| 1 |
#include "Integrator.hpp" |
| 2 |
#include "simError.h" |
| 3 |
#include <cmath> |
| 4 |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
| 5 |
: T(theInfo, the_ff), fz(NULL), |
| 6 |
indexOfZConsMols(NULL) |
| 7 |
{ |
| 8 |
|
| 9 |
//get properties from SimInfo |
| 10 |
GenericData* data; |
| 11 |
ZConsParaData* zConsParaData; |
| 12 |
DoubleData* sampleTime; |
| 13 |
DoubleData* tolerance; |
| 14 |
StringData* filename; |
| 15 |
double COM[3]; |
| 16 |
|
| 17 |
//by default, the direction of constraint is z |
| 18 |
// 0 --> x |
| 19 |
// 1 --> y |
| 20 |
// 2 --> z |
| 21 |
whichDirection = 2; |
| 22 |
|
| 23 |
//estimate the force constant of harmonical potential |
| 24 |
double Kb = 1.986E-3 ; //in kcal/K |
| 25 |
|
| 26 |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
| 27 |
zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
| 28 |
|
| 29 |
//retrieve sample time of z-contraint |
| 30 |
data = info->getProperty(ZCONSTIME_ID); |
| 31 |
|
| 32 |
if(!data) { |
| 33 |
|
| 34 |
sprintf( painCave.errMsg, |
| 35 |
"ZConstraint error: If you use an ZConstraint\n" |
| 36 |
" , you must set sample time.\n"); |
| 37 |
painCave.isFatal = 1; |
| 38 |
simError(); |
| 39 |
} |
| 40 |
else{ |
| 41 |
|
| 42 |
sampleTime = dynamic_cast<DoubleData*>(data); |
| 43 |
|
| 44 |
if(!sampleTime){ |
| 45 |
|
| 46 |
sprintf( painCave.errMsg, |
| 47 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 48 |
painCave.isFatal = 1; |
| 49 |
simError(); |
| 50 |
|
| 51 |
} |
| 52 |
else{ |
| 53 |
this->zconsTime = sampleTime->getData(); |
| 54 |
} |
| 55 |
|
| 56 |
} |
| 57 |
|
| 58 |
//retrieve output filename of z force |
| 59 |
data = info->getProperty(ZCONSFILENAME_ID); |
| 60 |
if(!data) { |
| 61 |
|
| 62 |
|
| 63 |
sprintf( painCave.errMsg, |
| 64 |
"ZConstraint error: If you use an ZConstraint\n" |
| 65 |
" , you must set output filename of z-force.\n"); |
| 66 |
painCave.isFatal = 1; |
| 67 |
simError(); |
| 68 |
|
| 69 |
} |
| 70 |
else{ |
| 71 |
|
| 72 |
filename = dynamic_cast<StringData*>(data); |
| 73 |
|
| 74 |
if(!filename){ |
| 75 |
|
| 76 |
sprintf( painCave.errMsg, |
| 77 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 78 |
painCave.isFatal = 1; |
| 79 |
simError(); |
| 80 |
|
| 81 |
} |
| 82 |
else{ |
| 83 |
this->zconsOutput = filename->getData(); |
| 84 |
} |
| 85 |
|
| 86 |
|
| 87 |
} |
| 88 |
|
| 89 |
//retrieve tolerance for z-constraint molecuels |
| 90 |
data = info->getProperty(ZCONSTOL_ID); |
| 91 |
|
| 92 |
if(!data) { |
| 93 |
|
| 94 |
sprintf( painCave.errMsg, |
| 95 |
"ZConstraint error: can not get tolerance \n"); |
| 96 |
painCave.isFatal = 1; |
| 97 |
simError(); |
| 98 |
} |
| 99 |
else{ |
| 100 |
|
| 101 |
tolerance = dynamic_cast<DoubleData*>(data); |
| 102 |
|
| 103 |
if(!tolerance){ |
| 104 |
|
| 105 |
sprintf( painCave.errMsg, |
| 106 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 107 |
painCave.isFatal = 1; |
| 108 |
simError(); |
| 109 |
|
| 110 |
} |
| 111 |
else{ |
| 112 |
this->zconsTol = tolerance->getData(); |
| 113 |
} |
| 114 |
|
| 115 |
} |
| 116 |
|
| 117 |
//retrieve index of z-constraint molecules |
| 118 |
data = info->getProperty(ZCONSPARADATA_ID); |
| 119 |
if(!data) { |
| 120 |
|
| 121 |
sprintf( painCave.errMsg, |
| 122 |
