| 35 |
|
* |
| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 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 "config.h" |
| 44 |
+ |
|
| 45 |
+ |
#ifdef IS_MPI |
| 46 |
+ |
#include <mpi.h> |
| 47 |
+ |
#endif |
| 48 |
|
|
| 49 |
|
#include "io/DumpWriter.hpp" |
| 50 |
|
#include "primitives/Molecule.hpp" |
| 51 |
|
#include "utils/simError.h" |
| 52 |
|
#include "io/basic_teebuf.hpp" |
| 53 |
+ |
#ifdef HAVE_ZLIB |
| 54 |
|
#include "io/gzstream.hpp" |
| 55 |
+ |
#endif |
| 56 |
|
#include "io/Globals.hpp" |
| 57 |
|
|
| 58 |
+ |
#ifdef _MSC_VER |
| 59 |
+ |
#define isnan(x) _isnan((x)) |
| 60 |
+ |
#define isinf(x) (!_finite(x) && !_isnan(x)) |
| 61 |
+ |
#endif |
| 62 |
|
|
| 50 |
– |
#ifdef IS_MPI |
| 51 |
– |
#include <mpi.h> |
| 52 |
– |
#endif //is_mpi |
| 53 |
– |
|
| 63 |
|
using namespace std; |
| 64 |
|
namespace OpenMD { |
| 65 |
|
|
| 66 |
|
DumpWriter::DumpWriter(SimInfo* info) |
| 67 |
< |
: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
| 67 |
> |
: info_(info), filename_(info->getDumpFileName()), |
| 68 |
> |
eorFilename_(info->getFinalConfigFileName()){ |
| 69 |
|
|
| 70 |
|
Globals* simParams = info->getSimParams(); |
| 71 |
< |
needCompression_ = simParams->getCompressDumpFile(); |
| 72 |
< |
needForceVector_ = simParams->getOutputForceVector(); |
| 71 |
> |
needCompression_ = simParams->getCompressDumpFile(); |
| 72 |
> |
needForceVector_ = simParams->getOutputForceVector(); |
| 73 |
> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 74 |
> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
| 75 |
> |
needElectricField_ = simParams->getOutputElectricField(); |
| 76 |
> |
needSitePotential_ = simParams->getOutputSitePotential(); |
| 77 |
> |
|
| 78 |
> |
if (needParticlePot_ || needFlucQ_ || needElectricField_ || |
| 79 |
> |
needSitePotential_) { |
| 80 |
> |
doSiteData_ = true; |
| 81 |
> |
} else { |
| 82 |
> |
doSiteData_ = false; |
| 83 |
> |
} |
| 84 |
> |
|
| 85 |
|
createDumpFile_ = true; |
| 86 |
|
#ifdef HAVE_LIBZ |
| 87 |
|
if (needCompression_) { |
| 119 |
|
Globals* simParams = info->getSimParams(); |
| 120 |
|
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
| 121 |
|
|
| 122 |
< |
needCompression_ = simParams->getCompressDumpFile(); |
| 123 |
< |
needForceVector_ = simParams->getOutputForceVector(); |
| 122 |
> |
needCompression_ = simParams->getCompressDumpFile(); |
| 123 |
> |
needForceVector_ = simParams->getOutputForceVector(); |
| 124 |
> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 125 |
> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
| 126 |
> |
needElectricField_ = simParams->getOutputElectricField(); |
| 127 |
> |
needSitePotential_ = simParams->getOutputSitePotential(); |
| 128 |
> |
|
| 129 |
> |
if (needParticlePot_ || needFlucQ_ || needElectricField_ || |
| 130 |
> |
needSitePotential_) { |
| 131 |
> |
doSiteData_ = true; |
| 132 |
> |
} else { |
| 133 |
> |
doSiteData_ = false; |
| 134 |
> |
} |
| 135 |
> |
|
| 136 |
|
createDumpFile_ = true; |
| 137 |
