# | 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), fzOut(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 Subtraction policy |
31 | + | data = info->getProperty(ZCONSFORCEPOLICY_ID); |
32 | + | if(!data){ |
33 | + | sprintf( painCave.errMsg, |
34 | + | "ZConstraint Warning: User does not set force Subtraction policy, " |
35 | + | "PolicyByMass is used\n"); |
36 | + | painCave.isFatal = 0; |
37 | + | simError(); |
38 | + | |
39 | + | forcePolicy = (ForceSubtractionPolicy*) 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 = (ForceSubtractionPolicy*) new PolicyByMass(this); |
52 | + | } |
53 | + | else{ |
54 | + | if(policy->getData() == "BYNUMBER") |
55 | + | forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this); |
56 | + | else if(policy->getData() == "BYMASS") |
57 | + | forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
58 | + | else{ |
59 | + | sprintf( painCave.errMsg, |
60 | + | "ZConstraint Warning: unknown force Subtraction policy, " |
61 | + | "PolicyByMass is used\n"); |
62 | + | painCave.isFatal = 0; |
63 | + | simError(); |
64 | + | forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
65 | + | } |
66 | + | } |
67 | + | } |
68 | + | |
69 | + | |
70 | //retrieve sample time of z-contraint | |
71 | data = info->getProperty(ZCONSTIME_ID); | |
72 | ||
# | Line 69 | Line 110 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
110 | } | |
111 | else{ | |
112 | ||
113 | < | filename = dynamic_cast<StringData*>(data); |
113 | > | filename = dynamic_cast<StringData*>(data); |
114 | ||
115 | if(!filename){ | |
116 | ||
# | Line 83 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
124 | this->zconsOutput = filename->getData(); | |
125 | } | |
126 | ||
86 | – | |
127 | } | |
128 | ||
129 | //retrieve tolerance for z-constraint molecuels | |
# | Line 113 | Line 153 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
153 | } | |
154 | ||
155 | } | |
156 | < | |
156 | > | |
157 | //retrieve index of z-constraint molecules | |
158 | data = info->getProperty(ZCONSPARADATA_ID); | |
159 | if(!data) { | |
# | Line 154 | Line 194 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
194 | "ZConstraint error: index is out of range\n"); | |
195 | painCave.isFatal = 1; | |
196 | simError(); | |
197 | < | } |
197 | > | } |
198 | ||
199 | < | maxIndex = (*parameters)[parameters->size()].zconsIndex; |
199 | > | maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
200 | ||
201 | #ifndef IS_MPI | |
202 | totalNumMol = nMols; | |
# | Line 175 | Line 215 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
215 | //its initial z coordinate will be used as default | |
216 | for(int i = 0; i < parameters->size(); i++){ | |
217 | ||
218 | < | if(!(*parameters)[i].havingZPos){ |
179 | < | |
218 | > | if(!(*parameters)[i].havingZPos){ |
219 | #ifndef IS_MPI | |
220 | < | for(int j = 0; j < nMols; j++){ |
221 | < | if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
222 | < | molecules[i].getCOM(COM); |
223 | < | break; |
185 | < | } |
220 | > | for(int j = 0; j < nMols; j++){ |
221 | > | if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
222 | > | molecules[j].getCOM(COM); |
223 | > | break; |
224 | } | |
225 | + | } |
226 | #else | |
227 | //query which processor current zconstraint molecule belongs to | |
228 | < | int *MolToProcMap; |
229 | < | int whichNode; |
230 | < | double initZPos; |
231 | < | MolToProcMap = mpiSim->getMolToProcMap(); |
232 | < | whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
233 | < | |
234 | < | //broadcast the zpos of current z-contraint molecule |
235 | < | //the node which contain this |
228 | > | int *MolToProcMap; |
229 | > | int whichNode; |
230 | > | double initZPos; |
231 | > | MolToProcMap = mpiSim->getMolToProcMap(); |
232 | > | whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
233 | > | |
234 | > | //broadcast the zpos of current z-contraint molecule |
235 | > | //the node which contain this |
236 | ||
237 | < | if (worldRank == whichNode ){ |
238 | < | |
239 | < | for(int i = 0; i < nMols; i++) |
