1 |
tim |
658 |
#include "Integrator.hpp" |
2 |
|
|
#include "simError.h" |
3 |
tim |
676 |
#include <cmath> |
4 |
tim |
658 |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
tim |
699 |
: T(theInfo, the_ff), fz(NULL), curZPos(NULL), |
6 |
tim |
701 |
indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
7 |
tim |
658 |
{ |
8 |
|
|
|
9 |
|
|
//get properties from SimInfo |
10 |
|
|
GenericData* data; |
11 |
tim |
682 |
ZConsParaData* zConsParaData; |
12 |
tim |
658 |
DoubleData* sampleTime; |
13 |
tim |
682 |
DoubleData* tolerance; |
14 |
tim |
699 |
StringData* policy; |
15 |
tim |
658 |
StringData* filename; |
16 |
tim |
682 |
double COM[3]; |
17 |
tim |
658 |
|
18 |
tim |
682 |
//by default, the direction of constraint is z |
19 |
|
|
// 0 --> x |
20 |
|
|
// 1 --> y |
21 |
|
|
// 2 --> z |
22 |
|
|
whichDirection = 2; |
23 |
tim |
658 |
|
24 |
tim |
682 |
//estimate the force constant of harmonical potential |
25 |
|
|
double Kb = 1.986E-3 ; //in kcal/K |
26 |
|
|
|
27 |
|
|
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
28 |
|
|
zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
29 |
tim |
676 |
|
30 |
tim |
699 |
//creat force substraction policy |
31 |
|
|
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
32 |
|
|
if(!data){ |
33 |
|
|
sprintf( painCave.errMsg, |
34 |
|
|
"ZConstraint Warning: User does not set force substraction policy, " |
35 |
|
|
"average force substraction policy is used\n"); |
36 |
|
|
painCave.isFatal = 0; |
37 |
|
|
simError(); |
38 |
|
|
|
39 |
|
|
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
40 |
|
|
} |
41 |
|
|
else{ |
42 |
|
|
policy = dynamic_cast<StringData*>(data); |
43 |
tim |
701 |
|
44 |
|
|
if(!policy){ |
45 |
tim |
699 |
sprintf( painCave.errMsg, |
46 |
|
|
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
47 |
|
|
"average force substraction policy is used\n"); |
48 |
|
|
painCave.isFatal = 0; |
49 |
|
|
simError(); |
50 |
|
|
|
51 |
|
|
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
52 |
tim |
701 |
} |
53 |
|
|
else{ |
54 |
|
|
if(policy->getData() == "BYNUMBER") |
55 |
|
|
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
56 |
|
|
else if(policy->getData() == "BYMASS") |
57 |
|
|
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
58 |
|
|
else{ |
59 |
tim |
699 |
sprintf( painCave.errMsg, |
60 |
|
|
"ZConstraint Warning: unknown force substraction policy, " |
61 |
|
|
"average force substraction policy is used\n"); |
62 |
|
|
painCave.isFatal = 0; |
63 |
|
|
simError(); |
64 |
tim |
701 |
} |
65 |
|
|
} |
66 |
tim |
699 |
} |
67 |
|
|
|
68 |
tim |
701 |
|
69 |
tim |
676 |
//retrieve sample time of z-contraint |
70 |
tim |
682 |
data = info->getProperty(ZCONSTIME_ID); |
71 |
tim |
658 |
|
72 |
|
|
if(!data) { |
73 |
|
|
|
74 |
|
|
sprintf( painCave.errMsg, |
75 |
|
|
"ZConstraint error: If you use an ZConstraint\n" |
76 |
|
|
" , you must set sample time.\n"); |
77 |
|
|
painCave.isFatal = 1; |
78 |
|
|
simError(); |
79 |
|
|
} |
80 |
|
|
else{ |
81 |
|
|
|
82 |
|
|
sampleTime = dynamic_cast<DoubleData*>(data); |
83 |
|
|
|
84 |
|
|
if(!sampleTime){ |
85 |
|
|
|
86 |
|
|
sprintf( painCave.errMsg, |
87 |
|
|
"ZConstraint error: Can not get property from SimInfo\n"); |
88 |
|
|
painCave.isFatal = 1; |
89 |
|
|
simError(); |
90 |
|
|
|
91 |
|
|
} |
92 |
|
|
else{ |
93 |
|
|
this->zconsTime = sampleTime->getData(); |
94 |
|
|
} |
95 |
|
|
|
96 |
|
|
} |
97 |
|
|
|
98 |
tim |
676 |
//retrieve output filename of z force |
99 |
tim |
682 |
data = info->getProperty(ZCONSFILENAME_ID); |
100 |
tim |
658 |
if(!data) { |
101 |
|
|
|
102 |
|
|
|
103 |
|
|
sprintf( painCave.errMsg, |
104 |
|
|
"ZConstraint error: If you use an ZConstraint\n" |
105 |
|
|
" , you must set output filename of z-force.\n"); |
106 |
|
|
painCave.isFatal = 1; |
107 |
|
|
simError(); |
108 |
|
|
|
109 |
|
|
} |
110 |
|
|
else{ |
111 |
|
|
|
112 |
tim |
701 |
filename = dynamic_cast<StringData*>(data); |
113 |
tim |
658 |
|
114 |
|
|
if(!filename){ |
115 |
|
|
|
116 |
|
|
sprintf( painCave.errMsg, |
117 |
|
|
"ZConstraint error: Can not get property from SimInfo\n"); |
118 |
|
|
painCave.isFatal = 1; |
119 |
|
|
simError(); |
120 |
|
|
|
121 |
|
|
} |
122 |
|
|
else{ |
123 |
|
|
this->zconsOutput = filename->getData(); |
124 |
|
|
} |
125 |
|
|
|
126 |
|
|
} |
127 |
tim |
682 |
|
128 |
|
|
//retrieve tolerance for z-constraint molecuels |
129 |
|
|
data = info->getProperty(ZCONSTOL_ID); |
130 |
tim |
658 |
|
131 |
tim |
682 |
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 |
tim |
701 |
|
156 |
tim |
682 |
//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 |
tim |
701 |
} |
197 |
tim |
682 |
|
198 |
tim |
693 |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
199 |
tim |
682 |
|
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 |
tim |
701 |
