# | Line 1 | Line 1 | |
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1 | #include "Integrator.hpp" | |
2 | #include "simError.h" | |
3 | < | #include <cmath> |
3 | > | #include <math.h> |
4 | template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) | |
5 | < | : T(theInfo, the_ff), fz(NULL), curZPos(NULL), |
6 | < | indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
5 | > | : T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL), |
6 | > | fzOut(NULL), curZconsTime(0), forcePolicy(NULL) |
7 | { | |
8 | ||
9 | //get properties from SimInfo | |
# | Line 27 | 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 |
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 substraction policy, " |
35 | < | "average force substraction policy is used\n"); |
34 | > | "ZConstraint Warning: User does not set force Subtraction policy, " |
35 | > | "PolicyByMass is used\n"); |
36 | painCave.isFatal = 0; | |
37 | simError(); | |
38 | ||
39 | < | forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
39 | > | forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
40 | } | |
41 | else{ | |
42 | policy = dynamic_cast<StringData*>(data); | |
43 | < | |
44 | < | if(!policy){ |
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"); |
47 | > | "PolicyByMass 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{ |
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 substraction policy, " |
61 | < | "average force substraction policy is used\n"); |
60 | > | "ZConstraint Warning: unknown force Subtraction policy, " |
61 | > | "PolicyByMass is used\n"); |
62 | painCave.isFatal = 0; | |
63 | simError(); | |
64 | < | } |
65 | < | } |
64 | > | forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
65 | > | } |
66 | > | } |
67 | } | |
67 | – | |
68 | ||
69 | < | |
69 | > | |
70 | //retrieve sample time of z-contraint | |
71 | data = info->getProperty(ZCONSTIME_ID); | |
72 | ||
# | Line 110 | 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 124 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
124 | this->zconsOutput = filename->getData(); | |
125 | } | |
126 | ||
127 | – | |
127 | } | |
128 | ||
129 | //retrieve tolerance for z-constraint molecuels | |
# | Line 154 | 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 195 | 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() - 1].zconsIndex; | |
200 | ||
# | Line 214 | Line 213 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
213 | ||
214 | //if user does not specify the zpos for the zconstraint molecule | |
215 | //its initial z coordinate will be used as default | |
216 | < | for(int i = 0; i < parameters->size(); i++){ |
216 | > | for(int i = 0; i < (int)(parameters->size()); i++){ |
217 | ||
218 | < | if(!(*parameters)[i].havingZPos){ |
220 | < | |
218 | > | if(!(*parameters)[i].havingZPos){ |
219 | #ifndef IS_MPI | |
220 | < | for(int j = 0; j < nMols; j++){ |
221 | < | if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
222 | < | molecules[j].getCOM(COM); |
223 | < | break; |
226 | < | } |
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 | > | |
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 j = 0; j < nMols; j++) |
240 | < | if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
241 | < | molecules[j].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, 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 279 | 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 | < | cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
281 | < | 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 305 | Line 304 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
304 | } | |
305 | ||
306 | //determine the states of z-constraint molecules | |
307 | < | for(int i = 0; i < zconsMols.size(); i++){ |
307 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
308 | indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); | |
309 | ||
310 | < | zconsMols[i]->getCOM(COM); |
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); |
312 | > | states.push_back(zcsFixed); |
313 | > | else |
314 | > | states.push_back(zcsMoving); |
315 | } | |
316 | ||
317 | #endif | |
# | Line 321 | Line 320 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
320 | double totalMassOfUncons_local; | |
321 | totalMassOfUncons_local = 0; | |
322 | ||
323 | < | for(int i = 0; i < unconsMols.size(); i++) |
