| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "io/DumpWriter.hpp" |
| 47 |
|
#include "io/gzstream.hpp" |
| 48 |
|
#include "io/Globals.hpp" |
| 49 |
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|
| 50 |
+ |
|
| 51 |
|
#ifdef IS_MPI |
| 52 |
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#include <mpi.h> |
| 53 |
|
#endif //is_mpi |
| 54 |
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|
| 55 |
+ |
using namespace std; |
| 56 |
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namespace OpenMD { |
| 57 |
|
|
| 58 |
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DumpWriter::DumpWriter(SimInfo* info) |
| 61 |
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Globals* simParams = info->getSimParams(); |
| 62 |
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needCompression_ = simParams->getCompressDumpFile(); |
| 63 |
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needForceVector_ = simParams->getOutputForceVector(); |
| 64 |
+ |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 65 |
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createDumpFile_ = true; |
| 66 |
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#ifdef HAVE_LIBZ |
| 67 |
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if (needCompression_) { |
| 140 |
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|
| 141 |
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needCompression_ = simParams->getCompressDumpFile(); |
| 142 |
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needForceVector_ = simParams->getOutputForceVector(); |
| 143 |
+ |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 144 |
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|
| 145 |
|
#ifdef HAVE_LIBZ |
| 146 |
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if (needCompression_) { |
| 199 |
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os << " <FrameData>\n"; |
| 200 |
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|
| 201 |
|
RealType currentTime = s->getTime(); |
| 202 |
+ |
|
| 203 |
+ |
if (isinf(currentTime) || isnan(currentTime)) { |
| 204 |
+ |
sprintf( painCave.errMsg, |
| 205 |
+ |
"DumpWriter detected a numerical error writing the time"); |
| 206 |
+ |
painCave.isFatal = 1; |
| 207 |
+ |
simError(); |
| 208 |
+ |
} |
| 209 |
+ |
|
| 210 |
|
sprintf(buffer, " Time: %.10g\n", currentTime); |
| 211 |
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os << buffer; |
| 212 |
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|
| 213 |
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Mat3x3d hmat; |
| 214 |
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hmat = s->getHmat(); |
| 215 |
+ |
|
| 216 |
+ |
for (unsigned int i = 0; i < 3; i++) { |
| 217 |
+ |
for (unsigned int j = 0; j < 3; j++) { |
| 218 |
+ |
if (isinf(hmat(i,j)) || isnan(hmat(i,j))) { |
| 219 |
+ |
sprintf( painCave.errMsg, |
| 220 |
+ |
"DumpWriter detected a numerical error writing the box"); |
| 221 |
+ |
painCave.isFatal = 1; |
| 222 |
+ |
simError(); |
| 223 |
+ |
} |
| 224 |
+ |
} |
| 225 |
+ |
} |
| 226 |
+ |
|
| 227 |
|
sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
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hmat(0, 0), hmat(1, 0), hmat(2, 0), |
| 229 |
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hmat(0, 1), hmat(1, 1), hmat(2, 1), |
| 232 |
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|
| 233 |
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RealType chi = s->getChi(); |
| 234 |
|
RealType integralOfChiDt = s->getIntegralOfChiDt(); |
| 235 |
+ |
if (isinf(chi) || isnan(chi) || |
| 236 |
+ |
isinf(integralOfChiDt) || isnan(integralOfChiDt)) { |
| 237 |
+ |
sprintf( painCave.errMsg, |
