1 |
#include "Integrator.hpp" |
2 |
#include "simError.h" |
3 |
#include <math.h> |
4 |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
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 |
10 |
GenericData* data; |
11 |
ZConsParaData* zConsParaData; |
12 |
DoubleData* sampleTime; |
13 |
DoubleData* tolerance; |
14 |
StringData* policy; |
15 |
StringData* filename; |
16 |
double COM[3]; |
17 |
|
18 |
//by default, the direction of constraint is z |
19 |
// 0 --> x |
20 |
// 1 --> y |
21 |
// 2 --> z |
22 |
whichDirection = 2; |
23 |
|
24 |
//estimate the force constant of harmonical potential |
25 |
double Kb = 1.986E-3 ; //in kcal/K |
26 |
|
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 |
|
73 |
if(!data) { |
74 |
|
75 |
sprintf( painCave.errMsg, |
76 |
"ZConstraint error: If you use an ZConstraint\n" |
77 |
" , you must set sample time.\n"); |
78 |
painCave.isFatal = 1; |
79 |
simError(); |
80 |
} |
81 |
else{ |
82 |
|
83 |
sampleTime = dynamic_cast<DoubleData*>(data); |
84 |
|
85 |
if(!sampleTime){ |
86 |
|
87 |
sprintf( painCave.errMsg, |
88 |
"ZConstraint error: Can not get property from SimInfo\n"); |
89 |
painCave.isFatal = 1; |
90 |
simError(); |
91 |
|
92 |
} |
93 |
else{ |
94 |
this->zconsTime = sampleTime->getData(); |
95 |
} |
96 |
|
97 |
} |
98 |
|
99 |
//retrieve output filename of z force |
100 |
data = info->getProperty(ZCONSFILENAME_ID); |
101 |
if(!data) { |
102 |
|
103 |
|
104 |
sprintf( painCave.errMsg, |
105 |
"ZConstraint error: If you use an ZConstraint\n" |
106 |
" , you must set output filename of z-force.\n"); |
107 |
painCave.isFatal = 1; |
108 |
simError(); |
109 |
|
110 |
} |
111 |
else{ |
112 |
|
113 |
filename = dynamic_cast<StringData*>(data); |
114 |
|
115 |
if(!filename){ |
116 |
|
117 |
sprintf( painCave.errMsg, |
118 |
"ZConstraint error: Can not get property from SimInfo\n"); |
119 |
painCave.isFatal = 1; |
120 |
simError(); |
121 |
|
122 |
} |
123 |
else{ |
124 |
this->zconsOutput = filename->getData(); |
125 |
} |
126 |
|
127 |
} |
128 |
|
129 |
//retrieve tolerance for z-constraint molecuels |
130 |
data = info->getProperty(ZCONSTOL_ID); |
131 |
|
132 |
if(!data) { |
133 |
|
134 |
sprintf( painCave.errMsg, |
135 |
"ZConstraint error: can not get tolerance \n"); |
136 |
painCave.isFatal = 1; |
137 |
simError(); |
138 |
} |
139 |
else{ |
140 |
|
141 |
tolerance = dynamic_cast<DoubleData*>(data); |
142 |
|
143 |
if(!tolerance){ |
144 |
|
145 |
sprintf( painCave.errMsg, |
146 |
"ZConstraint error: Can not get property from SimInfo\n"); |
147 |
painCave.isFatal = 1; |
148 |
simError(); |
149 |
|
150 |
} |
151 |
else{ |
152 |
this->zconsTol = tolerance->getData(); |
153 |
} |
154 |
|
155 |
} |
156 |
|
157 |
//retrieve index of z-constraint molecules |
158 |
data = info->getProperty(ZCONSPARADATA_ID); |
159 |
if(!data) { |
160 |
|
161 |
sprintf( painCave.errMsg, |
162 |
"ZConstraint error: If you use an ZConstraint\n" |
163 |
" , you must set index of z-constraint molecules.\n"); |
164 |
painCave.isFatal = 1; |
165 |
simError(); |
166 |
} |
167 |
else{ |
168 |
|
169 |
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
170 |
|
171 |
if(!zConsParaData){ |
172 |
|
173 |
sprintf( painCave.errMsg, |
174 |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
175 |
painCave.isFatal = 1; |
176 |
simError(); |
177 |
|
178 |
} |
179 |
else{ |
180 |
|
181 |
parameters = zConsParaData->getData(); |
182 |
|
183 |
//check the range of zconsIndex |
184 |
//and the minimum value of index is the first one (we already sorted the data) |
185 |
//the maximum value of index is the last one |
186 |
|
187 |
int maxIndex; |
188 |
int minIndex; |
189 |
int totalNumMol; |
190 |
|
191 |
minIndex = (*parameters)[0].zconsIndex; |
192 |
if(minIndex < 0){ |
193 |
sprintf( painCave.errMsg, |
194 |
"ZConstraint error: index is out of range\n"); |
195 |
painCave.isFatal = 1; |
196 |
simError(); |
197 |
} |
198 |
|
199 |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
200 |
|
201 |
#ifndef IS_MPI |
202 |
totalNumMol = nMols; |
203 |
#else |
204 |
totalNumMol = mpiSim->getTotNmol(); |
205 |
#endif |
206 |
|
207 |