323 | > | for(int i = 0; i < (int)(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, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
329 | > | MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
330 | > | MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 | #endif | |
332 | ||
333 | – | |
333 | //get total number of unconstrained atoms | |
334 | int nUnconsAtoms_local; | |
335 | nUnconsAtoms_local = 0; | |
336 | < | for(int i = 0; i < unconsMols.size(); i++) |
336 | > | for(int i = 0; i < (int)(unconsMols.size()); i++) |
337 | nUnconsAtoms_local += unconsMols[i]->getNAtoms(); | |
338 | ||
339 | #ifndef IS_MPI | |
340 | totNumOfUnconsAtoms = nUnconsAtoms_local; | |
341 | #else | |
342 | < | MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT,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(), parameters); |
348 | – | |
349 | – | if(!fzOut){ |
350 | – | sprintf( painCave.errMsg, |
351 | – | "Memory allocation failure in class Zconstraint\n"); |
352 | – | painCave.isFatal = 1; |
353 | – | simError(); |
354 | – | } |
355 | – | |
346 | forcePolicy->update(); | |
347 | } | |
348 | ||
# | Line 369 | Line 359 | template<typename T> ZConstraint<T>::~ZConstraint() | |
359 | ||
360 | if(fzOut) | |
361 | delete fzOut; | |
362 | < | |
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 398 | 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); |
402 | < | |
396 | > | kz.push_back((*parameters)[index].kRatio * zForceConst); |
397 | massOfZConsMols.push_back(molecules[i].getTotalMass()); | |
398 | ||
399 | molecules[i].getCOM(COM); | |
# | Line 414 | Line 408 | template<typename T> void ZConstraint<T>::update() | |
408 | } | |
409 | ||
410 | //determine the states of z-constraint molecules | |
411 | < | for(int i = 0; i < zconsMols.size(); i++){ |
412 | < | zconsMols[i]->getCOM(COM); |
411 | > | for(int i = 0; i < (int)(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); |
414 | > | states.push_back(zcsFixed); |
415 | > | else |
416 | > | states.push_back(zcsMoving); |
417 | } | |
418 | ||
419 | ||
# | Line 427 | Line 421 | template<typename T> void ZConstraint<T>::update() | |
421 | // that we want to make the MPI communication simple | |
422 | if(fz) | |
423 | delete[] fz; | |
424 | < | |
424 | > | |
425 | if(curZPos) | |
426 | delete[] curZPos; | |
427 | ||
# | Line 436 | Line 430 | template<typename T> void ZConstraint<T>::update() | |
430 | ||
431 | if (zconsMols.size() > 0){ | |
432 | fz = new double[zconsMols.size()]; | |
433 | < | curZPos = new double[zconsMols.size()]; |
433 | > | curZPos = new double[zconsMols.size()]; |
434 | indexOfZConsMols = new int[zconsMols.size()]; | |
435 | ||
436 | if(!fz || !curZPos || !indexOfZConsMols){ | |
# | Line 446 | Line 440 | template<typename T> void ZConstraint<T>::update() | |
440 | simError(); | |
441 | } | |
442 | ||
443 | < | for(int i = 0; i < zconsMols.size(); i++){ |
443 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
444 | indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); | |
445 | } | |
446 | ||
447 | } | |
448 | else{ | |
449 | fz = NULL; | |
450 | < | curZPos = NULL; |
450 | > | curZPos = NULL; |
451 | indexOfZConsMols = NULL; | |
452 | } | |
453 | < | |
453 | > | |
454 | // | |
455 | forcePolicy->update(); | |
456 | ||
# | Line 464 | Line 458 | template<typename T> void ZConstraint<T>::update() | |
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 499 | Line 494 | template<typename T> void ZConstraint<T>::integrate(){ | |
494 | } | |
495 | ||
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 519 | Line 526 | template<typename T> void ZConstraint<T>::calcForce(in | |
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(); |
535 | < | forcePolicy->update(); |
533 | > | if (checkZConsState()){ |
534 | > | zeroOutVel(); |
535 | > | forcePolicy->update(); |
536 | } | |
537 | + | |
538 | zsys = calcZSys(); | |
539 | < | cout << "---------------------------------------------------------------------" <<endl; |
540 | < | cout << "current time: " << info->getTime() << endl; |
541 | < | cout << "center of mass at z: " << zsys << endl; |
542 | < | //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
543 | < | cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
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 | < | //cout << "before doZConstraintForce, totalForce is " << calcTotalForce() << endl; |