"ZConstraint error: If you use an ZConstraint\n" |
| 123 |
" , you must set index of z-constraint molecules.\n"); |
| 124 |
painCave.isFatal = 1; |
| 125 |
simError(); |
| 126 |
} |
| 127 |
else{ |
| 128 |
|
| 129 |
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
| 130 |
|
| 131 |
if(!zConsParaData){ |
| 132 |
|
| 133 |
sprintf( painCave.errMsg, |
| 134 |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
| 135 |
painCave.isFatal = 1; |
| 136 |
simError(); |
| 137 |
|
| 138 |
} |
| 139 |
else{ |
| 140 |
|
| 141 |
parameters = zConsParaData->getData(); |
| 142 |
|
| 143 |
//check the range of zconsIndex |
| 144 |
//and the minimum value of index is the first one (we already sorted the data) |
| 145 |
//the maximum value of index is the last one |
| 146 |
|
| 147 |
int maxIndex; |
| 148 |
int minIndex; |
| 149 |
int totalNumMol; |
| 150 |
|
| 151 |
minIndex = (*parameters)[0].zconsIndex; |
| 152 |
if(minIndex < 0){ |
| 153 |
sprintf( painCave.errMsg, |
| 154 |
"ZConstraint error: index is out of range\n"); |
| 155 |
painCave.isFatal = 1; |
| 156 |
simError(); |
| 157 |
} |
| 158 |
|
| 159 |
maxIndex = (*parameters)[parameters->size()].zconsIndex; |
| 160 |
|
| 161 |
#ifndef IS_MPI |
| 162 |
totalNumMol = nMols; |
| 163 |
#else |
| 164 |
totalNumMol = mpiSim->getTotNmol(); |
| 165 |
#endif |
| 166 |
|
| 167 |
if(maxIndex > totalNumMol - 1){ |
| 168 |
sprintf( painCave.errMsg, |
| 169 |
"ZConstraint error: index is out of range\n"); |
| 170 |
painCave.isFatal = 1; |
| 171 |
simError(); |
| 172 |
} |
| 173 |
|
| 174 |
//if user does not specify the zpos for the zconstraint molecule |
| 175 |
//its initial z coordinate will be used as default |
| 176 |
for(int i = 0; i < parameters->size(); i++){ |
| 177 |
|
| 178 |
if(!(*parameters)[i].havingZPos){ |
| 179 |
|
| 180 |
#ifndef IS_MPI |
| 181 |
for(int j = 0; j < nMols; j++){ |
| 182 |
if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
| 183 |
molecules[i].getCOM(COM); |
| 184 |
break; |
| 185 |
} |
| 186 |
} |
| 187 |
#else |
| 188 |
//query which processor current zconstraint molecule belongs to |
| 189 |
int *MolToProcMap; |
| 190 |
int whichNode; |
| 191 |
double initZPos; |
| 192 |
MolToProcMap = mpiSim->getMolToProcMap(); |
| 193 |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
| 194 |
|
| 195 |
//broadcast the zpos of current z-contraint molecule |
| 196 |
//the node which contain this |
| 197 |
|
| 198 |
if (worldRank == whichNode ){ |
| 199 |
|
| 200 |
for(int i = 0; i < nMols; i++) |
| 201 |
if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
| 202 |
molecules[i].getCOM(COM); |
| 203 |
break; |
| 204 |
} |
| 205 |
|
| 206 |
} |
| 207 |
|
| 208 |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
| 209 |
#endif |
| 210 |
|
| 211 |
(*parameters)[i].zPos = COM[whichDirection]; |
| 212 |
|
| 213 |
sprintf( painCave.errMsg, |
| 214 |
"ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
| 215 |
"initial z coornidate will be used \n"); |
| 216 |
painCave.isFatal = 0; |
| 217 |
simError(); |
| 218 |
|
| 219 |
} |
| 220 |
} |
| 221 |
|
| 222 |
}//end if (!zConsParaData) |
| 223 |
}//end if (!data) |
| 224 |
|
| 225 |
// |
| 226 |
#ifdef IS_MPI |
| 227 |
update(); |
| 228 |
#else |
| 229 |
int searchResult; |
| 230 |
|
| 231 |
for(int i = 0; i < nMols; i++){ |