if(!(*parameters)[i].havingZPos){ |
218 |
tim |
682 |
#ifndef IS_MPI |
219 |
tim |
701 |
for(int j = 0; j < nMols; j++){ |
220 |
|
|
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
221 |
|
|
molecules[j].getCOM(COM); |
222 |
|
|
break; |
223 |
tim |
682 |
} |
224 |
tim |
701 |
} |
225 |
tim |
682 |
#else |
226 |
|
|
//query which processor current zconstraint molecule belongs to |
227 |
tim |
701 |
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 |
tim |
682 |
|
236 |
tim |
701 |
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 |
tim |
682 |
|
246 |
tim |
701 |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
247 |
tim |
682 |
#endif |
248 |
|
|
|
249 |
tim |
701 |
(*parameters)[i].zPos = COM[whichDirection]; |
250 |
tim |
682 |
|
251 |
tim |
701 |
sprintf( painCave.errMsg, |
252 |
tim |
682 |
"ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
253 |
|
|
"initial z coornidate will be used \n"); |
254 |
tim |
701 |
painCave.isFatal = 0; |
255 |
|
|
simError(); |
256 |
|
|
|
257 |
|
|
} |
258 |
|
|
} |
259 |
|
|
|
260 |
tim |
682 |
}//end if (!zConsParaData) |
261 |
|
|
}//end if (!data) |
262 |
|
|
|
263 |
|
|
// |
264 |
tim |
658 |
#ifdef IS_MPI |
265 |
|
|
update(); |
266 |
|
|
#else |
267 |
|
|
int searchResult; |
268 |
tim |
676 |
|
269 |
tim |
658 |
for(int i = 0; i < nMols; i++){ |
270 |
|
|
|
271 |
|
|
searchResult = isZConstraintMol(&molecules[i]); |
272 |
|
|
|
273 |
|
|
if(searchResult > -1){ |
274 |
|
|
|
275 |
|
|
zconsMols.push_back(&molecules[i]); |
276 |
|
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
277 |
tim |
682 |
|
278 |
|
|
zPos.push_back((*parameters)[searchResult].zPos); |
279 |
tim |
701 |
cout << "index: "<< (*parameters)[searchResult].zconsIndex |
280 |
|
|
<<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
281 |
|
|
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
282 |
tim |
676 |
|
283 |
tim |
658 |
molecules[i].getCOM(COM); |
284 |
|
|
} |
285 |
|
|
else |
286 |
|
|
{ |
287 |
|
|
|
288 |
|
|
unconsMols.push_back(&molecules[i]); |
289 |
|
|
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
290 |
|
|
|
291 |
|
|
} |
292 |
|
|
} |
293 |
|
|
|
294 |
|
|
fz = new double[zconsMols.size()]; |
295 |
tim |
699 |
curZPos = new double[zconsMols.size()]; |
296 |
tim |
658 |
indexOfZConsMols = new int [zconsMols.size()]; |
297 |
|
|
|
298 |
tim |
699 |
if(!fz || !curZPos || !indexOfZConsMols){ |
299 |
tim |
658 |
sprintf( painCave.errMsg, |
300 |
|
|
"Memory allocation failure in class Zconstraint\n"); |
301 |
|
|
painCave.isFatal = 1; |
302 |
|
|
simError(); |
303 |
|
|
} |
304 |
|
|
|
305 |
tim |
693 |
//determine the states of z-constraint molecules |
306 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
307 |
tim |
658 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
308 |
tim |
693 |
|
309 |
tim |
701 |
zconsMols[i]->getCOM(COM); |
310 |
tim |
693 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
311 |
tim |
701 |
states.push_back(zcsFixed); |
312 |
|
|
else |
313 |
|
|
states.push_back(zcsMoving); |
314 |
tim |
693 |
} |
315 |
tim |
658 |
|
316 |
|
|
#endif |
317 |
tim |
676 |
|
318 |
tim |
693 |
//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 |
tim |
701 |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
329 |
|
|
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
330 |
tim |
693 |
#endif |
331 |
|
|
|
332 |
|
|
|
333 |
tim |
676 |
//get total number of unconstrained atoms |
334 |
|
|
int nUnconsAtoms_local; |
335 |
|
|
nUnconsAtoms_local = 0; |
336 |
|
|
for(int i = 0; i < unconsMols.size(); i++) |
337 |
|
|
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
338 |
|
|
|
339 |
|
|
#ifndef IS_MPI |
340 |
|
|
totNumOfUnconsAtoms = nUnconsAtoms_local; |
341 |
|
|
#else |
342 |
tim |
701 |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
343 |
|
|
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
tim |
693 |
#endif |
345 |
tim |
676 |
|
346 |
tim |
693 |
// creat zconsWriter |
347 |
tim |
699 |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
348 |
tim |
658 |
|
349 |
|
|
if(!fzOut){ |
350 |
|
|
sprintf( painCave.errMsg, |
351 |
|
|
"Memory allocation failure in class Zconstraint\n"); |
352 |
|
|
painCave.isFatal = 1; |
353 |
|
|
simError(); |
354 |
|
|
} |
355 |
tim |
699 |
|
356 |
|
|
forcePolicy->update(); |
357 |
tim |
658 |
} |
358 |
|
|
|
359 |
|
|
template<typename T> ZConstraint<T>::~ZConstraint() |
360 |
|
|
{ |
361 |
|
|
if(fz) |
362 |
|
|
delete[] fz; |
363 |
tim |
699 |
|
364 |
|
|
if(curZPos) |
365 |
|
|
delete[] curZPos; |
366 |
tim |
658 |
|
367 |
|
|
if(indexOfZConsMols) |
368 |
|
|
delete[] indexOfZConsMols; |
369 |
|
|
|
370 |
|
|
if(fzOut) |
371 |
|
|
delete fzOut; |
372 |
tim |
701 |
|
373 |
tim |
699 |
if(forcePolicy) |
374 |
|
|
delete forcePolicy; |
375 |
tim |
658 |
} |
376 |
|
|
|
377 |
tim |
701 |
