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