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), |
6 |
< |
indexOfZConsMols(NULL) |
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 |
< |
IndexData* index; |
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 |
< |
//retrieve index of z-constraint molecules |
28 |
< |
data = info->getProperty("zconsindex"); |
17 |
< |
if(!data) { |
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 error: If you use an ZConstraint\n" |
35 |
< |
" , you must set index of z-constraint molecules.\n"); |
36 |
< |
painCave.isFatal = 1; |
37 |
< |
simError(); |
34 |
> |
"ZConstraint Warning: User does not set force substraction policy, " |
35 |
> |
"PolicyByMass is used\n"); |
36 |
> |
painCave.isFatal = 0; |
37 |
> |
simError(); |
38 |
> |
|
39 |
> |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
40 |
|
} |
41 |
|
else{ |
42 |
< |
index = dynamic_cast<IndexData*>(data); |
42 |
> |
policy = dynamic_cast<StringData*>(data); |
43 |
|
|
44 |
< |
if(!index){ |
29 |
< |
|
44 |
> |
if(!policy){ |
45 |
|
sprintf( painCave.errMsg, |
46 |
< |
"ZConstraint error: Can not get property from SimInfo\n"); |
47 |
< |
painCave.isFatal = 1; |
48 |
< |
simError(); |
49 |
< |
|
46 |
> |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
47 |
> |
"PolicyByMass is used\n"); |
48 |
> |
painCave.isFatal = 0; |
49 |
> |
simError(); |
50 |
> |
|
51 |
> |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
52 |
|
} |
53 |
|
else{ |
54 |
< |
|
55 |
< |
indexOfAllZConsMols = index->getIndexData(); |
56 |
< |
|
57 |
< |
//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp) |
58 |
< |
int maxIndex; |
42 |
< |
int minIndex; |
43 |
< |
int totalNumMol; |
44 |
< |
|
45 |
< |
minIndex = indexOfAllZConsMols[0]; |
46 |
< |
if(minIndex < 0){ |
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 error: index is out of range\n"); |
61 |
< |
painCave.isFatal = 1; |
62 |
< |
simError(); |
63 |
< |
} |
64 |
< |
|
53 |
< |
maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
54 |
< |
|
55 |
< |
#ifndef IS_MPI |
56 |
< |
totalNumMol = nMols; |
57 |
< |
#else |
58 |
< |
totalNumMol = mpiSim->getTotNmol(); |
59 |
< |
#endif |
60 |
< |
|
61 |
< |
if(maxIndex > totalNumMol - 1){ |
62 |
< |
sprintf( painCave.errMsg, |
63 |
< |
"ZConstraint error: index is out of range\n"); |
64 |
< |
painCave.isFatal = 1; |
65 |
< |
simError(); |
66 |
< |
|
67 |
< |
} |
68 |
< |
|
60 |
> |
"ZConstraint Warning: unknown force substraction policy, " |
61 |
> |
"average force substraction policy is used\n"); |
62 |
> |
painCave.isFatal = 0; |
63 |
> |
simError(); |
64 |
> |
} |
65 |
|
} |
70 |
– |
|
66 |
|
} |
67 |
|
|
68 |
+ |
|
69 |
|
//retrieve sample time of z-contraint |
70 |
< |
data = info->getProperty("zconstime"); |
70 |
> |
data = info->getProperty(ZCONSTIME_ID); |
71 |
|
|
72 |
|
if(!data) { |
73 |
|
|
95 |
|
|
96 |
|
} |
97 |
|
|
102 |
– |
|
98 |
|
//retrieve output filename of z force |
99 |
< |
data = info->getProperty("zconsfilename"); |
99 |
> |
data = info->getProperty(ZCONSFILENAME_ID); |
100 |
|
if(!data) { |
101 |
|
|
102 |
|
|
109 |
|
} |
110 |
|
else{ |
111 |
|
|
112 |
< |
filename = dynamic_cast<StringData*>(data); |
112 |
> |
filename = dynamic_cast<StringData*>(data); |
113 |
|
|
114 |
|
if(!filename){ |
115 |
|
|
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; |
138 |
– |
double COM[3]; |
268 |
|
|
269 |
|
for(int i = 0; i < nMols; i++){ |
270 |
|
|
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 |
|
} |
292 |
|
} |
293 |
|
|
294 |
|
fz = new double[zconsMols.size()]; |
295 |
+ |
curZPos = new double[zconsMols.size()]; |
296 |
|
indexOfZConsMols = new int [zconsMols.size()]; |
297 |
|
|
298 |
< |
if(!fz || !indexOfZConsMols){ |
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 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
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; |
339 |
|
#ifndef IS_MPI |
340 |
|
totNumOfUnconsAtoms = nUnconsAtoms_local; |
341 |
|
#else |
342 |
< |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
343 |
< |
