| 1 |
#include "Integrator.hpp" |
| 2 |
#include "simError.h" |
| 3 |
|
| 4 |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
| 5 |
: T(theInfo, the_ff), fz(NULL), indexOfZConsMols(NULL) |
| 6 |
{ |
| 7 |
|
| 8 |
//get properties from SimInfo |
| 9 |
GenericData* data; |
| 10 |
IndexData* index; |
| 11 |
DoubleData* sampleTime; |
| 12 |
StringData* filename; |
| 13 |
|
| 14 |
|
| 15 |
data = info->getProperty("zconsindex"); |
| 16 |
if(!data) { |
| 17 |
|
| 18 |
sprintf( painCave.errMsg, |
| 19 |
"ZConstraint error: If you use an ZConstraint\n" |
| 20 |
" , you must set index of z-constraint molecules.\n"); |
| 21 |
painCave.isFatal = 1; |
| 22 |
simError(); |
| 23 |
} |
| 24 |
else{ |
| 25 |
index = dynamic_cast<IndexData*>(data); |
| 26 |
|
| 27 |
if(!index){ |
| 28 |
|
| 29 |
sprintf( painCave.errMsg, |
| 30 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 31 |
painCave.isFatal = 1; |
| 32 |
simError(); |
| 33 |
|
| 34 |
} |
| 35 |
else{ |
| 36 |
indexOfAllZConsMols = index->getIndexData(); |
| 37 |
} |
| 38 |
|
| 39 |
} |
| 40 |
|
| 41 |
//retrive sample time of z-contraint |
| 42 |
data = info->getProperty("zconstime"); |
| 43 |
|
| 44 |
if(!data) { |
| 45 |
|
| 46 |
sprintf( painCave.errMsg, |
| 47 |
"ZConstraint error: If you use an ZConstraint\n" |
| 48 |
" , you must set sample time.\n"); |
| 49 |
painCave.isFatal = 1; |
| 50 |
simError(); |
| 51 |
} |
| 52 |
else{ |
| 53 |
|
| 54 |
sampleTime = dynamic_cast<DoubleData*>(data); |
| 55 |
|
| 56 |
if(!sampleTime){ |
| 57 |
|
| 58 |
sprintf( painCave.errMsg, |
| 59 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 60 |
painCave.isFatal = 1; |
| 61 |
simError(); |
| 62 |
|
| 63 |
} |
| 64 |
else{ |
| 65 |
this->zconsTime = sampleTime->getData(); |
| 66 |
} |
| 67 |
|
| 68 |
} |
| 69 |
|
| 70 |
|
| 71 |
//retrive output filename of z force |
| 72 |
data = info->getProperty("zconsfilename"); |
| 73 |
if(!data) { |
| 74 |
|
| 75 |
|
| 76 |
sprintf( painCave.errMsg, |
| 77 |
"ZConstraint error: If you use an ZConstraint\n" |
| 78 |
" , you must set output filename of z-force.\n"); |
| 79 |
painCave.isFatal = 1; |
| 80 |
simError(); |
| 81 |
|
| 82 |
} |
| 83 |
else{ |
| 84 |
|
| 85 |
filename = dynamic_cast<StringData*>(data); |
| 86 |
|
| 87 |
if(!filename){ |
| 88 |
|
| 89 |
sprintf( painCave.errMsg, |
| 90 |
"ZConstraint error: Can not get property from SimInfo\n"); |
| 91 |
painCave.isFatal = 1; |
| 92 |
simError(); |
| 93 |
|
| 94 |
} |
| 95 |
else{ |
| 96 |
this->zconsOutput = filename->getData(); |
| 97 |
} |
| 98 |
|
| 99 |
|
| 100 |
} |
| 101 |
|
| 102 |
|
| 103 |
//calculate reference z coordinate for z-constraint molecules |
| 104 |
double totalMass_local; |
| 105 |
double totalMass; |
| 106 |
double totalMZ_local; |
| 107 |
double totalMZ; |
| 108 |
double massOfUncons_local; |
| 109 |
double massOfCurMol; |
| 110 |
double COM[3]; |
| 111 |
|
| 112 |
totalMass_local = 0; |
| 113 |
totalMass = 0; |
| 114 |
totalMZ_local = 0; |
| 115 |
totalMZ = 0; |
| 116 |
massOfUncons_local = 0; |