| 232 |
|
| 233 |
searchResult = isZConstraintMol(&molecules[i]); |
| 234 |
|
| 235 |
if(searchResult > -1){ |
| 236 |
|
| 237 |
zconsMols.push_back(&molecules[i]); |
| 238 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 239 |
|
| 240 |
zPos.push_back((*parameters)[searchResult].zPos); |
| 241 |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
| 242 |
|
| 243 |
molecules[i].getCOM(COM); |
| 244 |
} |
| 245 |
else |
| 246 |
{ |
| 247 |
|
| 248 |
unconsMols.push_back(&molecules[i]); |
| 249 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 250 |
|
| 251 |
} |
| 252 |
} |
| 253 |
|
| 254 |
fz = new double[zconsMols.size()]; |
| 255 |
indexOfZConsMols = new int [zconsMols.size()]; |
| 256 |
|
| 257 |
if(!fz || !indexOfZConsMols){ |
| 258 |
sprintf( painCave.errMsg, |
| 259 |
"Memory allocation failure in class Zconstraint\n"); |
| 260 |
painCave.isFatal = 1; |
| 261 |
simError(); |
| 262 |
} |
| 263 |
|
| 264 |
for(int i = 0; i < zconsMols.size(); i++) |
| 265 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 266 |
|
| 267 |
#endif |
| 268 |
|
| 269 |
//get total number of unconstrained atoms |
| 270 |
int nUnconsAtoms_local; |
| 271 |
nUnconsAtoms_local = 0; |
| 272 |
for(int i = 0; i < unconsMols.size(); i++) |
| 273 |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
| 274 |
|
| 275 |
#ifndef IS_MPI |
| 276 |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
| 277 |
#else |
| 278 |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 279 |
#endif |
| 280 |
|
| 281 |
checkZConsState(); |
| 282 |
|
| 283 |
// |
| 284 |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
| 285 |
|
| 286 |
if(!fzOut){ |
| 287 |
sprintf( painCave.errMsg, |
| 288 |
"Memory allocation failure in class Zconstraint\n"); |
| 289 |
painCave.isFatal = 1; |
| 290 |
simError(); |
| 291 |
} |
| 292 |
|
| 293 |
} |
| 294 |
|
| 295 |
template<typename T> ZConstraint<T>::~ZConstraint() |
| 296 |
{ |
| 297 |
if(fz) |
| 298 |
delete[] fz; |
| 299 |
|
| 300 |
if(indexOfZConsMols) |
| 301 |
delete[] indexOfZConsMols; |
| 302 |
|
| 303 |
if(fzOut) |
| 304 |
delete fzOut; |
| 305 |
} |
| 306 |
|
| 307 |
#ifdef IS_MPI |
| 308 |
template<typename T> void ZConstraint<T>::update() |
| 309 |
{ |
| 310 |
double COM[3]; |
| 311 |
int index; |
| 312 |
|
| 313 |
zconsMols.clear(); |
| 314 |
massOfZConsMols.clear(); |
| 315 |
zPos.clear(); |
| 316 |
kz.clear(); |
| 317 |
|
| 318 |
unconsMols.clear(); |
| 319 |
massOfUnconsMols.clear(); |
| 320 |
|
| 321 |
|
| 322 |
//creat zconsMol and unconsMol lists |
| 323 |
for(int i = 0; i < nMols; i++){ |
| 324 |
|
| 325 |
index = isZConstraintMol(&molecules[i]); |
| 326 |
|
| 327 |
if(index > -1){ |
| 328 |
|
| 329 |
zconsMols.push_back(&molecules[i]); |
| 330 |
zPos.push_back((*parameters)[index].zPos); |
| 331 |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
| 332 |
|
| 333 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 334 |
|
| 335 |
molecules[i].getCOM(COM); |
| 336 |
} |
| 337 |
else |
| 338 |
{ |
| 339 |
|
| 340 |
unconsMols.push_back(&molecules[i]); |
| 341 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 342 |
|
| 343 |
} |
| 344 |
} |
| 345 |
|
| 346 |
//The reason to declare fz and indexOfZconsMols as pointer to array is |
| 347 |