|
#ifdef HAVE_LIBZ |
| 138 |
|
if (needCompression_) { |
| 170 |
|
Globals* simParams = info->getSimParams(); |
| 171 |
|
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
| 172 |
|
|
| 173 |
< |
needCompression_ = simParams->getCompressDumpFile(); |
| 174 |
< |
needForceVector_ = simParams->getOutputForceVector(); |
| 175 |
< |
|
| 173 |
> |
needCompression_ = simParams->getCompressDumpFile(); |
| 174 |
> |
needForceVector_ = simParams->getOutputForceVector(); |
| 175 |
> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 176 |
> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
| 177 |
> |
needElectricField_ = simParams->getOutputElectricField(); |
| 178 |
> |
needSitePotential_ = simParams->getOutputSitePotential(); |
| 179 |
> |
|
| 180 |
> |
if (needParticlePot_ || needFlucQ_ || needElectricField_ || |
| 181 |
> |
needSitePotential_) { |
| 182 |
> |
doSiteData_ = true; |
| 183 |
> |
} else { |
| 184 |
> |
doSiteData_ = false; |
| 185 |
> |
} |
| 186 |
> |
|
| 187 |
|
#ifdef HAVE_LIBZ |
| 188 |
|
if (needCompression_) { |
| 189 |
|
filename_ += ".gz"; |
| 272 |
|
hmat(0, 2), hmat(1, 2), hmat(2, 2)); |
| 273 |
|
os << buffer; |
| 274 |
|
|
| 275 |
< |
RealType chi = s->getChi(); |
| 276 |
< |
RealType integralOfChiDt = s->getIntegralOfChiDt(); |
| 277 |
< |
if (isinf(chi) || isnan(chi) || |
| 278 |
< |
isinf(integralOfChiDt) || isnan(integralOfChiDt)) { |
| 275 |
> |
pair<RealType, RealType> thermostat = s->getThermostat(); |
| 276 |
> |
|
| 277 |
> |
if (isinf(thermostat.first) || isnan(thermostat.first) || |
| 278 |
> |
isinf(thermostat.second) || isnan(thermostat.second)) { |
| 279 |
|
sprintf( painCave.errMsg, |
| 280 |
|
"DumpWriter detected a numerical error writing the thermostat"); |
| 281 |
|
painCave.isFatal = 1; |
| 282 |
|
simError(); |
| 283 |
|
} |
| 284 |
< |
sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
| 284 |
> |
sprintf(buffer, " Thermostat: %.10g , %.10g\n", thermostat.first, |
| 285 |
> |
thermostat.second); |
| 286 |
|
os << buffer; |
| 287 |
|
|
| 288 |
|
Mat3x3d eta; |
| 289 |
< |
eta = s->getEta(); |
| 289 |
> |
eta = s->getBarostat(); |
| 290 |
|
|
| 291 |
|
for (unsigned int i = 0; i < 3; i++) { |
| 292 |
|
for (unsigned int j = 0; j < 3; j++) { |
| 315 |
|
#endif |
| 316 |
|
|
| 317 |
|
Molecule* mol; |
| 318 |
< |
StuntDouble* integrableObject; |
| 318 |
> |
StuntDouble* sd; |
| 319 |
|
SimInfo::MoleculeIterator mi; |
| 320 |
|
Molecule::IntegrableObjectIterator ii; |
| 321 |
+ |
RigidBody::AtomIterator ai; |
| 322 |
|
|
| 323 |
|
#ifndef IS_MPI |
| 324 |
|
os << " <Snapshot>\n"; |
| 326 |
|
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 327 |
|
|
| 328 |
|
os << " <StuntDoubles>\n"; |
| 329 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 330 |
< |
|
| 329 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 330 |
> |
mol = info_->nextMolecule(mi)) { |
| 331 |
|
|
| 332 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 333 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 334 |