|
378 |
|
|
/** |
379 |
|
|
* |
380 |
|
|
*/ |
381 |
|
|
|
382 |
tim |
658 |
#ifdef IS_MPI |
383 |
|
|
template<typename T> void ZConstraint<T>::update() |
384 |
|
|
{ |
385 |
|
|
double COM[3]; |
386 |
|
|
int index; |
387 |
|
|
|
388 |
|
|
zconsMols.clear(); |
389 |
|
|
massOfZConsMols.clear(); |
390 |
tim |
682 |
zPos.clear(); |
391 |
|
|
kz.clear(); |
392 |
tim |
658 |
|
393 |
|
|
unconsMols.clear(); |
394 |
|
|
massOfUnconsMols.clear(); |
395 |
|
|
|
396 |
|
|
|
397 |
|
|
//creat zconsMol and unconsMol lists |
398 |
|
|
for(int i = 0; i < nMols; i++){ |
399 |
|
|
|
400 |
|
|
index = isZConstraintMol(&molecules[i]); |
401 |
|
|
|
402 |
|
|
if(index > -1){ |
403 |
|
|
|
404 |
|
|
zconsMols.push_back(&molecules[i]); |
405 |
tim |
682 |
zPos.push_back((*parameters)[index].zPos); |
406 |
tim |
701 |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
407 |
|
|
|
408 |
tim |
658 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
409 |
|
|
|
410 |
|
|
molecules[i].getCOM(COM); |
411 |
|
|
} |
412 |
|
|
else |
413 |
|
|
{ |
414 |
|
|
|
415 |
|
|
unconsMols.push_back(&molecules[i]); |
416 |
|
|
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
417 |
|
|
|
418 |
|
|
} |
419 |
|
|
} |
420 |
tim |
693 |
|
421 |
|
|
//determine the states of z-constraint molecules |
422 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
423 |
tim |
701 |
zconsMols[i]->getCOM(COM); |
424 |
tim |
693 |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
425 |
tim |
701 |
states.push_back(zcsFixed); |
426 |
|
|
else |
427 |
|
|
states.push_back(zcsMoving); |
428 |
tim |
693 |
} |
429 |
|
|
|
430 |
tim |
658 |
|
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 |
tim |
701 |
|
436 |
tim |
699 |
if(curZPos) |
437 |
|
|
delete[] curZPos; |
438 |
tim |
658 |
|
439 |
|
|
if(indexOfZConsMols) |
440 |
|
|
delete[] indexOfZConsMols; |
441 |
|
|
|
442 |
|
|
if (zconsMols.size() > 0){ |
443 |
|
|
fz = new double[zconsMols.size()]; |
444 |
tim |
701 |
curZPos = new double[zconsMols.size()]; |
445 |
tim |
658 |
indexOfZConsMols = new int[zconsMols.size()]; |
446 |
|
|
|
447 |
tim |
699 |
if(!fz || !curZPos || !indexOfZConsMols){ |
448 |
tim |
658 |
sprintf( painCave.errMsg, |
449 |
|
|
"Memory allocation failure in class Zconstraint\n"); |
450 |
|
|
painCave.isFatal = 1; |
451 |
|
|
simError(); |
452 |
|
|
} |
453 |
|
|
|
454 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
455 |
|
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
456 |
|
|
} |
457 |
|
|
|
458 |
|
|
} |
459 |
|
|
else{ |
460 |
|
|
fz = NULL; |
461 |
tim |
701 |
curZPos = NULL; |
462 |
tim |
658 |
indexOfZConsMols = NULL; |
463 |
|
|
} |
464 |
tim |
701 |
|
465 |
tim |
699 |
// |
466 |
|
|
forcePolicy->update(); |
467 |
tim |
658 |
|
468 |
|
|
} |
469 |
|
|
|
470 |
|
|
#endif |
471 |
|
|
|
472 |
tim |
701 |
/** |
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 |
tim |
658 |
*/ |
480 |
|
|
|
481 |
|
|
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
482 |
|
|
{ |
483 |
|
|
int index; |
484 |
|
|
int low; |
485 |
|
|
int high; |
486 |
|
|
int mid; |
487 |
|
|
|
488 |
|
|
index = mol->getGlobalIndex(); |
489 |
|
|
|
490 |
|
|
low = 0; |
491 |
tim |
682 |
high = parameters->size() - 1; |
492 |
tim |
658 |
|
493 |
|
|
//Binary Search (we have sorted the array) |
494 |
|
|
while(low <= high){ |
495 |
|
|
mid = (low + high) /2; |
496 |
tim |
682 |
if ((*parameters)[mid].zconsIndex == index) |
497 |
tim |
658 |
return mid; |
498 |
tim |
682 |
else if ((*parameters)[mid].zconsIndex > index ) |
499 |
tim |
658 |
high = mid -1; |
500 |
|
|
else |
501 |
|
|
low = mid + 1; |
502 |
|
|
} |
503 |
|
|
|
504 |
|
|
return -1; |
505 |
|
|
} |
506 |
|
|
|
507 |
tim |
676 |
template<typename T> void ZConstraint<T>::integrate(){ |
508 |
tim |
658 |
|
509 |
tim |
676 |
//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 |
mmeineke |
711 |
|
513 |
|
|
curZconsTime = zconsTime + info->getTime(); |
514 |
tim |
676 |
|
515 |
|
|
T::integrate(); |
516 |
|
|
|
517 |
tim |
658 |
} |
518 |
tim |
676 |
|
519 |
tim |
658 |
|
520 |
tim |
676 |
/** |
521 |
|
|
* |
522 |
|
|
* |
523 |
|
|
* |
524 |
|
|
* |
525 |
tim |
696 |
*/ |
526 |
tim |
676 |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
527 |
tim |
693 |
double zsys; |
528 |
tim |
699 |
double COM[3]; |
529 |
|
|
double force[3]; |
530 |
tim |
702 |
double zSysCOMVel; |
531 |
tim |
676 |
|
532 |
|
|
T::calcForce(calcPot, calcStress); |
533 |
|
|
|
534 |
tim |
699 |
if (checkZConsState()){ |
535 |
mmeineke |
711 |
|
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 |
tim |
696 |
zeroOutVel(); |
548 |
mmeineke |
711 |
|
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 |
tim |
699 |
} |
563 |
mmeineke |
711 |
|
564 |
tim |
693 |
zsys = calcZSys(); |
565 |
tim |
702 |
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 |