| 117 |
|
| 118 |
|
| 119 |
for(int i = 0; i < nMols; i++){ |
| 120 |
massOfCurMol = molecules[i].getTotalMass(); |
| 121 |
molecules[i].getCOM(COM); |
| 122 |
|
| 123 |
totalMass_local += massOfCurMol; |
| 124 |
totalMZ_local += massOfCurMol * COM[2]; |
| 125 |
|
| 126 |
if(isZConstraintMol(&molecules[i]) == -1){ |
| 127 |
|
| 128 |
massOfUncons_local += massOfCurMol; |
| 129 |
} |
| 130 |
|
| 131 |
} |
| 132 |
|
| 133 |
|
| 134 |
#ifdef IS_MPI |
| 135 |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 136 |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 137 |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 138 |
#else |
| 139 |
totalMass = totalMass_local; |
| 140 |
totalMZ = totalMZ_local; |
| 141 |
totalMassOfUncons = massOfUncons_local; |
| 142 |
#endif |
| 143 |
|
| 144 |
double zsys; |
| 145 |
zsys = totalMZ / totalMass; |
| 146 |
|
| 147 |
#ifndef IS_MPI |
| 148 |
for(int i = 0; i < nMols; i++){ |
| 149 |
|
| 150 |
if(isZConstraintMol(&molecules[i]) > -1 ){ |
| 151 |
molecules[i].getCOM(COM); |
| 152 |
allRefZ.push_back(COM[2] - zsys); |
| 153 |
} |
| 154 |
|
| 155 |
} |
| 156 |
#else |
| 157 |
|
| 158 |
int whichNode; |
| 159 |
enum CommType { RequestMolZPos, EndOfRequest} status; |
| 160 |
//int status; |
| 161 |
double zpos; |
| 162 |
int localIndex; |
| 163 |
MPI_Status ierr; |
| 164 |
int tag = 0; |
| 165 |
|
| 166 |
if(worldRank == 0){ |
| 167 |
|
| 168 |
int globalIndexOfCurMol; |
| 169 |
int *MolToProcMap; |
| 170 |
MolToProcMap = mpiSim->getMolToProcMap(); |
| 171 |
|
| 172 |
for(int i = 0; i < indexOfAllZConsMols.size(); i++){ |
| 173 |
|
| 174 |
whichNode = MolToProcMap[indexOfAllZConsMols[i]]; |
| 175 |
globalIndexOfCurMol = indexOfAllZConsMols[i]; |
| 176 |
|
| 177 |
if(whichNode == 0){ |
| 178 |
|
| 179 |
for(int j = 0; j < nMols; j++) |
| 180 |
if(molecules[j].getGlobalIndex() == globalIndexOfCurMol){ |
| 181 |
localIndex = j; |
| 182 |
break; |
| 183 |
} |
| 184 |
|
| 185 |
molecules[localIndex].getCOM(COM); |
| 186 |
allRefZ.push_back(COM[2] - zsys); |
| 187 |
|
| 188 |
} |
| 189 |
else{ |
| 190 |
status = RequestMolZPos; |
| 191 |
MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
| 192 |
MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
| 193 |
MPI_Recv(&zpos, 1, MPI_DOUBLE_PRECISION, whichNode, tag, MPI_COMM_WORLD, &ierr); |
| 194 |
|
| 195 |
allRefZ.push_back(zpos - zsys); |
| 196 |
|
| 197 |
} |
| 198 |
|
| 199 |
} //End of Request Loop |
| 200 |
|
| 201 |
//Send ending request message to slave nodes |
| 202 |
status = EndOfRequest; |
| 203 |
for(int i =1; i < mpiSim->getNumberProcessors(); i++) |
| 204 |
MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD); |
| 205 |
|
| 206 |
} |
| 207 |
else{ |
| 208 |
|
| 209 |
int whichMol; |
| 210 |
bool done = false; |
| 211 |
|
| 212 |
while (!done){ |
| 213 |
|
| 214 |
MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr); |
| 215 |
|
| 216 |
switch (status){ |
| 217 |
|
| 218 |
case RequestMolZPos : |
| 219 |
|
| 220 |
MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr); |
