1 |
#include "Integrator.hpp" |
2 |
#include "simError.h" |
3 |
|
4 |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
: T(theInfo, the_ff), fz(NULL), indexOfZConsMols(NULL) |
6 |
{ |
7 |
|
8 |
//get properties from SimInfo |
9 |
GenericData* data; |
10 |
IndexData* index; |
11 |
DoubleData* sampleTime; |
12 |
StringData* filename; |
13 |
|
14 |
|
15 |
data = info->getProperty("zconsindex"); |
16 |
if(!data) { |
17 |
|
18 |
sprintf( painCave.errMsg, |
19 |
"ZConstraint error: If you use an ZConstraint\n" |
20 |
" , you must set index of z-constraint molecules.\n"); |
21 |
painCave.isFatal = 1; |
22 |
simError(); |
23 |
} |
24 |
else{ |
25 |
index = dynamic_cast<IndexData*>(data); |
26 |
|
27 |
if(!index){ |
28 |
|
29 |
sprintf( painCave.errMsg, |
30 |
"ZConstraint error: Can not get property from SimInfo\n"); |
31 |
painCave.isFatal = 1; |
32 |
simError(); |
33 |
|
34 |
} |
35 |
else{ |
36 |
|
37 |
indexOfAllZConsMols = index->getIndexData(); |
38 |
|
39 |
//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp) |
40 |
int maxIndex; |
41 |
int totalNumMol; |
42 |
|
43 |
maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
44 |
|
45 |
#ifndef IS_MPI |
46 |
totalNumMol = nMols; |
47 |
#else |
48 |
totalNumMol = mpiSim->getTotNmol(); |
49 |
#endif |
50 |
|
51 |
if(maxIndex > totalNumMol - 1){ |
52 |
sprintf( painCave.errMsg, |
53 |
"ZConstraint error: index is out of range\n"); |
54 |
painCave.isFatal = 1; |
55 |
simError(); |
56 |
|
57 |
} |
58 |
|
59 |
} |
60 |
|
61 |
} |
62 |
|
63 |
//retrive sample time of z-contraint |
64 |
data = info->getProperty("zconstime"); |
65 |
|
66 |
if(!data) { |
67 |
|
68 |
sprintf( painCave.errMsg, |
69 |
"ZConstraint error: If you use an ZConstraint\n" |
70 |
" , you must set sample time.\n"); |
71 |
painCave.isFatal = 1; |
72 |
simError(); |
73 |
} |
74 |
else{ |
75 |
|
76 |
sampleTime = dynamic_cast<DoubleData*>(data); |
77 |
|
78 |
if(!sampleTime){ |
79 |
|
80 |
sprintf( painCave.errMsg, |
81 |
"ZConstraint error: Can not get property from SimInfo\n"); |
82 |
painCave.isFatal = 1; |
83 |
simError(); |
84 |
|
85 |
} |
86 |
else{ |
87 |
this->zconsTime = sampleTime->getData(); |
88 |
} |
89 |
|
90 |
} |
91 |
|
92 |
|
93 |
//retrive output filename of z force |
94 |
data = info->getProperty("zconsfilename"); |
95 |
if(!data) { |
96 |
|
97 |
|
98 |
sprintf( painCave.errMsg, |
99 |
"ZConstraint error: If you use an ZConstraint\n" |
100 |
" , you must set output filename of z-force.\n"); |
101 |
painCave.isFatal = 1; |
102 |
simError(); |
103 |
|
104 |
} |
105 |
else{ |
106 |
|
107 |
filename = dynamic_cast<StringData*>(data); |
108 |
|
109 |
if(!filename){ |
110 |
|
111 |
sprintf( painCave.errMsg, |
112 |
"ZConstraint error: Can not get property from SimInfo\n"); |
113 |
painCave.isFatal = 1; |
114 |
simError(); |
115 |
|
116 |
} |
117 |
else{ |
118 |
this->zconsOutput = filename->getData(); |
119 |
} |
120 |
|
121 |
|
122 |
} |
123 |
|
124 |
|
125 |
//calculate reference z coordinate for z-constraint molecules |
126 |
double totalMass_local; |
127 |
double totalMass; |
128 |
double totalMZ_local; |
129 |
double totalMZ; |
130 |
double massOfUncons_local; |
131 |
double massOfCurMol; |
132 |
double COM[3]; |
133 |
|
134 |
totalMass_local = 0; |
135 |
totalMass = 0; |
136 |
totalMZ_local = 0; |
137 |
totalMZ = 0; |
138 |
massOfUncons_local = 0; |
139 |
|
140 |
|
141 |
for(int i = 0; i < nMols; i++){ |
142 |
massOfCurMol = molecules[i].getTotalMass(); |
143 |
molecules[i].getCOM(COM); |
144 |
|
145 |
totalMass_local += massOfCurMol; |
146 |
totalMZ_local += massOfCurMol * COM[2]; |
147 |
|
148 |
if(isZConstraintMol(&molecules[i]) == -1){ |
