1 |
#include "Integrator.hpp" |
2 |
#include "simError.h" |
3 |
#include <math.h> |
4 |
|
5 |
const double INFINITE_TIME = 10e30; |
6 |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, |
7 |
ForceFields* the_ff): T(theInfo, the_ff), |
8 |
fzOut(NULL), |
9 |
curZconsTime(0), |
10 |
forcePolicy(NULL), |
11 |
usingSMD(false), |
12 |
hasZConsGap(false){ |
13 |
//get properties from SimInfo |
14 |
GenericData* data; |
15 |
ZConsParaData* zConsParaData; |
16 |
DoubleData* sampleTime; |
17 |
DoubleData* tolerance; |
18 |
DoubleData* gap; |
19 |
DoubleData* fixtime; |
20 |
StringData* policy; |
21 |
StringData* filename; |
22 |
IntData* smdFlag; |
23 |
double COM[3]; |
24 |
|
25 |
//by default, the direction of constraint is z |
26 |
// 0 --> x |
27 |
// 1 --> y |
28 |
// 2 --> z |
29 |
whichDirection = 2; |
30 |
|
31 |
//estimate the force constant of harmonical potential |
32 |
double Kb = 1.986E-3 ; //in kcal/K |
33 |
|
34 |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) / |
35 |
2; |
36 |
zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox); |
37 |
|
38 |
//creat force Subtraction policy |
39 |
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
40 |
if (!data){ |
41 |
sprintf(painCave.errMsg, |
42 |
"ZConstraint Warning: User does not set force Subtraction policy, " |
43 |
"PolicyByMass is used\n"); |
44 |
painCave.isFatal = 0; |
45 |
simError(); |
46 |
|
47 |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
48 |
} |
49 |
else{ |
50 |
policy = dynamic_cast<StringData*>(data); |
51 |
|
52 |
if (!policy){ |
53 |
sprintf(painCave.errMsg, |
54 |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
55 |
"PolicyByMass is used\n"); |
56 |
painCave.isFatal = 0; |
57 |
simError(); |
58 |
|
59 |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
60 |
} |
61 |
else{ |
62 |
if (policy->getData() == "BYNUMBER") |
63 |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this); |
64 |
else if (policy->getData() == "BYMASS") |
65 |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
66 |
else{ |
67 |
sprintf(painCave.errMsg, |
68 |
"ZConstraint Warning: unknown force Subtraction policy, " |
69 |
"PolicyByMass is used\n"); |
70 |
painCave.isFatal = 0; |
71 |
simError(); |
72 |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
73 |
} |
74 |
} |
75 |
} |
76 |
|
77 |
|
78 |
//retrieve sample time of z-contraint |
79 |
data = info->getProperty(ZCONSTIME_ID); |
80 |
|
81 |
if (!data){ |
82 |
sprintf(painCave.errMsg, |
83 |
"ZConstraint error: If you use an ZConstraint\n" |
84 |
" , you must set sample time.\n"); |
85 |
painCave.isFatal = 1; |
86 |
simError(); |
87 |
} |
88 |
else{ |
89 |
sampleTime = dynamic_cast<DoubleData*>(data); |
90 |
|
91 |
if (!sampleTime){ |
92 |
sprintf(painCave.errMsg, |
93 |
"ZConstraint error: Can not get property from SimInfo\n"); |
94 |
painCave.isFatal = 1; |
95 |
simError(); |
96 |
} |
97 |
else{ |
98 |
this->zconsTime = sampleTime->getData(); |
99 |
} |
100 |
} |
101 |
|
102 |
//retrieve output filename of z force |
103 |
data = info->getProperty(ZCONSFILENAME_ID); |
104 |
if (!data){ |
105 |
sprintf(painCave.errMsg, |
106 |
"ZConstraint error: If you use an ZConstraint\n" |
107 |
" , you must set output filename of z-force.\n"); |
108 |
painCave.isFatal = 1; |
109 |
simError(); |
110 |
} |
111 |
else{ |
112 |
filename = dynamic_cast<StringData*>(data); |
113 |
|
114 |
if (!filename){ |
115 |
sprintf(painCave.errMsg, |
116 |
"ZConstraint error: Can not get property from SimInfo\n"); |
117 |
painCave.isFatal = 1; |
118 |
simError(); |
119 |
} |
120 |
else{ |
121 |
this->zconsOutput = filename->getData(); |
122 |
} |
123 |
} |
124 |
|
125 |
//retrieve tolerance for z-constraint molecuels |
126 |
data = info->getProperty(ZCONSTOL_ID); |
127 |
|
128 |
if (!data){ |
129 |
sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n"); |
130 |
painCave.isFatal = 1; |
131 |
simError(); |
132 |
} |
133 |
else{ |
134 |
tolerance = dynamic_cast<DoubleData*>(data); |
135 |
|
136 |
if (!tolerance){ |
137 |
sprintf(painCave.errMsg, |
138 |
"ZConstraint error: Can not get property from SimInfo\n"); |
139 |
painCave.isFatal = 1; |
140 |
simError(); |
141 |
} |
142 |
else{ |
143 |
this->zconsTol = tolerance->getData(); |
144 |
} |
145 |
} |
146 |
|
147 |
//quick hack here |
148 |
data = info->getProperty(ZCONSGAP_ID); |
149 |
|
150 |
if (data){ |
151 |
gap = dynamic_cast<DoubleData*>(data); |
152 |
|
153 |
if (!gap){ |
154 |
sprintf(painCave.errMsg, |
155 |
"ZConstraint error: Can not get property from SimInfo\n"); |
156 |
painCave.isFatal = 1; |
157 |
simError(); |
158 |
} |
159 |
else{ |
160 |
this->hasZConsGap = true; |
161 |