#endif |
342 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
343 |
> |
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
> |
#endif |
345 |
|
|
346 |
< |
|
346 |
> |
// creat zconsWriter |
347 |
> |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
348 |
|
|
189 |
– |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
190 |
– |
|
349 |
|
if(!fzOut){ |
350 |
|
sprintf( painCave.errMsg, |
351 |
|
"Memory allocation failure in class Zconstraint\n"); |
352 |
|
painCave.isFatal = 1; |
353 |
|
simError(); |
354 |
|
} |
355 |
< |
|
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 |
|
{ |
387 |
|
|
388 |
|
zconsMols.clear(); |
389 |
|
massOfZConsMols.clear(); |
390 |
+ |
zPos.clear(); |
391 |
+ |
kz.clear(); |
392 |
|
|
393 |
|
unconsMols.clear(); |
394 |
|
massOfUnconsMols.clear(); |
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); |
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 || !indexOfZConsMols){ |
447 |
> |
if(!fz || !curZPos || !indexOfZConsMols){ |
448 |
|
sprintf( painCave.errMsg, |
449 |
|
"Memory allocation failure in class Zconstraint\n"); |
450 |
|
painCave.isFatal = 1; |
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 |
< |
/** Function Name: isZConstraintMol |
473 |
< |
** Parameter |
474 |
< |
** Molecule* mol |
475 |
< |
** Return value: |
476 |
< |
** -1, if the molecule is not z-constraint molecule, |
477 |
< |
** other non-negative values, its index in indexOfAllZConsMols vector |
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) |
488 |
|
index = mol->getGlobalIndex(); |
489 |
|
|
490 |
|
low = 0; |
491 |
< |
high = indexOfAllZConsMols.size() - 1; |
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 (indexOfAllZConsMols[mid] == index) |
496 |
> |
if ((*parameters)[mid].zconsIndex == index) |
497 |
|
return mid; |
498 |
< |
else if (indexOfAllZConsMols[mid] > index ) |
498 |
> |
else if ((*parameters)[mid].zconsIndex > index ) |
499 |
|
high = mid -1; |
500 |
|
else |
501 |
|
low = mid + 1; |
504 |
|
return -1; |
505 |
|
} |
506 |
|
|
313 |
– |
/** |
314 |
– |
* Description: |
315 |
– |
* Reset the z coordinates |
316 |
– |
*/ |
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 |
+ |
curZconsTime = zconsTime + info->getTime(); |
514 |
|
|
515 |
|
T::integrate(); |
516 |
|
|
522 |
|
* |
523 |
|
* |
524 |
|
* |
525 |
< |
*/ |
334 |
< |
|
335 |
< |
|
525 |
> |
*/ |
526 |
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
527 |
+ |
double zsys; |
528 |
+ |
double COM[3]; |
529 |
+ |
double force[3]; |
530 |
+ |
double zSysCOMVel; |
531 |
|
|
532 |
|
T::calcForce(calcPot, calcStress); |
533 |
|
|
534 |
< |
if (checkZConsState()) |
534 |
> |
if (checkZConsState()){ |
535 |
> |
|
536 |
> |
#ifdef IS_MPI |
537 |
> |
if(worldRank == 0){ |
538 |
> |
#endif |
539 |
> |
// std::cerr << "\n" |
540 |
> |
// << "*******************************************\n" |
541 |
> |
// << " about to call zeroOutVel()\n" |
542 |
> |
// << "*******************************************\n" |
543 |
> |
// << "\n"; |
544 |
> |
#ifdef IS_MPI |
545 |
> |
} |
546 |
> |
#endif |
547 |
|
zeroOutVel(); |
548 |
|
|
549 |
+ |
#ifdef IS_MPI |
550 |
+ |
if(worldRank == 0){ |
551 |
+ |
#endif |
552 |
+ |
// std::cerr << "\n" |
553 |
+ |
// << "*******************************************\n" |
554 |
+ |
// << " finished zeroOutVel()\n" |
555 |
+ |
// << "*******************************************\n" |
556 |
+ |
// << "\n"; |
557 |
+ |
#ifdef IS_MPI |
558 |
+ |
} |
559 |
+ |
#endif |
560 |
+ |
|
561 |
+ |
forcePolicy->update(); |
562 |
+ |
} |
563 |
+ |
|
564 |
+ |
zsys = calcZSys(); |
565 |
+ |
zSysCOMVel = calcSysCOMVel(); |
566 |
+ |
#ifdef IS_MPI |
567 |
+ |
if(worldRank == 0){ |
568 |
+ |
#endif |
569 |
+ |
// cout << "---------------------------------------------------------------------" <<endl; |
570 |
+ |
// cout << "current time: " << info->getTime() << endl; |
571 |
+ |
// cout << "center of mass at z: " << zsys << endl; |
572 |
+ |
// cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
573 |
+ |
|
574 |