149 |
|
150 |
massOfUncons_local += massOfCurMol; |
151 |
} |
152 |
|
153 |
} |
154 |
|
155 |
|
156 |
#ifdef IS_MPI |
157 |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
158 |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
159 |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
160 |
#else |
161 |
totalMass = totalMass_local; |
162 |
totalMZ = totalMZ_local; |
163 |
totalMassOfUncons = massOfUncons_local; |
164 |
#endif |
165 |
|
166 |
double zsys; |
167 |
zsys = totalMZ / totalMass; |
168 |
|
169 |
#ifndef IS_MPI |
170 |
for(int i = 0; i < nMols; i++){ |
171 |
|
172 |
if(isZConstraintMol(&molecules[i]) > -1 ){ |
173 |
molecules[i].getCOM(COM); |
174 |
allRefZ.push_back(COM[2] - zsys); |
175 |
} |
176 |
|
177 |
} |
178 |
#else |
179 |
|
180 |
int whichNode; |
181 |
enum CommType { RequestMolZPos, EndOfRequest} status; |
182 |
//int status; |
183 |
double zpos; |
184 |
int localIndex; |
185 |
MPI_Status ierr; |
186 |
int tag = 0; |
187 |
|
188 |
if(worldRank == 0){ |
189 |
|
190 |
int globalIndexOfCurMol; |
191 |
int *MolToProcMap; |
192 |
MolToProcMap = mpiSim->getMolToProcMap(); |
193 |
|
194 |
for(int i = 0; i < indexOfAllZConsMols.size(); i++){ |
195 |
|
196 |
whichNode = MolToProcMap[indexOfAllZConsMols[i]]; |
197 |
globalIndexOfCurMol = indexOfAllZConsMols[i]; |
198 |
|
199 |
if(whichNode == 0){ |
200 |
|
201 |
for(int j = 0; j < nMols; j++) |
202 |
if(molecules[j].getGlobalIndex() == globalIndexOfCurMol){ |
203 |
localIndex = j; |
204 |
break; |
205 |
} |
206 |
|
207 |
molecules[localIndex].getCOM(COM); |
208 |
allRefZ.push_back(COM[2] - zsys); |
209 |
|
210 |
} |
211 |
else{ |
212 |
status = RequestMolZPos; |
213 |
MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
214 |
MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
215 |
MPI_Recv(&zpos, 1, MPI_DOUBLE_PRECISION, whichNode, tag, MPI_COMM_WORLD, &ierr); |
216 |
|
217 |
allRefZ.push_back(zpos - zsys); |
218 |
|
219 |
} |
220 |
|
221 |
} //End of Request Loop |
222 |
|
223 |
//Send ending request message to slave nodes |
224 |
status = EndOfRequest; |
225 |
for(int i =1; i < mpiSim->getNumberProcessors(); i++) |
226 |
MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD); |
227 |
|
228 |
} |
229 |
else{ |
230 |
|
231 |
int whichMol; |
232 |
bool done = false; |
233 |
|
234 |
while (!done){ |
235 |
|
236 |
MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr); |
237 |
|
238 |
switch (status){ |
239 |
|
240 |
case RequestMolZPos : |
241 |
|
242 |
MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr); |
243 |
|
244 |
for(int i = 0; i < nMols; i++) |
245 |
if(molecules[i].getGlobalIndex() == whichMol){ |
246 |
localIndex = i; |
247 |
break; |
248 |
} |
249 |
|
250 |
molecules[localIndex].getCOM(COM); |
251 |
zpos = COM[2]; |
252 |
MPI_Send(&zpos, 1, MPI_DOUBLE_PRECISION, 0, tag, MPI_COMM_WORLD); |
253 |
|
254 |
break; |
255 |
|
256 |
case EndOfRequest : |
257 |
|
258 |
done = true; |
259 |
break; |
260 |
} |
261 |
|
262 |
} |
263 |
|
264 |
} |
265 |
|
266 |
//Brocast the allRefZ to slave nodes; |
267 |
double* allRefZBuf; |
268 |
int nZConsMols; |
269 |
nZConsMols = indexOfAllZConsMols.size(); |
270 |
|
271 |
allRefZBuf = new double[nZConsMols]; |
272 |
|
273 |
if(worldRank == 0){ |
274 |
|
275 |
for(int i = 0; i < nZConsMols; i++) |
276 |
allRefZBuf[i] = allRefZ[i]; |
277 |
} |
278 |
|
279 |
MPI_Bcast(allRefZBuf, nZConsMols, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD); |
280 |
|
281 |
if(worldRank != 0){ |
282 |
|
283 |
for(int i = 0; i < nZConsMols; i++) |
284 |
allRefZ.push_back(allRefZBuf[i]); |
285 |
} |
286 |
|
287 |
delete[] allRefZBuf; |
288 |
#endif |
289 |
|
290 |
|