| 238 |
+ |
"DumpWriter detected a numerical error writing the thermostat"); |
| 239 |
+ |
painCave.isFatal = 1; |
| 240 |
+ |
simError(); |
| 241 |
+ |
} |
| 242 |
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sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
| 243 |
|
os << buffer; |
| 244 |
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|
| 245 |
|
Mat3x3d eta; |
| 246 |
|
eta = s->getEta(); |
| 247 |
+ |
|
| 248 |
+ |
for (unsigned int i = 0; i < 3; i++) { |
| 249 |
+ |
for (unsigned int j = 0; j < 3; j++) { |
| 250 |
+ |
if (isinf(eta(i,j)) || isnan(eta(i,j))) { |
| 251 |
+ |
sprintf( painCave.errMsg, |
| 252 |
+ |
"DumpWriter detected a numerical error writing the barostat"); |
| 253 |
+ |
painCave.isFatal = 1; |
| 254 |
+ |
simError(); |
| 255 |
+ |
} |
| 256 |
+ |
} |
| 257 |
+ |
} |
| 258 |
+ |
|
| 259 |
|
sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
| 260 |
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eta(0, 0), eta(1, 0), eta(2, 0), |
| 261 |
|
eta(0, 1), eta(1, 1), eta(2, 1), |
| 309 |
|
} |
| 310 |
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|
| 311 |
|
const int masterNode = 0; |
| 312 |
< |
|
| 312 |
> |
int nProc; |
| 313 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 314 |
|
if (worldRank == masterNode) { |
| 315 |
|
os << " <Snapshot>\n"; |
| 316 |
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writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 318 |
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|
| 319 |
|
os << buffer; |
| 320 |
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|
| 276 |
– |
int nProc; |
| 277 |
– |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 321 |
|
for (int i = 1; i < nProc; ++i) { |
| 322 |
|
|
| 323 |
|
// receive the length of the string buffer that was |
| 324 |
|
// prepared by processor i |
| 325 |
|
|
| 326 |
+ |
MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD); |
| 327 |
|
int recvLength; |
| 328 |
|
MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
| 329 |
|
char* recvBuffer = new char[recvLength]; |
| 340 |
|
os.flush(); |
| 341 |
|
} else { |
| 342 |
|
int sendBufferLength = buffer.size() + 1; |
| 343 |
< |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 344 |
< |
MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 343 |
> |
int myturn = 0; |
| 344 |
> |
for (int i = 1; i < nProc; ++i){ |
| 345 |
> |
MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD); |
| 346 |
> |
if (myturn == worldRank){ |
| 347 |
> |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 348 |
> |
MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 349 |
> |
} |
| 350 |
> |
} |
| 351 |
|
} |
| 352 |
|
|
| 353 |
|
#endif // is_mpi |
| 364 |
|
Vector3d pos; |
| 365 |
|
Vector3d vel; |
| 366 |
|
pos = integrableObject->getPos(); |
| 367 |
+ |
|
| 368 |
+ |
if (isinf(pos[0]) || isnan(pos[0]) || |
| 369 |
+ |
isinf(pos[1]) || isnan(pos[1]) || |
| 370 |
+ |
isinf(pos[2]) || isnan(pos[2]) ) { |
| 371 |
+ |
sprintf( painCave.errMsg, |
| 372 |
+ |
"DumpWriter detected a numerical error writing the position" |
| 373 |
+ |
" for object %d", index); |
| 374 |
+ |
painCave.isFatal = 1; |
| 375 |
+ |
simError(); |
| 376 |
+ |
} |
| 377 |
+ |
|
| 378 |
|
vel = integrableObject->getVel(); |
| 379 |
+ |
|
| 380 |
+ |
if (isinf(vel[0]) || isnan(vel[0]) || |
| 381 |
+ |
isinf(vel[1]) || isnan(vel[1]) || |
| 382 |
+ |
isinf(vel[2]) || isnan(vel[2]) ) { |
| 383 |
+ |
sprintf( painCave.errMsg, |
| 384 |
+ |
"DumpWriter detected a numerical error writing the velocity" |
| 385 |
+ |
" for object %d", index); |
| 386 |
+ |
painCave.isFatal = 1; |
| 387 |
+ |
simError(); |
| 388 |
+ |
} |
| 389 |
+ |
|
| 390 |
|
sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", |
| 391 |
|
pos[0], pos[1], pos[2], |
| 392 |
|
vel[0], vel[1], vel[2]); |
| 397 |
|
Quat4d q; |
| 398 |
|
Vector3d ji; |
| 399 |
|
q = integrableObject->getQ(); |
| 400 |
+ |
|
| 401 |
+ |
if (isinf(q[0]) || isnan(q[0]) || |
| 402 |
+ |
isinf(q[1]) || isnan(q[1]) || |
| 403 |
+ |
isinf(q[2]) || isnan(q[2]) || |
| 404 |
+ |
isinf(q[3]) || isnan(q[3]) ) { |
| 405 |
+ |
sprintf( painCave.errMsg, |
| 406 |
+ |
"DumpWriter detected a numerical error writing the quaternion" |
| 407 |
+ |
" for object %d", index); |
| 408 |
+ |
painCave.isFatal = 1; |
| 409 |
+ |
simError(); |
| 410 |
+ |
} |
| 411 |
+ |
|
| 412 |
|
ji = integrableObject->getJ(); |
| 413 |
+ |
|
| 414 |
+ |
if (isinf(ji[0]) || isnan(ji[0]) || |
| 415 |
+ |
isinf(ji[1]) || isnan(ji[1]) || |
| 416 |
+ |
isinf(ji[2]) || isnan(ji[2]) ) { |
| 417 |
+ |
sprintf( painCave.errMsg, |
| 418 |
+ |
"DumpWriter detected a numerical error writing the angular" |
| 419 |
+ |
" momentum for object %d", index); |
| 420 |
+ |
painCave.isFatal = 1; |
| 421 |
+ |
simError(); |
| 422 |
+ |
} |
| 423 |
+ |
|
| 424 |
|
sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
| 425 |
|
q[0], q[1], q[2], q[3], |
| 426 |
|
ji[0], ji[1], ji[2]); |
| 428 |
|
} |
| 429 |
|
|
| 430 |
|
if (needForceVector_) { |
| 431 |
< |
type += "ft"; |
| 431 |
> |
type += "f"; |
| 432 |
|
Vector3d frc; |
| 433 |
< |
Vector3d trq; |
| 433 |
> |
|
| 434 |
|
frc = integrableObject->getFrc(); |
| 435 |
< |
trq = integrableObject->getTrq(); |
| 436 |
< |
|
| 437 |
< |
sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e", |
| 438 |
< |
frc[0], frc[1], frc[2], |
| 439 |
< |
trq[0], trq[1], trq[2]); |
| 435 |
> |
|
| 436 |
> |
if (isinf(frc[0]) || isnan(frc[0]) || |
| 437 |
> |
isinf(frc[1]) || isnan(frc[1]) || |
| 438 |
> |
isinf(frc[2]) || isnan(frc[2]) ) { |
| 439 |
> |
sprintf( painCave.errMsg, |
| 440 |
> |
"DumpWriter detected a numerical error writing the force" |
| 441 |
> |
" for object %d", index); |
| 442 |
> |
painCave.isFatal = 1; |
| 443 |
> |
simError(); |
| 444 |
> |
} |
| 445 |
> |
sprintf(tempBuffer, " %13e %13e %13e", |
| 446 |
> |
frc[0], frc[1], frc[2]); |
| 447 |
|
line += tempBuffer; |
| 448 |
+ |
|
| 449 |
+ |
if (integrableObject->isDirectional()) { |
| 450 |
+ |
type += "t"; |
| 451 |
+ |
Vector3d trq; |
| 452 |
+ |
|
| 453 |
+ |
trq = integrableObject->getTrq(); |
| 454 |
+ |
|
| 455 |
+ |
if (isinf(trq[0]) || isnan(trq[0]) || |
| 456 |
+ |
isinf(trq[1]) || isnan(trq[1]) || |
| 457 |
+ |
isinf(trq[2]) || isnan(trq[2]) ) { |
| 458 |
+ |
sprintf( painCave.errMsg, |
| 459 |
+ |
"DumpWriter detected a numerical error writing the torque" |
| 460 |
+ |
" for object %d", index); |
| 461 |
+ |
painCave.isFatal = 1; |
| 462 |
+ |
simError(); |
| 463 |
+ |
} |
| 464 |
+ |
|
| 465 |
+ |
sprintf(tempBuffer, " %13e %13e %13e", |
| 466 |
+ |
trq[0], trq[1], trq[2]); |
| 467 |
+ |
line += tempBuffer; |
| 468 |
+ |
} |
| 469 |
|
} |
| 470 |
< |
|
| 470 |
> |
if (needParticlePot_) { |
| 471 |
> |
type += "u"; |
| 472 |
> |
RealType particlePot; |
| 473 |
> |
|
| 474 |
> |
particlePot = integrableObject->getParticlePot(); |
| 475 |
> |
|
| 476 |
> |
if (isinf(particlePot) || isnan(particlePot)) { |
| 477 |
> |
sprintf( painCave.errMsg, |
| 478 |
> |
"DumpWriter detected a numerical error writing the particle " |
| 479 |
> |
" potential for object %d", index); |
| 480 |
> |
painCave.isFatal = 1; |
| 481 |
> |
simError(); |
| 482 |
> |
} |
| 483 |
> |
sprintf(tempBuffer, " %13e", particlePot); |
| 484 |
> |
line += tempBuffer; |
| 485 |
> |
} |
| 486 |
> |
|
| 487 |
|
sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
| 488 |
|
return std::string(tempBuffer); |
| 489 |
|
} |