+ |
#ifdef IS_MPI |
575 |
+ |
} |
576 |
+ |
#endif |
577 |
+ |
|
578 |
|
//do zconstraint force; |
579 |
|
if (haveFixedZMols()) |
580 |
|
this->doZconstraintForce(); |
581 |
< |
|
581 |
> |
|
582 |
|
//use harmonical poteintial to move the molecules to the specified positions |
583 |
|
if (haveMovingZMols()) |
584 |
< |
//this->doHarmonic(); |
585 |
< |
|
586 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
587 |
< |
|
584 |
> |
this->doHarmonic(); |
585 |
> |
|
586 |
> |
//write out forces and current positions of z-constraint molecules |
587 |
> |
if(info->getTime() >= curZconsTime){ |
588 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
589 |
> |
zconsMols[i]->getCOM(COM); |
590 |
> |
curZPos[i] = COM[whichDirection]; |
591 |
> |
|
592 |
> |
//if the z-constraint molecule is still moving, just record its force |
593 |
> |
if(states[i] == zcsMoving){ |
594 |
> |
fz[i] = 0; |
595 |
> |
Atom** movingZAtoms; |
596 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
597 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
598 |
> |
movingZAtoms[j]->getFrc(force); |
599 |
> |
fz[i] += force[whichDirection]; |
600 |
> |
} |
601 |
> |
} |
602 |
> |
} |
603 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
604 |
> |
curZconsTime += zconsTime; |
605 |
> |
} |
606 |
> |
|
607 |
> |
zSysCOMVel = calcSysCOMVel(); |
608 |
> |
#ifdef IS_MPI |
609 |
> |
if(worldRank == 0){ |
610 |
> |
#endif |
611 |
> |
// cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
612 |
> |
#ifdef IS_MPI |
613 |
> |
} |
614 |
> |
#endif |
615 |
> |
|
616 |
|
} |
617 |
+ |
|
618 |
+ |
|
619 |
+ |
/** |
620 |
+ |
* |
621 |
+ |
*/ |
622 |
|
|
623 |
|
template<typename T> double ZConstraint<T>::calcZSys() |
624 |
|
{ |
627 |
|
double totalMass; |
628 |
|
double totalMZ_local; |
629 |
|
double totalMZ; |
362 |
– |
double massOfUncons_local; |
630 |
|
double massOfCurMol; |
631 |
|
double COM[3]; |
632 |
|
|
633 |
|
totalMass_local = 0; |
367 |
– |
totalMass = 0; |
634 |
|
totalMZ_local = 0; |
369 |
– |
totalMZ = 0; |
370 |
– |
massOfUncons_local = 0; |
371 |
– |
|
635 |
|
|
636 |
|
for(int i = 0; i < nMols; i++){ |
637 |
|
massOfCurMol = molecules[i].getTotalMass(); |
639 |
|
|
640 |
|
totalMass_local += massOfCurMol; |
641 |
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
642 |
< |
|
380 |
< |
if(isZConstraintMol(&molecules[i]) == -1){ |
381 |
< |
|
382 |
< |
massOfUncons_local += massOfCurMol; |
383 |
< |
} |
384 |
< |
|
642 |
> |
|
643 |
|
} |
644 |
+ |
|
645 |
|
|
387 |
– |
|
646 |
|
#ifdef IS_MPI |
647 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
648 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
649 |
< |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
650 |
< |
#else |
647 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, |
648 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
649 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
650 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
651 |
> |
#else |
652 |
|
totalMass = totalMass_local; |
653 |
|
totalMZ = totalMZ_local; |
654 |
< |
totalMassOfUncons = massOfUncons_local; |
396 |
< |
#endif |
654 |
> |
#endif |
655 |
|
|
656 |
|
double zsys; |
657 |
|
zsys = totalMZ / totalMass; |
670 |
|
|
671 |
|
/** |
672 |
|
* |
415 |
– |
* |
416 |
– |
* |
673 |
|
*/ |
674 |
|
|
675 |
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
677 |
|
Atom** fixedZAtoms; |
678 |
|
double COMvel[3]; |
679 |
|
double vel[3]; |
680 |
< |
|
680 |
> |
double zSysCOMVel; |
681 |
> |
|
682 |
|
//zero out the velocities of center of mass of fixed z-constrained molecules |
683 |
|
|
684 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
685 |
|
|
686 |
< |
if (states[i] == zcsFixed){ |
686 |
> |
if (states[i] == zcsFixed){ |
687 |
|
|
688 |
< |
zconsMols[i]->getCOMvel(COMvel); |
688 |
> |
zconsMols[i]->getCOMvel(COMvel); |
689 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
690 |
> |
|
691 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
692 |
< |
|
692 |
> |
|