this->zconsGap = gap->getData(); |
162 |
} |
163 |
} |
164 |
|
165 |
|
166 |
|
167 |
data = info->getProperty(ZCONSFIXTIME_ID); |
168 |
|
169 |
if (data){ |
170 |
fixtime = dynamic_cast<DoubleData*>(data); |
171 |
if (!fixtime){ |
172 |
sprintf(painCave.errMsg, |
173 |
"ZConstraint error: Can not get zconsFixTime from SimInfo\n"); |
174 |
painCave.isFatal = 1; |
175 |
simError(); |
176 |
} |
177 |
else{ |
178 |
this->zconsFixTime = fixtime->getData(); |
179 |
} |
180 |
} |
181 |
else if(hasZConsGap){ |
182 |
sprintf(painCave.errMsg, |
183 |
"ZConstraint error: must set fixtime if already set zconsGap\n"); |
184 |
painCave.isFatal = 1; |
185 |
simError(); |
186 |
} |
187 |
|
188 |
|
189 |
|
190 |
data = info->getProperty(ZCONSUSINGSMD_ID); |
191 |
|
192 |
if (data){ |
193 |
smdFlag = dynamic_cast<IntData*>(data); |
194 |
|
195 |
if (!smdFlag){ |
196 |
sprintf(painCave.errMsg, |
197 |
"ZConstraint error: Can not get property from SimInfo\n"); |
198 |
painCave.isFatal = 1; |
199 |
simError(); |
200 |
} |
201 |
else{ |
202 |
this->usingSMD= smdFlag->getData() ? true : false; |
203 |
} |
204 |
|
205 |
} |
206 |
|
207 |
|
208 |
|
209 |
//retrieve index of z-constraint molecules |
210 |
data = info->getProperty(ZCONSPARADATA_ID); |
211 |
if (!data){ |
212 |
sprintf(painCave.errMsg, |
213 |
"ZConstraint error: If you use an ZConstraint\n" |
214 |
" , you must set index of z-constraint molecules.\n"); |
215 |
painCave.isFatal = 1; |
216 |
simError(); |
217 |
} |
218 |
else{ |
219 |
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
220 |
|
221 |
if (!zConsParaData){ |
222 |
sprintf(painCave.errMsg, |
223 |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
224 |
painCave.isFatal = 1; |
225 |
simError(); |
226 |
} |
227 |
else{ |
228 |
parameters = zConsParaData->getData(); |
229 |
|
230 |
//check the range of zconsIndex |
231 |
//and the minimum value of index is the first one (we already sorted the data) |
232 |
//the maximum value of index is the last one |
233 |
|
234 |
int maxIndex; |
235 |
int minIndex; |
236 |
int totalNumMol; |
237 |
|
238 |
minIndex = (*parameters)[0].zconsIndex; |
239 |
if (minIndex < 0){ |
240 |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
241 |
painCave.isFatal = 1; |
242 |
simError(); |
243 |
} |
244 |
|
245 |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
246 |
|
247 |
#ifndef IS_MPI |
248 |
totalNumMol = nMols; |
249 |
#else |
250 |
totalNumMol = mpiSim->getNMolGlobal(); |
251 |
#endif |
252 |
|
253 |
if (maxIndex > totalNumMol - 1){ |
254 |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
255 |
painCave.isFatal = 1; |
256 |
simError(); |
257 |
} |
258 |
|
259 |
//if user does not specify the zpos for the zconstraint molecule |
260 |
//its initial z coordinate will be used as default |
261 |
for (int i = 0; i < (int) (parameters->size()); i++){ |
262 |
if (!(*parameters)[i].havingZPos){ |
263 |
#ifndef IS_MPI |
264 |
for (int j = 0; j < nMols; j++){ |
265 |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
266 |
molecules[j].getCOM(COM); |
267 |
break; |
268 |
} |
269 |
} |
270 |
#else |
271 |
//query which processor current zconstraint molecule belongs to |
272 |
int* MolToProcMap; |
273 |
int whichNode; |
274 |
|
275 |
MolToProcMap = mpiSim->getMolToProcMap(); |
276 |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
277 |
|
278 |
//broadcast the zpos of current z-contraint molecule |
279 |
//the node which contain this |
280 |
|
281 |
if (worldRank == whichNode){ |
282 |
for (int j = 0; j < nMols; j++) |
283 |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
284 |
molecules[j].getCOM(COM); |
285 |
break; |
286 |
} |
287 |
} |
288 |
|
289 |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, |
290 |
MPI_COMM_WORLD); |
291 |
#endif |
292 |
|
293 |
(*parameters)[i].zPos = COM[whichDirection]; |
294 |
|
295 |
sprintf(painCave.errMsg, |
296 |
"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
297 |
"initial z coornidate will be used \n"); |
298 |
painCave.isFatal = 0; |
299 |
simError(); |
300 |
} |
301 |
} |
302 |
}//end if (!zConsParaData) |
303 |
|
304 |
}//end if (!data) |
305 |
|
306 |
// |
307 |
#ifdef IS_MPI |
308 |
update(); |
309 |
#else |
310 |
int searchResult; |
311 |
|
312 |
for (int i = 0; i < nMols; i++){ |
313 |
searchResult = isZConstraintMol(&molecules[i]); |
314 |
|
315 |
if (searchResult > -1){ |
316 |
zconsMols.push_back(&molecules[i]); |
317 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
318 |
|
319 |
zPos.push_back((*parameters)[searchResult].zPos); |
320 |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
321 |
|
322 |
if(usingSMD) |
323 |
cantVel.push_back((*parameters)[searchResult].cantVel); |