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 | ||
546 | – | //cout << "after doHarmonic, totalForce is " << calcTotalForce() << endl; |
547 | – | |
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++){ |
561 | > | if(info->getTime() >= curZconsTime){ |
562 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
563 | zconsMols[i]->getCOM(COM); | |
564 | < | curZPos[i] = COM[whichDirection]; |
564 | > | curZPos[i] = COM[whichDirection]; |
565 | ||
566 | < | //if the z-constraint molecule is still moving, just record its force |
567 | < | if(states[i] == zcsMoving){ |
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++){ |
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 | < | } |
574 | > | } |
575 | > | } |
576 | > | } |
577 | fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); | |
578 | < | curZconsTime += zconsTime; |
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 | < | |
569 | < | //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
570 | < | cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
588 | > | #endif |
589 | } | |
590 | + | |
591 | + | |
592 | + | /** |
593 | + | * |
594 | + | */ |
595 | ||
596 | template<typename T> double ZConstraint<T>::calcZSys() | |
597 | { | |
# | Line 579 | Line 602 | template<typename T> double ZConstraint<T>::calcZSys() | |
602 | double totalMZ; | |
603 | double massOfCurMol; | |
604 | double COM[3]; | |
605 | < | |
605 | > | |
606 | totalMass_local = 0; | |
607 | totalMZ_local = 0; | |
608 | ||
# | Line 594 | Line 617 | template<typename T> double ZConstraint<T>::calcZSys() | |
617 | ||
618 | ||
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); |
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; | |
# | Line 618 | Line 643 | template<typename T> void ZConstraint<T>::thermalize( | |
643 | ||
644 | /** | |
645 | * | |
621 | – | * |
622 | – | * |
646 | */ | |
647 | ||
648 | template<typename T> void ZConstraint<T>::zeroOutVel(){ | |
# | Line 627 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
650 | Atom** fixedZAtoms; | |
651 | double COMvel[3]; | |
652 | double vel[3]; | |
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++){ |
657 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
658 | ||
659 | < | if (states[i] == zcsFixed){ |
659 | > | if (states[i] == zcsFixed){ |
660 | ||
661 | < | zconsMols[i]->getCOMvel(COMvel); |
662 | < | //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
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 | < | zconsMols[i]->getCOMvel(COMvel); |
673 | < | //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
672 | > | zconsMols[i]->getCOMvel(COMvel); |
673 | > | //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
674 | } | |
675 | < | |
675 | > | |
676 | } | |
677 | ||
678 | < | //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
678 | > | //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
679 | ||
680 | + | zSysCOMVel = calcSysCOMVel(); |
681 | #ifdef IS_MPI | |
682 | < | if (worldRank == 0){ |
682 | > | if(worldRank == 0){ |
683 | #endif | |
684 | < | cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl; |
684 | > | //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
685 | #ifdef IS_MPI | |
686 | } | |
687 | #endif | |
688 | < | |
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 670 | Line 695 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
695 | MVzOfMovingMols_local = 0; | |
696 | totalMassOfMovingZMols_local = 0; | |
697 | ||
698 | < | for(int i =0; i < unconsMols.size(); i++){ |
698 | > | for(int i =0; i < (int)(unconsMols.size()); i++){ |
699 | unconsMols[i]->getCOMvel(COMvel); | |
700 | MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; | |
701 | } | |
702 | ||
703 | < | for(int i = 0; i < zconsMols.size(); i++){ |
703 | > | for(int i = 0; i < (int)(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 697 | Line 722 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
722 | ||
723 | //modify the velocites of unconstrained molecules | |
724 | Atom** unconsAtoms; | |
725 | < | for(int i = 0; i < unconsMols.size(); i++){ |
725 | > | for(int i = 0; i < (int)(unconsMols.size()); i++){ |
726 | ||
727 | unconsAtoms = unconsMols[i]->getMyAtoms(); | |
728 | for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ | |
# | Line 710 | 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.size(); i++){ |
738 | > | for(int i = 0; i < (int)(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); |
