 735 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
735 | ||
736 | //modify the velocities of moving z-constrained molecuels | |
737 | Atom** movingZAtoms; | |
738 | < | for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
738 | > | for(int i = 0; i < zconsMols.size(); i++){ |
739 | ||
740 | if (states[i] ==zcsMoving){ | |
741 | ||
742 | movingZAtoms = zconsMols[i]->getMyAtoms(); | |
743 | < | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
743 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
744 | movingZAtoms[j]->getVel(vel); | |
745 | vel[whichDirection] -= vzOfMovingMols; | |
746 | < | movingZAtoms[j]->setVel(vel); |
603 | < | } |
604 | < | |
746 | > | movingZAtoms[j]->setVel(vel); |
747 | } | |
748 | + | |
749 | + | } |
750 | ||
751 | + | } |
752 | + | |
753 | + | |
754 | + | zSysCOMVel = calcSysCOMVel(); |
755 | + | #ifdef IS_MPI |
756 | + | if(worldRank == 0){ |
757 | + | #endif |
758 | + | cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
759 | + | #ifdef IS_MPI |
760 | } | |
761 | + | #endif |
762 | ||
763 | } | |
764 | ||
765 | + | /** |
766 | + | * |
767 | + | */ |
768 | + | |
769 | template<typename T> void ZConstraint<T>::doZconstraintForce(){ | |
770 | ||
771 | Atom** zconsAtoms; | |
# | Line 616 | Line 774 | template<typename T> void ZConstraint<T>::doZconstrain | |
774 | double COMvel[3]; | |
775 | double COM[3]; | |
776 | double force[3]; | |
619 | – | double zsys; |
777 | ||
621 | – | int nMovingZMols_local; |
622 | – | int nMovingZMols; |
778 | ||
624 | – | //constrain the molecules which do not reach the specified positions |
779 | ||
780 | < | zsys = calcZSys(); |
627 | < | cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
780 | > | //constrain the molecules which do not reach the specified positions |
781 | ||
782 | //Zero Out the force of z-contrained molecules | |
783 | totalFZ_local = 0; | |
784 | ||
785 | //calculate the total z-contrained force of fixed z-contrained molecules | |
786 | < | cout << "Fixed Molecules" << endl; |
786 | > | |
787 | for(int i = 0; i < zconsMols.size(); i++){ | |
788 | < | |
788 | > | |
789 | if (states[i] == zcsFixed){ | |
790 | < | |
790 | > | |
791 | zconsMols[i]->getCOM(COM); | |
792 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
793 | ||
# | Line 642 | Line 795 | template<typename T> void ZConstraint<T>::doZconstrain | |
795 | for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { | |
796 | zconsAtoms[j]->getFrc(force); | |
797 | fz[i] += force[whichDirection]; | |
798 | < | } |
798 | > | } |
799 | totalFZ_local += fz[i]; | |
800 | ||
801 | < | cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
801 | > | cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
802 | > | <<"\tcurrent zpos: " << COM[whichDirection] |
803 | > | << "\tcurrent fz: " <<fz[i] << endl; |
804 | ||
805 | } | |
806 | < | |
806 | > | |
807 | } | |
808 | ||
809 | < | //calculate the number of atoms of moving z-constrained molecules |
655 | < | nMovingZMols_local = 0; |
656 | < | for(int i = 0; zconsMols.size(); i++){ |
657 | < | if(states[i] == zcsMoving) |
658 | < | nMovingZMols_local += massOfZConsMols[i]; |
659 | < | } |
809 | > | //calculate total z-constraint force |
810 | #ifdef IS_MPI | |
811 | MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); | |
662 | – | MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
812 | #else | |
813 | totalFZ = totalFZ_local; | |
665 | – | nMovingZMols = nMovingZMols_local; |
814 | #endif | |
815 | ||
816 | < | force[0]= 0; |
669 | < | force[1]= 0; |
670 | < | force[2]= 0; |
671 | < | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
672 | < | |
673 | < | //modify the velocites of unconstrained molecules |
674 | < | for(int i = 0; i < unconsMols.size(); i++){ |
675 | < | |
676 | < | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
677 | < | |
678 | < | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