693 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
694 |
|
fixedZAtoms[j]->getVel(vel); |
695 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
696 |
< |
fixedZAtoms[j]->setVel(vel); |
695 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
696 |
> |
fixedZAtoms[j]->setVel(vel); |
697 |
|
} |
698 |
< |
|
698 |
> |
|
699 |
> |
zconsMols[i]->getCOMvel(COMvel); |
700 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
701 |
|
} |
441 |
– |
|
442 |
– |
} |
702 |
|
|
703 |
+ |
} |
704 |
+ |
|
705 |
+ |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
706 |
+ |
|
707 |
+ |
zSysCOMVel = calcSysCOMVel(); |
708 |
+ |
#ifdef IS_MPI |
709 |
+ |
if(worldRank == 0){ |
710 |
+ |
#endif |
711 |
+ |
// cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
712 |
+ |
#ifdef IS_MPI |
713 |
+ |
} |
714 |
+ |
#endif |
715 |
+ |
|
716 |
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
717 |
|
double MVzOfMovingMols_local; |
718 |
|
double MVzOfMovingMols; |
727 |
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
728 |
|
} |
729 |
|
|
730 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
459 |
< |
|
730 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
731 |
|
if (states[i] == zcsMoving){ |
732 |
|
zconsMols[i]->getCOMvel(COMvel); |
733 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
734 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
734 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
735 |
|
} |
736 |
< |
|
736 |
> |
|
737 |
|
} |
738 |
|
|
739 |
|
#ifndef IS_MPI |
762 |
|
|
763 |
|
//modify the velocities of moving z-constrained molecuels |
764 |
|
Atom** movingZAtoms; |
765 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
765 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
766 |
|
|
767 |
|
if (states[i] ==zcsMoving){ |
768 |
|
|
769 |
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
770 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
770 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
771 |
|
movingZAtoms[j]->getVel(vel); |
772 |
|
vel[whichDirection] -= vzOfMovingMols; |
773 |
< |
movingZAtoms[j]->setVel(vel); |
503 |
< |
} |
504 |
< |
|
773 |
> |
movingZAtoms[j]->setVel(vel); |
774 |
|
} |
775 |
+ |
|
776 |
+ |
} |
777 |
|
|
778 |
+ |
} |
779 |
+ |
|
780 |
+ |
|
781 |
+ |
zSysCOMVel = calcSysCOMVel(); |
782 |
+ |
#ifdef IS_MPI |
783 |
+ |
if(worldRank == 0){ |
784 |
+ |
#endif |
785 |
+ |
// cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
786 |
+ |
#ifdef IS_MPI |
787 |
|
} |
788 |
+ |
#endif |
789 |
|
|
790 |
|
} |
791 |
|
|
792 |
+ |
/** |
793 |
+ |
* |
794 |
+ |
*/ |
795 |
+ |
|
796 |
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
797 |
|
|
798 |
|
Atom** zconsAtoms; |
801 |
|
double COMvel[3]; |
802 |
|
double COM[3]; |
803 |
|
double force[3]; |
519 |
– |
double zsys; |
804 |
|
|
521 |
– |
int nMovingZMols_local; |
522 |
– |
int nMovingZMols; |
805 |
|
|
524 |
– |
//constrain the molecules which do not reach the specified positions |
806 |
|
|
807 |
< |
zsys = calcZSys(); |
527 |
< |
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
807 |
> |
//constrain the molecules which do not reach the specified positions |
808 |
|
|
809 |
|
//Zero Out the force of z-contrained molecules |
810 |
|
totalFZ_local = 0; |
811 |
|
|
812 |
|
//calculate the total z-contrained force of fixed z-contrained molecules |
813 |
+ |
|
814 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
815 |
< |
|
815 |
> |
|
816 |
|
if (states[i] == zcsFixed){ |
817 |
< |
|
817 |
> |
|
818 |
|
zconsMols[i]->getCOM(COM); |
819 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
820 |
|
|
822 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
823 |
|
zconsAtoms[j]->getFrc(force); |
824 |
|
fz[i] += force[whichDirection]; |
825 |
< |
} |
825 |
> |
} |
826 |
|
totalFZ_local += fz[i]; |
827 |
|
|
828 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
828 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
829 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
830 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