324 |
|
325 |
} |
326 |
else{ |
327 |
unconsMols.push_back(&molecules[i]); |
328 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
329 |
} |
330 |
} |
331 |
|
332 |
fz.resize(zconsMols.size()); |
333 |
curZPos.resize(zconsMols.size()); |
334 |
indexOfZConsMols.resize(zconsMols.size()); |
335 |
|
336 |
//determine the states of z-constraint molecules |
337 |
for (size_t i = 0; i < zconsMols.size(); i++){ |
338 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
339 |
|
340 |
zconsMols[i]->getCOM(COM); |
341 |
|
342 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
343 |
states.push_back(zcsFixed); |
344 |
|
345 |
if (hasZConsGap) |
346 |
endFixTime.push_back(info->getTime() + zconsFixTime); |
347 |
} |
348 |
else{ |
349 |
states.push_back(zcsMoving); |
350 |
|
351 |
if (hasZConsGap) |
352 |
endFixTime.push_back(INFINITE_TIME); |
353 |
} |
354 |
|
355 |
if(usingSMD) |
356 |
cantPos.push_back(COM[whichDirection]); |
357 |
} |
358 |
|
359 |
if(usingSMD) |
360 |
prevCantPos = cantPos; |
361 |
#endif |
362 |
|
363 |
|
364 |
//get total masss of unconstraint molecules |
365 |
double totalMassOfUncons_local; |
366 |
totalMassOfUncons_local = 0; |
367 |
|
368 |
for (size_t i = 0; i < unconsMols.size(); i++) |
369 |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
370 |
|
371 |
#ifndef IS_MPI |
372 |
totalMassOfUncons = totalMassOfUncons_local; |
373 |
#else |
374 |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, |
375 |
MPI_SUM, MPI_COMM_WORLD); |
376 |
#endif |
377 |
|
378 |
//get total number of unconstrained atoms |
379 |
int nUnconsAtoms_local; |
380 |
nUnconsAtoms_local = 0; |
381 |
for (int i = 0; i < (int) (unconsMols.size()); i++) |
382 |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
383 |
|
384 |
#ifndef IS_MPI |
385 |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
386 |
#else |
387 |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM, |
388 |
MPI_COMM_WORLD); |
389 |
#endif |
390 |
|
391 |
forcePolicy->update(); |
392 |
} |
393 |
|
394 |
template<typename T> ZConstraint<T>::~ZConstraint(){ |
395 |
|
396 |
if (fzOut){ |
397 |
delete fzOut; |
398 |
} |
399 |
|
400 |
if (forcePolicy){ |
401 |
delete forcePolicy; |
402 |
} |
403 |
} |
404 |
|
405 |
|
406 |
/** |
407 |
* |
408 |
*/ |
409 |
|
410 |
#ifdef IS_MPI |
411 |
template<typename T> void ZConstraint<T>::update(){ |
412 |
double COM[3]; |
413 |
int index; |
414 |
|
415 |
zconsMols.clear(); |
416 |
massOfZConsMols.clear(); |
417 |
zPos.clear(); |
418 |
kz.clear(); |
419 |
cantPos.clear(); |
420 |
cantVel.clear(); |
421 |
|
422 |
unconsMols.clear(); |
423 |
massOfUnconsMols.clear(); |
424 |
|
425 |
|
426 |
//creat zconsMol and unconsMol lists |
427 |
for (int i = 0; i < nMols; i++){ |
428 |
index = isZConstraintMol(&molecules[i]); |
429 |
|
430 |
if (index > -1){ |
431 |
zconsMols.push_back(&molecules[i]); |
432 |
zPos.push_back((*parameters)[index].zPos); |
433 |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
434 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
435 |
|
436 |
if(usingSMD) |
437 |
cantVel.push_back((*parameters)[index].cantVel); |
438 |
|
439 |
} |
440 |
else{ |
441 |
unconsMols.push_back(&molecules[i]); |
442 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
443 |
} |
444 |
} |
445 |
|
446 |
fz.resize(zconsMols.size()); |
447 |
curZPos.resize(zconsMols.size()); |
448 |
indexOfZConsMols.resize(zconsMols.size()); |
449 |
|
450 |
for (size_t i = 0; i < zconsMols.size(); i++){ |
451 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
452 |
} |
453 |
|
454 |
//determine the states of z-constraint molecules |
455 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
456 |
|
457 |
zconsMols[i]->getCOM(COM); |
458 |
|
459 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
460 |
states.push_back(zcsFixed); |
461 |
|
462 |
if (hasZConsGap) |
463 |
endFixTime.push_back(info->getTime() + zconsFixTime); |
464 |
} |
465 |
else{ |
466 |
states.push_back(zcsMoving); |
467 |
|
468 |
if (hasZConsGap) |
469 |
endFixTime.push_back(INFINITE_TIME); |
470 |
} |
471 |
|
472 |
if(usingSMD) |
473 |
cantPos.push_back(COM[whichDirection]); |
474 |
} |
475 |
|
476 |
if(usingSMD) |
477 |
prevCantPos = cantPos; |
478 |
|
479 |
// |
480 |
forcePolicy->update(); |
481 |
} |
482 |
|
483 |
#endif |
484 |
|
485 |
/** |
486 |
* Function Name: isZConstraintMol |
487 |
* Parameter |
488 |
* Molecule* mol |
489 |
* Return value: |
490 |
* -1, if the molecule is not z-constraint molecule, |
491 |
* other non-negative values, its index in indexOfAllZConsMols vector |
492 |
*/ |
493 |
|
494 |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){ |
495 |
int index; |
496 |