tim |
676 |
|
574 |
tim |
702 |
#ifdef IS_MPI |
575 |
|
|
} |
576 |
|
|
#endif |
577 |
tim |
696 |
|
578 |
tim |
676 |
//do zconstraint force; |
579 |
|
|
if (haveFixedZMols()) |
580 |
|
|
this->doZconstraintForce(); |
581 |
tim |
696 |
|
582 |
tim |
676 |
//use harmonical poteintial to move the molecules to the specified positions |
583 |
|
|
if (haveMovingZMols()) |
584 |
tim |
693 |
this->doHarmonic(); |
585 |
tim |
696 |
|
586 |
tim |
699 |
//write out forces and current positions of z-constraint molecules |
587 |
tim |
701 |
if(info->getTime() >= curZconsTime){ |
588 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
589 |
tim |
699 |
zconsMols[i]->getCOM(COM); |
590 |
tim |
701 |
curZPos[i] = COM[whichDirection]; |
591 |
tim |
699 |
|
592 |
tim |
701 |
//if the z-constraint molecule is still moving, just record its force |
593 |
|
|
if(states[i] == zcsMoving){ |
594 |
tim |
699 |
fz[i] = 0; |
595 |
tim |
701 |
Atom** movingZAtoms; |
596 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
597 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
598 |
tim |
699 |
movingZAtoms[j]->getFrc(force); |
599 |
|
|
fz[i] += force[whichDirection]; |
600 |
tim |
701 |
} |
601 |
|
|
} |
602 |
|
|
} |
603 |
tim |
699 |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
604 |
tim |
701 |
curZconsTime += zconsTime; |
605 |
tim |
699 |
} |
606 |
tim |
702 |
|
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 |
tim |
676 |
} |
617 |
tim |
701 |
|
618 |
|
|
|
619 |
|
|
/** |
620 |
|
|
* |
621 |
|
|
*/ |
622 |
tim |
676 |
|
623 |
|
|
template<typename T> double ZConstraint<T>::calcZSys() |
624 |
tim |
658 |
{ |
625 |
tim |
676 |
//calculate reference z coordinate for z-constraint molecules |
626 |
|
|
double totalMass_local; |
627 |
|
|
double totalMass; |
628 |
|
|
double totalMZ_local; |
629 |
|
|
double totalMZ; |
630 |
|
|
double massOfCurMol; |
631 |
|
|
double COM[3]; |
632 |
tim |
701 |
|
633 |
tim |
676 |
totalMass_local = 0; |
634 |
|
|
totalMZ_local = 0; |
635 |
|
|
|
636 |
|
|
for(int i = 0; i < nMols; i++){ |
637 |
|
|
massOfCurMol = molecules[i].getTotalMass(); |
638 |
|
|
molecules[i].getCOM(COM); |
639 |
|
|
|
640 |
|
|
totalMass_local += massOfCurMol; |
641 |
|
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
642 |
tim |
696 |
|
643 |
tim |
676 |
} |
644 |
tim |
696 |
|
645 |
tim |
676 |
|
646 |
|
|
#ifdef IS_MPI |
647 |
tim |
701 |
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 |
tim |
696 |
#else |
652 |
tim |
676 |
totalMass = totalMass_local; |
653 |
|
|
totalMZ = totalMZ_local; |
654 |
tim |
696 |
#endif |
655 |
mmeineke |
671 |
|
656 |
tim |
658 |
double zsys; |
657 |
tim |
676 |
zsys = totalMZ / totalMass; |
658 |
tim |
658 |
|
659 |
tim |
676 |
return zsys; |
660 |
|
|
} |
661 |
|
|
|
662 |
|
|
/** |
663 |
|
|
* |
664 |
|
|
*/ |
665 |
|
|
template<typename T> void ZConstraint<T>::thermalize( void ){ |
666 |
|
|
|
667 |
|
|
T::thermalize(); |
668 |
|
|
zeroOutVel(); |
669 |
|
|
} |
670 |
|
|
|
671 |
|
|
/** |
672 |
|
|
* |
673 |
|
|
*/ |
674 |
|
|
|
675 |
|
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
676 |
|
|
|
677 |
|
|
Atom** fixedZAtoms; |
678 |
|
|
double COMvel[3]; |
679 |
|
|
double vel[3]; |
680 |
tim |
701 |
double zSysCOMVel; |
681 |
tim |
693 |
|
682 |
tim |
676 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
683 |
|
|
|
684 |
tim |
658 |
for(int i = 0; i < zconsMols.size(); i++){ |
685 |
tim |
676 |
|
686 |
tim |
701 |
if (states[i] == zcsFixed){ |
687 |
tim |
676 |
|
688 |
tim |
701 |
zconsMols[i]->getCOMvel(COMvel); |
689 |
|
|
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
690 |
tim |
693 |
|
691 |
tim |
676 |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
692 |
tim |
701 |
|
693 |
tim |
676 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
694 |
|
|
fixedZAtoms[j]->getVel(vel); |
695 |
tim |
701 |
vel[whichDirection] -= COMvel[whichDirection]; |
696 |
|
|
fixedZAtoms[j]->setVel(vel); |
697 |
tim |
676 |
} |
698 |
tim |
693 |
|
699 |
tim |
701 |
zconsMols[i]->getCOMvel(COMvel); |
700 |
|
|
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
701 |
tim |
676 |
} |
702 |
tim |
701 |
|
703 |
tim |
658 |
} |
704 |
tim |
693 |
|
705 |
tim |
701 |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
706 |
tim |
699 |
|
707 |
tim |
701 |
zSysCOMVel = calcSysCOMVel(); |
708 |
tim |
699 |
#ifdef IS_MPI |
709 |
tim |
701 |
if(worldRank == 0){ |
710 |
tim |
699 |
#endif |
711 |
tim |
701 |
cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
712 |
tim |
699 |
#ifdef IS_MPI |
713 |
|
|
} |
714 |
|
|
#endif |
715 |
tim |
701 |
|
716 |
tim |
676 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
717 |
|
|
double MVzOfMovingMols_local; |
718 |
|
|
double MVzOfMovingMols; |
719 |
|
|
double totalMassOfMovingZMols_local; |
720 |
|
|
double totalMassOfMovingZMols; |