831 |
|
|
832 |
+ |
|
833 |
|
} |
834 |
< |
|
834 |
> |
|
835 |
|
} |
836 |
|
|
837 |
< |
//calculate the number of atoms of moving z-constrained molecules |
554 |
< |
nMovingZMols_local = 0; |
555 |
< |
for(int i = 0; zconsMols.size(); i++){ |
556 |
< |
if(states[i] == zcsMoving) |
557 |
< |
nMovingZMols_local += massOfZConsMols[i]; |
558 |
< |
} |
837 |
> |
//calculate total z-constraint force |
838 |
|
#ifdef IS_MPI |
839 |
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
561 |
– |
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
840 |
|
#else |
841 |
|
totalFZ = totalFZ_local; |
564 |
– |
nMovingZMols = nMovingZMols_local; |
842 |
|
#endif |
843 |
|
|
844 |
+ |
|
845 |
+ |
// apply negative to fixed z-constrained molecues; |
846 |
|
force[0]= 0; |
847 |
|
force[1]= 0; |
848 |
|
force[2]= 0; |
570 |
– |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
849 |
|
|
850 |
< |
//modify the velocites of unconstrained molecules |
850 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
851 |
> |
|
852 |
> |
if (states[i] == zcsFixed){ |
853 |
> |
|
854 |
> |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
855 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
856 |
> |
|
857 |
> |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
858 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
859 |
> |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
860 |
> |
zconsAtoms[j]->addFrc(force); |
861 |
> |
} |
862 |
> |
|
863 |
> |
} |
864 |
> |
|
865 |
> |
} |
866 |
> |
|
867 |
> |
// cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
868 |
> |
// << "total force is " << calcTotalForce() << endl; |
869 |
> |
|
870 |
> |
//calculate the number of atoms of moving z-constrained molecules |
871 |
> |
int nMovingZAtoms_local; |
872 |
> |
int nMovingZAtoms; |
873 |
> |
|
874 |
> |
nMovingZAtoms_local = 0; |
875 |
> |
for(int i = 0; i < zconsMols.size(); i++) |
876 |
> |
if(states[i] == zcsMoving) |
877 |
> |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
878 |
> |
|
879 |
> |
#ifdef IS_MPI |
880 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, |
881 |
> |
MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
882 |
> |
#else |
883 |
> |
nMovingZAtoms = nMovingZAtoms_local; |
884 |
> |
#endif |
885 |
> |
|
886 |
> |
force[0]= 0; |
887 |
> |
force[1]= 0; |
888 |
> |
force[2]= 0; |
889 |
> |
|
890 |
> |
//modify the forces of unconstrained molecules |
891 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
892 |
|
|
893 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
894 |
|
|
895 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
895 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
896 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
897 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
898 |
|
unconsAtoms[j]->addFrc(force); |
899 |
+ |
} |
900 |
|
|
901 |
|
} |
902 |
|
|
903 |
< |
//modify the velocities of moving z-constrained molecules |
903 |
> |
//modify the forces of moving z-constrained molecules |
904 |
|
for(int i = 0; i < zconsMols.size(); i++) { |
905 |
< |
if (states[i] == zcsMoving){ |
906 |
< |
|
907 |
< |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
905 |
> |
if (states[i] == zcsMoving){ |
906 |
> |
|
907 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
908 |
|
|
909 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
910 |
< |
movingZAtoms[j]->addFrc(force); |
911 |
< |
} |
909 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
910 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
911 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
912 |
> |
movingZAtoms[j]->addFrc(force); |
913 |
> |
} |
914 |
> |
} |
915 |
|
} |
916 |
|
|
917 |
< |
// apply negative to fixed z-constrained molecues; |
918 |
< |
force[0]= 0; |
595 |
< |
force[1]= 0; |
596 |
< |
force[2]= 0; |
917 |
> |
//cout << "after substracting z-constraint force from moving molecuels " |
918 |
> |
// << "total force is " << calcTotalForce() << endl; |
919 |
|
|