int low; |
497 |
int high; |
498 |
int mid; |
499 |
|
500 |
index = mol->getGlobalIndex(); |
501 |
|
502 |
low = 0; |
503 |
high = parameters->size() - 1; |
504 |
|
505 |
//Binary Search (we have sorted the array) |
506 |
while (low <= high){ |
507 |
mid = (low + high) / 2; |
508 |
if ((*parameters)[mid].zconsIndex == index) |
509 |
return mid; |
510 |
else if ((*parameters)[mid].zconsIndex > index) |
511 |
high = mid - 1; |
512 |
else |
513 |
low = mid + 1; |
514 |
} |
515 |
|
516 |
return -1; |
517 |
} |
518 |
|
519 |
template<typename T> void ZConstraint<T>::integrate(){ |
520 |
// creat zconsWriter |
521 |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
522 |
|
523 |
if (!fzOut){ |
524 |
sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n"); |
525 |
painCave.isFatal = 1; |
526 |
simError(); |
527 |
} |
528 |
|
529 |
//zero out the velocities of center of mass of unconstrained molecules |
530 |
//and the velocities of center of mass of every single z-constrained molecueles |
531 |
zeroOutVel(); |
532 |
|
533 |
curZconsTime = zconsTime + info->getTime(); |
534 |
|
535 |
T::integrate(); |
536 |
} |
537 |
|
538 |
|
539 |
/** |
540 |
* |
541 |
* |
542 |
* |
543 |
* |
544 |
*/ |
545 |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
546 |
double zsys; |
547 |
double COM[3]; |
548 |
double force[3]; |
549 |
double zSysCOMVel; |
550 |
|
551 |
T::calcForce(calcPot, calcStress); |
552 |
|
553 |
|
554 |
if (hasZConsGap){ |
555 |
updateZPos(); |
556 |
} |
557 |
|
558 |
if (checkZConsState()){ |
559 |
zeroOutVel(); |
560 |
forcePolicy->update(); |
561 |
} |
562 |
|
563 |
zsys = calcZSys(); |
564 |
zSysCOMVel = calcSysCOMVel(); |
565 |
#ifdef IS_MPI |
566 |
if (worldRank == 0){ |
567 |
#endif |
568 |
//cout << "---------------------------------------------------------------------" <<endl; |
569 |
//cout << "current time: " << info->getTime() << endl; |
570 |
//cout << "center of mass at z: " << zsys << endl; |
571 |
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
572 |
|
573 |
#ifdef IS_MPI |
574 |
} |
575 |
#endif |
576 |
|
577 |
//do zconstraint force; |
578 |
if (haveFixedZMols()){ |
579 |
this->doZconstraintForce(); |
580 |
} |
581 |
|
582 |
//use external force to move the molecules to the specified positions |
583 |
if (haveMovingZMols()){ |
584 |
if (usingSMD) |
585 |
this->doHarmonic(cantPos); |
586 |
else |
587 |
this->doHarmonic(zPos); |
588 |
} |
589 |
|
590 |
//write out forces and current positions of z-constraint molecules |
591 |
if (info->getTime() >= curZconsTime){ |
592 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
593 |
zconsMols[i]->getCOM(COM); |
594 |
curZPos[i] = COM[whichDirection]; |
595 |
|
596 |
//if the z-constraint molecule is still moving, just record its force |
597 |
if (states[i] == zcsMoving){ |
598 |
fz[i] = 0; |
599 |
Atom** movingZAtoms; |
600 |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
601 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
602 |
movingZAtoms[j]->getFrc(force); |
603 |
fz[i] += force[whichDirection]; |
604 |
} |
605 |
} |
606 |
} |
607 |
fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0], |
608 |
&curZPos[0], &zPos[0]); |
609 |
curZconsTime += zconsTime; |
610 |
} |
611 |
|
612 |
zSysCOMVel = calcSysCOMVel(); |
613 |
#ifdef IS_MPI |
614 |
if (worldRank == 0){ |
615 |
#endif |
616 |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
617 |
#ifdef IS_MPI |
618 |
} |
619 |
#endif |
620 |
} |
621 |
|
622 |
|
623 |
/** |
624 |
* |
625 |
*/ |
626 |
|
627 |
template<typename T> double ZConstraint<T>::calcZSys(){ |
628 |
//calculate reference z coordinate for z-constraint molecules |
629 |
double totalMass_local; |
630 |
double totalMass; |
631 |
double totalMZ_local; |
632 |
double totalMZ; |
633 |
double massOfCurMol; |
634 |
double COM[3]; |
635 |
|
636 |
totalMass_local = 0; |
637 |
totalMZ_local = 0; |
638 |
|
639 |
for (int i = 0; i < nMols; i++){ |
640 |
massOfCurMol = molecules[i].getTotalMass(); |
641 |
molecules[i].getCOM(COM); |
642 |
|
643 |
totalMass_local += massOfCurMol; |
644 |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
645 |
} |
646 |
|
647 |
|
648 |
#ifdef IS_MPI |
649 |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, |
650 |
MPI_COMM_WORLD); |
651 |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
652 |
#else |
653 |
totalMass = totalMass_local; |
654 |
totalMZ = totalMZ_local; |
655 |
#endif |
656 |
|
657 |
double zsys; |
658 |
zsys = totalMZ / totalMass; |
659 |
|
660 |
return zsys; |
661 |
} |
662 |
|
663 |
/** |
664 |
* |
665 |
*/ |
666 |
template<typename T> void ZConstraint<T>::thermalize(void){ |
667 |
T::thermalize(); |
668 |