// that we want to make the MPI communication simple |
| 348 |
if(fz) |
| 349 |
delete[] fz; |
| 350 |
|
| 351 |
if(indexOfZConsMols) |
| 352 |
delete[] indexOfZConsMols; |
| 353 |
|
| 354 |
if (zconsMols.size() > 0){ |
| 355 |
fz = new double[zconsMols.size()]; |
| 356 |
indexOfZConsMols = new int[zconsMols.size()]; |
| 357 |
|
| 358 |
if(!fz || !indexOfZConsMols){ |
| 359 |
sprintf( painCave.errMsg, |
| 360 |
"Memory allocation failure in class Zconstraint\n"); |
| 361 |
painCave.isFatal = 1; |
| 362 |
simError(); |
| 363 |
} |
| 364 |
|
| 365 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 366 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 367 |
} |
| 368 |
|
| 369 |
} |
| 370 |
else{ |
| 371 |
fz = NULL; |
| 372 |
indexOfZConsMols = NULL; |
| 373 |
} |
| 374 |
|
| 375 |
} |
| 376 |
|
| 377 |
#endif |
| 378 |
|
| 379 |
/** Function Name: isZConstraintMol |
| 380 |
** Parameter |
| 381 |
** Molecule* mol |
| 382 |
** Return value: |
| 383 |
** -1, if the molecule is not z-constraint molecule, |
| 384 |
** other non-negative values, its index in indexOfAllZConsMols vector |
| 385 |
*/ |
| 386 |
|
| 387 |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
| 388 |
{ |
| 389 |
int index; |
| 390 |
int low; |
| 391 |
int high; |
| 392 |
int mid; |
| 393 |
|
| 394 |
index = mol->getGlobalIndex(); |
| 395 |
|
| 396 |
low = 0; |
| 397 |
high = parameters->size() - 1; |
| 398 |
|
| 399 |
//Binary Search (we have sorted the array) |
| 400 |
while(low <= high){ |
| 401 |
mid = (low + high) /2; |
| 402 |
if ((*parameters)[mid].zconsIndex == index) |
| 403 |
return mid; |
| 404 |
else if ((*parameters)[mid].zconsIndex > index ) |
| 405 |
high = mid -1; |
| 406 |
else |
| 407 |
low = mid + 1; |
| 408 |
} |
| 409 |
|
| 410 |
return -1; |
| 411 |
} |
| 412 |
|
| 413 |
/** |
| 414 |
* Description: |
| 415 |
* Reset the z coordinates |
| 416 |
*/ |
| 417 |
template<typename T> void ZConstraint<T>::integrate(){ |
| 418 |
|
| 419 |
//zero out the velocities of center of mass of unconstrained molecules |
| 420 |
//and the velocities of center of mass of every single z-constrained molecueles |
| 421 |
zeroOutVel(); |
| 422 |
|
| 423 |
T::integrate(); |
| 424 |
|
| 425 |
} |
| 426 |
|
| 427 |
|
| 428 |
/** |
| 429 |
* |
| 430 |
* |
| 431 |
* |
| 432 |
* |
| 433 |
*/ |
| 434 |
|
| 435 |
|
| 436 |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
| 437 |
|
| 438 |
T::calcForce(calcPot, calcStress); |
| 439 |
|
| 440 |
if (checkZConsState()) |
| 441 |
zeroOutVel(); |
| 442 |
|
| 443 |
//do zconstraint force; |
| 444 |
if (haveFixedZMols()) |
| 445 |
this->doZconstraintForce(); |
| 446 |
|
| 447 |
//use harmonical poteintial to move the molecules to the specified positions |
| 448 |
if (haveMovingZMols()) |
| 449 |
//this->doHarmonic(); |
| 450 |
|
| 451 |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
| 452 |
|
| 453 |
} |
| 454 |
|
| 455 |
template<typename T> double ZConstraint<T>::calcZSys() |
| 456 |
{ |
| 457 |
//calculate reference z coordinate for z-constraint molecules |
| 458 |
double totalMass_local; |
| 459 |
double totalMass; |
| 460 |
double totalMZ_local; |
| 461 |
double totalMZ; |
| 462 |
double massOfUncons_local; |
| 463 |
double massOfCurMol; |
| 464 |
double COM[3]; |
| 465 |
|
| 466 |
totalMass_local = 0; |