679 | < | unconsAtoms[j]->addFrc(force); |
680 | < | |
681 | < | } |
682 | < | |
683 | < | //modify the velocities of moving z-constrained molecules |
684 | < | for(int i = 0; i < zconsMols.size(); i++) { |
685 | < | if (states[i] == zcsMoving){ |
686 | < | |
687 | < | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
688 | < | |
689 | < | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
690 | < | movingZAtoms[j]->addFrc(force); |
691 | < | } |
692 | < | } |
693 | < | |
816 | > | |
817 | // apply negative to fixed z-constrained molecues; | |
818 | force[0]= 0; | |
819 | force[1]= 0; | |
# | Line 699 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain | |
822 | for(int i = 0; i < zconsMols.size(); i++){ | |
823 | ||
824 | if (states[i] == zcsFixed){ | |
825 | < | |
825 | > | |
826 | int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); | |
827 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
828 | ||
829 | for(int j =0; j < nAtomOfCurZConsMol; j++) { | |
830 | < | force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
830 | > | force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
831 | > | //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
832 | zconsAtoms[j]->addFrc(force); | |
833 | } | |
834 | < | |
834 | > | |
835 | } | |
836 | < | |
836 | > | |
837 | } | |
838 | ||
839 | + | //cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
840 | + | // << "total force is " << calcTotalForce() << endl; |
841 | + | |
842 | + | //calculate the number of atoms of moving z-constrained molecules |
843 | + | int nMovingZAtoms_local; |
844 | + | int nMovingZAtoms; |
845 | + | |
846 | + | nMovingZAtoms_local = 0; |
847 | + | for(int i = 0; i < zconsMols.size(); i++) |
848 | + | if(states[i] == zcsMoving) |
849 | + | nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
850 | + | |
851 | + | #ifdef IS_MPI |
852 | + | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, |
853 | + | MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
854 | + | #else |
855 | + | nMovingZAtoms = nMovingZAtoms_local; |
856 | + | #endif |
857 | + | |
858 | + | force[0]= 0; |
859 | + | force[1]= 0; |
860 | + | force[2]= 0; |
861 | + | |
862 | + | //modify the forces of unconstrained molecules |
863 | + | for(int i = 0; i < unconsMols.size(); i++){ |
864 | + | |
865 | + | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
866 | + | |
867 | + | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
868 | + | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
869 | + | //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
870 | + | unconsAtoms[j]->addFrc(force); |
871 | + | } |
872 | + | |
873 | + | } |
874 | + | |
875 | + | //modify the forces of moving z-constrained molecules |
876 | + | for(int i = 0; i < zconsMols.size(); i++) { |
877 | + | if (states[i] == zcsMoving){ |
878 | + | |
879 | + | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
880 | + | |
881 | + | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
882 | + | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
883 | + | //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
884 | + | movingZAtoms[j]->addFrc(force); |
885 | + | } |
886 | + | } |
887 | + | } |
888 | + | |
889 | + | //cout << "after substracting z-constraint force from moving molecuels " |
890 | + | // << "total force is " << calcTotalForce() << endl; |
891 | + | |
892 | } | |
893 | ||
894 | + | /** |
895 | + | * |
896 | + | * |
897 | + | */ |
898 | + | |
899 | + | template<typename T> void ZConstraint<T>::doHarmonic(){ |
900 | + | double force[3]; |
901 | + | double harmonicU; |
902 | + | double harmonicF; |
903 | + | double COM[3]; |
904 | + | double diff; |
905 | + | double totalFZ_local; |
906 | + | double totalFZ; |
907 | + | |
908 | + | force[0] = 0; |
909 | + | force[1] = 0; |
910 | + | force[2] = 0; |
911 | + | |
912 | + | totalFZ_local = 0; |
913 | + | |
914 | + | for(int i = 0; i < zconsMols.size(); i++) { |
