| 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 |
IndexData* index; |
| 12 |
DoubleData* sampleTime; |
| 13 |
StringData* filename; |
| 14 |
|
| 15 |
//retrieve index of z-constraint molecules |
| 16 |
data = info->getProperty("zconsindex"); |
| 17 |
if(!data) { |
| 18 |
|
| 19 |
sprintf( painCave.errMsg, |
| 20 |
"ZConstraint error: If you use an ZConstraint\n" |
| 21 |
" , you must set index of z-constraint molecules.\n"); |
| 22 |
painCave.isFatal = 1; |
| 23 |
simError(); |
| 24 |
} |
| 25 |
else{ |
| 26 |
index = dynamic_cast<IndexData*>(data); |
| 27 |
|
| 28 |
if(!index){ |
| 29 |
|
| 30 |
sprintf( painCave.errMsg, |
| 31 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 32 |
painCave.isFatal = 1; |
| 33 |
simError(); |
| 34 |
|
| 35 |
} |
| 36 |
else{ |
| 37 |
|
| 38 |
indexOfAllZConsMols = index->getIndexData(); |
| 39 |
|
| 40 |
//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp) |
| 41 |
int maxIndex; |
| 42 |
int minIndex; |
| 43 |
int totalNumMol; |
| 44 |
|
| 45 |
minIndex = indexOfAllZConsMols[0]; |
| 46 |
if(minIndex < 0){ |
| 47 |
sprintf( painCave.errMsg, |
| 48 |
"ZConstraint error: index is out of range\n"); |
| 49 |
painCave.isFatal = 1; |
| 50 |
simError(); |
| 51 |
} |
| 52 |
|
| 53 |
maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
| 54 |
|
| 55 |
#ifndef IS_MPI |
| 56 |
totalNumMol = nMols; |
| 57 |
#else |
| 58 |
totalNumMol = mpiSim->getTotNmol(); |
| 59 |
#endif |
| 60 |
|
| 61 |
if(maxIndex > totalNumMol - 1){ |
| 62 |
sprintf( painCave.errMsg, |
| 63 |
"ZConstraint error: index is out of range\n"); |
| 64 |
painCave.isFatal = 1; |
| 65 |
simError(); |
| 66 |
|
| 67 |
} |
| 68 |
|
| 69 |
} |
| 70 |
|
| 71 |
} |
| 72 |
|
| 73 |
//retrieve sample time of z-contraint |
| 74 |
data = info->getProperty("zconstime"); |
| 75 |
|
| 76 |
if(!data) { |
| 77 |
|
| 78 |
sprintf( painCave.errMsg, |
| 79 |
"ZConstraint error: If you use an ZConstraint\n" |
| 80 |
" , you must set sample time.\n"); |
| 81 |
painCave.isFatal = 1; |
| 82 |
simError(); |
| 83 |
} |
| 84 |
else{ |
| 85 |
|
| 86 |
sampleTime = dynamic_cast<DoubleData*>(data); |
| 87 |
|
| 88 |
if(!sampleTime){ |
| 89 |
|
| 90 |
sprintf( painCave.errMsg, |
| 91 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 92 |
painCave.isFatal = 1; |
| 93 |
simError(); |
| 94 |
|
| 95 |
} |
| 96 |
else{ |
| 97 |
this->zconsTime = sampleTime->getData(); |
| 98 |
} |
| 99 |
|
| 100 |
} |
| 101 |
|
| 102 |
|
| 103 |
//retrieve output filename of z force |
| 104 |
data = info->getProperty("zconsfilename"); |
| 105 |
if(!data) { |
| 106 |
|
| 107 |
|
| 108 |
sprintf( painCave.errMsg, |
| 109 |
"ZConstraint error: If you use an ZConstraint\n" |
| 110 |
" , you must set output filename of z-force.\n"); |
| 111 |
painCave.isFatal = 1; |
| 112 |
simError(); |
| 113 |
|
| 114 |
} |
| 115 |
else{ |
| 116 |
|
| 117 |
filename = dynamic_cast<StringData*>(data); |
| 118 |
|
| 119 |
if(!filename){ |
| 120 |
|
| 121 |
sprintf( painCave.errMsg, |
| 122 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 123 |
painCave.isFatal = 1; |
| 124 |
simError(); |
| 125 |
|
| 126 |
} |
| 127 |
else{ |
| 128 |
this->zconsOutput = filename->getData(); |
| 129 |
} |
| 130 |
|
| 131 |
|
| 132 |
} |
| 133 |
|
| 134 |
#ifdef IS_MPI |
| 135 |
update(); |
| 136 |
#else |
| 137 |
int searchResult; |
| 138 |
double COM[3]; |
| 139 |
|
| 140 |
for(int i = 0; i < nMols; i++){ |
| 141 |
|
| 142 |
searchResult = isZConstraintMol(&molecules[i]); |
| 143 |
|
| 144 |
if(searchResult > -1){ |
| 145 |
|
| 146 |
zconsMols.push_back(&molecules[i]); |
| 147 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 148 |
|
| 149 |
molecules[i].getCOM(COM); |