| 467 |
totalMass = 0; |
| 468 |
totalMZ_local = 0; |
| 469 |
totalMZ = 0; |
| 470 |
massOfUncons_local = 0; |
| 471 |
|
| 472 |
|
| 473 |
for(int i = 0; i < nMols; i++){ |
| 474 |
massOfCurMol = molecules[i].getTotalMass(); |
| 475 |
molecules[i].getCOM(COM); |
| 476 |
|
| 477 |
totalMass_local += massOfCurMol; |
| 478 |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
| 479 |
|
| 480 |
if(isZConstraintMol(&molecules[i]) == -1){ |
| 481 |
|
| 482 |
massOfUncons_local += massOfCurMol; |
| 483 |
} |
| 484 |
|
| 485 |
} |
| 486 |
|
| 487 |
|
| 488 |
#ifdef IS_MPI |
| 489 |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 490 |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 491 |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 492 |
#else |
| 493 |
totalMass = totalMass_local; |
| 494 |
totalMZ = totalMZ_local; |
| 495 |
totalMassOfUncons = massOfUncons_local; |
| 496 |
#endif |
| 497 |
|
| 498 |
double zsys; |
| 499 |
zsys = totalMZ / totalMass; |
| 500 |
|
| 501 |
return zsys; |
| 502 |
} |
| 503 |
|
| 504 |
/** |
| 505 |
* |
| 506 |
*/ |
| 507 |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
| 508 |
|
| 509 |
T::thermalize(); |
| 510 |
zeroOutVel(); |
| 511 |
} |
| 512 |
|
| 513 |
/** |
| 514 |
* |
| 515 |
* |
| 516 |
* |
| 517 |
*/ |
| 518 |
|
| 519 |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
| 520 |
|
| 521 |
Atom** fixedZAtoms; |
| 522 |
double COMvel[3]; |
| 523 |
double vel[3]; |
| 524 |
|
| 525 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
| 526 |
|
| 527 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 528 |
|
| 529 |
if (states[i] == zcsFixed){ |
| 530 |
|
| 531 |
zconsMols[i]->getCOMvel(COMvel); |
| 532 |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
| 533 |
|
| 534 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
| 535 |
fixedZAtoms[j]->getVel(vel); |
| 536 |
vel[whichDirection] -= COMvel[whichDirection]; |
| 537 |
fixedZAtoms[j]->setVel(vel); |
| 538 |
} |
| 539 |
|
| 540 |
} |
| 541 |
|
| 542 |
} |
| 543 |
|
| 544 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
| 545 |
double MVzOfMovingMols_local; |
| 546 |
double MVzOfMovingMols; |
| 547 |
double totalMassOfMovingZMols_local; |
| 548 |
double totalMassOfMovingZMols; |
| 549 |
|
| 550 |
MVzOfMovingMols_local = 0; |
| 551 |
totalMassOfMovingZMols_local = 0; |
| 552 |
|
| 553 |
for(int i =0; i < unconsMols.size(); i++){ |
| 554 |
unconsMols[i]->getCOMvel(COMvel); |
| 555 |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
| 556 |
} |
| 557 |
|
| 558 |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
| 559 |
|
| 560 |
if (states[i] == zcsMoving){ |
| 561 |
zconsMols[i]->getCOMvel(COMvel); |
| 562 |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
| 563 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
| 564 |
} |
| 565 |
|
| 566 |
} |
| 567 |
|
| 568 |
#ifndef IS_MPI |
| 569 |
MVzOfMovingMols = MVzOfMovingMols_local; |
| 570 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
| 571 |
#else |
| 572 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 573 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 574 |
#endif |
| 575 |
|
| 576 |
double vzOfMovingMols; |
| 577 |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
| 578 |
|
| 579 |