291 |
#ifdef IS_MPI |
292 |
update(); |
293 |
#else |
294 |
int searchResult; |
295 |
|
296 |
refZ = allRefZ; |
297 |
|
298 |
for(int i = 0; i < nMols; i++){ |
299 |
|
300 |
searchResult = isZConstraintMol(&molecules[i]); |
301 |
|
302 |
if(searchResult > -1){ |
303 |
|
304 |
zconsMols.push_back(&molecules[i]); |
305 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
306 |
|
307 |
molecules[i].getCOM(COM); |
308 |
} |
309 |
else |
310 |
{ |
311 |
|
312 |
unconsMols.push_back(&molecules[i]); |
313 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
314 |
|
315 |
} |
316 |
} |
317 |
|
318 |
fz = new double[zconsMols.size()]; |
319 |
indexOfZConsMols = new int [zconsMols.size()]; |
320 |
|
321 |
if(!fz || !indexOfZConsMols){ |
322 |
sprintf( painCave.errMsg, |
323 |
"Memory allocation failure in class Zconstraint\n"); |
324 |
painCave.isFatal = 1; |
325 |
simError(); |
326 |
} |
327 |
|
328 |
for(int i = 0; i < zconsMols.size(); i++) |
329 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
330 |
|
331 |
#endif |
332 |
|
333 |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
334 |
|
335 |
if(!fzOut){ |
336 |
sprintf( painCave.errMsg, |
337 |
"Memory allocation failure in class Zconstraint\n"); |
338 |
painCave.isFatal = 1; |
339 |
simError(); |
340 |
} |
341 |
|
342 |
fzOut->writeRefZ(indexOfAllZConsMols, allRefZ); |
343 |
} |
344 |
|
345 |
template<typename T> ZConstraint<T>::~ZConstraint() |
346 |
{ |
347 |
if(fz) |
348 |
delete[] fz; |
349 |
|
350 |
if(indexOfZConsMols) |
351 |
delete[] indexOfZConsMols; |
352 |
|
353 |
if(fzOut) |
354 |
delete fzOut; |
355 |
} |
356 |
|
357 |
#ifdef IS_MPI |
358 |
template<typename T> void ZConstraint<T>::update() |
359 |
{ |
360 |
double COM[3]; |
361 |
int index; |
362 |
|
363 |
zconsMols.clear(); |
364 |
massOfZConsMols.clear(); |
365 |
refZ.clear(); |
366 |
|
367 |
unconsMols.clear(); |
368 |
massOfUnconsMols.clear(); |
369 |
|
370 |
|
371 |
//creat zconsMol and unconsMol lists |
372 |
for(int i = 0; i < nMols; i++){ |
373 |
|
374 |
index = isZConstraintMol(&molecules[i]); |
375 |
|
376 |
if(index > -1){ |
377 |
|
378 |
zconsMols.push_back(&molecules[i]); |
379 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
380 |
|
381 |
molecules[i].getCOM(COM); |
382 |
refZ.push_back(allRefZ[index]); |
383 |
} |
384 |
else |
385 |
{ |
386 |
|
387 |
unconsMols.push_back(&molecules[i]); |
388 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
389 |
|
390 |
} |
391 |
} |
392 |
|
393 |
//The reason to declare fz and indexOfZconsMols as pointer to array is |
394 |
// that we want to make the MPI communication simple |
395 |
if(fz) |
396 |
delete[] fz; |
397 |
|
398 |
if(indexOfZConsMols) |
399 |
delete[] indexOfZConsMols; |
400 |
|
401 |
if (zconsMols.size() > 0){ |
402 |
fz = new double[zconsMols.size()]; |
403 |
indexOfZConsMols = new int[zconsMols.size()]; |
404 |
|
405 |
if(!fz || !indexOfZConsMols){ |
406 |
sprintf( painCave.errMsg, |
407 |
"Memory allocation failure in class Zconstraint\n"); |
408 |
painCave.isFatal = 1; |
409 |
simError(); |
410 |
} |
411 |
|
412 |
for(int i = 0; i < zconsMols.size(); i++){ |
413 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
414 |
} |
415 |
|
416 |
} |
417 |
else{ |
418 |
fz = NULL; |
419 |
indexOfZConsMols = NULL; |
420 |
} |
421 |
|
422 |
} |
423 |
|
424 |
#endif |
425 |
|
426 |
/** Function Name: isZConstraintMol |
427 |
** Parameter |
428 |
** Molecule* mol |
429 |
** Return value: |
430 |
** -1, if the molecule is not z-constraint molecule, |
431 |
** other non-negative values, its index in indexOfAllZConsMols vector |
432 |
*/ |
433 |
|
434 |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