if(maxIndex > totalNumMol - 1){ |
208 |
sprintf( painCave.errMsg, |
209 |
"ZConstraint error: index is out of range\n"); |
210 |
painCave.isFatal = 1; |
211 |
simError(); |
212 |
} |
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 < (int)(parameters->size()); i++){ |
217 |
|
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; |
224 |
} |
225 |
} |
226 |
#else |
227 |
//query which processor current zconstraint molecule belongs to |
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 |
} |
246 |
|
247 |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
248 |
#endif |
249 |
|
250 |
(*parameters)[i].zPos = COM[whichDirection]; |
251 |
|
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 |
|
261 |
}//end if (!zConsParaData) |
262 |
}//end if (!data) |
263 |
|
264 |
// |
265 |
#ifdef IS_MPI |
266 |
update(); |
267 |
#else |
268 |
int searchResult; |
269 |
|
270 |
for(int i = 0; i < nMols; i++){ |
271 |
|
272 |
searchResult = isZConstraintMol(&molecules[i]); |
273 |
|
274 |
if(searchResult > -1){ |
275 |
|
276 |
zconsMols.push_back(&molecules[i]); |
277 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
278 |
|
279 |
zPos.push_back((*parameters)[searchResult].zPos); |
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 |
287 |
{ |
288 |
|
289 |
unconsMols.push_back(&molecules[i]); |
290 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
291 |
|
292 |
} |
293 |
} |
294 |
|
295 |
fz = new double[zconsMols.size()]; |
296 |
curZPos = new double[zconsMols.size()]; |
297 |
indexOfZConsMols = new int [zconsMols.size()]; |
298 |
|
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 |
//determine the states of z-constraint molecules |
307 |
for(int i = 0; i < (int)(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 < (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, |
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; |
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, |
343 |
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
#endif |
345 |
|
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 |
{ |
375 |
double COM[3]; |
376 |
int index; |
377 |
|
378 |
zconsMols.clear(); |
379 |
massOfZConsMols.clear(); |
380 |
zPos.clear(); |
381 |
kz.clear(); |
382 |
|
383 |
unconsMols.clear(); |
384 |
massOfUnconsMols.clear(); |
385 |
|
386 |
|
387 |
//creat zconsMol and unconsMol lists |
388 |
for(int i = 0; i < nMols; i++){ |
389 |
|
390 |
index = isZConstraintMol(&molecules[i]); |
391 |
|
392 |
if(index > -1){ |
393 |
|
394 |
zconsMols.push_back(&molecules[i]); |
395 |
zPos.push_back((*parameters)[index].zPos); |
396 |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
397 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
398 |
|
399 |
molecules[i].getCOM(COM); |
400 |
} |
401 |
else |
402 |
{ |
403 |
|
404 |
unconsMols.push_back(&molecules[i]); |
405 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
406 |
|
407 |
} |
408 |
} |
409 |
|
410 |
//determine the states of z-constraint molecules |
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); |
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 || !curZPos || !indexOfZConsMols){ |
437 |
sprintf( painCave.errMsg, |
438 |
"Memory allocation failure in class Zconstraint\n"); |
439 |
painCave.isFatal = 1; |
440 |
simError(); |
441 |
} |
442 |
|
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; |
451 |
indexOfZConsMols = NULL; |
452 |
} |
453 |
|
454 |
// |
455 |
forcePolicy->update(); |
456 |
|
457 |
} |
458 |
|
459 |
#endif |
460 |
|
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) |
471 |
{ |
472 |
int index; |
473 |
int low; |
474 |
int high; |
475 |
int mid; |
476 |
|
477 |
index = mol->getGlobalIndex(); |
478 |
|
479 |
low = 0; |
480 |
high = parameters->size() - 1; |
481 |
|
482 |
//Binary Search (we have sorted the array) |
483 |
while(low <= high){ |
484 |
mid = (low + high) /2; |
485 |
if ((*parameters)[mid].zconsIndex == index) |
486 |
return mid; |
487 |
else if ((*parameters)[mid].zconsIndex > index ) |
488 |
high = mid -1; |
489 |
else |
490 |
low = mid + 1; |
491 |
} |
492 |
|
493 |
return -1; |
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 |