920 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
920 |
> |
} |
921 |
|
|
922 |
< |
if (states[i] == zcsFixed){ |
923 |
< |
|
924 |
< |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
925 |
< |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
922 |
> |
/** |
923 |
> |
* |
924 |
> |
* |
925 |
> |
*/ |
926 |
> |
|
927 |
> |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
928 |
> |
double force[3]; |
929 |
> |
double harmonicU; |
930 |
> |
double harmonicF; |
931 |
> |
double COM[3]; |
932 |
> |
double diff; |
933 |
> |
double totalFZ_local; |
934 |
> |
double totalFZ; |
935 |
> |
|
936 |
> |
force[0] = 0; |
937 |
> |
force[1] = 0; |
938 |
> |
force[2] = 0; |
939 |
> |
|
940 |
> |
totalFZ_local = 0; |
941 |
> |
|
942 |
> |
for(int i = 0; i < zconsMols.size(); i++) { |
943 |
> |
|
944 |
> |
if (states[i] == zcsMoving){ |
945 |
> |
zconsMols[i]->getCOM(COM); |
946 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
947 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
948 |
> |
|
949 |
> |
diff = COM[whichDirection] -zPos[i]; |
950 |
|
|
951 |
< |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
952 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
953 |
< |
zconsAtoms[j]->addFrc(force); |
954 |
< |
} |
955 |
< |
|
951 |
> |
harmonicU = 0.5 * kz[i] * diff * diff; |
952 |
> |
info->lrPot += harmonicU; |
953 |
> |
|
954 |
> |
harmonicF = - kz[i] * diff; |
955 |
> |
totalFZ_local += harmonicF; |
956 |
> |
|
957 |
> |
//adjust force |
958 |
> |
|
959 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
960 |
> |
|
961 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
962 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
963 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
964 |
> |
movingZAtoms[j]->addFrc(force); |
965 |
> |
} |
966 |
|
} |
611 |
– |
|
612 |
– |
} |
967 |
|
|
968 |
+ |
} |
969 |
+ |
|
970 |
+ |
#ifndef IS_MPI |
971 |
+ |
totalFZ = totalFZ_local; |
972 |
+ |
#else |
973 |
+ |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
974 |
+ |
#endif |
975 |
+ |
|
976 |
+ |
force[0]= 0; |
977 |
+ |
force[1]= 0; |
978 |
+ |
force[2]= 0; |
979 |
+ |
|
980 |
+ |
//modify the forces of unconstrained molecules |
981 |
+ |
for(int i = 0; i < unconsMols.size(); i++){ |
982 |
+ |
|
983 |
+ |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
984 |
+ |
|
985 |
+ |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
986 |
+ |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
987 |
+ |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
988 |
+ |
unconsAtoms[j]->addFrc(force); |
989 |
+ |
} |
990 |
+ |
} |
991 |
+ |
|
992 |
|
} |
993 |
|
|
994 |
+ |
/** |
995 |
+ |
* |
996 |
+ |
*/ |
997 |
+ |
|
998 |
|
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
999 |
|
double COM[3]; |
1000 |
|
double diff; |
1001 |
|
|
1002 |
< |
bool changed; |
1002 |
> |
int changed_local; |
1003 |
> |
int changed; |
1004 |
|
|
1005 |
< |
changed = false; |
1005 |
> |
changed_local = 0; |
1006 |
|
|
1007 |
|
for(int i =0; i < zconsMols.size(); i++){ |
1008 |
|
|
1009 |
|
zconsMols[i]->getCOM(COM); |
1010 |
< |
diff = fabs(COM[whichDirection] - ZPos[i]); |
1011 |
< |
if ( diff <= ztol && states[i] == zcsMoving){ |
1010 |
> |
diff = fabs(COM[whichDirection] - zPos[i]); |
1011 |
> |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
1012 |
|
states[i] = zcsFixed; |
1013 |
< |
changed = true; |
1013 |
> |
changed_local = 1; |
1014 |
|
} |
1015 |
< |
else if ( diff > ztol && states[i] == zcsFixed){ |
1015 |
> |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
1016 |
|
states[i] = zcsMoving; |
1017 |
< |
changed = true; |
1017 |
> |
changed_local = 1; |
1018 |
|
} |
1019 |
|
|
1020 |
|
} |
1021 |
|
|
1022 |
< |
return changed; |
1022 |
> |
#ifndef IS_MPI |
1023 |
> |
changed =changed_local; |
1024 |
> |
#else |
1025 |
> |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1026 |
> |
#endif |
1027 |
> |
|
1028 |
> |
return (changed > 0); |
1029 |
> |
|
1030 |
|
} |
1031 |
|
|
1032 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