240 | < | if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
241 | < | molecules[i].getCOM(COM); |
242 | < | break; |
243 | < | } |
244 | < | |
245 | < | } |
237 | > | if (worldRank == whichNode ){ |
238 | > | |
239 | > | for(int j = 0; j < nMols; j++) |
240 | > | if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
241 | > | molecules[j].getCOM(COM); |
242 | > | break; |
243 | > | } |
244 | > | |
245 | > | } |
246 | ||
247 | < | MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
247 | > | MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
248 | #endif | |
249 | ||
250 | < | (*parameters)[i].zPos = COM[whichDirection]; |
250 | > | (*parameters)[i].zPos = COM[whichDirection]; |
251 | ||
252 | < | sprintf( painCave.errMsg, |
253 | < | "ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
252 | > | sprintf( painCave.errMsg, |
253 | > | "ZConstraint warning: Does not specify zpos for z-constraint molecule " |
254 | "initial z coornidate will be used \n"); | |
255 | < | painCave.isFatal = 0; |
256 | < | simError(); |
257 | < | |
258 | < | } |
259 | < | } |
260 | < | |
255 | > | painCave.isFatal = 0; |
256 | > | simError(); |
257 | > | |
258 | > | } |
259 | > | } |
260 | > | |
261 | }//end if (!zConsParaData) | |
262 | }//end if (!data) | |
263 | ||
# | Line 238 | Line 277 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
277 | massOfZConsMols.push_back(molecules[i].getTotalMass()); | |
278 | ||
279 | zPos.push_back((*parameters)[searchResult].zPos); | |
280 | < | kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
280 | > | // cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 | > | // <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
282 | ||
283 | + | kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
284 | molecules[i].getCOM(COM); | |
285 | } | |
286 | else | |
# | Line 252 | Line 293 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
293 | } | |
294 | ||
295 | fz = new double[zconsMols.size()]; | |
296 | + | curZPos = new double[zconsMols.size()]; |
297 | indexOfZConsMols = new int [zconsMols.size()]; | |
298 | ||
299 | < | if(!fz || !indexOfZConsMols){ |
299 | > | if(!fz || !curZPos || !indexOfZConsMols){ |
300 | sprintf( painCave.errMsg, | |
301 | "Memory allocation failure in class Zconstraint\n"); | |
302 | painCave.isFatal = 1; | |
303 | simError(); | |
304 | } | |
305 | ||
306 | < | for(int i = 0; i < zconsMols.size(); i++) |
306 | > | //determine the states of z-constraint molecules |
307 | > | for(int i = 0; i < zconsMols.size(); i++){ |
308 | indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); | |
309 | + | |
310 | + | zconsMols[i]->getCOM(COM); |
311 | + | if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
312 | + | states.push_back(zcsFixed); |
313 | + | else |
314 | + | states.push_back(zcsMoving); |
315 | + | } |
316 | ||
317 | #endif | |
318 | ||
319 | + | //get total masss of unconstraint molecules |
320 | + | double totalMassOfUncons_local; |
321 | + | totalMassOfUncons_local = 0; |
322 | + | |
323 | + | for(int i = 0; i < unconsMols.size(); i++) |
324 | + | totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
325 | + | |
326 | + | #ifndef IS_MPI |
327 | + | totalMassOfUncons = totalMassOfUncons_local; |
328 | + | #else |
329 | + | MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
330 | + | MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 | + | #endif |
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(); |
282 | < | |
283 | < | // |
284 | < | fzOut = new ZConsWriter(zconsOutput.c_str()); |
285 | < | |
286 | < | if(!fzOut){ |
287 | < | sprintf( painCave.errMsg, |
288 | < | "Memory allocation failure in class Zconstraint\n"); |
289 | < | painCave.isFatal = 1; |
290 | < | simError(); |
291 | < | } |
292 | < | |
346 | > | forcePolicy->update(); |
347 | } | |
348 | ||
349 | template<typename T> ZConstraint<T>::~ZConstraint() | |
350 | { | |
351 | if(fz) | |
352 | delete[] fz; | |
353 | + | |
354 | + | if(curZPos) |
355 | + | delete[] curZPos; |
356 | ||
357 | if(indexOfZConsMols) | |
358 | delete[] indexOfZConsMols; | |
359 | ||
360 | if(fzOut) | |