zeroOutVel(); |
669 |
} |
670 |
|
671 |
/** |
672 |
* |
673 |
*/ |
674 |
|
675 |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
676 |
Atom** fixedZAtoms; |
677 |
double COMvel[3]; |
678 |
double vel[3]; |
679 |
double zSysCOMVel; |
680 |
|
681 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
682 |
|
683 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
684 |
if (states[i] == zcsFixed){ |
685 |
zconsMols[i]->getCOMvel(COMvel); |
686 |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
687 |
|
688 |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
689 |
|
690 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
691 |
fixedZAtoms[j]->getVel(vel); |
692 |
vel[whichDirection] -= COMvel[whichDirection]; |
693 |
fixedZAtoms[j]->setVel(vel); |
694 |
} |
695 |
|
696 |
zconsMols[i]->getCOMvel(COMvel); |
697 |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
698 |
} |
699 |
} |
700 |
|
701 |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
702 |
|
703 |
zSysCOMVel = calcSysCOMVel(); |
704 |
#ifdef IS_MPI |
705 |
if (worldRank == 0){ |
706 |
#endif |
707 |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
708 |
#ifdef IS_MPI |
709 |
} |
710 |
#endif |
711 |
|
712 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
713 |
double MVzOfMovingMols_local; |
714 |
double MVzOfMovingMols; |
715 |
double totalMassOfMovingZMols_local; |
716 |
double totalMassOfMovingZMols; |
717 |
|
718 |
MVzOfMovingMols_local = 0; |
719 |
totalMassOfMovingZMols_local = 0; |
720 |
|
721 |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
722 |
unconsMols[i]->getCOMvel(COMvel); |
723 |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
724 |
} |
725 |
|
726 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
727 |
if (states[i] == zcsMoving){ |
728 |
zconsMols[i]->getCOMvel(COMvel); |
729 |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
730 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
731 |
} |
732 |
} |
733 |
|
734 |
#ifndef IS_MPI |
735 |
MVzOfMovingMols = MVzOfMovingMols_local; |
736 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
737 |
#else |
738 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
739 |
MPI_SUM, MPI_COMM_WORLD); |
740 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
741 |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
742 |
#endif |
743 |
|
744 |
double vzOfMovingMols; |
745 |
vzOfMovingMols = MVzOfMovingMols / |
746 |
(totalMassOfUncons + totalMassOfMovingZMols); |
747 |
|
748 |
//modify the velocites of unconstrained molecules |
749 |
Atom** unconsAtoms; |
750 |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
751 |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
752 |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
753 |
unconsAtoms[j]->getVel(vel); |
754 |
vel[whichDirection] -= vzOfMovingMols; |
755 |
unconsAtoms[j]->setVel(vel); |
756 |
} |
757 |
} |
758 |
|
759 |
//modify the velocities of moving z-constrained molecuels |
760 |
Atom** movingZAtoms; |
761 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
762 |
if (states[i] == zcsMoving){ |
763 |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
764 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
765 |
movingZAtoms[j]->getVel(vel); |
766 |
vel[whichDirection] -= vzOfMovingMols; |
767 |
movingZAtoms[j]->setVel(vel); |
768 |
} |
769 |
} |
770 |
} |
771 |
|
772 |
|
773 |
zSysCOMVel = calcSysCOMVel(); |
774 |
#ifdef IS_MPI |
775 |
if (worldRank == 0){ |
776 |
#endif |
777 |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
778 |
#ifdef IS_MPI |
779 |
} |
780 |
#endif |
781 |
} |
782 |
|
783 |
/** |
784 |
* |
785 |
*/ |
786 |
|
787 |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
788 |
Atom** zconsAtoms; |
789 |
double totalFZ; |
790 |
double totalFZ_local; |
791 |
double COM[3]; |
792 |
double force[3]; |
793 |
|
794 |
//constrain the molecules which do not reach the specified positions |
795 |
|
796 |
//Zero Out the force of z-contrained molecules |
797 |
totalFZ_local = 0; |
798 |
|
799 |
//calculate the total z-contrained force of fixed z-contrained molecules |
800 |
|
801 |
//cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
802 |
// << "total force is " << calcTotalForce() << endl; |
803 |
|
804 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
805 |
if (states[i] == zcsFixed){ |
806 |
zconsMols[i]->getCOM(COM); |
807 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
808 |
|
809 |
fz[i] = 0; |
810 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
811 |
zconsAtoms[j]->getFrc(force); |
812 |
fz[i] += force[whichDirection]; |
813 |
} |
814 |
totalFZ_local += fz[i]; |
815 |
|
816 |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