747 | < | } |
748 | < | |
746 | > | movingZAtoms[j]->setVel(vel); |
747 | > | } |
748 | > | |
749 | } | |
750 | ||
751 | } | |
752 | ||
753 | + | |
754 | + | zSysCOMVel = calcSysCOMVel(); |
755 | #ifdef IS_MPI | |
756 | < | if (worldRank == 0){ |
756 | > | if(worldRank == 0){ |
757 | #endif | |
758 | < | cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl; |
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; | |
772 | double totalFZ; | |
773 | double totalFZ_local; | |
743 | – | double COMvel[3]; |
774 | double COM[3]; | |
775 | double force[3]; | |
776 | ||
777 | < | |
748 | < | |
749 | < | //constrain the molecules which do not reach the specified positions |
777 | > | //constrain the molecules which do not reach the specified positions |
778 | ||
779 | //Zero Out the force of z-contrained molecules | |
780 | totalFZ_local = 0; | |
781 | ||
782 | //calculate the total z-contrained force of fixed z-contrained molecules | |
783 | + | |
784 | + | //cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
785 | + | // << "total force is " << calcTotalForce() << endl; |
786 | ||
787 | < | #ifdef IS_MPI |
788 | < | if (worldRank == 0){ |
758 | < | #endif |
759 | < | cout << "Fixed Molecules" << endl; |
760 | < | #ifdef IS_MPI |
761 | < | } |
762 | < | #endif |
763 | < | |
764 | < | for(int i = 0; i < zconsMols.size(); i++){ |
765 | < | |
787 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
788 | > | |
789 | if (states[i] == zcsFixed){ | |
790 | < | |
790 | > | |
791 | zconsMols[i]->getCOM(COM); | |
792 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
793 | ||
# | Line 772 | 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] |
802 | < | <<"\tcurrent zpos: " << COM[whichDirection] |
803 | < | << "\tcurrent fz: " <<fz[i] << endl; |
801 | > | //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
802 | > | // <<"\tcurrent zpos: " << COM[whichDirection] |
803 | > | // << "\tcurrent fz: " <<fz[i] << endl; |
804 | ||
805 | + | |
806 | } | |
807 | < | |
807 | > | |
808 | } | |
809 | ||
810 | //calculate total z-constraint force | |
# | Line 790 | Line 814 | template<typename T> void ZConstraint<T>::doZconstrain | |
814 | totalFZ = totalFZ_local; | |
815 | #endif | |
816 | ||
817 | < | |
817 | > | |
818 | // apply negative to fixed z-constrained molecues; | |
819 | force[0]= 0; | |
820 | force[1]= 0; | |
821 | force[2]= 0; | |
822 | ||
823 | < | for(int i = 0; i < zconsMols.size(); i++){ |
823 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
824 | ||
825 | if (states[i] == zcsFixed){ | |
826 | < | |
826 | > | |
827 | int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); | |
828 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
829 | ||
830 | for(int j =0; j < nAtomOfCurZConsMol; j++) { | |
831 | < | force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
832 | < | //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
831 | > | //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
832 | > | force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
833 | zconsAtoms[j]->addFrc(force); | |
834 | } | |
835 | < | |
835 | > | |
836 | } | |
837 | < | |
837 | > | |
838 | } | |
839 | ||
840 | //cout << "after zero out z-constraint force on fixed z-constraint molecuels " | |
841 | < | // << "total force is " << calcTotalForce() << endl; |
841 | > | // << "total force is " << calcTotalForce() << endl; |
842 | > | |
843 | ||
819 | – | //calculate the number of atoms of moving z-constrained molecules |
820 | – | int nMovingZAtoms_local; |
821 | – | int nMovingZAtoms; |
822 | – | |
823 | – | nMovingZAtoms_local = 0; |
824 | – | for(int i = 0; i < zconsMols.size(); i++) |
825 | – | if(states[i] == zcsMoving) |
826 | – | nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
827 | – | |
828 | – | #ifdef IS_MPI |
829 | – | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
830 | – | #else |
831 | – | nMovingZAtoms = nMovingZAtoms_local; |
832 | – | #endif |
833 | – | |
844 | force[0]= 0; | |
845 | force[1]= 0; | |
846 | force[2]= 0; | |
847 | ||
848 | //modify the forces of unconstrained molecules | |
849 | < | for(int i = 0; i < unconsMols.size(); i++){ |
849 | > | for(int i = 0; i < (int)(unconsMols.size()); i++){ |
850 | ||
851 | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); | |
852 | ||
853 | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ | |
854 | < | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
855 | < | //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
854 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
855 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
856 | unconsAtoms[j]->addFrc(force); | |
857 | } | |
858 | ||
859 | } | |
860 | ||
861 | //modify the forces of moving z-constrained molecules | |
862 | < | for(int i = 0; i < zconsMols.size(); i++) { |
862 | > | for(int i = 0; i < (int)(zconsMols.size()); i++) { |
863 | if (states[i] == zcsMoving){ | |
864 | < | |
864 | > | |
865 | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); | |
866 | ||
867 | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ | |
868 | < | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
869 | < | //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
868 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
869 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
870 | movingZAtoms[j]->addFrc(force); | |
871 | } | |
872 | } | |
873 | } | |
874 | + | // cout << "after substracting z-constraint force from moving molecuels " |
875 | + | // << "total force is " << calcTotalForce() << endl; |
876 | ||
877 | < | //cout << "after substracting z-constraint force from moving molecuels " |
866 | < | // << "total force is " << calcTotalForce() << endl; |
877 | > | } |
878 | ||
879 | + | /** |
880 | + | * |
881 | + | * |
882 | + | */ |
883 | + | |
884 | + | template<typename T> void ZConstraint<T>::doHarmonic(){ |
885 | + | double force[3]; |
886 | + | double harmonicU; |
887 | + | double harmonicF; |
888 | + | double COM[3]; |
889 | + | double diff; |
890 | + | double totalFZ_local; |
891 | + | double totalFZ; |
892 | + | |
893 | + | force[0] = 0; |
894 | + | force[1] = 0; |
895 | + | force[2] = 0; |
896 | + | |
897 | + | totalFZ_local = 0; |
898 | + | |
899 | + | for(int i = 0; i < (int)(zconsMols.size()); i++) { |
900 | + | |
901 | + | if (states[i] == zcsMoving){ |
902 | + | zconsMols[i]->getCOM(COM); |
903 | + | // cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
904 | + | // << "\tcurrent zpos: " << COM[whichDirection] << endl; |
905 | + | |
906 | + | diff = COM[whichDirection] -zPos[i]; |
907 | + | |
908 | + | harmonicU = 0.5 * kz[i] * diff * diff; |
909 | + | info->lrPot += harmonicU; |
910 | + | |
911 | + | harmonicF = - kz[i] * diff; |
912 | + | totalFZ_local += harmonicF; |
913 | + | |
914 | + | //adjust force |
915 | + | |
916 | + | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
917 | + | |
918 | + | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
919 | + | //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
920 | + | force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
921 | + | movingZAtoms[j]->addFrc(force); |
922 | + | } |
923 | + | } |
924 | + | |
925 | + | } |
926 | + | |
927 | + | #ifndef IS_MPI |
928 | + | totalFZ = totalFZ_local; |
929 | + | #else |
930 | + | MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
931 | + | #endif |
932 | + | |
933 | + | //cout << "before substracting harmonic force from moving molecuels " |
934 | + | // << "total force is " << calcTotalForce() << endl; |
935 | + | |
936 | + | force[0]= 0; |
937 | + | force[1]= 0; |
938 | + | force[2]= 0; |
939 | + | |
940 | + | //modify the forces of unconstrained molecules |
941 | + | for(int i = 0; i < (int)(unconsMols.size()); i++){ |
942 | + | |
943 | + | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
944 | + | |
945 | + | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
946 | + | //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
947 | + | force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
948 | + | unconsAtoms[j]->addFrc(force); |
949 | + | } |
950 | + | } |
951 | + | |
952 | + | //cout << "after substracting harmonic force from moving molecuels " |
953 | + | // << "total force is " << calcTotalForce() << endl; |
954 | + | |
955 | } | |
956 | ||
957 | + | /** |
958 | + | * |
959 | + | */ |
960 | + | |
961 | template<typename T> bool ZConstraint<T>::checkZConsState(){ | |
962 | double COM[3]; | |
963 | double diff; | |
964 | ||
965 | int changed_local; | |
966 | int changed; | |
967 | < | |
967 | > | |
968 | changed_local = 0; | |
969 | ||
970 | < | for(int i =0; i < zconsMols.size(); i++){ |
970 | > | for(int i =0; i < (int)(zconsMols.size()); i++){ |