361 | delete fzOut; | |
362 | + | |
363 | + | if(forcePolicy) |
364 | + | delete forcePolicy; |
365 | } | |
366 | ||
367 | + | |
368 | + | /** |
369 | + | * |
370 | + | */ |
371 | + | |
372 | #ifdef IS_MPI | |
373 | template<typename T> void ZConstraint<T>::update() | |
374 | { | |
# | Line 328 | Line 393 | template<typename T> void ZConstraint<T>::update() | |
393 | ||
394 | zconsMols.push_back(&molecules[i]); | |
395 | zPos.push_back((*parameters)[index].zPos); | |
396 | < | kz.push_back((*parameters)[index].kRatio * zForceConst); |
332 | < | |
396 | > | kz.push_back((*parameters)[index].kRatio * zForceConst); |
397 | massOfZConsMols.push_back(molecules[i].getTotalMass()); | |
398 | ||
399 | molecules[i].getCOM(COM); | |
# | Line 342 | Line 406 | template<typename T> void ZConstraint<T>::update() | |
406 | ||
407 | } | |
408 | } | |
409 | + | |
410 | + | //determine the states of z-constraint molecules |
411 | + | for(int i = 0; i < zconsMols.size(); i++){ |
412 | + | zconsMols[i]->getCOM(COM); |
413 | + | if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
414 | + | states.push_back(zcsFixed); |
415 | + | else |
416 | + | states.push_back(zcsMoving); |
417 | + | } |
418 | + | |
419 | ||
420 | //The reason to declare fz and indexOfZconsMols as pointer to array is | |
421 | // that we want to make the MPI communication simple | |
422 | if(fz) | |
423 | delete[] fz; | |
424 | + | |
425 | + | if(curZPos) |
426 | + | delete[] curZPos; |
427 | ||
428 | if(indexOfZConsMols) | |
429 | delete[] indexOfZConsMols; | |
430 | ||
431 | if (zconsMols.size() > 0){ | |
432 | fz = new double[zconsMols.size()]; | |
433 | + | curZPos = new double[zconsMols.size()]; |
434 | indexOfZConsMols = new int[zconsMols.size()]; | |
435 | ||
436 | < | if(!fz || !indexOfZConsMols){ |
436 | > | if(!fz || !curZPos || !indexOfZConsMols){ |
437 | sprintf( painCave.errMsg, | |
438 | "Memory allocation failure in class Zconstraint\n"); | |
439 | painCave.isFatal = 1; | |
# | Line 369 | Line 447 | template<typename T> void ZConstraint<T>::update() | |
447 | } | |
448 | else{ | |
449 | fz = NULL; | |
450 | + | curZPos = NULL; |
451 | indexOfZConsMols = NULL; | |
452 | } | |
453 | ||
454 | + | // |
455 | + | forcePolicy->update(); |
456 | + | |
457 | } | |
458 | ||
459 | #endif | |
460 | ||
461 | < | /** Function Name: isZConstraintMol |
462 | < | ** Parameter |
463 | < | ** Molecule* mol |
464 | < | ** Return value: |
465 | < | ** -1, if the molecule is not z-constraint molecule, |
466 | < | ** other non-negative values, its index in indexOfAllZConsMols vector |
461 | > | /** |
462 | > | * Function Name: isZConstraintMol |
463 | > | * Parameter |
464 | > | * Molecule* mol |
465 | > | * Return value: |
466 | > | * -1, if the molecule is not z-constraint molecule, |
467 | > | * other non-negative values, its index in indexOfAllZConsMols vector |
468 | */ | |
469 | ||
470 | template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) | |
# | Line 410 | Line 493 | template<typename T> int ZConstraint<T>::isZConstraint | |
493 | return -1; | |
494 | } | |
495 | ||
413 | – | /** |
414 | – | * Description: |
415 | – | * Reset the z coordinates |
416 | – | */ |
496 | template<typename T> void ZConstraint<T>::integrate(){ | |
497 | + | |
498 | + | // creat zconsWriter |
499 | + | fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
500 | ||
501 | + | if(!fzOut){ |
502 | + | sprintf( painCave.errMsg, |
503 | + | "Memory allocation failure in class Zconstraint\n"); |
504 | + | painCave.isFatal = 1; |
505 | + | simError(); |
506 | + | } |
507 | + | |
508 | //zero out the velocities of center of mass of unconstrained molecules | |
509 | //and the velocities of center of mass of every single z-constrained molecueles | |
510 | zeroOutVel(); | |
511 | + | |
512 | + | curZconsTime = zconsTime + info->getTime(); |
513 | ||
514 | T::integrate(); | |
515 | ||
# | Line 430 | Line 521 | template<typename T> void ZConstraint<T>::integrate(){ | |
521 | * | |
522 | * | |
523 | * | |
524 | < | */ |
434 | < | |
435 | < | |
524 | > | */ |