435 |
{ |
436 |
int index; |
437 |
int low; |
438 |
int high; |
439 |
int mid; |
440 |
|
441 |
index = mol->getGlobalIndex(); |
442 |
|
443 |
low = 0; |
444 |
high = indexOfAllZConsMols.size() - 1; |
445 |
|
446 |
//Binary Search (we have sorted the array) |
447 |
while(low <= high){ |
448 |
mid = (low + high) /2; |
449 |
if (indexOfAllZConsMols[mid] == index) |
450 |
return mid; |
451 |
else if (indexOfAllZConsMols[mid] > index ) |
452 |
high = mid -1; |
453 |
else |
454 |
low = mid + 1; |
455 |
} |
456 |
|
457 |
return -1; |
458 |
} |
459 |
|
460 |
/** Function Name: integrateStep |
461 |
** Parameter: |
462 |
** int calcPot; |
463 |
** int calcStress; |
464 |
** Description: |
465 |
** Advance One Step. |
466 |
** Memo: |
467 |
** The best way to implement z-constraint is to override integrateStep |
468 |
** Overriding constrainB is not a good choice, since in integrateStep, |
469 |
** constrainB is invoked by below line, |
470 |
** if(nConstrained) constrainB(); |
471 |
** For instance, we would like to apply z-constraint without bond contrain, |
472 |
** In that case, if we override constrainB, Z-constrain method will never be executed; |
473 |
*/ |
474 |
template<typename T> void ZConstraint<T>::integrateStep( int calcPot, int calcStress ) |
475 |
{ |
476 |
T::integrateStep( calcPot, calcStress ); |
477 |
resetZ(); |
478 |
|
479 |
double currZConsTime = 0; |
480 |
|
481 |
//write out forces of z constraint |
482 |
if( info->getTime() >= currZConsTime){ |
483 |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
484 |
} |
485 |
} |
486 |
|
487 |
/** Function Name: resetZ |
488 |
** Description: |
489 |
** Reset the z coordinates |
490 |
*/ |
491 |
|
492 |
template<typename T> void ZConstraint<T>::resetZ() |
493 |
{ |
494 |
double deltaZ; |
495 |
double mzOfZCons; //total sum of m*z of z-constrain molecules |
496 |
double mzOfUncons; //total sum of m*z of unconstrain molecuels; |
497 |
double totalMZOfZCons; |
498 |
double totalMZOfUncons; |
499 |
double COM[3]; |
500 |
double zsys; |
501 |
Atom** zconsAtoms; |
502 |
|
503 |
mzOfZCons = 0; |
504 |
mzOfUncons = 0; |
505 |
|
506 |
for(int i = 0; i < zconsMols.size(); i++){ |
507 |
mzOfZCons += massOfZConsMols[i] * refZ[i]; |
508 |
} |
509 |
|
510 |
#ifdef IS_MPI |
511 |
MPI_Allreduce(&mzOfZCons, &totalMZOfZCons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
512 |
#else |
513 |
totalMZOfZCons = mzOfZCons; |
514 |
#endif |
515 |
|
516 |
for(int i = 0; i < unconsMols.size(); i++){ |
517 |
unconsMols[i]->getCOM(COM); |
518 |
mzOfUncons += massOfUnconsMols[i] * COM[2]; |
519 |
} |
520 |
|
521 |
#ifdef IS_MPI |
522 |
MPI_Allreduce(&mzOfUncons, &totalMZOfUncons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
523 |
#else |
524 |
totalMZOfUncons = mzOfUncons; |
525 |
#endif |
526 |
|
527 |
zsys = (totalMZOfZCons + totalMZOfUncons) /totalMassOfUncons; |
528 |
|
529 |
cout << "current time: " << info->getTime() <<endl; |
530 |
for(int i = 0; i < zconsMols.size(); i++){ |
531 |
|
532 |
zconsMols[i]->getCOM(COM); |
533 |
|
534 |
cout << "global index: " << zconsMols[i]->getGlobalIndex() << "\tZ: " << COM[2] << "\t"; |
535 |
deltaZ = zsys + refZ[i] - COM[2]; |
536 |
cout << "\tdistance: " << COM[2] +deltaZ - zsys; |
537 |
//update z coordinate |
538 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
539 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
540 |
zconsAtoms[j]->setZ(zconsAtoms[j]->getZ() + deltaZ); |
541 |
} |
542 |
|
543 |
//calculate z constrain force |
544 |
fz[i] = massOfZConsMols[i]* deltaZ / dt2; |
545 |
|
546 |
cout << "\tforce: " << fz[i] << endl; |
547 |
} |
548 |
|
549 |
|
550 |
} |