971 | ||
972 | zconsMols[i]->getCOM(COM); | |
973 | diff = fabs(COM[whichDirection] - zPos[i]); | |
974 | if ( diff <= zconsTol && states[i] == zcsMoving){ | |
975 | states[i] = zcsFixed; | |
976 | < | changed_local = 1; |
976 | > | changed_local = 1; |
977 | } | |
978 | else if ( diff > zconsTol && states[i] == zcsFixed){ | |
979 | states[i] = zcsMoving; | |
980 | < | changed_local = 1; |
980 | > | changed_local = 1; |
981 | } | |
982 | ||
983 | } | |
# | Line 897 | Line 988 | template<typename T> bool ZConstraint<T>::checkZConsSt | |
988 | MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
989 | #endif | |
990 | ||
991 | < | return changed > 0 ? true : false; |
991 | > | return (changed > 0); |
992 | > | |
993 | } | |
994 | ||
995 | template<typename T> bool ZConstraint<T>::haveFixedZMols(){ | |
# | Line 907 | Line 999 | template<typename T> bool ZConstraint<T>::haveFixedZMo | |
999 | ||
1000 | havingFixed_local = 0; | |
1001 | ||
1002 | < | for(int i = 0; i < zconsMols.size(); i++) |
1002 | > | for(int i = 0; i < (int)(zconsMols.size()); i++) |
1003 | if (states[i] == zcsFixed){ | |
1004 | havingFixed_local = 1; | |
1005 | < | break; |
1005 | > | break; |
1006 | } | |
1007 | ||
1008 | #ifndef IS_MPI | |
# | Line 919 | Line 1011 | template<typename T> bool ZConstraint<T>::haveFixedZMo | |
1011 | MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
1012 | #endif | |
1013 | ||
1014 | < | return havingFixed > 0 ? true : false; |
1014 | > | return (havingFixed > 0); |
1015 | } | |
1016 | ||
1017 | ||
# | Line 933 | Line 1025 | template<typename T> bool ZConstraint<T>::haveMovingZM | |
1025 | ||
1026 | havingMoving_local = 0; | |
1027 | ||
1028 | < | for(int i = 0; i < zconsMols.size(); i++) |
1028 | > | for(int i = 0; i < (int)(zconsMols.size()); i++) |
1029 | if (states[i] == zcsMoving){ | |
1030 | havingMoving_local = 1; | |
1031 | < | break; |
1031 | > | break; |
1032 | } | |
1033 | ||
1034 | #ifndef IS_MPI | |
# | Line 945 | Line 1037 | template<typename T> bool ZConstraint<T>::haveMovingZM | |
1037 | MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
1038 | #endif | |
1039 | ||
1040 | < | return havingMoving > 0 ? true : false; |
1040 | > | return (havingMoving > 0); |
1041 | ||
1042 | } | |
1043 | ||
1044 | /** | |
1045 | < | * |
1046 | < | * |
955 | < | */ |
956 | < | |
957 | < | template<typename T> void ZConstraint<T>::doHarmonic(){ |
958 | < | double force[3]; |
959 | < | double harmonicU; |
960 | < | double harmonicF; |
961 | < | double COM[3]; |
962 | < | double diff; |
963 | < | double totalFZ_local; |
964 | < | double totalFZ; |
965 | < | |
966 | < | force[0] = 0; |
967 | < | force[1] = 0; |
968 | < | force[2] = 0; |
969 | < | |
970 | < | totalFZ_local = 0; |
971 | < | |
972 | < | #ifdef IS_MPI |
973 | < | if (worldRank == 0){ |
974 | < | #endif |
975 | < | cout << "Moving Molecules" << endl; |
976 | < | #ifdef IS_MPI |
977 | < | } |
978 | < | #endif |
979 | < | |
980 | < | |
981 | < | for(int i = 0; i < zconsMols.size(); i++) { |
982 | < | |
983 | < | if (states[i] == zcsMoving){ |
984 | < | zconsMols[i]->getCOM(COM); |
985 | < | cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
986 | < | |
987 | < | diff = COM[whichDirection] -zPos[i]; |
988 | < | |
989 | < | harmonicU = 0.5 * kz[i] * diff * diff; |
990 | < | info->lrPot += harmonicU; |
991 | < | |
992 | < | harmonicF = - kz[i] * diff; |
993 | < | totalFZ_local += harmonicF; |
994 | < | |
995 | < | //adjust force |
996 | < | |
997 | < | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
1045 | > | * |
1046 | > | */ |
1047 | ||
999 | – | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
1000 | – | force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
1001 | – | //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
1002 | – | movingZAtoms[j]->addFrc(force); |
1003 | – | } |
1004 | – | } |
1005 | – | |
1006 | – | } |
1007 | – | |
1008 | – | #ifndef IS_MPI |
1009 | – | totalFZ = totalFZ_local; |
1010 | – | #else |
1011 | – | MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1012 | – | #endif |
1013 | – | |
1014 | – | force[0]= 0; |
1015 | – | force[1]= 0; |
1016 | – | force[2]= 0; |
1017 | – | |
1018 | – | //modify the forces of unconstrained molecules |
1019 | – | for(int i = 0; i < unconsMols.size(); i++){ |
1020 | – | |
1021 | – | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
1022 | – | |