525 | template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ | |
526 | + | double zsys; |
527 | + | double COM[3]; |
528 | + | double force[3]; |
529 | + | double zSysCOMVel; |
530 | ||
531 | T::calcForce(calcPot, calcStress); | |
532 | ||
533 | < | if (checkZConsState()) |
534 | < | zeroOutVel(); |
533 | > | if (checkZConsState()){ |
534 | > | zeroOutVel(); |
535 | > | forcePolicy->update(); |
536 | > | } |
537 | > | |
538 | > | zsys = calcZSys(); |
539 | > | zSysCOMVel = calcSysCOMVel(); |
540 | > | #ifdef IS_MPI |
541 | > | if(worldRank == 0){ |
542 | > | #endif |
543 | > | //cout << "---------------------------------------------------------------------" <<endl; |
544 | > | //cout << "current time: " << info->getTime() << endl; |
545 | > | //cout << "center of mass at z: " << zsys << endl; |
546 | > | //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
547 | ||
548 | + | #ifdef IS_MPI |
549 | + | } |
550 | + | #endif |
551 | + | |
552 | //do zconstraint force; | |
553 | if (haveFixedZMols()) | |
554 | this->doZconstraintForce(); | |
555 | < | |
555 | > | |
556 | //use harmonical poteintial to move the molecules to the specified positions | |
557 | if (haveMovingZMols()) | |
558 | < | //this->doHarmonic(); |
559 | < | |
560 | < | fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
561 | < | |
558 | > | this->doHarmonic(); |
559 | > | |
560 | > | //write out forces and current positions of z-constraint molecules |
561 | > | if(info->getTime() >= curZconsTime){ |
562 | > | for(int i = 0; i < zconsMols.size(); i++){ |
563 | > | zconsMols[i]->getCOM(COM); |
564 | > | curZPos[i] = COM[whichDirection]; |
565 | > | |
566 | > | //if the z-constraint molecule is still moving, just record its force |
567 | > | if(states[i] == zcsMoving){ |
568 | > | fz[i] = 0; |
569 | > | Atom** movingZAtoms; |
570 | > | movingZAtoms = zconsMols[i]->getMyAtoms(); |
571 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
572 | > | movingZAtoms[j]->getFrc(force); |
573 | > | fz[i] += force[whichDirection]; |
574 | > | } |
575 | > | } |
576 | > | } |
577 | > | fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
578 | > | curZconsTime += zconsTime; |
579 | > | } |
580 | > | |
581 | > | zSysCOMVel = calcSysCOMVel(); |
582 | > | #ifdef IS_MPI |
583 | > | if(worldRank == 0){ |
584 | > | #endif |
585 | > | //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
586 | > | #ifdef IS_MPI |
587 | > | } |
588 | > | #endif |
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 | < | |
671 | > | |
672 | > | zconsMols[i]->getCOMvel(COMvel); |
673 | > | //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
674 | } | |
541 | – | |
542 | – | } |
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 | ||
778 | < | int nMovingZMols_local; |
622 | < | int nMovingZMols; |
623 | < | |
624 | < | //constrain the molecules which do not reach the specified positions |
625 | < | |
626 | < | zsys = calcZSys(); |
627 | < | cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
778 | > | //constrain the molecules which do not reach the specified positions |
779 | ||
780 | //Zero Out the force of z-contrained molecules | |
781 | totalFZ_local = 0; | |
782 | ||
783 | //calculate the total z-contrained force of fixed z-contrained molecules | |
784 | < | cout << "Fixed Molecules" << endl; |
784 | > | |
785 | > | //cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
786 | > | // << "total force is " << calcTotalForce() << endl; |
787 | > | |
788 | for(int i = 0; i < zconsMols.size(); i++){ | |
789 | < | |
789 | > | |
790 | if (states[i] == zcsFixed){ | |
791 | < | |
791 | > | |
792 | zconsMols[i]->getCOM(COM); | |
793 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
794 | ||
# | Line 642 | Line 796 | template<typename T> void ZConstraint<T>::doZconstrain | |
796 | for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { | |
797 | zconsAtoms[j]->getFrc(force); | |
798 | fz[i] += force[whichDirection]; | |
799 | < | } |
799 | > | } |
800 | totalFZ_local += fz[i]; | |
801 | ||
802 | < | cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