817 |
// <<"\tcurrent zpos: " << COM[whichDirection] |
818 |
// << "\tcurrent fz: " <<fz[i] << endl; |
819 |
} |
820 |
} |
821 |
|
822 |
//calculate total z-constraint force |
823 |
#ifdef IS_MPI |
824 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
825 |
#else |
826 |
totalFZ = totalFZ_local; |
827 |
#endif |
828 |
|
829 |
|
830 |
// apply negative to fixed z-constrained molecues; |
831 |
force[0] = 0; |
832 |
force[1] = 0; |
833 |
force[2] = 0; |
834 |
|
835 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
836 |
if (states[i] == zcsFixed){ |
837 |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
838 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
839 |
|
840 |
for (int j = 0; j < nAtomOfCurZConsMol; j++){ |
841 |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
842 |
force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i], |
843 |
zconsAtoms[j], |
844 |
fz[i]); |
845 |
zconsAtoms[j]->addFrc(force); |
846 |
} |
847 |
} |
848 |
} |
849 |
|
850 |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
851 |
// << "total force is " << calcTotalForce() << endl; |
852 |
|
853 |
|
854 |
force[0] = 0; |
855 |
force[1] = 0; |
856 |
force[2] = 0; |
857 |
|
858 |
//modify the forces of unconstrained molecules |
859 |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
860 |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
861 |
|
862 |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
863 |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
864 |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j], |
865 |
totalFZ); |
866 |
unconsAtoms[j]->addFrc(force); |
867 |
} |
868 |
} |
869 |
|
870 |
//modify the forces of moving z-constrained molecules |
871 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
872 |
if (states[i] == zcsMoving){ |
873 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
874 |
|
875 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
876 |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
877 |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j], |
878 |
totalFZ); |
879 |
movingZAtoms[j]->addFrc(force); |
880 |
} |
881 |
} |
882 |
} |
883 |
// cout << "after substracting z-constraint force from moving molecuels " |
884 |
// << "total force is " << calcTotalForce() << endl; |
885 |
} |
886 |
|
887 |
/** |
888 |
* |
889 |
* |
890 |
*/ |
891 |
|
892 |
template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){ |
893 |
double force[3]; |
894 |
double harmonicU; |
895 |
double harmonicF; |
896 |
double COM[3]; |
897 |
double diff; |
898 |
double totalFZ_local; |
899 |
double totalFZ; |
900 |
|
901 |
force[0] = 0; |
902 |
force[1] = 0; |
903 |
force[2] = 0; |
904 |
|
905 |
totalFZ_local = 0; |
906 |
|
907 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
908 |
if (states[i] == zcsMoving){ |
909 |
zconsMols[i]->getCOM(COM); |
910 |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
911 |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
912 |
|
913 |
diff = COM[whichDirection] - resPos[i]; |
914 |
|
915 |
harmonicU = 0.5 * kz[i] * diff * diff; |
916 |
info->lrPot += harmonicU; |
917 |
|
918 |
harmonicF = -kz[i] * diff; |
919 |
totalFZ_local += harmonicF; |
920 |
|
921 |
//adjust force |
922 |
|
923 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
924 |
|
925 |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
926 |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
927 |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], |
928 |
movingZAtoms[j], |
929 |
harmonicF); |
930 |
movingZAtoms[j]->addFrc(force); |
931 |
} |
932 |
} |
933 |
} |
934 |
|
935 |
#ifndef IS_MPI |
936 |
totalFZ = totalFZ_local; |
937 |
#else |
938 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
939 |
#endif |
940 |
|
941 |
//cout << "before substracting harmonic force from moving molecuels " |
942 |
// << "total force is " << calcTotalForce() << endl; |
943 |
|
944 |
force[0] = 0; |
945 |
force[1] = 0; |
946 |
force[2] = 0; |
947 |
|
948 |
//modify the forces of unconstrained molecules |
949 |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
950 |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
951 |
|
952 |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
953 |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
954 |
force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j], |
955 |
totalFZ); |
956 |
unconsAtoms[j]->addFrc(force); |
957 |
} |
958 |
} |
959 |
|
960 |
//cout << "after substracting harmonic force from moving molecuels " |
961 |
// << "total force is " << calcTotalForce() << endl; |
962 |
} |
963 |
|
964 |
/** |
965 |
* |
966 |
*/ |
967 |
|