915 | + | |
916 | + | if (states[i] == zcsMoving){ |
917 | + | zconsMols[i]->getCOM(COM); |
918 | + | cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
919 | + | |
920 | + | diff = COM[whichDirection] -zPos[i]; |
921 | + | |
922 | + | harmonicU = 0.5 * kz[i] * diff * diff; |
923 | + | info->lrPot += harmonicU; |
924 | + | |
925 | + | harmonicF = - kz[i] * diff; |
926 | + | totalFZ_local += harmonicF; |
927 | + | |
928 | + | //adjust force |
929 | + | |
930 | + | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
931 | + | |
932 | + | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
933 | + | force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
934 | + | //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
935 | + | movingZAtoms[j]->addFrc(force); |
936 | + | } |
937 | + | } |
938 | + | |
939 | + | } |
940 | + | |
941 | + | #ifndef IS_MPI |
942 | + | totalFZ = totalFZ_local; |
943 | + | #else |
944 | + | MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
945 | + | #endif |
946 | + | |
947 | + | force[0]= 0; |
948 | + | force[1]= 0; |
949 | + | force[2]= 0; |
950 | + | |
951 | + | //modify the forces of unconstrained molecules |
952 | + | for(int i = 0; i < unconsMols.size(); i++){ |
953 | + | |
954 | + | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
955 | + | |
956 | + | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
957 | + | force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
958 | + | //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
959 | + | unconsAtoms[j]->addFrc(force); |
960 | + | } |
961 | + | } |
962 | + | |
963 | + | } |
964 | + | |
965 | + | /** |
966 | + | * |
967 | + | */ |
968 | + | |
969 | template<typename T> bool ZConstraint<T>::checkZConsState(){ | |
970 | double COM[3]; | |
971 | double diff; | |
972 | ||
973 | < | bool changed; |
973 | > | int changed_local; |
974 | > | int changed; |
975 | ||
976 | < | changed = false; |
976 | > | changed_local = 0; |
977 | ||
978 | for(int i =0; i < zconsMols.size(); i++){ | |
979 | ||
# | Line 728 | Line 981 | template<typename T> bool ZConstraint<T>::checkZConsSt | |
981 | diff = fabs(COM[whichDirection] - zPos[i]); | |
982 | if ( diff <= zconsTol && states[i] == zcsMoving){ | |
983 | states[i] = zcsFixed; | |
984 | < | changed = true; |
984 | > | changed_local = 1; |
985 | } | |
986 | else if ( diff > zconsTol && states[i] == zcsFixed){ | |
987 | states[i] = zcsMoving; | |
988 | < | changed = true; |
988 | > | changed_local = 1; |
989 | } | |
990 | ||
991 | } | |
992 | ||
993 | < | return changed; |
993 | > | #ifndef IS_MPI |
994 | > | changed =changed_local; |
995 | > | #else |
996 | > | MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
997 | > | #endif |
998 | > | |
999 | > | return changed > 0 ? true : false; |
1000 | } | |
1001 | ||
1002 | template<typename T> bool ZConstraint<T>::haveFixedZMols(){ | |
1003 | + | |
1004 | + | int havingFixed_local; |
1005 | + | int havingFixed; |
1006 | + | |
1007 | + | havingFixed_local = 0; |
1008 | + | |
1009 | for(int i = 0; i < zconsMols.size(); i++) | |
1010 | < | if (states[i] == zcsFixed) |
1011 | < | return true; |
1010 | > | if (states[i] == zcsFixed){ |
1011 | > | havingFixed_local = 1; |
1012 | > | break; |
1013 | > | } |
1014 | ||
1015 | < | return false; |
1015 | > | #ifndef IS_MPI |
1016 | > | havingFixed = havingFixed_local; |
1017 | > | #else |
1018 | > | MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1019 | > | #endif |
1020 | > | |
1021 | > | return havingFixed > 0 ? true : false; |
1022 | } | |
1023 | ||
1024 | ||
# | Line 753 | Line 1026 | template<typename T> bool ZConstraint<T>::haveMovingZM | |
1026 | * | |
1027 | */ | |
1028 | template<typename T> bool ZConstraint<T>::haveMovingZMols(){ | |
1029 | + | |
1030 | + | int havingMoving_local; |
1031 | + | int havingMoving; |
1032 | + | |
1033 | + | havingMoving_local = 0; |