//modify the velocites of unconstrained molecules |
| 580 |
Atom** unconsAtoms; |
| 581 |
for(int i = 0; i < unconsMols.size(); i++){ |
| 582 |
|
| 583 |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
| 584 |
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
| 585 |
unconsAtoms[j]->getVel(vel); |
| 586 |
vel[whichDirection] -= vzOfMovingMols; |
| 587 |
unconsAtoms[j]->setVel(vel); |
| 588 |
} |
| 589 |
|
| 590 |
} |
| 591 |
|
| 592 |
//modify the velocities of moving z-constrained molecuels |
| 593 |
Atom** movingZAtoms; |
| 594 |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
| 595 |
|
| 596 |
if (states[i] ==zcsMoving){ |
| 597 |
|
| 598 |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 599 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 600 |
movingZAtoms[j]->getVel(vel); |
| 601 |
vel[whichDirection] -= vzOfMovingMols; |
| 602 |
movingZAtoms[j]->setVel(vel); |
| 603 |
} |
| 604 |
|
| 605 |
} |
| 606 |
|
| 607 |
} |
| 608 |
|
| 609 |
} |
| 610 |
|
| 611 |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
| 612 |
|
| 613 |
Atom** zconsAtoms; |
| 614 |
double totalFZ; |
| 615 |
double totalFZ_local; |
| 616 |
double COMvel[3]; |
| 617 |
double COM[3]; |
| 618 |
double force[3]; |
| 619 |
double zsys; |
| 620 |
|
| 621 |
int nMovingZMols_local; |
| 622 |
int nMovingZMols; |
| 623 |
|
| 624 |
//constrain the molecules which do not reach the specified positions |
| 625 |
|
| 626 |
zsys = calcZSys(); |
| 627 |
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
| 628 |
|
| 629 |
//Zero Out the force of z-contrained molecules |
| 630 |
totalFZ_local = 0; |
| 631 |
|
| 632 |
//calculate the total z-contrained force of fixed z-contrained molecules |
| 633 |
cout << "Fixed Molecules" << endl; |
| 634 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 635 |
|
| 636 |
if (states[i] == zcsFixed){ |
| 637 |
|
| 638 |
zconsMols[i]->getCOM(COM); |
| 639 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
| 640 |
|
| 641 |
fz[i] = 0; |
| 642 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
| 643 |
zconsAtoms[j]->getFrc(force); |
| 644 |
fz[i] += force[whichDirection]; |
| 645 |
} |
| 646 |
totalFZ_local += fz[i]; |
| 647 |
|
| 648 |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
| 649 |
|
| 650 |
} |
| 651 |
|
| 652 |
} |
| 653 |
|
| 654 |
//calculate the number of atoms of moving z-constrained molecules |
| 655 |
nMovingZMols_local = 0; |
| 656 |
for(int i = 0; zconsMols.size(); i++){ |
| 657 |
if(states[i] == zcsMoving) |
| 658 |
nMovingZMols_local += massOfZConsMols[i]; |
| 659 |
} |
| 660 |
#ifdef IS_MPI |
| 661 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 662 |
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 663 |
#else |
| 664 |
totalFZ = totalFZ_local; |
| 665 |
nMovingZMols = nMovingZMols_local; |
| 666 |
#endif |
| 667 |
|
| 668 |
force[0]= 0; |
| 669 |
force[1]= 0; |
| 670 |
force[2]= 0; |
| 671 |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
| 672 |
|
| 673 |
//modify the velocites of unconstrained molecules |
| 674 |
for(int i = 0; i < unconsMols.size(); i++){ |
| 675 |
|
| 676 |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
| 677 |
|
| 678 |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
| 679 |
unconsAtoms[j]->addFrc(force); |
| 680 |
|