721 |
|
|
|
722 |
|
|
MVzOfMovingMols_local = 0; |
723 |
|
|
totalMassOfMovingZMols_local = 0; |
724 |
tim |
658 |
|
725 |
tim |
676 |
for(int i =0; i < unconsMols.size(); i++){ |
726 |
|
|
unconsMols[i]->getCOMvel(COMvel); |
727 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
728 |
|
|
} |
729 |
|
|
|
730 |
tim |
693 |
for(int i = 0; i < zconsMols.size(); i++){ |
731 |
tim |
676 |
if (states[i] == zcsMoving){ |
732 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
733 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
734 |
tim |
701 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
735 |
tim |
676 |
} |
736 |
tim |
701 |
|
737 |
tim |
676 |
} |
738 |
|
|
|
739 |
|
|
#ifndef IS_MPI |
740 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
741 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
742 |
tim |
658 |
#else |
743 |
tim |
676 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
744 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
745 |
tim |
658 |
#endif |
746 |
|
|
|
747 |
tim |
676 |
double vzOfMovingMols; |
748 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
749 |
|
|
|
750 |
|
|
//modify the velocites of unconstrained molecules |
751 |
|
|
Atom** unconsAtoms; |
752 |
tim |
658 |
for(int i = 0; i < unconsMols.size(); i++){ |
753 |
tim |
676 |
|
754 |
|
|
unconsAtoms = unconsMols[i]->getMyAtoms(); |
755 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
756 |
|
|
unconsAtoms[j]->getVel(vel); |
757 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
758 |
|
|
unconsAtoms[j]->setVel(vel); |
759 |
|
|
} |
760 |
|
|
|
761 |
|
|
} |
762 |
|
|
|
763 |
|
|
//modify the velocities of moving z-constrained molecuels |
764 |
|
|
Atom** movingZAtoms; |
765 |
tim |
693 |
for(int i = 0; i < zconsMols.size(); i++){ |
766 |
tim |
676 |
|
767 |
|
|
if (states[i] ==zcsMoving){ |
768 |
|
|
|
769 |
|
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
770 |
tim |
701 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
771 |
tim |
676 |
movingZAtoms[j]->getVel(vel); |
772 |
|
|
vel[whichDirection] -= vzOfMovingMols; |
773 |
tim |
701 |
movingZAtoms[j]->setVel(vel); |
774 |
|
|
} |
775 |
|
|
|
776 |
tim |
693 |
} |
777 |
tim |
676 |
|
778 |
tim |
693 |
} |
779 |
tim |
676 |
|
780 |
tim |
701 |
|
781 |
|
|
zSysCOMVel = calcSysCOMVel(); |
782 |
tim |
699 |
#ifdef IS_MPI |
783 |
tim |
701 |
if(worldRank == 0){ |
784 |
tim |
699 |
#endif |
785 |
tim |
701 |
cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
786 |
tim |
699 |
#ifdef IS_MPI |
787 |
|
|
} |
788 |
|
|
#endif |
789 |
tim |
693 |
|
790 |
tim |
676 |
} |
791 |
|
|
|
792 |
tim |
701 |
/** |
793 |
|
|
* |
794 |
|
|
*/ |
795 |
|
|
|
796 |
tim |
676 |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
797 |
|
|
|
798 |
|
|
Atom** zconsAtoms; |
799 |
|
|
double totalFZ; |
800 |
|
|
double totalFZ_local; |
801 |
|
|
double COMvel[3]; |
802 |
|
|
double COM[3]; |
803 |
|
|
double force[3]; |
804 |
|
|
|
805 |
|
|
|
806 |
tim |
696 |
|
807 |
tim |
701 |
//constrain the molecules which do not reach the specified positions |
808 |
tim |
676 |
|
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 |
tim |
699 |
|
814 |
tim |
676 |
for(int i = 0; i < zconsMols.size(); i++){ |
815 |
tim |
701 |
|
816 |
tim |
676 |
if (states[i] == zcsFixed){ |
817 |
tim |
701 |
|
818 |
tim |
676 |
zconsMols[i]->getCOM(COM); |
819 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
820 |
|
|
|
821 |
|
|
fz[i] = 0; |
822 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
823 |
|
|
zconsAtoms[j]->getFrc(force); |
824 |
|
|
fz[i] += force[whichDirection]; |
825 |
tim |
701 |
} |
826 |
tim |
676 |
totalFZ_local += fz[i]; |
827 |
|
|
|
828 |
mmeineke |
711 |
// cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
829 |
|
|
// <<"\tcurrent zpos: " << COM[whichDirection] |
830 |
|
|
// << "\tcurrent fz: " <<fz[i] << endl; |
831 |
tim |
676 |
|
832 |
|
|
} |
833 |
tim |
701 |
|
834 |
tim |
676 |
} |
835 |
tim |
699 |
|
836 |
|
|
//calculate total z-constraint force |
837 |
|
|
#ifdef IS_MPI |
838 |
|
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
839 |
|
|
#else |
840 |
|
|
totalFZ = totalFZ_local; |
841 |
|
|
#endif |
842 |
|
|
|
843 |
tim |
701 |
|
844 |
tim |
696 |
// apply negative to fixed z-constrained molecues; |
845 |
|
|
force[0]= 0; |
846 |
|
|
force[1]= 0; |
847 |
|
|
force[2]= 0; |
848 |
tim |
676 |
|
849 |
tim |
696 |
for(int i = 0; i < zconsMols.size(); i++){ |
850 |
|
|
|
851 |
|
|
if (states[i] == zcsFixed){ |
852 |
tim |
701 |
|
853 |
tim |
696 |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
854 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
855 |
|
|
|
856 |
|
|
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
857 |
tim |
701 |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
858 |
tim |
699 |