| 150 |
} |
| 151 |
else |
| 152 |
{ |
| 153 |
|
| 154 |
unconsMols.push_back(&molecules[i]); |
| 155 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 156 |
|
| 157 |
} |
| 158 |
} |
| 159 |
|
| 160 |
fz = new double[zconsMols.size()]; |
| 161 |
indexOfZConsMols = new int [zconsMols.size()]; |
| 162 |
|
| 163 |
if(!fz || !indexOfZConsMols){ |
| 164 |
sprintf( painCave.errMsg, |
| 165 |
"Memory allocation failure in class Zconstraint\n"); |
| 166 |
painCave.isFatal = 1; |
| 167 |
simError(); |
| 168 |
} |
| 169 |
|
| 170 |
for(int i = 0; i < zconsMols.size(); i++) |
| 171 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 172 |
|
| 173 |
#endif |
| 174 |
|
| 175 |
//get total number of unconstrained atoms |
| 176 |
int nUnconsAtoms_local; |
| 177 |
nUnconsAtoms_local = 0; |
| 178 |
for(int i = 0; i < unconsMols.size(); i++) |
| 179 |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
| 180 |
|
| 181 |
#ifndef IS_MPI |
| 182 |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
| 183 |
#else |
| 184 |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 185 |
#endif |
| 186 |
|
| 187 |
|
| 188 |
|
| 189 |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
| 190 |
|
| 191 |
if(!fzOut){ |
| 192 |
sprintf( painCave.errMsg, |
| 193 |
"Memory allocation failure in class Zconstraint\n"); |
| 194 |
painCave.isFatal = 1; |
| 195 |
simError(); |
| 196 |
} |
| 197 |
|
| 198 |
} |
| 199 |
|
| 200 |
template<typename T> ZConstraint<T>::~ZConstraint() |
| 201 |
{ |
| 202 |
if(fz) |
| 203 |
delete[] fz; |
| 204 |
|
| 205 |
if(indexOfZConsMols) |
| 206 |
delete[] indexOfZConsMols; |
| 207 |
|
| 208 |
if(fzOut) |
| 209 |
delete fzOut; |
| 210 |
} |
| 211 |
|
| 212 |
#ifdef IS_MPI |
| 213 |
template<typename T> void ZConstraint<T>::update() |
| 214 |
{ |
| 215 |
double COM[3]; |
| 216 |
int index; |
| 217 |
|
| 218 |
zconsMols.clear(); |
| 219 |
massOfZConsMols.clear(); |
| 220 |
|
| 221 |
unconsMols.clear(); |
| 222 |
massOfUnconsMols.clear(); |
| 223 |
|
| 224 |
|
| 225 |
//creat zconsMol and unconsMol lists |
| 226 |
for(int i = 0; i < nMols; i++){ |
| 227 |
|
| 228 |
index = isZConstraintMol(&molecules[i]); |
| 229 |
|
| 230 |
if(index > -1){ |
| 231 |
|
| 232 |
zconsMols.push_back(&molecules[i]); |
| 233 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 234 |
|
| 235 |
molecules[i].getCOM(COM); |
| 236 |
} |
| 237 |
else |
| 238 |
{ |
| 239 |
|
| 240 |
unconsMols.push_back(&molecules[i]); |
| 241 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 242 |
|
| 243 |
} |
| 244 |
} |
| 245 |
|
| 246 |
//The reason to declare fz and indexOfZconsMols as pointer to array is |
| 247 |
// that we want to make the MPI communication simple |
| 248 |
if(fz) |
| 249 |
delete[] fz; |
| 250 |
|
| 251 |
if(indexOfZConsMols) |
| 252 |
delete[] indexOfZConsMols; |
| 253 |
|
| 254 |
if (zconsMols.size() > 0){ |
| 255 |
fz = new double[zconsMols.size()]; |
| 256 |
indexOfZConsMols = new int[zconsMols.size()]; |
| 257 |
|
| 258 |
if(!fz || !indexOfZConsMols){ |
| 259 |
sprintf( painCave.errMsg, |
| 260 |
"Memory allocation failure in class Zconstraint\n"); |
| 261 |
painCave.isFatal = 1; |
| 262 |
simError(); |
| 263 |
} |
| 264 |
|
| 265 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 266 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 267 |
} |
| 268 |
|
| 269 |
} |
| 270 |
else{ |
| 271 |
fz = NULL; |
| 272 |
indexOfZConsMols = NULL; |
| 273 |
} |
| 274 |
|
| 275 |
} |
| 276 |
|
| 277 |
#endif |
| 278 |
|
| 279 |
/** Function Name: isZConstraintMol |
| 280 |
** Parameter |
| 281 |
** Molecule* mol |
| 282 |
** Return value: |
| 283 |
** -1, if the molecule is not z-constraint molecule, |
| 284 |