643 |
– |
for(int i = 0; i < zconsMols.size(); i++) |
644 |
– |
if (states[i] == zcsFixed) |
645 |
– |
return true; |
1033 |
|
|
1034 |
< |
return false; |
1034 |
> |
int havingFixed_local; |
1035 |
> |
int havingFixed; |
1036 |
> |
|
1037 |
> |
havingFixed_local = 0; |
1038 |
> |
|
1039 |
> |
for(int i = 0; i < zconsMols.size(); i++) |
1040 |
> |
if (states[i] == zcsFixed){ |
1041 |
> |
havingFixed_local = 1; |
1042 |
> |
break; |
1043 |
> |
} |
1044 |
> |
|
1045 |
> |
#ifndef IS_MPI |
1046 |
> |
havingFixed = havingFixed_local; |
1047 |
> |
#else |
1048 |
> |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1049 |
> |
#endif |
1050 |
> |
|
1051 |
> |
return (havingFixed > 0); |
1052 |
|
} |
1053 |
|
|
1054 |
|
|
1056 |
|
* |
1057 |
|
*/ |
1058 |
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1059 |
+ |
|
1060 |
+ |
int havingMoving_local; |
1061 |
+ |
int havingMoving; |
1062 |
+ |
|
1063 |
+ |
havingMoving_local = 0; |
1064 |
+ |
|
1065 |
|
for(int i = 0; i < zconsMols.size(); i++) |
1066 |
< |
if (states[i] == zcsMoving) |
1067 |
< |
return true; |
1066 |
> |
if (states[i] == zcsMoving){ |
1067 |
> |
havingMoving_local = 1; |
1068 |
> |
break; |
1069 |
> |
} |
1070 |
|
|
1071 |
< |
return false; |
1071 |
> |
#ifndef IS_MPI |
1072 |
> |
havingMoving = havingMoving_local; |
1073 |
> |
#else |
1074 |
> |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1075 |
> |
#endif |
1076 |
> |
|
1077 |
> |
return (havingMoving > 0); |
1078 |
|
|
1079 |
< |
} |
1079 |
> |
} |
1080 |
> |
|
1081 |
> |
/** |
1082 |
> |
* |
1083 |
> |
*/ |
1084 |
> |
|
1085 |
> |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1086 |
> |
{ |
1087 |
> |
double MVzOfMovingMols_local; |
1088 |
> |
double MVzOfMovingMols; |
1089 |
> |
double totalMassOfMovingZMols_local; |
1090 |
> |
double totalMassOfMovingZMols; |
1091 |
> |
double COMvel[3]; |
1092 |
> |
|
1093 |
> |
MVzOfMovingMols_local = 0; |
1094 |
> |
totalMassOfMovingZMols_local = 0; |
1095 |
> |
|
1096 |
> |
for(int i =0; i < unconsMols.size(); i++){ |
1097 |
> |
unconsMols[i]->getCOMvel(COMvel); |
1098 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1099 |
> |
} |
1100 |
> |
|
1101 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
1102 |
> |
|
1103 |
> |
if (states[i] == zcsMoving){ |
1104 |
> |
zconsMols[i]->getCOMvel(COMvel); |
1105 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1106 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1107 |
> |
} |
1108 |
> |
|
1109 |
> |
} |
1110 |
> |
|
1111 |
> |
#ifndef IS_MPI |
1112 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
1113 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1114 |
> |
#else |
1115 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1116 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1117 |
> |
#endif |
1118 |
> |
|
1119 |
> |
double vzOfMovingMols; |
1120 |
> |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1121 |
> |
|
1122 |
> |
return vzOfMovingMols; |
1123 |
> |
} |
1124 |
> |
|
1125 |
> |
/** |
1126 |
> |
* |
1127 |
> |
*/ |
1128 |
> |
|
1129 |
> |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1130 |
> |
{ |
1131 |
> |
double COMvel[3]; |
1132 |
> |
double tempMVz_local; |
1133 |
> |
double tempMVz; |
1134 |
> |
double massOfZCons_local; |
1135 |
> |
double massOfZCons; |
1136 |
> |
|
1137 |
> |
|
1138 |
> |
tempMVz_local = 0; |
1139 |
> |
|
1140 |
> |
for(int i =0 ; i < nMols; i++){ |
1141 |
> |
molecules[i].getCOMvel(COMvel); |
1142 |
> |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1143 |
> |
} |
1144 |
> |
|
1145 |
> |
massOfZCons_local = 0; |
1146 |
> |
|
1147 |
> |
for(int i = 0; i < massOfZConsMols.size(); i++){ |
1148 |
> |
massOfZCons_local += massOfZConsMols[i]; |
1149 |
> |
} |
1150 |
> |
#ifndef IS_MPI |
1151 |
> |
massOfZCons = massOfZCons_local; |
1152 |
> |
tempMVz = tempMVz_local; |
1153 |
> |
#else |
1154 |
> |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1155 |
> |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1156 |
> |