968 |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
969 |
double COM[3]; |
970 |
double diff; |
971 |
|
972 |
int changed_local; |
973 |
int changed; |
974 |
|
975 |
changed_local = 0; |
976 |
|
977 |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
978 |
zconsMols[i]->getCOM(COM); |
979 |
diff = fabs(COM[whichDirection] - zPos[i]); |
980 |
if (diff <= zconsTol && states[i] == zcsMoving){ |
981 |
states[i] = zcsFixed; |
982 |
changed_local = 1; |
983 |
|
984 |
if(usingSMD) |
985 |
prevCantPos = cantPos; |
986 |
|
987 |
if (hasZConsGap) |
988 |
endFixTime[i] = info->getTime() + zconsFixTime; |
989 |
} |
990 |
else if (diff > zconsTol && states[i] == zcsFixed){ |
991 |
states[i] = zcsMoving; |
992 |
changed_local = 1; |
993 |
|
994 |
if(usingSMD) |
995 |
cantPos = prevCantPos; |
996 |
|
997 |
if (hasZConsGap) |
998 |
endFixTime[i] = INFINITE_TIME; |
999 |
} |
1000 |
} |
1001 |
|
1002 |
#ifndef IS_MPI |
1003 |
changed = changed_local; |
1004 |
#else |
1005 |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1006 |
#endif |
1007 |
|
1008 |
return (changed > 0); |
1009 |
} |
1010 |
|
1011 |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1012 |
int havingFixed_local; |
1013 |
int havingFixed; |
1014 |
|
1015 |
havingFixed_local = 0; |
1016 |
|
1017 |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
1018 |
if (states[i] == zcsFixed){ |
1019 |
havingFixed_local = 1; |
1020 |
break; |
1021 |
} |
1022 |
|
1023 |
#ifndef IS_MPI |
1024 |
havingFixed = havingFixed_local; |
1025 |
#else |
1026 |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM, |
1027 |
MPI_COMM_WORLD); |
1028 |
#endif |
1029 |
|
1030 |
return (havingFixed > 0); |
1031 |
} |
1032 |
|
1033 |
|
1034 |
/** |
1035 |
* |
1036 |
*/ |
1037 |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1038 |
int havingMoving_local; |
1039 |
int havingMoving; |
1040 |
|
1041 |
havingMoving_local = 0; |
1042 |
|
1043 |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
1044 |
if (states[i] == zcsMoving){ |
1045 |
havingMoving_local = 1; |
1046 |
break; |
1047 |
} |
1048 |
|
1049 |
#ifndef IS_MPI |
1050 |
havingMoving = havingMoving_local; |
1051 |
#else |
1052 |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM, |
1053 |
MPI_COMM_WORLD); |
1054 |
#endif |
1055 |
|
1056 |
return (havingMoving > 0); |
1057 |
} |
1058 |
|
1059 |
/** |
1060 |
* |
1061 |
*/ |
1062 |
|
1063 |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){ |
1064 |
double MVzOfMovingMols_local; |
1065 |
double MVzOfMovingMols; |
1066 |
double totalMassOfMovingZMols_local; |
1067 |
double totalMassOfMovingZMols; |
1068 |
double COMvel[3]; |
1069 |
|
1070 |
MVzOfMovingMols_local = 0; |
1071 |
totalMassOfMovingZMols_local = 0; |
1072 |
|
1073 |
for (int i = 0; i < unconsMols.size(); i++){ |
1074 |
unconsMols[i]->getCOMvel(COMvel); |
1075 |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1076 |
} |
1077 |
|
1078 |
for (int i = 0; i < zconsMols.size(); i++){ |
1079 |
if (states[i] == zcsMoving){ |
1080 |
zconsMols[i]->getCOMvel(COMvel); |
1081 |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1082 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1083 |
} |
1084 |
} |
1085 |
|
1086 |
#ifndef IS_MPI |
1087 |
MVzOfMovingMols = MVzOfMovingMols_local; |
1088 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1089 |
#else |
1090 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
1091 |
MPI_SUM, MPI_COMM_WORLD); |
1092 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
1093 |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
1094 |
#endif |
1095 |
|
1096 |
double vzOfMovingMols; |
1097 |
vzOfMovingMols = MVzOfMovingMols / |
1098 |
(totalMassOfUncons + totalMassOfMovingZMols); |
1099 |
|
1100 |
return vzOfMovingMols; |
1101 |
} |
1102 |
|
1103 |
/** |
1104 |
* |
1105 |
*/ |
1106 |
|
1107 |
template<typename T> double ZConstraint<T>::calcSysCOMVel(){ |
1108 |
double COMvel[3]; |
1109 |
double tempMVz_local; |
1110 |
double tempMVz; |
1111 |
double massOfZCons_local; |
1112 |
double massOfZCons; |
1113 |
|
1114 |
|
1115 |
tempMVz_local = 0; |
1116 |
|
1117 |
for (int i = 0 ; i < nMols; i++){ |
1118 |
molecules[i].getCOMvel(COMvel); |
1119 |
tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection]; |
1120 |
} |
1121 |
|
1122 |
massOfZCons_local = 0; |
1123 |
|
1124 |
for (int i = 0; i < (int) (massOfZConsMols.size()); i++){ |
1125 |
massOfZCons_local += massOfZConsMols[i]; |
1126 |
} |
1127 |
#ifndef IS_MPI |
1128 |
massOfZCons = massOfZCons_local; |
1129 |
tempMVz = tempMVz_local; |
1130 |
#else |
1131 |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM, |
1132 |
MPI_COMM_WORLD); |
1133 |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