1034 | + | |
1035 | for(int i = 0; i < zconsMols.size(); i++) | |
1036 | < | if (states[i] == zcsMoving) |
1037 | < | return true; |
1036 | > | if (states[i] == zcsMoving){ |
1037 | > | havingMoving_local = 1; |
1038 | > | break; |
1039 | > | } |
1040 | ||
1041 | < | return false; |
1041 | > | #ifndef IS_MPI |
1042 | > | havingMoving = havingMoving_local; |
1043 | > | #else |
1044 | > | MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1045 | > | #endif |
1046 | > | |
1047 | > | return havingMoving > 0 ? true : false; |
1048 | ||
1049 | } | |
1050 | ||
1051 | /** | |
1052 | < | * |
1053 | < | * |
767 | < | */ |
1052 | > | * |
1053 | > | */ |
1054 | ||
1055 | < | template<typename T> void ZConstraint<T>::doHarmonic(){ |
1056 | < | double force[3]; |
1057 | < | double harmonicU; |
1058 | < | double COM[3]; |
1059 | < | double diff; |
1060 | < | |
1061 | < | force[0] = 0; |
1062 | < | force[1] = 0; |
1063 | < | force[2] = 0; |
1055 | > | template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1056 | > | { |
1057 | > | double MVzOfMovingMols_local; |
1058 | > | double MVzOfMovingMols; |
1059 | > | double totalMassOfMovingZMols_local; |
1060 | > | double totalMassOfMovingZMols; |
1061 | > | double COMvel[3]; |
1062 | > | |
1063 | > | MVzOfMovingMols_local = 0; |
1064 | > | totalMassOfMovingZMols_local = 0; |
1065 | ||
1066 | < | cout << "Moving Molecules" << endl; |
1067 | < | for(int i = 0; i < zconsMols.size(); i++) { |
1066 | > | for(int i =0; i < unconsMols.size(); i++){ |
1067 | > | unconsMols[i]->getCOMvel(COMvel); |
1068 | > | MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1069 | > | } |
1070 | ||
1071 | + | for(int i = 0; i < zconsMols.size(); i++){ |
1072 | + | |
1073 | if (states[i] == zcsMoving){ | |
1074 | < | zconsMols[i]->getCOM(COM): |
1075 | < | cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
1076 | < | |
1077 | < | diff = COM[whichDirection] -zPos[i]; |
1078 | < | |
1079 | < | harmonicU = 0.5 * kz[i] * diff * diff; |
789 | < | info->ltPot += harmonicU; |
1074 | > | zconsMols[i]->getCOMvel(COMvel); |
1075 | > | MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1076 | > | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1077 | > | } |
1078 | > | |
1079 | > | } |
1080 | ||
1081 | < | force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
1082 | < | |
1083 | < | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
1081 | > | #ifndef IS_MPI |
1082 | > | MVzOfMovingMols = MVzOfMovingMols_local; |
1083 | > | totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1084 | > | #else |
1085 | > | MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1086 | > | MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1087 | > | #endif |
1088 | ||
1089 | < | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
1090 | < | movingZAtoms[j]->addFrc(force); |
797 | < | } |
1089 | > | double vzOfMovingMols; |
1090 | > | vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1091 | ||
1092 | + | return vzOfMovingMols; |
1093 | + | } |
1094 | + | |
1095 | + | /** |
1096 | + | * |
1097 | + | */ |
1098 | + | |
1099 | + | template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1100 | + | { |
1101 | + | double COMvel[3]; |
1102 | + | double tempMVz_local; |
1103 | + | double tempMVz; |
1104 | + | double massOfZCons_local; |
1105 | + | double massOfZCons; |
1106 | + | |
1107 | + | |
1108 | + | tempMVz_local = 0; |
1109 | + | |
1110 | + | for(int i =0 ; i < nMols; i++){ |
1111 | + | molecules[i].getCOMvel(COMvel); |
1112 | + | tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1113 | } | |
1114 | ||
1115 | + | massOfZCons_local = 0; |
1116 | + | |
1117 | + | for(int i = 0; i < massOfZConsMols.size(); i++){ |
1118 | + | massOfZCons_local += massOfZConsMols[i]; |
1119 | + | } |
1120 | + | #ifndef IS_MPI |
1121 | + | massOfZCons = massOfZCons_local; |
1122 | + | tempMVz = tempMVz_local; |
1123 | + | #else |