** other non-negative values, its index in indexOfAllZConsMols vector |
| 285 |
*/ |
| 286 |
|
| 287 |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
| 288 |
{ |
| 289 |
int index; |
| 290 |
int low; |
| 291 |
int high; |
| 292 |
int mid; |
| 293 |
|
| 294 |
index = mol->getGlobalIndex(); |
| 295 |
|
| 296 |
low = 0; |
| 297 |
high = indexOfAllZConsMols.size() - 1; |
| 298 |
|
| 299 |
//Binary Search (we have sorted the array) |
| 300 |
while(low <= high){ |
| 301 |
mid = (low + high) /2; |
| 302 |
if (indexOfAllZConsMols[mid] == index) |
| 303 |
return mid; |
| 304 |
else if (indexOfAllZConsMols[mid] > index ) |
| 305 |
high = mid -1; |
| 306 |
else |
| 307 |
low = mid + 1; |
| 308 |
} |
| 309 |
|
| 310 |
return -1; |
| 311 |
} |
| 312 |
|
| 313 |
/** |
| 314 |
* Description: |
| 315 |
* Reset the z coordinates |
| 316 |
*/ |
| 317 |
template<typename T> void ZConstraint<T>::integrate(){ |
| 318 |
|
| 319 |
//zero out the velocities of center of mass of unconstrained molecules |
| 320 |
//and the velocities of center of mass of every single z-constrained molecueles |
| 321 |
zeroOutVel(); |
| 322 |
|
| 323 |
T::integrate(); |
| 324 |
|
| 325 |
} |
| 326 |
|
| 327 |
|
| 328 |
/** |
| 329 |
* |
| 330 |
* |
| 331 |
* |
| 332 |
* |
| 333 |
*/ |
| 334 |
|
| 335 |
|
| 336 |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
| 337 |
|
| 338 |
T::calcForce(calcPot, calcStress); |
| 339 |
|
| 340 |
if (checkZConsState()) |
| 341 |
zeroOutVel(); |
| 342 |
|
| 343 |
//do zconstraint force; |
| 344 |
if (haveFixedZMols()) |
| 345 |
this->doZconstraintForce(); |
| 346 |
|
| 347 |
//use harmonical poteintial to move the molecules to the specified positions |
| 348 |
if (haveMovingZMols()) |
| 349 |
//this->doHarmonic(); |
| 350 |
|
| 351 |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
| 352 |
|
| 353 |
} |
| 354 |
|
| 355 |
template<typename T> double ZConstraint<T>::calcZSys() |
| 356 |
{ |
| 357 |
//calculate reference z coordinate for z-constraint molecules |
| 358 |
double totalMass_local; |
| 359 |
double totalMass; |
| 360 |
double totalMZ_local; |
| 361 |
double totalMZ; |
| 362 |
double massOfUncons_local; |
| 363 |
double massOfCurMol; |
| 364 |
double COM[3]; |
| 365 |
|
| 366 |
totalMass_local = 0; |
| 367 |
totalMass = 0; |
| 368 |
totalMZ_local = 0; |
| 369 |
totalMZ = 0; |
| 370 |
massOfUncons_local = 0; |
| 371 |
|
| 372 |
|
| 373 |
for(int i = 0; i < nMols; i++){ |
| 374 |
massOfCurMol = molecules[i].getTotalMass(); |
| 375 |
molecules[i].getCOM(COM); |
| 376 |
|
| 377 |
totalMass_local += massOfCurMol; |
| 378 |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
| 379 |
|
| 380 |
if(isZConstraintMol(&molecules[i]) == -1){ |
| 381 |
|
| 382 |
massOfUncons_local += massOfCurMol; |
| 383 |
} |
| 384 |
|
| 385 |
} |
| 386 |
|
| 387 |
|
| 388 |
#ifdef IS_MPI |
| 389 |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 390 |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 391 |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 392 |
#else |
| 393 |
totalMass = totalMass_local; |
| 394 |
totalMZ = totalMZ_local; |
| 395 |
totalMassOfUncons = massOfUncons_local; |
| 396 |
#endif |
| 397 |
|
| 398 |
double zsys; |
| 399 |
zsys = totalMZ / totalMass; |
| 400 |
|
| 401 |
return zsys; |
| 402 |
} |
| 403 |
|
| 404 |
/** |
| 405 |
* |
| 406 |
*/ |
| 407 |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
| 408 |
|
| 409 |
T::thermalize(); |
| 410 |
zeroOutVel(); |
| 411 |
} |
| 412 |
|
| 413 |
/** |
| 414 |
* |
| 415 |
* |
| 416 |
* |
| 417 |
*/ |
| 418 |
|
| 419 |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
| 420 |
|
| 421 |
Atom** fixedZAtoms; |
| 422 |