< |
os << prepareDumpLine(integrableObject); |
| 332 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 333 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 334 |
> |
os << prepareDumpLine(sd); |
| 335 |
|
|
| 336 |
|
} |
| 337 |
|
} |
| 338 |
|
os << " </StuntDoubles>\n"; |
| 339 |
< |
|
| 339 |
> |
|
| 340 |
> |
if (doSiteData_) { |
| 341 |
> |
os << " <SiteData>\n"; |
| 342 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 343 |
> |
mol = info_->nextMolecule(mi)) { |
| 344 |
> |
|
| 345 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 346 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 347 |
> |
|
| 348 |
> |
int ioIndex = sd->getGlobalIntegrableObjectIndex(); |
| 349 |
> |
// do one for the IO itself |
| 350 |
> |
os << prepareSiteLine(sd, ioIndex, 0); |
| 351 |
> |
|
| 352 |
> |
if (sd->isRigidBody()) { |
| 353 |
> |
|
| 354 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 355 |
> |
int siteIndex = 0; |
| 356 |
> |
for (Atom* atom = rb->beginAtom(ai); atom != NULL; |
| 357 |
> |
atom = rb->nextAtom(ai)) { |
| 358 |
> |
os << prepareSiteLine(atom, ioIndex, siteIndex); |
| 359 |
> |
siteIndex++; |
| 360 |
> |
} |
| 361 |
> |
} |
| 362 |
> |
} |
| 363 |
> |
} |
| 364 |
> |
os << " </SiteData>\n"; |
| 365 |
> |
} |
| 366 |
|
os << " </Snapshot>\n"; |
| 367 |
|
|
| 368 |
|
os.flush(); |
| 369 |
|
#else |
| 297 |
– |
//every node prepares the dump lines for integrable objects belong to itself |
| 298 |
– |
std::string buffer; |
| 299 |
– |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 370 |
|
|
| 301 |
– |
|
| 302 |
– |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 303 |
– |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 304 |
– |
buffer += prepareDumpLine(integrableObject); |
| 305 |
– |
} |
| 306 |
– |
} |
| 307 |
– |
|
| 371 |
|
const int masterNode = 0; |
| 372 |
+ |
int worldRank; |
| 373 |
+ |
int nProc; |
| 374 |
|
|
| 375 |
+ |
MPI_Comm_size( MPI_COMM_WORLD, &nProc); |
| 376 |
+ |
MPI_Comm_rank( MPI_COMM_WORLD, &worldRank); |
| 377 |
+ |
|
| 378 |
+ |
|
| 379 |
|
if (worldRank == masterNode) { |
| 380 |
|
os << " <Snapshot>\n"; |
| 381 |
< |
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 381 |
> |
writeFrameProperties(os, |
| 382 |
> |
info_->getSnapshotManager()->getCurrentSnapshot()); |
| 383 |
|
os << " <StuntDoubles>\n"; |
| 384 |
< |
|
| 315 |
< |
os << buffer; |
| 384 |
> |
} |
| 385 |
|
|
| 386 |
< |
int nProc; |
| 387 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 386 |
> |
//every node prepares the dump lines for integrable objects belong to itself |
| 387 |
> |
std::string buffer; |
| 388 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 389 |
> |
mol = info_->nextMolecule(mi)) { |
| 390 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 391 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 392 |
> |
buffer += prepareDumpLine(sd); |
| 393 |
> |
} |
| 394 |
> |
} |
| 395 |
> |
|
| 396 |
> |
if (worldRank == masterNode) { |
| 397 |
> |
os << buffer; |