| 221 |
|
| 222 |
for(int i = 0; i < nMols; i++) |
| 223 |
if(molecules[i].getGlobalIndex() == whichMol){ |
| 224 |
localIndex = i; |
| 225 |
break; |
| 226 |
} |
| 227 |
|
| 228 |
molecules[localIndex].getCOM(COM); |
| 229 |
zpos = COM[2]; |
| 230 |
MPI_Send(&zpos, 1, MPI_DOUBLE_PRECISION, 0, tag, MPI_COMM_WORLD); |
| 231 |
|
| 232 |
break; |
| 233 |
|
| 234 |
case EndOfRequest : |
| 235 |
|
| 236 |
done = true; |
| 237 |
break; |
| 238 |
} |
| 239 |
|
| 240 |
} |
| 241 |
|
| 242 |
} |
| 243 |
|
| 244 |
//Brocast the allRefZ to slave nodes; |
| 245 |
double* allRefZBuf; |
| 246 |
int nZConsMols; |
| 247 |
nZConsMols = indexOfAllZConsMols.size(); |
| 248 |
|
| 249 |
allRefZBuf = new double[nZConsMols]; |
| 250 |
|
| 251 |
if(worldRank == 0){ |
| 252 |
|
| 253 |
for(int i = 0; i < nZConsMols; i++) |
| 254 |
allRefZBuf[i] = allRefZ[i]; |
| 255 |
} |
| 256 |
|
| 257 |
MPI_Bcast(allRefZBuf, nZConsMols, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD); |
| 258 |
|
| 259 |
if(worldRank != 0){ |
| 260 |
|
| 261 |
for(int i = 0; i < nZConsMols; i++) |
| 262 |
allRefZ.push_back(allRefZBuf[i]); |
| 263 |
} |
| 264 |
|
| 265 |
delete[] allRefZBuf; |
| 266 |
#endif |
| 267 |
|
| 268 |
|
| 269 |
#ifdef IS_MPI |
| 270 |
update(); |
| 271 |
#else |
| 272 |
int searchResult; |
| 273 |
|
| 274 |
refZ = allRefZ; |
| 275 |
|
| 276 |
for(int i = 0; i < nMols; i++){ |
| 277 |
|
| 278 |
searchResult = isZConstraintMol(&molecules[i]); |
| 279 |
|
| 280 |
if(searchResult > -1){ |
| 281 |
|
| 282 |
zconsMols.push_back(&molecules[i]); |
| 283 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 284 |
|
| 285 |
molecules[i].getCOM(COM); |
| 286 |
} |
| 287 |
else |
| 288 |
{ |
| 289 |
|
| 290 |
unconsMols.push_back(&molecules[i]); |
| 291 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 292 |
|
| 293 |
} |
| 294 |
} |
| 295 |
|
| 296 |
fz = new double[zconsMols.size()]; |
| 297 |
indexOfZConsMols = new int [zconsMols.size()]; |
| 298 |
|
| 299 |
if(!fz || !indexOfZConsMols){ |
| 300 |
sprintf( painCave.errMsg, |
| 301 |
"Memory allocation failure in class Zconstraint\n"); |
| 302 |
painCave.isFatal = 1; |
| 303 |
simError(); |
| 304 |
} |
| 305 |
|
| 306 |
for(int i = 0; i < zconsMols.size(); i++) |
| 307 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 308 |
|
| 309 |
#endif |
| 310 |
|
| 311 |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
| 312 |
|
| 313 |
if(!fzOut){ |
| 314 |
sprintf( painCave.errMsg, |
| 315 |
"Memory allocation failure in class Zconstraint\n"); |
| 316 |
painCave.isFatal = 1; |
| 317 |
simError(); |
| 318 |
} |
| 319 |
|
| 320 |
fzOut->writeRefZ(indexOfAllZConsMols, allRefZ); |
| 321 |
} |
| 322 |
|
| 323 |
template<typename T> ZConstraint<T>::~ZConstraint() |
| 324 |
{ |
| 325 |
if(fz) |
| 326 |
delete[] fz; |
| 327 |
|
| 328 |
if(indexOfZConsMols) |
| 329 |
delete[] indexOfZConsMols; |
| 330 |
|
| 331 |
if(fzOut) |
| 332 |
delete fzOut; |
| 333 |
} |
| 334 |
|
| 335 |
#ifdef IS_MPI |
| 336 |