//force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
859 |
tim |
696 |
zconsAtoms[j]->addFrc(force); |
860 |
|
|
} |
861 |
tim |
701 |
|
862 |
tim |
696 |
} |
863 |
tim |
701 |
|
864 |
tim |
696 |
} |
865 |
|
|
|
866 |
mmeineke |
711 |
// cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
867 |
|
|
// << "total force is " << calcTotalForce() << endl; |
868 |
tim |
699 |
|
869 |
tim |
676 |
//calculate the number of atoms of moving z-constrained molecules |
870 |
tim |
696 |
int nMovingZAtoms_local; |
871 |
|
|
int nMovingZAtoms; |
872 |
tim |
701 |
|
873 |
tim |
696 |
nMovingZAtoms_local = 0; |
874 |
tim |
693 |
for(int i = 0; i < zconsMols.size(); i++) |
875 |
tim |
676 |
if(states[i] == zcsMoving) |
876 |
tim |
701 |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
877 |
tim |
693 |
|
878 |
tim |
658 |
#ifdef IS_MPI |
879 |
tim |
701 |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, |
880 |
|
|
MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
881 |
tim |
658 |
#else |
882 |
tim |
696 |
nMovingZAtoms = nMovingZAtoms_local; |
883 |
tim |
676 |
#endif |
884 |
|
|
|
885 |
|
|
force[0]= 0; |
886 |
|
|
force[1]= 0; |
887 |
|
|
force[2]= 0; |
888 |
|
|
|
889 |
tim |
693 |
//modify the forces of unconstrained molecules |
890 |
tim |
676 |
for(int i = 0; i < unconsMols.size(); i++){ |
891 |
|
|
|
892 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
893 |
|
|
|
894 |
tim |
699 |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
895 |
|
|
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
896 |
|
|
//force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
897 |
tim |
676 |
unconsAtoms[j]->addFrc(force); |
898 |
tim |
699 |
} |
899 |
tim |
676 |
|
900 |
|
|
} |
901 |
|
|
|
902 |
tim |
693 |
//modify the forces of moving z-constrained molecules |
903 |
tim |
676 |
for(int i = 0; i < zconsMols.size(); i++) { |
904 |
tim |
696 |
if (states[i] == zcsMoving){ |
905 |
tim |
701 |
|
906 |
tim |
696 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
907 |
tim |
676 |
|
908 |
tim |
699 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
909 |
|
|
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
910 |
|
|
//force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
911 |
tim |
696 |
movingZAtoms[j]->addFrc(force); |
912 |
tim |
699 |
} |
913 |
tim |
696 |
} |
914 |
tim |
676 |
} |
915 |
|
|
|
916 |
tim |
699 |
//cout << "after substracting z-constraint force from moving molecuels " |
917 |
tim |
701 |
// << "total force is " << calcTotalForce() << endl; |
918 |
tim |
699 |
|
919 |
tim |
676 |
} |
920 |
|
|
|
921 |
tim |
701 |
/** |
922 |
|
|
* |
923 |
|
|
* |
924 |
|
|
*/ |
925 |
|
|
|
926 |
|
|
template<typename T> void ZConstraint<T>::doHarmonic(){ |
927 |
|
|
double force[3]; |
928 |
|
|
double harmonicU; |
929 |
|
|
double harmonicF; |
930 |
|
|
double COM[3]; |
931 |
|
|
double diff; |
932 |
|
|
double totalFZ_local; |
933 |
|
|
double totalFZ; |
934 |
|
|
|
935 |
|
|
force[0] = 0; |
936 |
|
|
force[1] = 0; |
937 |
|
|
force[2] = 0; |
938 |
|
|
|
939 |
|
|
totalFZ_local = 0; |
940 |
|
|
|
941 |
|
|
for(int i = 0; i < zconsMols.size(); i++) { |
942 |
|
|
|
943 |
|
|
if (states[i] == zcsMoving){ |
944 |
|
|
zconsMols[i]->getCOM(COM); |
945 |
mmeineke |
711 |
cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
946 |
|
|
<< "\tcurrent zpos: " << COM[whichDirection] << endl; |
947 |
tim |
701 |
|
948 |
|
|
diff = COM[whichDirection] -zPos[i]; |
949 |
|
|
|
950 |
|
|
harmonicU = 0.5 * kz[i] * diff * diff; |
951 |
|
|
info->lrPot += harmonicU; |
952 |
|
|
|
953 |
|
|
harmonicF = - kz[i] * diff; |
954 |
|
|
totalFZ_local += harmonicF; |
955 |
|
|
|
956 |
|
|
//adjust force |
957 |
|
|
|
958 |
|
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
959 |
|
|
|
960 |
|
|
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
961 |
|
|
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
962 |
|
|
//force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
963 |
|
|
movingZAtoms[j]->addFrc(force); |
964 |
|
|
} |
965 |
|
|
} |
966 |
|
|
|
967 |
|
|
} |
968 |
|
|
|
969 |
|
|
#ifndef IS_MPI |
970 |
|
|
totalFZ = totalFZ_local; |
971 |
|
|
#else |
972 |
|
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
973 |
|
|
#endif |
974 |
|
|
|
975 |
|
|
force[0]= 0; |
976 |
|
|
force[1]= 0; |
977 |
|
|
force[2]= 0; |
978 |
|
|
|
979 |
|
|
//modify the forces of unconstrained molecules |
980 |
|
|
for(int i = 0; i < unconsMols.size(); i++){ |
981 |
|
|
|
982 |
|
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
983 |
|
|
|
984 |
|
|
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
985 |
|
|
force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
986 |
|
|
//force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
987 |
|
|
unconsAtoms[j]->addFrc(force); |
988 |
|
|
} |
989 |
|
|
} |
990 |
|
|
|