#endif |
1157 |
> |
|
1158 |
> |
return tempMVz /(totalMassOfUncons + massOfZCons); |
1159 |
> |
} |
1160 |
> |
|
1161 |
> |
/** |
1162 |
> |
* |
1163 |
> |
*/ |
1164 |
> |
|
1165 |
> |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1166 |
> |
|
1167 |
> |
double force[3]; |
1168 |
> |
double totalForce_local; |
1169 |
> |
double totalForce; |
1170 |
> |
|
1171 |
> |
totalForce_local = 0; |
1172 |
> |
|
1173 |
> |
for(int i = 0; i < nAtoms; i++){ |
1174 |
> |
atoms[i]->getFrc(force); |
1175 |
> |
totalForce_local += force[whichDirection]; |
1176 |
> |
} |
1177 |
> |
|
1178 |
> |
#ifndef IS_MPI |
1179 |
> |
totalForce = totalForce_local; |
1180 |
> |
#else |
1181 |
> |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1182 |
> |
#endif |
1183 |
> |
|
1184 |
> |
return totalForce; |
1185 |
> |
|
1186 |
> |
} |
1187 |
> |
|
1188 |
> |
/** |
1189 |
> |
* |
1190 |
> |
*/ |
1191 |
> |
|
1192 |
> |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1193 |
> |
//calculate the number of atoms of moving z-constrained molecules |
1194 |
> |
int nMovingZAtoms_local; |
1195 |
> |
int nMovingZAtoms; |
1196 |
> |
|
1197 |
> |
nMovingZAtoms_local = 0; |
1198 |
> |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1199 |
> |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1200 |
> |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1201 |
> |
|
1202 |
> |
#ifdef IS_MPI |
1203 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1204 |
> |
#else |
1205 |
> |
nMovingZAtoms = nMovingZAtoms_local; |
1206 |
> |
#endif |
1207 |
> |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1208 |
> |
|
1209 |
> |
#ifdef IS_MPI |
1210 |
> |
if(worldRank == 0){ |
1211 |
> |
#endif |
1212 |
> |
// std::cerr << "\n" |
1213 |
> |
// << "*******************************************\n" |
1214 |
> |
// << " fiished Policy by numbr()\n" |
1215 |
> |
// << "*******************************************\n" |
1216 |
> |
// << "\n"; |
1217 |
> |
#ifdef IS_MPI |
1218 |
> |
} |
1219 |
> |
#endif |
1220 |
> |
} |
1221 |
> |
|
1222 |
> |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1223 |
> |
return totalForce / mol->getNAtoms(); |
1224 |
> |
} |
1225 |
> |
|
1226 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1227 |
> |
return totalForce / totNumOfMovingAtoms; |
1228 |
> |
} |
1229 |
> |
|
1230 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1231 |
> |
return totalForce / mol->getNAtoms(); |
1232 |
> |
} |
1233 |
> |
|
1234 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1235 |
> |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1236 |
> |
} |
1237 |
> |
|
1238 |
> |
/** |
1239 |
> |
* |
1240 |
> |
*/ |
1241 |
> |
|
1242 |
> |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1243 |
> |
//calculate the number of atoms of moving z-constrained molecules |
1244 |
> |
double massOfMovingZAtoms_local; |
1245 |
> |
double massOfMovingZAtoms; |
1246 |
> |
|
1247 |
> |
massOfMovingZAtoms_local = 0; |
1248 |
> |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1249 |
> |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1250 |
> |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1251 |
> |
|
1252 |
> |
#ifdef IS_MPI |
1253 |
> |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1254 |
> |
#else |
1255 |
> |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1256 |
> |
#endif |
1257 |
> |
totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1258 |
> |
} |
1259 |
> |
|
1260 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1261 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1262 |
> |
} |
1263 |
> |
|
1264 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1265 |
> |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1266 |
> |
} |
1267 |
> |
|
1268 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1269 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1270 |
> |
} |
1271 |
> |
|
1272 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1273 |
> |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1274 |
> |
} |
1275 |
> |
|