double COMvel[3]; |
| 423 |
double vel[3]; |
| 424 |
|
| 425 |
//zero out the velocities of center of mass of fixed z-constrained molecules |
| 426 |
|
| 427 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 428 |
|
| 429 |
if (states[i] == zcsFixed){ |
| 430 |
|
| 431 |
zconsMols[i]->getCOMvel(COMvel); |
| 432 |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
| 433 |
|
| 434 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
| 435 |
fixedZAtoms[j]->getVel(vel); |
| 436 |
vel[whichDirection] -= COMvel[whichDirection]; |
| 437 |
fixedZAtoms[j]->setVel(vel); |
| 438 |
} |
| 439 |
|
| 440 |
} |
| 441 |
|
| 442 |
} |
| 443 |
|
| 444 |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
| 445 |
double MVzOfMovingMols_local; |
| 446 |
double MVzOfMovingMols; |
| 447 |
double totalMassOfMovingZMols_local; |
| 448 |
double totalMassOfMovingZMols; |
| 449 |
|
| 450 |
MVzOfMovingMols_local = 0; |
| 451 |
totalMassOfMovingZMols_local = 0; |
| 452 |
|
| 453 |
for(int i =0; i < unconsMols.size(); i++){ |
| 454 |
unconsMols[i]->getCOMvel(COMvel); |
| 455 |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
| 456 |
} |
| 457 |
|
| 458 |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
| 459 |
|
| 460 |
if (states[i] == zcsMoving){ |
| 461 |
zconsMols[i]->getCOMvel(COMvel); |
| 462 |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
| 463 |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
| 464 |
} |
| 465 |
|
| 466 |
} |
| 467 |
|
| 468 |
#ifndef IS_MPI |
| 469 |
MVzOfMovingMols = MVzOfMovingMols_local; |
| 470 |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
| 471 |
#else |
| 472 |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 473 |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 474 |
#endif |
| 475 |
|
| 476 |
double vzOfMovingMols; |
| 477 |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
| 478 |
|
| 479 |
//modify the velocites of unconstrained molecules |
| 480 |
Atom** unconsAtoms; |
| 481 |
for(int i = 0; i < unconsMols.size(); i++){ |
| 482 |
|
| 483 |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
| 484 |
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
| 485 |
unconsAtoms[j]->getVel(vel); |
| 486 |
vel[whichDirection] -= vzOfMovingMols; |
| 487 |
unconsAtoms[j]->setVel(vel); |
| 488 |
} |
| 489 |
|
| 490 |
} |
| 491 |
|
| 492 |
//modify the velocities of moving z-constrained molecuels |
| 493 |
Atom** movingZAtoms; |
| 494 |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
| 495 |
|
| 496 |
if (states[i] ==zcsMoving){ |
| 497 |
|
| 498 |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 499 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
| 500 |
movingZAtoms[j]->getVel(vel); |
| 501 |
vel[whichDirection] -= vzOfMovingMols; |
| 502 |
movingZAtoms[j]->setVel(vel); |
| 503 |
} |
| 504 |
|
| 505 |
} |
| 506 |
|
| 507 |
} |
| 508 |
|
| 509 |
} |
| 510 |
|
| 511 |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
| 512 |
|
| 513 |
Atom** zconsAtoms; |
| 514 |
double totalFZ; |
| 515 |
double totalFZ_local; |
| 516 |
double COMvel[3]; |
| 517 |
double COM[3]; |
| 518 |
double force[3]; |
| 519 |
double zsys; |
| 520 |
|
| 521 |
int nMovingZMols_local; |
| 522 |
int nMovingZMols; |
| 523 |
|
| 524 |
//constrain the molecules which do not reach the specified positions |
| 525 |
|
| 526 |
zsys = calcZSys(); |
| 527 |
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
| 528 |
|
| 529 |
//Zero Out the force of z-contrained molecules |
| 530 |
totalFZ_local = 0; |
| 531 |
|
| 532 |
//calculate the total z-contrained force of fixed z-contrained molecules |
| 533 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 534 |
|
| 535 |