991 |
|
|
} |
992 |
|
|
|
993 |
|
|
/** |
994 |
|
|
* |
995 |
|
|
*/ |
996 |
|
|
|
997 |
tim |
676 |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
998 |
|
|
double COM[3]; |
999 |
|
|
double diff; |
1000 |
tim |
658 |
|
1001 |
tim |
699 |
int changed_local; |
1002 |
|
|
int changed; |
1003 |
tim |
701 |
|
1004 |
tim |
699 |
changed_local = 0; |
1005 |
tim |
676 |
|
1006 |
|
|
for(int i =0; i < zconsMols.size(); i++){ |
1007 |
|
|
|
1008 |
tim |
658 |
zconsMols[i]->getCOM(COM); |
1009 |
tim |
682 |
diff = fabs(COM[whichDirection] - zPos[i]); |
1010 |
|
|
if ( diff <= zconsTol && states[i] == zcsMoving){ |
1011 |
tim |
676 |
states[i] = zcsFixed; |
1012 |
tim |
701 |
changed_local = 1; |
1013 |
tim |
676 |
} |
1014 |
tim |
682 |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
1015 |
tim |
676 |
states[i] = zcsMoving; |
1016 |
tim |
701 |
changed_local = 1; |
1017 |
tim |
676 |
} |
1018 |
|
|
|
1019 |
tim |
658 |
} |
1020 |
|
|
|
1021 |
tim |
699 |
#ifndef IS_MPI |
1022 |
|
|
changed =changed_local; |
1023 |
|
|
#else |
1024 |
|
|
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1025 |
|
|
#endif |
1026 |
mmeineke |
711 |
|
1027 |
|
|
return (changed > 0); |
1028 |
tim |
658 |
} |
1029 |
tim |
676 |
|
1030 |
|
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1031 |
tim |
699 |
|
1032 |
|
|
int havingFixed_local; |
1033 |
|
|
int havingFixed; |
1034 |
|
|
|
1035 |
|
|
havingFixed_local = 0; |
1036 |
|
|
|
1037 |
tim |
676 |
for(int i = 0; i < zconsMols.size(); i++) |
1038 |
tim |
699 |
if (states[i] == zcsFixed){ |
1039 |
|
|
havingFixed_local = 1; |
1040 |
tim |
701 |
break; |
1041 |
tim |
699 |
} |
1042 |
tim |
676 |
|
1043 |
tim |
699 |
#ifndef IS_MPI |
1044 |
|
|
havingFixed = havingFixed_local; |
1045 |
|
|
#else |
1046 |
|
|
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1047 |
|
|
#endif |
1048 |
|
|
|
1049 |
|
|
return havingFixed > 0 ? true : false; |
1050 |
tim |
676 |
} |
1051 |
|
|
|
1052 |
|
|
|
1053 |
|
|
/** |
1054 |
|
|
* |
1055 |
|
|
*/ |
1056 |
|
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1057 |
tim |
699 |
|
1058 |
|
|
int havingMoving_local; |
1059 |
|
|
int havingMoving; |
1060 |
|
|
|
1061 |
|
|
havingMoving_local = 0; |
1062 |
|
|
|
1063 |
tim |
676 |
for(int i = 0; i < zconsMols.size(); i++) |
1064 |
tim |
699 |
if (states[i] == zcsMoving){ |
1065 |
|
|
havingMoving_local = 1; |
1066 |
tim |
701 |
break; |
1067 |
tim |
699 |
} |
1068 |
tim |
676 |
|
1069 |
tim |
699 |
#ifndef IS_MPI |
1070 |
|
|
havingMoving = havingMoving_local; |
1071 |
|
|
#else |
1072 |
|
|
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1073 |
|
|
#endif |
1074 |
|
|
|
1075 |
|
|
return havingMoving > 0 ? true : false; |
1076 |
tim |
676 |
|
1077 |
tim |
682 |
} |
1078 |
|
|
|
1079 |
|
|
/** |
1080 |
tim |
701 |
* |
1081 |
|
|
*/ |
1082 |
tim |
682 |
|
1083 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1084 |
tim |
693 |
{ |
1085 |
|
|
double MVzOfMovingMols_local; |
1086 |
|
|
double MVzOfMovingMols; |
1087 |
|
|
double totalMassOfMovingZMols_local; |
1088 |
|
|
double totalMassOfMovingZMols; |
1089 |
|
|
double COMvel[3]; |
1090 |
|
|
|
1091 |
|
|
MVzOfMovingMols_local = 0; |
1092 |
|
|
totalMassOfMovingZMols_local = 0; |
1093 |
|
|
|
1094 |
|
|
for(int i =0; i < unconsMols.size(); i++){ |
1095 |
|
|
unconsMols[i]->getCOMvel(COMvel); |
1096 |
|
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1097 |
|
|
} |
1098 |
|
|
|
1099 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
1100 |
|
|
|
1101 |
|
|
if (states[i] == zcsMoving){ |
1102 |
|
|
zconsMols[i]->getCOMvel(COMvel); |
1103 |
|
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1104 |
tim |
701 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1105 |
tim |
693 |
} |
1106 |
tim |
701 |
|
1107 |
tim |
693 |
} |
1108 |
|
|
|
1109 |
|
|
#ifndef IS_MPI |
1110 |
|
|
MVzOfMovingMols = MVzOfMovingMols_local; |
1111 |
|
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1112 |
|
|
#else |
1113 |
|
|
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1114 |
|
|
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1115 |
|
|
#endif |
1116 |
|
|
|
1117 |
|
|
double vzOfMovingMols; |
1118 |
|
|
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1119 |
|
|
|
1120 |
|
|
return vzOfMovingMols; |
1121 |
|
|
} |
1122 |
|
|
|
1123 |
tim |
701 |
/** |
1124 |
|
|
* |
1125 |
|
|
*/ |
1126 |
tim |
693 |
|
1127 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1128 |
tim |
693 |
{ |
1129 |
|
|
double COMvel[3]; |
1130 |
tim |
699 |
double tempMVz_local; |
1131 |
|
|
double tempMVz; |
1132 |
|
|
double massOfZCons_local; |
1133 |
|
|
double massOfZCons; |
1134 |
|
|
|
1135 |
|
|
|
1136 |
|
|
tempMVz_local = 0; |
1137 |
|
|
|
1138 |
tim |
693 |
for(int i =0 ; i < nMols; i++){ |
1139 |
tim |
696 |
molecules[i].getCOMvel(COMvel); |
