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