if (states[i] == zcsFixed){ |
| 536 |
|
| 537 |
zconsMols[i]->getCOM(COM); |
| 538 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
| 539 |
|
| 540 |
fz[i] = 0; |
| 541 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
| 542 |
zconsAtoms[j]->getFrc(force); |
| 543 |
fz[i] += force[whichDirection]; |
| 544 |
} |
| 545 |
totalFZ_local += fz[i]; |
| 546 |
|
| 547 |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
| 548 |
|
| 549 |
} |
| 550 |
|
| 551 |
} |
| 552 |
|
| 553 |
//calculate the number of atoms of moving z-constrained molecules |
| 554 |
nMovingZMols_local = 0; |
| 555 |
for(int i = 0; zconsMols.size(); i++){ |
| 556 |
if(states[i] == zcsMoving) |
| 557 |
nMovingZMols_local += massOfZConsMols[i]; |
| 558 |
} |
| 559 |
#ifdef IS_MPI |
| 560 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 561 |
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 562 |
#else |
| 563 |
totalFZ = totalFZ_local; |
| 564 |
nMovingZMols = nMovingZMols_local; |
| 565 |
#endif |
| 566 |
|
| 567 |
force[0]= 0; |
| 568 |
force[1]= 0; |
| 569 |
force[2]= 0; |
| 570 |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
| 571 |
|
| 572 |
//modify the velocites of unconstrained molecules |
| 573 |
for(int i = 0; i < unconsMols.size(); i++){ |
| 574 |
|
| 575 |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
| 576 |
|
| 577 |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
| 578 |
unconsAtoms[j]->addFrc(force); |
| 579 |
|
| 580 |
} |
| 581 |
|
| 582 |
//modify the velocities of moving z-constrained molecules |
| 583 |
for(int i = 0; i < zconsMols.size(); i++) { |
| 584 |
if (states[i] == zcsMoving){ |
| 585 |
|
| 586 |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
| 587 |
|
| 588 |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
| 589 |
movingZAtoms[j]->addFrc(force); |
| 590 |
} |
| 591 |
} |
| 592 |
|
| 593 |
// apply negative to fixed z-constrained molecues; |
| 594 |
force[0]= 0; |
| 595 |
force[1]= 0; |
| 596 |
force[2]= 0; |
| 597 |
|
| 598 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 599 |
|
| 600 |
if (states[i] == zcsFixed){ |
| 601 |
|
| 602 |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
| 603 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
| 604 |
|
| 605 |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
| 606 |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
| 607 |
zconsAtoms[j]->addFrc(force); |
| 608 |
} |
| 609 |
|
| 610 |
} |
| 611 |
|
| 612 |
} |
| 613 |
|
| 614 |
} |
| 615 |
|
| 616 |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
| 617 |
double COM[3]; |
| 618 |
double diff; |
| 619 |
|
| 620 |
bool changed; |
| 621 |
|
| 622 |
changed = false; |
| 623 |
|
| 624 |
for(int i =0; i < zconsMols.size(); i++){ |
| 625 |
|
| 626 |
zconsMols[i]->getCOM(COM); |
| 627 |
diff = fabs(COM[whichDirection] - ZPos[i]); |
| 628 |
if ( diff <= ztol && states[i] == zcsMoving){ |
| 629 |
states[i] = zcsFixed; |
| 630 |
changed = true; |
| 631 |
} |
| 632 |
else if ( diff > ztol && states[i] == zcsFixed){ |
| 633 |
states[i] = zcsMoving; |
| 634 |
changed = true; |
| 635 |
} |
| 636 |
|
| 637 |
} |
| 638 |
|
| 639 |
return changed; |
| 640 |
} |
| 641 |
|
| 642 |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
| 643 |
for(int i = 0; i < zconsMols.size(); i++) |
| 644 |
if (states[i] == zcsFixed) |
| 645 |
return true; |
| 646 |
|
| 647 |
return false; |
| 648 |
} |
| 649 |
|
| 650 |
|
| 651 |
/** |
| 652 |
* |
| 653 |
*/ |
| 654 |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
| 655 |
for(int i = 0; i < zconsMols.size(); i++) |
| 656 |
if (states[i] == zcsMoving) |
| 657 |
return true; |
| 658 |
|
| 659 |
return false; |
| 660 |
|
| 661 |
} |