|
516 |
} |
517 |
|
518 |
|
519 |
/** |
520 |
* |
521 |
* |
522 |
* |
523 |
* |
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(); |
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 |
|
556 |
//use harmonical poteintial to move the molecules to the specified positions |
557 |
if (haveMovingZMols()) |
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 < (int)(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 |
{ |
598 |
//calculate reference z coordinate for z-constraint molecules |
599 |
double totalMass_local; |
600 |
double totalMass; |
601 |
double totalMZ_local; |
602 |
double totalMZ; |
603 |
double massOfCurMol; |
604 |
double COM[3]; |
605 |
|
606 |
totalMass_local = 0; |
607 |
totalMZ_local = 0; |
608 |
|
609 |
for(int i = 0; i < nMols; i++){ |
610 |
massOfCurMol = molecules[i].getTotalMass(); |
611 |
molecules[i].getCOM(COM); |
612 |
|
613 |
totalMass_local += massOfCurMol; |
614 |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
615 |
|
616 |
} |
617 |
|
618 |
|
619 |
#ifdef IS_MPI |
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 |
#endif |
628 |
|
629 |
double zsys; |
630 |
zsys = totalMZ / totalMass; |
631 |
|
632 |
return zsys; |
633 |
} |
634 |
|
635 |
/** |
636 |
* |
637 |
*/ |
638 |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
639 |
|
640 |
T::thermalize(); |
641 |
zeroOutVel(); |
642 |
} |
643 |
|
644 |
/** |
645 |
* |
646 |
*/ |
647 |
|
648 |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
649 |
|
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 < (int)(zconsMols.size()); i++){ |
658 |
|
659 |
if (states[i] == zcsFixed){ |
660 |
|
661 |
zconsMols[i]->getCOMvel(COMvel); |
662 |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
663 |
|
664 |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
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); |
670 |
} |
671 |
|
672 |
zconsMols[i]->getCOMvel(COMvel); |
673 |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
674 |
} |
675 |
|
676 |
} |
677 |
|
678 |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
679 |
|
680 |
zSysCOMVel = calcSysCOMVel(); |
681 |
#ifdef IS_MPI |
682 |
if(worldRank == 0){ |
683 |
#endif |
684 |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
685 |
#ifdef IS_MPI |
686 |
} |
687 |
#endif |
688 |
|
689 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
690 |
double MVzOfMovingMols_local; |
691 |
double MVzOfMovingMols; |
692 |
double totalMassOfMovingZMols_local; |
693 |
double totalMassOfMovingZMols; |
694 |
|
695 |
MVzOfMovingMols_local = 0; |
696 |
totalMassOfMovingZMols_local = 0; |
697 |
|
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 < (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]; |
708 |
} |
709 |
|
710 |
} |
711 |
|
712 |
#ifndef IS_MPI |
713 |
MVzOfMovingMols = MVzOfMovingMols_local; |
714 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
715 |
#else |
716 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
717 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
718 |
#endif |
719 |
|
720 |
double vzOfMovingMols; |
721 |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
722 |
|
723 |
//modify the velocites of unconstrained molecules |
724 |
Atom** unconsAtoms; |
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++){ |
729 |
unconsAtoms[j]->getVel(vel); |
730 |
vel[whichDirection] -= vzOfMovingMols; |
731 |
unconsAtoms[j]->setVel(vel); |
732 |
} |
733 |
|
734 |
} |
735 |
|
736 |
//modify the velocities of moving z-constrained molecuels |
737 |
Atom** movingZAtoms; |
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++){ |
744 |
movingZAtoms[j]->getVel(vel); |
745 |
vel[whichDirection] -= vzOfMovingMols; |
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; |
772 |
double totalFZ; |
773 |
double totalFZ_local; |
774 |
double COM[3]; |
775 |
double force[3]; |
776 |
|
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 |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
788 |
|
789 |
if (states[i] == zcsFixed){ |
790 |
|
791 |
zconsMols[i]->getCOM(COM); |
792 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
793 |
|
794 |