802 | > | //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
803 | > | // <<"\tcurrent zpos: " << COM[whichDirection] |
804 | > | // << "\tcurrent fz: " <<fz[i] << endl; |
805 | ||
806 | + | |
807 | } | |
808 | < | |
808 | > | |
809 | } | |
810 | ||
811 | < | //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 | < | } |
811 | > | //calculate total z-constraint force |
812 | #ifdef IS_MPI | |
813 | 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); |
814 | #else | |
815 | totalFZ = totalFZ_local; | |
665 | – | nMovingZMols = nMovingZMols_local; |
816 | #endif | |
817 | ||
818 | + | |
819 | + | // apply negative to fixed z-constrained molecues; |
820 | force[0]= 0; | |
821 | force[1]= 0; | |
822 | force[2]= 0; | |
671 | – | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
823 | ||
824 | < | //modify the velocites of unconstrained molecules |
824 | > | for(int i = 0; i < zconsMols.size(); i++){ |
825 | > | |
826 | > | if (states[i] == zcsFixed){ |
827 | > | |
828 | > | int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
829 | > | zconsAtoms = zconsMols[i]->getMyAtoms(); |
830 | > | |
831 | > | for(int j =0; j < nAtomOfCurZConsMol; j++) { |
832 | > | //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
833 | > | force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
834 | > | zconsAtoms[j]->addFrc(force); |
835 | > | } |
836 | > | |
837 | > | } |
838 | > | |
839 | > | } |
840 | > | |
841 | > | //cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
842 | > | // << "total force is " << calcTotalForce() << endl; |
843 | > | |
844 | > | |
845 | > | force[0]= 0; |
846 | > | force[1]= 0; |
847 | > | force[2]= 0; |
848 | > | |
849 | > | //modify the forces of unconstrained molecules |
850 | for(int i = 0; i < unconsMols.size(); i++){ | |
851 | ||
852 | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); | |
853 | ||
854 | < | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
854 | > | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
855 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
856 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
857 | unconsAtoms[j]->addFrc(force); | |
858 | + | } |
859 | ||
860 | } | |
861 | ||
862 | < | //modify the velocities of moving z-constrained molecules |
862 | > | //modify the forces of moving z-constrained molecules |
863 | for(int i = 0; i < zconsMols.size(); i++) { | |
864 | < | if (states[i] == zcsMoving){ |
865 | < | |
866 | < | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
864 | > | if (states[i] == zcsMoving){ |
865 | > | |
866 | > | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
867 | ||
868 | < | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
869 | < | movingZAtoms[j]->addFrc(force); |
870 | < | } |
868 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
869 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
870 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
871 | > | movingZAtoms[j]->addFrc(force); |
872 | > | } |
873 | > | } |
874 | } | |
875 | + | // cout << "after substracting z-constraint force from moving molecuels " |
876 | + | // << "total force is " << calcTotalForce() << endl; |
877 | ||
878 | < | // apply negative to fixed z-constrained molecues; |
878 | > | } |
879 | > | |
880 | > | /** |
881 | > | * |
882 | > | * |
883 | > | */ |
884 | > | |
885 | > | template<typename T> void ZConstraint<T>::doHarmonic(){ |
886 | > | double force[3]; |
887 | > | double harmonicU; |
888 | > | double harmonicF; |
889 | > | double COM[3]; |
890 | > | double diff; |
891 | > | double totalFZ_local; |
892 | > | double totalFZ; |
893 | > | |
894 | > | force[0] = 0; |
895 | > | force[1] = 0; |
896 | > | force[2] = 0; |
897 | > | |
898 | > | totalFZ_local = 0; |
899 | > | |
900 | > | for(int i = 0; i < zconsMols.size(); i++) { |
901 | > | |
902 | > | if (states[i] == zcsMoving){ |
903 | > | zconsMols[i]->getCOM(COM); |
904 | > | // cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
905 | > | // << "\tcurrent zpos: " << COM[whichDirection] << endl; |
906 | > | |
907 | > | diff = COM[whichDirection] -zPos[i]; |