1023 | – | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
1024 | – | force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
1025 | – | //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
1026 | – | unconsAtoms[j]->addFrc(force); |
1027 | – | } |
1028 | – | } |
1029 | – | |
1030 | – | } |
1031 | – | |
1048 | template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() | |
1049 | { | |
1050 | double MVzOfMovingMols_local; | |
# | Line 1050 | Line 1066 | template<typename T> double ZConstraint<T>::calcMoving | |
1066 | if (states[i] == zcsMoving){ | |
1067 | zconsMols[i]->getCOMvel(COMvel); | |
1068 | MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; | |
1069 | < | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1069 | > | totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1070 | } | |
1071 | < | |
1071 | > | |
1072 | } | |
1073 | ||
1074 | #ifndef IS_MPI | |
# | Line 1069 | Line 1085 | template<typename T> double ZConstraint<T>::calcMoving | |
1085 | return vzOfMovingMols; | |
1086 | } | |
1087 | ||
1088 | + | /** |
1089 | + | * |
1090 | + | */ |
1091 | ||
1092 | template<typename T> double ZConstraint<T>::calcSysCOMVel() | |
1093 | { | |
# | Line 1083 | Line 1102 | template<typename T> double ZConstraint<T>::calcSysCOM | |
1102 | ||
1103 | for(int i =0 ; i < nMols; i++){ | |
1104 | molecules[i].getCOMvel(COMvel); | |
1105 | < | tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1105 | > | tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1106 | } | |
1107 | ||
1108 | massOfZCons_local = 0; | |
1109 | < | |
1110 | < | for(int i = 0; i < massOfZConsMols.size(); i++){ |
1109 | > | |
1110 | > | for(int i = 0; i < (int)(massOfZConsMols.size()); i++){ |
1111 | massOfZCons_local += massOfZConsMols[i]; | |
1112 | } | |
1113 | #ifndef IS_MPI | |
# | Line 1102 | Line 1121 | template<typename T> double ZConstraint<T>::calcSysCOM | |
1121 | return tempMVz /(totalMassOfUncons + massOfZCons); | |
1122 | } | |
1123 | ||
1124 | + | /** |
1125 | + | * |
1126 | + | */ |
1127 | + | |
1128 | template<typename T> double ZConstraint<T>::calcTotalForce(){ | |
1129 | ||
1130 | double force[3]; | |
# | Line 1133 | Line 1156 | template<typename T> void ZConstraint<T>::PolicyByNumb | |
1156 | //calculate the number of atoms of moving z-constrained molecules | |
1157 | int nMovingZAtoms_local; | |
1158 | int nMovingZAtoms; | |
1159 | < | |
1159 | > | |
1160 | nMovingZAtoms_local = 0; | |
1161 | < | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1161 | > | for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1162 | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) | |
1163 | < | nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1163 | > | nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1164 | ||
1165 | #ifdef IS_MPI | |
1166 | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
# | Line 1147 | Line 1170 | template<typename T> void ZConstraint<T>::PolicyByNumb | |
1170 | totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; | |
1171 | } | |
1172 | ||
1173 | < | template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1173 | > | template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1174 | return totalForce / mol->getNAtoms(); | |
1175 | } | |
1176 | ||
# | Line 1171 | Line 1194 | template<typename T> void ZConstraint<T>::PolicyByMass | |
1194 | //calculate the number of atoms of moving z-constrained molecules | |
1195 | double massOfMovingZAtoms_local; | |
1196 | double massOfMovingZAtoms; | |
1197 | < | |
1197 | > | |
1198 | massOfMovingZAtoms_local = 0; | |
1199 | < | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1199 | > | for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1200 | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) | |
1201 | < | massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1201 | > | massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1202 | ||
1203 | #ifdef IS_MPI | |
1204 | MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); | |
1205 | #else | |
1206 | massOfMovingZAtoms = massOfMovingZAtoms_local; | |
1207 | #endif | |
1208 | < | totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1208 | > | totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons; |
1209 | } | |
1210 | ||
1211 | template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
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