| 398 |
> |
|
| 399 |
|
for (int i = 1; i < nProc; ++i) { |
| 400 |
+ |
// tell processor i to start sending us data: |
| 401 |
+ |
MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 402 |
|
|
| 403 |
|
// receive the length of the string buffer that was |
| 404 |
< |
// prepared by processor i |
| 323 |
< |
|
| 404 |
> |
// prepared by processor i: |
| 405 |
|
int recvLength; |
| 406 |
< |
MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
| 406 |
> |
MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD, |
| 407 |
> |
&istatus); |
| 408 |
> |
|
| 409 |
> |
// create a buffer to receive the data |
| 410 |
|
char* recvBuffer = new char[recvLength]; |
| 411 |
|
if (recvBuffer == NULL) { |
| 412 |
|
} else { |
| 413 |
< |
MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
| 413 |
> |
// receive the data: |
| 414 |
> |
MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, |
| 415 |
> |
MPI_ANY_TAG, MPI_COMM_WORLD, &istatus); |
| 416 |
> |
// send it to the file: |
| 417 |
|
os << recvBuffer; |
| 418 |
+ |
// get rid of the receive buffer: |
| 419 |
|
delete [] recvBuffer; |
| 420 |
|
} |
| 421 |
|
} |
| 334 |
– |
os << " </StuntDoubles>\n"; |
| 335 |
– |
|
| 336 |
– |
os << " </Snapshot>\n"; |
| 337 |
– |
os.flush(); |
| 422 |
|
} else { |
| 423 |
|
int sendBufferLength = buffer.size() + 1; |
| 424 |
< |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 425 |
< |
MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 424 |
> |
int myturn = 0; |
| 425 |
> |
for (int i = 1; i < nProc; ++i){ |
| 426 |
> |
// wait for the master node to call our number: |
| 427 |
> |
MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 428 |
> |
if (myturn == worldRank){ |
| 429 |
> |
// send the length of our buffer: |
| 430 |
> |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 431 |
> |
|
| 432 |
> |
// send our buffer: |
| 433 |
> |
MPI_Send((void *)buffer.c_str(), sendBufferLength, |
| 434 |
> |
MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 435 |
> |
|
| 436 |
> |
} |
| 437 |
> |
} |
| 438 |
|
} |
| 439 |
+ |
|
| 440 |
+ |
if (worldRank == masterNode) { |
| 441 |
+ |
os << " </StuntDoubles>\n"; |
| 442 |
+ |
} |
| 443 |
|
|
| 444 |
< |
#endif // is_mpi |
| 444 |
> |
if (doSiteData_) { |
| 445 |
> |
if (worldRank == masterNode) { |
| 446 |
> |
os << " <SiteData>\n"; |
| 447 |
> |
} |
| 448 |
> |
buffer.clear(); |
| 449 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 450 |
> |
mol = info_->nextMolecule(mi)) { |
| 451 |
> |
|
| 452 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 453 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 454 |
> |
|
| 455 |
> |
int ioIndex = sd->getGlobalIntegrableObjectIndex(); |
| 456 |
> |
// do one for the IO itself |
| 457 |
> |
buffer += prepareSiteLine(sd, ioIndex, 0); |
| 458 |
|
|
| 459 |
< |
} |
| 459 |
> |
if (sd->isRigidBody()) { |
| 460 |
> |
|
| 461 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 462 |
> |
int siteIndex = 0; |
| 463 |
> |
for (Atom* atom = rb->beginAtom(ai); atom != NULL; |