| 681 |
} |
| 682 |
|
| 683 |
//modify the velocities of moving z-constrained molecules |
| 684 |
for(int i = 0; i < zconsMols.size(); i++) { |
| 685 |
if (states[i] == zcsMoving){ |
| 686 |
|
| 687 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 688 |
|
| 689 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
| 690 |
movingZAtoms[j]->addFrc(force); |
| 691 |
} |
| 692 |
} |
| 693 |
|
| 694 |
// apply negative to fixed z-constrained molecues; |
| 695 |
force[0]= 0; |
| 696 |
force[1]= 0; |
| 697 |
force[2]= 0; |
| 698 |
|
| 699 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 700 |
|
| 701 |
if (states[i] == zcsFixed){ |
| 702 |
|
| 703 |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
| 704 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
| 705 |
|
| 706 |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
| 707 |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
| 708 |
zconsAtoms[j]->addFrc(force); |
| 709 |
} |
| 710 |
|
| 711 |
} |
| 712 |
|
| 713 |
} |
| 714 |
|
| 715 |
} |
| 716 |
|
| 717 |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
| 718 |
double COM[3]; |
| 719 |
double diff; |
| 720 |
|
| 721 |
bool changed; |
| 722 |
|
| 723 |
changed = false; |
| 724 |
|
| 725 |
for(int i =0; i < zconsMols.size(); i++){ |
| 726 |
|
| 727 |
zconsMols[i]->getCOM(COM); |
| 728 |
diff = fabs(COM[whichDirection] - zPos[i]); |
| 729 |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
| 730 |
states[i] = zcsFixed; |
| 731 |
changed = true; |
| 732 |
} |
| 733 |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
| 734 |
states[i] = zcsMoving; |
| 735 |
changed = true; |
| 736 |
} |
| 737 |
|
| 738 |
} |
| 739 |
|
| 740 |
return changed; |
| 741 |
} |
| 742 |
|
| 743 |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
| 744 |
for(int i = 0; i < zconsMols.size(); i++) |
| 745 |
if (states[i] == zcsFixed) |
| 746 |
return true; |
| 747 |
|
| 748 |
return false; |
| 749 |
} |
| 750 |
|
| 751 |
|
| 752 |
/** |
| 753 |
* |
| 754 |
*/ |
| 755 |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
| 756 |
for(int i = 0; i < zconsMols.size(); i++) |
| 757 |
if (states[i] == zcsMoving) |
| 758 |
return true; |
| 759 |
|
| 760 |
return false; |
| 761 |
|
| 762 |
} |
| 763 |
|
| 764 |
/** |
| 765 |
* |
| 766 |
* |
| 767 |
*/ |
| 768 |
|
| 769 |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
| 770 |
double force[3]; |
| 771 |
double harmonicU; |
| 772 |
double COM[3]; |
| 773 |
double diff; |
| 774 |
|
| 775 |
force[0] = 0; |
| 776 |
force[1] = 0; |
| 777 |
force[2] = 0; |
| 778 |
|
| 779 |
cout << "Moving Molecules" << endl; |
| 780 |
for(int i = 0; i < zconsMols.size(); i++) { |
| 781 |
|
| 782 |
if (states[i] == zcsMoving){ |
| 783 |
zconsMols[i]->getCOM(COM): |
| 784 |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
| 785 |
|
| 786 |
diff = COM[whichDirection] -zPos[i]; |
| 787 |
|
| 788 |
harmonicU = 0.5 * kz[i] * diff * diff; |
| 789 |
info->ltPot += harmonicU; |
| 790 |
|
| 791 |
force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
| 792 |
|
| 793 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 794 |
|
| 795 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
| 796 |
movingZAtoms[j]->addFrc(force); |
| 797 |
} |
| 798 |
|
| 799 |
} |
| 800 |
|
| 801 |
} |