908 | > | |
909 | > | harmonicU = 0.5 * kz[i] * diff * diff; |
910 | > | info->lrPot += harmonicU; |
911 | > | |
912 | > | harmonicF = - kz[i] * diff; |
913 | > | totalFZ_local += harmonicF; |
914 | > | |
915 | > | //adjust force |
916 | > | |
917 | > | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
918 | > | |
919 | > | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
920 | > | //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
921 | > | force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
922 | > | movingZAtoms[j]->addFrc(force); |
923 | > | } |
924 | > | } |
925 | > | |
926 | > | } |
927 | > | |
928 | > | #ifndef IS_MPI |
929 | > | totalFZ = totalFZ_local; |
930 | > | #else |
931 | > | MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
932 | > | #endif |
933 | > | |
934 | > | //cout << "before substracting harmonic force from moving molecuels " |
935 | > | // << "total force is " << calcTotalForce() << endl; |
936 | > | |
937 | force[0]= 0; | |
938 | force[1]= 0; | |
939 | force[2]= 0; | |
940 | ||
941 | < | for(int i = 0; i < zconsMols.size(); i++){ |
941 | > | //modify the forces of unconstrained molecules |
942 | > | for(int i = 0; i < unconsMols.size(); i++){ |
943 | > | |
944 | > | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
945 | > | |
946 | > | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
947 | > | //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
948 | > | force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
949 | > | unconsAtoms[j]->addFrc(force); |
950 | > | } |
951 | > | } |
952 | ||
953 | < | if (states[i] == zcsFixed){ |
954 | < | |
703 | < | int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
704 | < | zconsAtoms = zconsMols[i]->getMyAtoms(); |
705 | < | |
706 | < | for(int j =0; j < nAtomOfCurZConsMol; j++) { |
707 | < | force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
708 | < | zconsAtoms[j]->addFrc(force); |
709 | < | } |
710 | < | |
711 | < | } |
712 | < | |
713 | < | } |
953 | > | //cout << "after substracting harmonic force from moving molecuels " |
954 | > | // << "total force is " << calcTotalForce() << endl; |
955 | ||
956 | } | |
957 | ||
958 | + | /** |
959 | + | * |
960 | + | */ |
961 | + | |
962 | template<typename T> bool ZConstraint<T>::checkZConsState(){ | |
963 | double COM[3]; | |
964 | double diff; | |
965 | ||
966 | < | bool changed; |
966 | > | int changed_local; |
967 | > | int changed; |
968 | ||
969 | < | changed = false; |
969 | > | changed_local = 0; |
970 | ||
971 | for(int i =0; i < zconsMols.size(); i++){ | |
972 | ||
# | Line 728 | Line 974 | template<typename T> bool ZConstraint<T>::checkZConsSt | |
974 | diff = fabs(COM[whichDirection] - zPos[i]); | |
975 | if ( diff <= zconsTol && states[i] == zcsMoving){ | |
976 | states[i] = zcsFixed; | |
977 | < | changed = true; |
977 | > | changed_local = 1; |
978 | } | |
979 | else if ( diff > zconsTol && states[i] == zcsFixed){ | |
980 | states[i] = zcsMoving; | |
981 | < | changed = true; |
981 | > | changed_local = 1; |
982 | } | |
983 | ||
984 | } | |
985 | ||
986 | < | return changed; |
986 | > | #ifndef IS_MPI |
987 | > | changed =changed_local; |
988 | > | #else |
989 | > | MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
990 | > | #endif |
991 | > | |
992 | > | return (changed > 0); |
993 | > | |
994 | } | |
995 | ||
996 | template<typename T> bool ZConstraint<T>::haveFixedZMols(){ | |
997 | + | |
998 | + | int havingFixed_local; |
999 | + | int havingFixed; |
1000 | + | |
1001 | + | havingFixed_local = 0; |
1002 | + | |
1003 | for(int i = 0; i < zconsMols.size(); i++) | |
1004 | < | if (states[i] == zcsFixed) |
1005 | < | return true; |
1004 | > | if (states[i] == zcsFixed){ |
1005 | > | havingFixed_local = 1; |
1006 | > | break; |
1007 | > | } |
1008 | ||
1009 | < | return false; |
1009 | > | #ifndef IS_MPI |
1010 | > | havingFixed = havingFixed_local; |
1011 | > | #else |
1012 | > | MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1013 | > | #endif |
1014 | > | |
1015 | > | return (havingFixed > 0); |
1016 | } | |
1017 | ||