| 464 |
> |
atom = rb->nextAtom(ai)) { |
| 465 |
> |
buffer += prepareSiteLine(atom, ioIndex, siteIndex); |
| 466 |
> |
siteIndex++; |
| 467 |
> |
} |
| 468 |
> |
} |
| 469 |
> |
} |
| 470 |
> |
} |
| 471 |
|
|
| 472 |
< |
std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { |
| 472 |
> |
if (worldRank == masterNode) { |
| 473 |
> |
os << buffer; |
| 474 |
> |
|
| 475 |
> |
for (int i = 1; i < nProc; ++i) { |
| 476 |
> |
|
| 477 |
> |
// tell processor i to start sending us data: |
| 478 |
> |
MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 479 |
> |
|
| 480 |
> |
// receive the length of the string buffer that was |
| 481 |
> |
// prepared by processor i: |
| 482 |
> |
int recvLength; |
| 483 |
> |
MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD, |
| 484 |
> |
&istatus); |
| 485 |
> |
|
| 486 |
> |
// create a buffer to receive the data |
| 487 |
> |
char* recvBuffer = new char[recvLength]; |
| 488 |
> |
if (recvBuffer == NULL) { |
| 489 |
> |
} else { |
| 490 |
> |
// receive the data: |
| 491 |
> |
MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, |
| 492 |
> |
MPI_ANY_TAG, MPI_COMM_WORLD, &istatus); |
| 493 |
> |
// send it to the file: |
| 494 |
> |
os << recvBuffer; |
| 495 |
> |
// get rid of the receive buffer: |
| 496 |
> |
delete [] recvBuffer; |
| 497 |
> |
} |
| 498 |
> |
} |
| 499 |
> |
} else { |
| 500 |
> |
int sendBufferLength = buffer.size() + 1; |
| 501 |
> |
int myturn = 0; |
| 502 |
> |
for (int i = 1; i < nProc; ++i){ |
| 503 |
> |
// wait for the master node to call our number: |
| 504 |
> |
MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 505 |
> |
if (myturn == worldRank){ |
| 506 |
> |
// send the length of our buffer: |
| 507 |
> |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 508 |
> |
// send our buffer: |
| 509 |
> |
MPI_Send((void *)buffer.c_str(), sendBufferLength, |
| 510 |
> |
MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 511 |
> |
} |
| 512 |
> |
} |
| 513 |
> |
} |
| 514 |
> |
|
| 515 |
> |
if (worldRank == masterNode) { |
| 516 |
> |
os << " </SiteData>\n"; |
| 517 |
> |
} |
| 518 |
> |
} |
| 519 |
> |
|
| 520 |
> |
if (worldRank == masterNode) { |
| 521 |
> |
os << " </Snapshot>\n"; |
| 522 |
> |
os.flush(); |
| 523 |
> |
} |
| 524 |
> |
|
| 525 |
> |
#endif // is_mpi |
| 526 |
> |
|
| 527 |
> |
} |
| 528 |
> |
|
| 529 |
> |
std::string DumpWriter::prepareDumpLine(StuntDouble* sd) { |
| 530 |
|
|
| 531 |
< |
int index = integrableObject->getGlobalIntegrableObjectIndex(); |
| 531 |
> |
int index = sd->getGlobalIntegrableObjectIndex(); |
| 532 |
|
std::string type("pv"); |
| 533 |
|
std::string line; |
| 534 |
|
char tempBuffer[4096]; |
| 535 |
|
|
| 536 |
|
Vector3d pos; |
| 537 |
|
Vector3d vel; |
| 538 |
< |
pos = integrableObject->getPos(); |
| 538 |
> |
pos = sd->getPos(); |
| 539 |
|
|
| 540 |
|
if (isinf(pos[0]) || isnan(pos[0]) || |
| 541 |
|
isinf(pos[1]) || isnan(pos[1]) || |
| 547 |
|
simError(); |
| 548 |
|
} |
| 549 |
|
|
| 550 |
< |