1134 |
#endif |
1135 |
|
1136 |
return tempMVz / (totalMassOfUncons + massOfZCons); |
1137 |
} |
1138 |
|
1139 |
/** |
1140 |
* |
1141 |
*/ |
1142 |
|
1143 |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1144 |
double force[3]; |
1145 |
double totalForce_local; |
1146 |
double totalForce; |
1147 |
|
1148 |
totalForce_local = 0; |
1149 |
|
1150 |
for (int i = 0; i < nAtoms; i++){ |
1151 |
atoms[i]->getFrc(force); |
1152 |
totalForce_local += force[whichDirection]; |
1153 |
} |
1154 |
|
1155 |
#ifndef IS_MPI |
1156 |
totalForce = totalForce_local; |
1157 |
#else |
1158 |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM, |
1159 |
MPI_COMM_WORLD); |
1160 |
#endif |
1161 |
|
1162 |
return totalForce; |
1163 |
} |
1164 |
|
1165 |
/** |
1166 |
* |
1167 |
*/ |
1168 |
|
1169 |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1170 |
//calculate the number of atoms of moving z-constrained molecules |
1171 |
int nMovingZAtoms_local; |
1172 |
int nMovingZAtoms; |
1173 |
|
1174 |
nMovingZAtoms_local = 0; |
1175 |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
1176 |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
1177 |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1178 |
} |
1179 |
|
1180 |
#ifdef IS_MPI |
1181 |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, |
1182 |
MPI_COMM_WORLD); |
1183 |
#else |
1184 |
nMovingZAtoms = nMovingZAtoms_local; |
1185 |
#endif |
1186 |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1187 |
} |
1188 |
|
1189 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, |
1190 |
Atom* atom, |
1191 |
double totalForce){ |
1192 |
return totalForce / mol->getNAtoms(); |
1193 |
} |
1194 |
|
1195 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, |
1196 |
double totalForce){ |
1197 |
return totalForce / totNumOfMovingAtoms; |
1198 |
} |
1199 |
|
1200 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, |
1201 |
Atom* atom, |
1202 |
double totalForce){ |
1203 |
return totalForce / mol->getNAtoms(); |
1204 |
} |
1205 |
|
1206 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, |
1207 |
double totalForce){ |
1208 |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1209 |
} |
1210 |
|
1211 |
/** |
1212 |
* |
1213 |
*/ |
1214 |
|
1215 |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1216 |
//calculate the number of atoms of moving z-constrained molecules |
1217 |
double massOfMovingZAtoms_local; |
1218 |
double massOfMovingZAtoms; |
1219 |
|
1220 |
massOfMovingZAtoms_local = 0; |
1221 |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
1222 |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
1223 |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1224 |
} |
1225 |
|
1226 |
#ifdef IS_MPI |
1227 |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE, |
1228 |
MPI_SUM, MPI_COMM_WORLD); |
1229 |
#else |
1230 |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1231 |
#endif |
1232 |
totMassOfMovingAtoms = massOfMovingZAtoms + |
1233 |
zconsIntegrator->totalMassOfUncons; |
1234 |
} |
1235 |
|
1236 |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, |
1237 |
Atom* atom, |
1238 |
double totalForce){ |
1239 |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1240 |
} |
1241 |
|
1242 |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom, |
1243 |
double totalForce){ |
1244 |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1245 |
} |
1246 |
|
1247 |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, |
1248 |
Atom* atom, |
1249 |
double totalForce){ |
1250 |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1251 |
} |
1252 |
|
1253 |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, |
1254 |
double totalForce){ |
1255 |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1256 |
} |
1257 |
|
1258 |
template<typename T> void ZConstraint<T>::updateZPos(){ |
1259 |
double curTime; |
1260 |
double COM[3]; |
1261 |
|
1262 |
curTime = info->getTime(); |
1263 |
|
1264 |
for (size_t i = 0; i < zconsMols.size(); i++){ |
1265 |
|
1266 |
if (states[i] == zcsFixed && curTime >= endFixTime[i]){ |
1267 |
zPos[i] += zconsGap; |
1268 |
|
1269 |
if (usingSMD){ |
1270 |
zconsMols[i]->getCOM(COM); |
1271 |
cantPos[i] = COM[whichDirection]; |
1272 |
} |
1273 |
|
1274 |
} |
1275 |
|
1276 |
} |
1277 |
|
1278 |
} |
1279 |
|
1280 |
template<typename T> void ZConstraint<T>::updateCantPos(){ |
1281 |
double curTime; |
1282 |
double dt; |
1283 |
|
1284 |
curTime = info->getTime(); |
1285 |
dt = info->dt; |
1286 |
|
1287 |
for (size_t i = 0; i < zconsMols.size(); i++){ |
1288 |
if (states[i] == zcsMoving){ |
1289 |
cantPos[i] += cantVel[i] * dt; |
1290 |
} |
1291 |
} |
1292 |
|
1293 |
} |