1018 | ||
# | Line 753 | Line 1020 | template<typename T> bool ZConstraint<T>::haveMovingZM | |
1020 | * | |
1021 | */ | |
1022 | template<typename T> bool ZConstraint<T>::haveMovingZMols(){ | |
1023 | + | |
1024 | + | int havingMoving_local; |
1025 | + | int havingMoving; |
1026 | + | |
1027 | + | havingMoving_local = 0; |
1028 | + | |
1029 | for(int i = 0; i < zconsMols.size(); i++) | |
1030 | < | if (states[i] == zcsMoving) |
1031 | < | return true; |
1030 | > | if (states[i] == zcsMoving){ |
1031 | > | havingMoving_local = 1; |
1032 | > | break; |
1033 | > | } |
1034 | ||
1035 | < | return false; |
1035 | > | #ifndef IS_MPI |
1036 | > | havingMoving = havingMoving_local; |
1037 | > | #else |
1038 | > | MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1039 | > | #endif |
1040 | > | |
1041 | > | return (havingMoving > 0); |
1042 | ||
1043 | } | |
1044 | ||
1045 | /** | |
1046 | < | * |
1047 | < | * |
767 | < | */ |
1046 | > | * |
1047 | > | */ |
1048 | ||
1049 | < | template<typename T> void ZConstraint<T>::doHarmonic(){ |
1050 | < | double force[3]; |
1051 | < | double harmonicU; |
1052 | < | double COM[3]; |
1053 | < | double diff; |
1054 | < | |
1055 | < | force[0] = 0; |
1056 | < | force[1] = 0; |
1057 | < | force[2] = 0; |
1049 | > | template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1050 | > | { |
1051 | > | double MVzOfMovingMols_local; |
1052 | > | double MVzOfMovingMols; |
1053 | > | double totalMassOfMovingZMols_local; |
1054 | > | double totalMassOfMovingZMols; |
1055 | > | double COMvel[3]; |
1056 | > | |
1057 | > | MVzOfMovingMols_local = 0; |
1058 | > | totalMassOfMovingZMols_local = 0; |
1059 | ||
1060 | < | cout << "Moving Molecules" << endl; |
1061 | < | for(int i = 0; i < zconsMols.size(); i++) { |
1060 | > | for(int i =0; i < unconsMols.size(); i++){ |
1061 | > | unconsMols[i]->getCOMvel(COMvel); |
1062 | > | MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1063 | > | } |
1064 | ||
1065 | + | for(int i = 0; i < zconsMols.size(); i++){ |
1066 | + | |
1067 | if (states[i] == zcsMoving){ | |
1068 | < | zconsMols[i]->getCOM(COM): |
1069 | < | cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
1070 | < | |
1071 | < | diff = COM[whichDirection] -zPos[i]; |
1072 | < | |
1073 | < | harmonicU = 0.5 * kz[i] * diff * diff; |
789 | < | info->ltPot += harmonicU; |
1068 | > | zconsMols[i]->getCOMvel(COMvel); |
1069 | > | MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1070 | > | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1071 | > | } |
1072 | > | |
1073 | > | } |
1074 | ||
1075 | < | force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
1076 | < | |
1077 | < | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
1075 | > | #ifndef IS_MPI |
1076 | > | MVzOfMovingMols = MVzOfMovingMols_local; |
1077 | > | totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1078 | > | #else |
1079 | > | MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1080 | > | MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1081 | > | #endif |
1082 | ||
1083 | < | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
1084 | < | movingZAtoms[j]->addFrc(force); |
797 | < | } |
1083 | > | double vzOfMovingMols; |
1084 | > | vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1085 | ||
1086 | + | return vzOfMovingMols; |
1087 | + | } |
1088 | + | |
1089 | + | /** |
1090 | + | * |
1091 | + | */ |
1092 | + | |
1093 | + | template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1094 | + | { |
1095 | + | double COMvel[3]; |
1096 | + | double tempMVz_local; |
1097 | + | double tempMVz; |
1098 | + | double massOfZCons_local; |
1099 | + | double massOfZCons; |
1100 | + | |
1101 | + | |
1102 | + | tempMVz_local = 0; |
1103 | + | |
1104 | + | for(int i =0 ; i < nMols; i++){ |
1105 | + | molecules[i].getCOMvel(COMvel); |
1106 | + | tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1107 | } | |
1108 | ||
1109 | + | massOfZCons_local = 0; |
1110 | + | |
1111 | + | for(int i = 0; i < massOfZConsMols.size(); i++){ |
1112 | + | massOfZCons_local += massOfZConsMols[i]; |
1113 | + | } |