template<typename T> void ZConstraint<T>::update() |
| 337 |
{ |
| 338 |
double COM[3]; |
| 339 |
int index; |
| 340 |
|
| 341 |
zconsMols.clear(); |
| 342 |
massOfZConsMols.clear(); |
| 343 |
refZ.clear(); |
| 344 |
|
| 345 |
unconsMols.clear(); |
| 346 |
massOfUnconsMols.clear(); |
| 347 |
|
| 348 |
|
| 349 |
//creat zconsMol and unconsMol lists |
| 350 |
for(int i = 0; i < nMols; i++){ |
| 351 |
|
| 352 |
index = isZConstraintMol(&molecules[i]); |
| 353 |
|
| 354 |
if(index > -1){ |
| 355 |
|
| 356 |
zconsMols.push_back(&molecules[i]); |
| 357 |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
| 358 |
|
| 359 |
molecules[i].getCOM(COM); |
| 360 |
refZ.push_back(allRefZ[index]); |
| 361 |
} |
| 362 |
else |
| 363 |
{ |
| 364 |
|
| 365 |
unconsMols.push_back(&molecules[i]); |
| 366 |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
| 367 |
|
| 368 |
} |
| 369 |
} |
| 370 |
|
| 371 |
//The reason to declare fz and indexOfZconsMols as pointer to array is |
| 372 |
// that we want to make the MPI communication simple |
| 373 |
if(fz) |
| 374 |
delete[] fz; |
| 375 |
|
| 376 |
if(indexOfZConsMols) |
| 377 |
delete[] indexOfZConsMols; |
| 378 |
|
| 379 |
if (zconsMols.size() > 0){ |
| 380 |
fz = new double[zconsMols.size()]; |
| 381 |
indexOfZConsMols = new int[zconsMols.size()]; |
| 382 |
|
| 383 |
if(!fz || !indexOfZConsMols){ |
| 384 |
sprintf( painCave.errMsg, |
| 385 |
"Memory allocation failure in class Zconstraint\n"); |
| 386 |
painCave.isFatal = 1; |
| 387 |
simError(); |
| 388 |
} |
| 389 |
|
| 390 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 391 |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
| 392 |
} |
| 393 |
|
| 394 |
} |
| 395 |
else{ |
| 396 |
fz = NULL; |
| 397 |
indexOfZConsMols = NULL; |
| 398 |
} |
| 399 |
|
| 400 |
} |
| 401 |
|
| 402 |
#endif |
| 403 |
|
| 404 |
/** Function Name: isZConstraintMol |
| 405 |
** Parameter |
| 406 |
** Molecule* mol |
| 407 |
** Return value: |
| 408 |
** -1, if the molecule is not z-constraint molecule, |
| 409 |
** other non-negative values, its index in indexOfAllZConsMols vector |
| 410 |
*/ |
| 411 |
|
| 412 |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
| 413 |
{ |
| 414 |
int index; |
| 415 |
int low; |
| 416 |
int high; |
| 417 |
int mid; |
| 418 |
|
| 419 |
index = mol->getGlobalIndex(); |
| 420 |
|
| 421 |
low = 0; |
| 422 |
high = indexOfAllZConsMols.size() - 1; |
| 423 |
|
| 424 |
//Binary Search (we have sorted the array) |
| 425 |
while(low <= high){ |
| 426 |
mid = (low + high) /2; |
| 427 |
if (indexOfAllZConsMols[mid] == index) |
| 428 |
return mid; |
| 429 |
else if (indexOfAllZConsMols[mid] > index ) |
| 430 |
high = mid -1; |
| 431 |
else |
| 432 |
low = mid + 1; |
| 433 |
} |
| 434 |
|
| 435 |
return -1; |
| 436 |
} |
| 437 |
|
| 438 |
/** Function Name: integrateStep |
| 439 |
** Parameter: |
| 440 |
** int calcPot; |
| 441 |
** int calcStress; |
| 442 |
** Description: |
| 443 |
** Advance One Step. |
| 444 |
** Memo: |
| 445 |
** The best way to implement z-constraint is to override integrateStep |
| 446 |