vel = integrableObject->getVel(); |
| 550 |
> |
vel = sd->getVel(); |
| 551 |
|
|
| 552 |
|
if (isinf(vel[0]) || isnan(vel[0]) || |
| 553 |
|
isinf(vel[1]) || isnan(vel[1]) || |
| 564 |
|
vel[0], vel[1], vel[2]); |
| 565 |
|
line += tempBuffer; |
| 566 |
|
|
| 567 |
< |
if (integrableObject->isDirectional()) { |
| 567 |
> |
if (sd->isDirectional()) { |
| 568 |
|
type += "qj"; |
| 569 |
|
Quat4d q; |
| 570 |
|
Vector3d ji; |
| 571 |
< |
q = integrableObject->getQ(); |
| 571 |
> |
q = sd->getQ(); |
| 572 |
|
|
| 573 |
|
if (isinf(q[0]) || isnan(q[0]) || |
| 574 |
|
isinf(q[1]) || isnan(q[1]) || |
| 581 |
|
simError(); |
| 582 |
|
} |
| 583 |
|
|
| 584 |
< |
ji = integrableObject->getJ(); |
| 584 |
> |
ji = sd->getJ(); |
| 585 |
|
|
| 586 |
|
if (isinf(ji[0]) || isnan(ji[0]) || |
| 587 |
|
isinf(ji[1]) || isnan(ji[1]) || |
| 601 |
|
|
| 602 |
|
if (needForceVector_) { |
| 603 |
|
type += "f"; |
| 604 |
< |
Vector3d frc; |
| 424 |
< |
|
| 425 |
< |
frc = integrableObject->getFrc(); |
| 426 |
< |
|
| 604 |
> |
Vector3d frc = sd->getFrc(); |
| 605 |
|
if (isinf(frc[0]) || isnan(frc[0]) || |
| 606 |
|
isinf(frc[1]) || isnan(frc[1]) || |
| 607 |
|
isinf(frc[2]) || isnan(frc[2]) ) { |
| 615 |
|
frc[0], frc[1], frc[2]); |
| 616 |
|
line += tempBuffer; |
| 617 |
|
|
| 618 |
< |
if (integrableObject->isDirectional()) { |
| 618 |
> |
if (sd->isDirectional()) { |
| 619 |
|
type += "t"; |
| 620 |
< |
Vector3d trq; |
| 443 |
< |
|
| 444 |
< |
trq = integrableObject->getTrq(); |
| 445 |
< |
|
| 620 |
> |
Vector3d trq = sd->getTrq(); |
| 621 |
|
if (isinf(trq[0]) || isnan(trq[0]) || |
| 622 |
|
isinf(trq[1]) || isnan(trq[1]) || |
| 623 |
|
isinf(trq[2]) || isnan(trq[2]) ) { |
| 626 |
|
" for object %d", index); |
| 627 |
|
painCave.isFatal = 1; |
| 628 |
|
simError(); |
| 629 |
< |
} |
| 455 |
< |
|
| 629 |
> |
} |
| 630 |
|
sprintf(tempBuffer, " %13e %13e %13e", |
| 631 |
|
trq[0], trq[1], trq[2]); |
| 632 |
|
line += tempBuffer; |
| 633 |
|
} |
| 634 |
|
} |
| 635 |
< |
|
| 635 |
> |
|
| 636 |
|
sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
| 637 |
+ |
return std::string(tempBuffer); |
| 638 |
+ |
} |
| 639 |
+ |
|
| 640 |
+ |
std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) { |
| 641 |
+ |
int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
| 642 |
+ |
|
| 643 |
+ |
std::string id; |
| 644 |
+ |
std::string type; |
| 645 |
+ |
std::string line; |
| 646 |
+ |
char tempBuffer[4096]; |
| 647 |
+ |
|
| 648 |
+ |
if (sd->isRigidBody()) { |
| 649 |
+ |
sprintf(tempBuffer, "%10d ", ioIndex); |
| 650 |
+ |
id = std::string(tempBuffer); |
| 651 |
+ |
} else { |
| 652 |
+ |
sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex); |
| 653 |
+ |
id = std::string(tempBuffer); |
| 654 |
+ |
} |
| 655 |
+ |
|
| 656 |
+ |
if (needFlucQ_) { |
| 657 |
+ |
if (storageLayout & DataStorage::dslFlucQPosition) { |
| 658 |
+ |
type += "c"; |
| 659 |
+ |
RealType fqPos = sd->getFlucQPos(); |
| 660 |
+ |
if (isinf(fqPos) || isnan(fqPos) ) { |
| 661 |
+ |