1114 | + | #ifndef IS_MPI |
1115 | + | massOfZCons = massOfZCons_local; |
1116 | + | tempMVz = tempMVz_local; |
1117 | + | #else |
1118 | + | MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1119 | + | MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1120 | + | #endif |
1121 | + | |
1122 | + | return tempMVz /(totalMassOfUncons + massOfZCons); |
1123 | } | |
1124 | + | |
1125 | + | /** |
1126 | + | * |
1127 | + | */ |
1128 | + | |
1129 | + | template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1130 | + | |
1131 | + | double force[3]; |
1132 | + | double totalForce_local; |
1133 | + | double totalForce; |
1134 | + | |
1135 | + | totalForce_local = 0; |
1136 | + | |
1137 | + | for(int i = 0; i < nAtoms; i++){ |
1138 | + | atoms[i]->getFrc(force); |
1139 | + | totalForce_local += force[whichDirection]; |
1140 | + | } |
1141 | + | |
1142 | + | #ifndef IS_MPI |
1143 | + | totalForce = totalForce_local; |
1144 | + | #else |
1145 | + | MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1146 | + | #endif |
1147 | + | |
1148 | + | return totalForce; |
1149 | + | |
1150 | + | } |
1151 | + | |
1152 | + | /** |
1153 | + | * |
1154 | + | */ |
1155 | + | |
1156 | + | template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1157 | + | //calculate the number of atoms of moving z-constrained molecules |
1158 | + | int nMovingZAtoms_local; |
1159 | + | int nMovingZAtoms; |
1160 | + | |
1161 | + | nMovingZAtoms_local = 0; |
1162 | + | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1163 | + | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1164 | + | nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1165 | + | |
1166 | + | #ifdef IS_MPI |
1167 | + | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1168 | + | #else |
1169 | + | nMovingZAtoms = nMovingZAtoms_local; |
1170 | + | #endif |
1171 | + | totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1172 | + | } |
1173 | + | |
1174 | + | template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1175 | + | return totalForce / mol->getNAtoms(); |
1176 | + | } |
1177 | + | |
1178 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1179 | + | return totalForce / totNumOfMovingAtoms; |
1180 | + | } |
1181 | + | |
1182 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1183 | + | return totalForce / mol->getNAtoms(); |
1184 | + | } |
1185 | + | |
1186 | + | template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1187 | + | return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1188 | + | } |
1189 | + | |
1190 | + | /** |
1191 | + | * |
1192 | + | */ |
1193 | + | |
1194 | + | template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1195 | + | //calculate the number of atoms of moving z-constrained molecules |
1196 | + | double massOfMovingZAtoms_local; |
1197 | + | double massOfMovingZAtoms; |
1198 | + | |
1199 | + | massOfMovingZAtoms_local = 0; |
1200 | + | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1201 | + | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1202 | + | massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1203 | + | |
1204 | + | #ifdef IS_MPI |
1205 | + | MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1206 | + | #else |
1207 | + | massOfMovingZAtoms = massOfMovingZAtoms_local; |
1208 | + | #endif |
1209 | + | totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons; |
1210 | + | } |
1211 | + | |
1212 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1213 | + | return totalForce * atom->getMass() / mol->getTotalMass(); |
1214 | + | } |
1215 | + | |
1216 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1217 | + | return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1218 | + | } |
1219 | + | |
1220 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1221 | + | return totalForce * atom->getMass() / mol->getTotalMass(); |
1222 | + | } |
1223 | + | |
1224 | + | template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1225 | + | return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1226 | + | } |
1227 | + |
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