1140 |
tim |
701 |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1141 |
tim |
693 |
} |
1142 |
tim |
696 |
|
1143 |
|
|
massOfZCons_local = 0; |
1144 |
tim |
701 |
|
1145 |
tim |
696 |
for(int i = 0; i < massOfZConsMols.size(); i++){ |
1146 |
|
|
massOfZCons_local += massOfZConsMols[i]; |
1147 |
|
|
} |
1148 |
|
|
#ifndef IS_MPI |
1149 |
|
|
massOfZCons = massOfZCons_local; |
1150 |
tim |
699 |
tempMVz = tempMVz_local; |
1151 |
tim |
696 |
#else |
1152 |
|
|
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1153 |
tim |
699 |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1154 |
tim |
696 |
#endif |
1155 |
|
|
|
1156 |
|
|
return tempMVz /(totalMassOfUncons + massOfZCons); |
1157 |
tim |
693 |
} |
1158 |
tim |
696 |
|
1159 |
tim |
701 |
/** |
1160 |
|
|
* |
1161 |
|
|
*/ |
1162 |
|
|
|
1163 |
tim |
696 |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1164 |
|
|
|
1165 |
|
|
double force[3]; |
1166 |
|
|
double totalForce_local; |
1167 |
|
|
double totalForce; |
1168 |
|
|
|
1169 |
|
|
totalForce_local = 0; |
1170 |
|
|
|
1171 |
|
|
for(int i = 0; i < nAtoms; i++){ |
1172 |
|
|
atoms[i]->getFrc(force); |
1173 |
|
|
totalForce_local += force[whichDirection]; |
1174 |
|
|
} |
1175 |
|
|
|
1176 |
|
|
#ifndef IS_MPI |
1177 |
|
|
totalForce = totalForce_local; |
1178 |
|
|
#else |
1179 |
|
|
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1180 |
|
|
#endif |
1181 |
|
|
|
1182 |
|
|
return totalForce; |
1183 |
|
|
|
1184 |
|
|
} |
1185 |
tim |
699 |
|
1186 |
|
|
/** |
1187 |
|
|
* |
1188 |
|
|
*/ |
1189 |
|
|
|
1190 |
|
|
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1191 |
|
|
//calculate the number of atoms of moving z-constrained molecules |
1192 |
|
|
int nMovingZAtoms_local; |
1193 |
|
|
int nMovingZAtoms; |
1194 |
tim |
701 |
|
1195 |
tim |
699 |
nMovingZAtoms_local = 0; |
1196 |
|
|
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1197 |
|
|
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1198 |
tim |
701 |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1199 |
tim |
699 |
|
1200 |
|
|
#ifdef IS_MPI |
1201 |
|
|
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1202 |
|
|
#else |
1203 |
|
|
nMovingZAtoms = nMovingZAtoms_local; |
1204 |
|
|
#endif |
1205 |
|
|
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1206 |
mmeineke |
711 |
|
1207 |
|
|
#ifdef IS_MPI |
1208 |
|
|
if(worldRank == 0){ |
1209 |
|
|
#endif |
1210 |
|
|
std::cerr << "\n" |
1211 |
|
|
<< "*******************************************\n" |
1212 |
|
|
<< " fiished Policy by numbr()\n" |
1213 |
|
|
<< "*******************************************\n" |
1214 |
|
|
<< "\n"; |
1215 |
|
|
#ifdef IS_MPI |
1216 |
|
|
} |
1217 |
|
|
#endif |
1218 |
tim |
699 |
} |
1219 |
|
|
|
1220 |
tim |
701 |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1221 |
tim |
699 |
return totalForce / mol->getNAtoms(); |
1222 |
|
|
} |
1223 |
|
|
|
1224 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1225 |
|
|
return totalForce / totNumOfMovingAtoms; |
1226 |
|
|
} |
1227 |
|
|
|
1228 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1229 |
|
|
return totalForce / mol->getNAtoms(); |
1230 |
|
|
} |
1231 |
|
|
|
1232 |
|
|
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1233 |
|
|
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1234 |
|
|
} |
1235 |
|
|
|
1236 |
|
|
/** |
1237 |
|
|
* |
1238 |
|
|
*/ |
1239 |
|
|
|
1240 |
|
|
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1241 |
|
|
//calculate the number of atoms of moving z-constrained molecules |
1242 |
|
|
double massOfMovingZAtoms_local; |
1243 |
|
|
double massOfMovingZAtoms; |
1244 |
tim |
701 |
|
1245 |
tim |
699 |
massOfMovingZAtoms_local = 0; |
1246 |
|
|
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1247 |
|
|
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1248 |
tim |
701 |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1249 |
tim |
699 |
|
1250 |
|
|
#ifdef IS_MPI |
1251 |
|
|
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1252 |
|
|
#else |
1253 |
|
|
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1254 |
|
|
#endif |
1255 |
|
|
totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1256 |
|
|
} |
1257 |
|
|
|
1258 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1259 |
|
|
return totalForce * atom->getMass() / mol->getTotalMass(); |
1260 |
|
|
} |
1261 |
|
|
|
1262 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1263 |
|
|
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1264 |
|
|
} |
1265 |
|
|
|
1266 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1267 |
|
|
return totalForce * atom->getMass() / mol->getTotalMass(); |
1268 |
|
|
} |
1269 |
|
|
|
1270 |
|
|
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1271 |
|
|
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1272 |
|
|
} |
1273 |
|
|
|