sprintf( painCave.errMsg, |
| 662 |
+ |
"DumpWriter detected a numerical error writing the" |
| 663 |
+ |
" fluctuating charge for object %s", id.c_str()); |
| 664 |
+ |
painCave.isFatal = 1; |
| 665 |
+ |
simError(); |
| 666 |
+ |
} |
| 667 |
+ |
sprintf(tempBuffer, " %13e ", fqPos); |
| 668 |
+ |
line += tempBuffer; |
| 669 |
+ |
} |
| 670 |
+ |
|
| 671 |
+ |
if (storageLayout & DataStorage::dslFlucQVelocity) { |
| 672 |
+ |
type += "w"; |
| 673 |
+ |
RealType fqVel = sd->getFlucQVel(); |
| 674 |
+ |
if (isinf(fqVel) || isnan(fqVel) ) { |
| 675 |
+ |
sprintf( painCave.errMsg, |
| 676 |
+ |
"DumpWriter detected a numerical error writing the" |
| 677 |
+ |
" fluctuating charge velocity for object %s", id.c_str()); |
| 678 |
+ |
painCave.isFatal = 1; |
| 679 |
+ |
simError(); |
| 680 |
+ |
} |
| 681 |
+ |
sprintf(tempBuffer, " %13e ", fqVel); |
| 682 |
+ |
line += tempBuffer; |
| 683 |
+ |
} |
| 684 |
+ |
|
| 685 |
+ |
if (needForceVector_) { |
| 686 |
+ |
if (storageLayout & DataStorage::dslFlucQForce) { |
| 687 |
+ |
type += "g"; |
| 688 |
+ |
RealType fqFrc = sd->getFlucQFrc(); |
| 689 |
+ |
if (isinf(fqFrc) || isnan(fqFrc) ) { |
| 690 |
+ |
sprintf( painCave.errMsg, |
| 691 |
+ |
"DumpWriter detected a numerical error writing the" |
| 692 |
+ |
" fluctuating charge force for object %s", id.c_str()); |
| 693 |
+ |
painCave.isFatal = 1; |
| 694 |
+ |
simError(); |
| 695 |
+ |
} |
| 696 |
+ |
sprintf(tempBuffer, " %13e ", fqFrc); |
| 697 |
+ |
line += tempBuffer; |
| 698 |
+ |
} |
| 699 |
+ |
} |
| 700 |
+ |
} |
| 701 |
+ |
|
| 702 |
+ |
if (needElectricField_) { |
| 703 |
+ |
if (storageLayout & DataStorage::dslElectricField) { |
| 704 |
+ |
type += "e"; |
| 705 |
+ |
Vector3d eField= sd->getElectricField(); |
| 706 |
+ |
if (isinf(eField[0]) || isnan(eField[0]) || |
| 707 |
+ |
isinf(eField[1]) || isnan(eField[1]) || |
| 708 |
+ |
isinf(eField[2]) || isnan(eField[2]) ) { |
| 709 |
+ |
sprintf( painCave.errMsg, |
| 710 |
+ |
"DumpWriter detected a numerical error writing the electric" |
| 711 |
+ |
" field for object %s", id.c_str()); |
| 712 |
+ |
painCave.isFatal = 1; |
| 713 |
+ |
simError(); |
| 714 |
+ |
} |
| 715 |
+ |
sprintf(tempBuffer, " %13e %13e %13e", |
| 716 |
+ |
eField[0], eField[1], eField[2]); |
| 717 |
+ |
line += tempBuffer; |
| 718 |
+ |
} |
| 719 |
+ |
} |
| 720 |
+ |
|
| 721 |
+ |
if (needSitePotential_) { |
| 722 |
+ |
if (storageLayout & DataStorage::dslSitePotential) { |
| 723 |
+ |
type += "s"; |
| 724 |
+ |
RealType sPot = sd->getSitePotential(); |
| 725 |
+ |
if (isinf(sPot) || isnan(sPot) ) { |
| 726 |
+ |
sprintf( painCave.errMsg, |
| 727 |
+ |
"DumpWriter detected a numerical error writing the" |
| 728 |
+ |
" site potential for object %s", id.c_str()); |
| 729 |
+ |
painCave.isFatal = 1; |
| 730 |
+ |
simError(); |
| 731 |
+ |
} |
| 732 |
+ |
sprintf(tempBuffer, " %13e ", sPot); |
| 733 |
+ |
line += tempBuffer; |
| 734 |
+ |
} |
| 735 |
+ |
} |
| 736 |
+ |
|
| 737 |
+ |
if (needParticlePot_) { |
| 738 |
+ |