fz[i] = 0; |
795 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
796 |
zconsAtoms[j]->getFrc(force); |
797 |
fz[i] += force[whichDirection]; |
798 |
} |
799 |
totalFZ_local += fz[i]; |
800 |
|
801 |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
802 |
// <<"\tcurrent zpos: " << COM[whichDirection] |
803 |
// << "\tcurrent fz: " <<fz[i] << endl; |
804 |
|
805 |
|
806 |
} |
807 |
|
808 |
} |
809 |
|
810 |
//calculate total z-constraint force |
811 |
#ifdef IS_MPI |
812 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
813 |
#else |
814 |
totalFZ = totalFZ_local; |
815 |
#endif |
816 |
|
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 < (int)(zconsMols.size()); i++){ |
824 |
|
825 |
if (states[i] == zcsFixed){ |
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]); |
833 |
zconsAtoms[j]->addFrc(force); |
834 |
} |
835 |
|
836 |
} |
837 |
|
838 |
} |
839 |
|
840 |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
841 |
// << "total force is " << calcTotalForce() << endl; |
842 |
|
843 |
|
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 < (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); |
856 |
unconsAtoms[j]->addFrc(force); |
857 |
} |
858 |
|
859 |
} |
860 |
|
861 |
//modify the forces of moving z-constrained molecules |
862 |
for(int i = 0; i < (int)(zconsMols.size()); i++) { |
863 |
if (states[i] == zcsMoving){ |
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); |
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 |
} |
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 |
|
968 |
changed_local = 0; |
969 |
|
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; |
977 |
} |
978 |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
979 |
states[i] = zcsMoving; |
980 |
changed_local = 1; |
981 |
} |
982 |
|
983 |
} |
984 |
|
985 |
#ifndef IS_MPI |
986 |
changed =changed_local; |
987 |
#else |
988 |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
989 |
#endif |
990 |
|
991 |
return (changed > 0); |
992 |
|
993 |
} |
994 |
|
995 |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
996 |
|
997 |
int havingFixed_local; |
998 |
int havingFixed; |
999 |
|
1000 |
havingFixed_local = 0; |
1001 |
|
1002 |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1003 |
if (states[i] == zcsFixed){ |
1004 |
havingFixed_local = 1; |
1005 |
break; |
1006 |
} |
1007 |
|
1008 |
#ifndef IS_MPI |
1009 |
havingFixed = havingFixed_local; |
1010 |
#else |
1011 |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1012 |
#endif |
1013 |
|
1014 |
return (havingFixed > 0); |
1015 |
} |
1016 |
|
1017 |
|
1018 |
/** |
1019 |
* |
1020 |
*/ |
1021 |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1022 |
|
1023 |
int havingMoving_local; |
1024 |
int havingMoving; |
1025 |
|
1026 |
havingMoving_local = 0; |
1027 |
|
1028 |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1029 |
if (states[i] == zcsMoving){ |
1030 |
havingMoving_local = 1; |
1031 |
break; |
1032 |
} |
1033 |
|
1034 |
#ifndef IS_MPI |
1035 |
havingMoving = havingMoving_local; |
1036 |
#else |
1037 |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1038 |
#endif |
1039 |
|
1040 |
return (havingMoving > 0); |
1041 |
|
1042 |
} |
1043 |
|
1044 |
/** |
1045 |
* |
1046 |
*/ |
1047 |
|
1048 |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1049 |
{ |
1050 |
double MVzOfMovingMols_local; |
1051 |
double MVzOfMovingMols; |
1052 |
double totalMassOfMovingZMols_local; |
1053 |
double totalMassOfMovingZMols; |
1054 |
double COMvel[3]; |
1055 |
|
1056 |
MVzOfMovingMols_local = 0; |
1057 |
totalMassOfMovingZMols_local = 0; |
1058 |
|
1059 |
for(int i =0; i < unconsMols.size(); i++){ |
1060 |
unconsMols[i]->getCOMvel(COMvel); |
1061 |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1062 |
} |
1063 |
|
1064 |
for(int i = 0; i < zconsMols.size(); i++){ |
1065 |
|
1066 |
if (states[i] == zcsMoving){ |
1067 |
zconsMols[i]->getCOMvel(COMvel); |
1068 |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1069 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1070 |
} |
1071 |
|
1072 |
} |
1073 |
|
1074 |
#ifndef IS_MPI |
1075 |
MVzOfMovingMols = MVzOfMovingMols_local; |