** Overriding constrainB is not a good choice, since in integrateStep, |
| 447 |
** constrainB is invoked by below line, |
| 448 |
** if(nConstrained) constrainB(); |
| 449 |
** For instance, we would like to apply z-constraint without bond contrain, |
| 450 |
** In that case, if we override constrainB, Z-constrain method will never be executed; |
| 451 |
*/ |
| 452 |
template<typename T> void ZConstraint<T>::integrateStep( int calcPot, int calcStress ) |
| 453 |
{ |
| 454 |
T::integrateStep( calcPot, calcStress ); |
| 455 |
resetZ(); |
| 456 |
|
| 457 |
double currZConsTime = 0; |
| 458 |
|
| 459 |
//write out forces of z constraint |
| 460 |
if( info->getTime() >= currZConsTime){ |
| 461 |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
| 462 |
} |
| 463 |
} |
| 464 |
|
| 465 |
/** Function Name: resetZ |
| 466 |
** Description: |
| 467 |
** Reset the z coordinates |
| 468 |
*/ |
| 469 |
|
| 470 |
template<typename T> void ZConstraint<T>::resetZ() |
| 471 |
{ |
| 472 |
double deltaZ; |
| 473 |
double mzOfZCons; //total sum of m*z of z-constrain molecules |
| 474 |
double mzOfUncons; //total sum of m*z of unconstrain molecuels; |
| 475 |
double totalMZOfZCons; |
| 476 |
double totalMZOfUncons; |
| 477 |
double COM[3]; |
| 478 |
double zsys; |
| 479 |
Atom** zconsAtoms; |
| 480 |
|
| 481 |
mzOfZCons = 0; |
| 482 |
mzOfUncons = 0; |
| 483 |
|
| 484 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 485 |
mzOfZCons += massOfZConsMols[i] * refZ[i]; |
| 486 |
} |
| 487 |
|
| 488 |
#ifdef IS_MPI |
| 489 |
MPI_Allreduce(&mzOfZCons, &totalMZOfZCons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 490 |
#else |
| 491 |
totalMZOfZCons = mzOfZCons; |
| 492 |
#endif |
| 493 |
|
| 494 |
for(int i = 0; i < unconsMols.size(); i++){ |
| 495 |
unconsMols[i]->getCOM(COM); |
| 496 |
mzOfUncons += massOfUnconsMols[i] * COM[2]; |
| 497 |
} |
| 498 |
|
| 499 |
#ifdef IS_MPI |
| 500 |
MPI_Allreduce(&mzOfUncons, &totalMZOfUncons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 501 |
#else |
| 502 |
totalMZOfUncons = mzOfUncons; |
| 503 |
#endif |
| 504 |
|
| 505 |
zsys = (totalMZOfZCons + totalMZOfUncons) /totalMassOfUncons; |
| 506 |
|
| 507 |
cout << "current time: " << info->getTime() <<endl; |
| 508 |
for(int i = 0; i < zconsMols.size(); i++){ |
| 509 |
|
| 510 |
zconsMols[i]->getCOM(COM); |
| 511 |
|
| 512 |
cout << "global index: " << zconsMols[i]->getGlobalIndex() << "\tZ: " << COM[2] << "\t"; |
| 513 |
deltaZ = zsys + refZ[i] - COM[2]; |
| 514 |
cout << "\tdistance: " << COM[2] +deltaZ - zsys; |
| 515 |
//update z coordinate |
| 516 |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
| 517 |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
| 518 |
zconsAtoms[j]->setZ(zconsAtoms[j]->getZ() + deltaZ); |
| 519 |
} |
| 520 |
|
| 521 |
//calculate z constrain force |
| 522 |
fz[i] = massOfZConsMols[i]* deltaZ / dt2; |
| 523 |
|
| 524 |
cout << "\tforce: " << fz[i] << endl; |
| 525 |
} |
| 526 |
|
| 527 |
|
| 528 |
} |