1124 | + | MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1125 | + | MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1126 | + | #endif |
1127 | + | |
1128 | + | return tempMVz /(totalMassOfUncons + massOfZCons); |
1129 | } | |
1130 | + | |
1131 | + | /** |
1132 | + | * |
1133 | + | */ |
1134 | + | |
1135 | + | template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1136 | + | |
1137 | + | double force[3]; |
1138 | + | double totalForce_local; |
1139 | + | double totalForce; |
1140 | + | |
1141 | + | totalForce_local = 0; |
1142 | + | |
1143 | + | for(int i = 0; i < nAtoms; i++){ |
1144 | + | atoms[i]->getFrc(force); |
1145 | + | totalForce_local += force[whichDirection]; |
1146 | + | } |
1147 | + | |
1148 | + | #ifndef IS_MPI |
1149 | + | totalForce = totalForce_local; |
1150 | + | #else |
1151 | + | MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1152 | + | #endif |
1153 | + | |
1154 | + | return totalForce; |
1155 | + | |
1156 | + | } |
1157 | + | |
1158 | + | /** |
1159 | + | * |
1160 | + | */ |
1161 | + | |
1162 | + | template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1163 | + | //calculate the number of atoms of moving z-constrained molecules |
1164 | + | int nMovingZAtoms_local; |
1165 | + | int nMovingZAtoms; |
1166 | + | |
1167 | + | nMovingZAtoms_local = 0; |
1168 | + | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1169 | + | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1170 | + | nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1171 | + | |
1172 | + | #ifdef IS_MPI |
1173 | + | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1174 | + | #else |
1175 | + | nMovingZAtoms = nMovingZAtoms_local; |
1176 | + | #endif |
1177 | + | totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1178 | + | } |
1179 | + | |
1180 | + | template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1181 | + | return totalForce / mol->getNAtoms(); |
1182 | + | } |
1183 | + | |
1184 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1185 | + | return totalForce / totNumOfMovingAtoms; |
1186 | + | } |
1187 | + | |
1188 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1189 | + | return totalForce / mol->getNAtoms(); |
1190 | + | } |
1191 | + | |
1192 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1193 | + | return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1194 | + | } |
1195 | + | |
1196 | + | /** |
1197 | + | * |
1198 | + | */ |
1199 | + | |
1200 | + | template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1201 | + | //calculate the number of atoms of moving z-constrained molecules |
1202 | + | double massOfMovingZAtoms_local; |
1203 | + | double massOfMovingZAtoms; |
1204 | + | |
1205 | + | massOfMovingZAtoms_local = 0; |
1206 | + | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1207 | + | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1208 | + | massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1209 | + | |
1210 | + | #ifdef IS_MPI |
1211 | + | MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1212 | + | #else |
1213 | + | massOfMovingZAtoms = massOfMovingZAtoms_local; |
1214 | + | #endif |
1215 | + | totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1216 | + | } |
1217 | + | |
1218 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1219 | + | return totalForce * atom->getMass() / mol->getTotalMass(); |
1220 | + | } |
1221 | + | |
1222 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1223 | + | return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1224 | + | } |
1225 | + | |
1226 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1227 | + | return totalForce * atom->getMass() / mol->getTotalMass(); |
1228 | + | } |
1229 | + | |
1230 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1231 | + | return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1232 | + | } |
1233 | + |
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