if (storageLayout & DataStorage::dslParticlePot) { |
| 739 |
+ |
type += "u"; |
| 740 |
+ |
RealType particlePot = sd->getParticlePot(); |
| 741 |
+ |
if (isinf(particlePot) || isnan(particlePot)) { |
| 742 |
+ |
sprintf( painCave.errMsg, |
| 743 |
+ |
"DumpWriter detected a numerical error writing the particle " |
| 744 |
+ |
" potential for object %s", id.c_str()); |
| 745 |
+ |
painCave.isFatal = 1; |
| 746 |
+ |
simError(); |
| 747 |
+ |
} |
| 748 |
+ |
sprintf(tempBuffer, " %13e", particlePot); |
| 749 |
+ |
line += tempBuffer; |
| 750 |
+ |
} |
| 751 |
+ |
} |
| 752 |
+ |
|
| 753 |
+ |
sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str()); |
| 754 |
|
return std::string(tempBuffer); |
| 755 |
|
} |
| 756 |
|
|
| 759 |
|
} |
| 760 |
|
|
| 761 |
|
void DumpWriter::writeEor() { |
| 762 |
< |
std::ostream* eorStream; |
| 763 |
< |
|
| 762 |
> |
|
| 763 |
> |
std::ostream* eorStream = NULL; |
| 764 |
> |
|
| 765 |
|
#ifdef IS_MPI |
| 766 |
|
if (worldRank == 0) { |
| 767 |
|
#endif // is_mpi |
| 768 |
< |
|
| 768 |
> |
|
| 769 |
|
eorStream = createOStream(eorFilename_); |
| 770 |
|
|
| 771 |
|
#ifdef IS_MPI |
| 772 |
|
} |
| 773 |
< |
#endif // is_mpi |
| 774 |
< |
|
| 773 |
> |
#endif |
| 774 |
> |
|
| 775 |
|
writeFrame(*eorStream); |
| 776 |
< |
|
| 776 |
> |
|
| 777 |
|
#ifdef IS_MPI |
| 778 |
|
if (worldRank == 0) { |
| 779 |
< |
#endif // is_mpi |
| 779 |
> |
#endif |
| 780 |
> |
|
| 781 |
|
writeClosing(*eorStream); |
| 782 |
|
delete eorStream; |
| 783 |
+ |
|
| 784 |
|
#ifdef IS_MPI |
| 785 |
|
} |
| 786 |
|
#endif // is_mpi |
| 794 |
|
#ifdef IS_MPI |
| 795 |
|
if (worldRank == 0) { |
| 796 |
|
#endif // is_mpi |
| 503 |
– |
|
| 797 |
|
buffers.push_back(dumpFile_->rdbuf()); |
| 505 |
– |
|
| 798 |
|
eorStream = createOStream(eorFilename_); |
| 507 |
– |
|
| 799 |
|
buffers.push_back(eorStream->rdbuf()); |
| 509 |
– |
|
| 800 |
|
#ifdef IS_MPI |
| 801 |
|
} |
| 802 |
|
#endif // is_mpi |
| 803 |
|
|
| 804 |
|
TeeBuf tbuf(buffers.begin(), buffers.end()); |
| 805 |
|
std::ostream os(&tbuf); |
| 516 |
– |
|
| 806 |
|
writeFrame(os); |
| 807 |
|
|
| 808 |
|
#ifdef IS_MPI |
| 812 |
|
delete eorStream; |
| 813 |
|
#ifdef IS_MPI |
| 814 |
|
} |
| 815 |
< |
#endif // is_mpi |
| 527 |
< |
|
| 815 |
> |
#endif // is_mpi |
| 816 |
|
} |
| 817 |
|
|
| 818 |
|
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
| 819 |
|
|
| 820 |
|
std::ostream* newOStream; |
| 821 |
< |
#ifdef HAVE_LIBZ |
| 821 |
> |
#ifdef HAVE_ZLIB |
| 822 |
|
if (needCompression_) { |
| 823 |
|
newOStream = new ogzstream(filename.c_str()); |
| 824 |
|
} else { |
| 828 |
|
newOStream = new std::ofstream(filename.c_str()); |
| 829 |
|
#endif |
| 830 |
|
//write out MetaData first |
| 831 |
< |
(*newOStream) << "<OpenMD version=1>" << std::endl; |
| 831 |
> |
(*newOStream) << "<OpenMD version=2>" << std::endl; |
| 832 |
|
(*newOStream) << " <MetaData>" << std::endl; |
| 833 |
|
(*newOStream) << info_->getRawMetaData(); |
| 834 |
|
(*newOStream) << " </MetaData>" << std::endl; |