1076 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1077 |
#else |
1078 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1079 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1080 |
#endif |
1081 |
|
1082 |
double vzOfMovingMols; |
1083 |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1084 |
|
1085 |
return vzOfMovingMols; |
1086 |
} |
1087 |
|
1088 |
/** |
1089 |
* |
1090 |
*/ |
1091 |
|
1092 |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1093 |
{ |
1094 |
double COMvel[3]; |
1095 |
double tempMVz_local; |
1096 |
double tempMVz; |
1097 |
double massOfZCons_local; |
1098 |
double massOfZCons; |
1099 |
|
1100 |
|
1101 |
tempMVz_local = 0; |
1102 |
|
1103 |
for(int i =0 ; i < nMols; i++){ |
1104 |
molecules[i].getCOMvel(COMvel); |
1105 |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1106 |
} |
1107 |
|
1108 |
massOfZCons_local = 0; |
1109 |
|
1110 |
for(int i = 0; i < (int)(massOfZConsMols.size()); i++){ |
1111 |
massOfZCons_local += massOfZConsMols[i]; |
1112 |
} |
1113 |
#ifndef IS_MPI |
1114 |
massOfZCons = massOfZCons_local; |
1115 |
tempMVz = tempMVz_local; |
1116 |
#else |
1117 |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1118 |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1119 |
#endif |
1120 |
|
1121 |
return tempMVz /(totalMassOfUncons + massOfZCons); |
1122 |
} |
1123 |
|
1124 |
/** |
1125 |
* |
1126 |
*/ |
1127 |
|
1128 |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1129 |
|
1130 |
double force[3]; |
1131 |
double totalForce_local; |
1132 |
double totalForce; |
1133 |
|
1134 |
totalForce_local = 0; |
1135 |
|
1136 |
for(int i = 0; i < nAtoms; i++){ |
1137 |
atoms[i]->getFrc(force); |
1138 |
totalForce_local += force[whichDirection]; |
1139 |
} |
1140 |
|
1141 |
#ifndef IS_MPI |
1142 |
totalForce = totalForce_local; |
1143 |
#else |
1144 |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1145 |
#endif |
1146 |
|
1147 |
return totalForce; |
1148 |
|
1149 |
} |
1150 |
|
1151 |
/** |
1152 |
* |
1153 |
*/ |
1154 |
|
1155 |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1156 |
//calculate the number of atoms of moving z-constrained molecules |
1157 |
int nMovingZAtoms_local; |
1158 |
int nMovingZAtoms; |
1159 |
|
1160 |
nMovingZAtoms_local = 0; |
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(); |
1164 |
|
1165 |
#ifdef IS_MPI |
1166 |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1167 |
#else |
1168 |
nMovingZAtoms = nMovingZAtoms_local; |
1169 |
#endif |
1170 |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1171 |
} |
1172 |
|
1173 |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1174 |
return totalForce / mol->getNAtoms(); |
1175 |
} |
1176 |
|
1177 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1178 |
return totalForce / totNumOfMovingAtoms; |
1179 |
} |
1180 |
|
1181 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1182 |
return totalForce / mol->getNAtoms(); |
1183 |
} |
1184 |
|
1185 |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1186 |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1187 |
} |
1188 |
|
1189 |
/** |
1190 |
* |
1191 |
*/ |
1192 |
|
1193 |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1194 |
//calculate the number of atoms of moving z-constrained molecules |
1195 |
double massOfMovingZAtoms_local; |
1196 |
double massOfMovingZAtoms; |
1197 |
|
1198 |
massOfMovingZAtoms_local = 0; |
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(); |
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 + zconsIntegrator->totalMassOfUncons; |
1209 |
} |
1210 |
|
1211 |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1212 |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1213 |
} |
1214 |
|
1215 |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1216 |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1217 |
} |
1218 |
|
1219 |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1220 |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1221 |
} |
1222 |
|
1223 |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1224 |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1225 |
} |
1226 |
|