| 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 "io/DumpWriter.hpp" |
| 44 |
|
#include "primitives/Molecule.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
|
#include "io/basic_teebuf.hpp" |
| 47 |
+ |
#ifdef HAVE_ZLIB |
| 48 |
|
#include "io/gzstream.hpp" |
| 49 |
+ |
#endif |
| 50 |
|
#include "io/Globals.hpp" |
| 51 |
|
|
| 52 |
+ |
#ifdef _MSC_VER |
| 53 |
+ |
#define isnan(x) _isnan((x)) |
| 54 |
+ |
#define isinf(x) (!_finite(x) && !_isnan(x)) |
| 55 |
+ |
#endif |
| 56 |
|
|
| 57 |
|
#ifdef IS_MPI |
| 58 |
|
#include <mpi.h> |
| 59 |
< |
#endif //is_mpi |
| 59 |
> |
#endif |
| 60 |
|
|
| 61 |
|
using namespace std; |
| 62 |
|
namespace OpenMD { |
| 65 |
|
: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
| 66 |
|
|
| 67 |
|
Globals* simParams = info->getSimParams(); |
| 68 |
< |
needCompression_ = simParams->getCompressDumpFile(); |
| 69 |
< |
needForceVector_ = simParams->getOutputForceVector(); |
| 68 |
> |
needCompression_ = simParams->getCompressDumpFile(); |
| 69 |
> |
needForceVector_ = simParams->getOutputForceVector(); |
| 70 |
> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 71 |
> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
| 72 |
> |
needElectricField_ = simParams->getOutputElectricField(); |
| 73 |
> |
|
| 74 |
> |
if (needParticlePot_ || needFlucQ_ || needElectricField_) { |
| 75 |
> |
doSiteData_ = true; |
| 76 |
> |
} else { |
| 77 |
> |
doSiteData_ = false; |
| 78 |
> |
} |
| 79 |
> |
|
| 80 |
|
createDumpFile_ = true; |
| 81 |
|
#ifdef HAVE_LIBZ |
| 82 |
|
if (needCompression_) { |
| 114 |
|
Globals* simParams = info->getSimParams(); |
| 115 |
|
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
| 116 |
|
|
| 117 |
< |
needCompression_ = simParams->getCompressDumpFile(); |
| 118 |
< |
needForceVector_ = simParams->getOutputForceVector(); |
| 117 |
> |
needCompression_ = simParams->getCompressDumpFile(); |
| 118 |
> |
needForceVector_ = simParams->getOutputForceVector(); |
| 119 |
> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 120 |
> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
| 121 |
> |
needElectricField_ = simParams->getOutputElectricField(); |
| 122 |
> |
|
| 123 |
> |
if (needParticlePot_ || needFlucQ_ || needElectricField_) { |
| 124 |
> |
doSiteData_ = true; |
| 125 |
> |
} else { |
| 126 |
> |
doSiteData_ = false; |
| 127 |
> |
} |
| 128 |
> |
|
| 129 |
|
createDumpFile_ = true; |
| 130 |
|
#ifdef HAVE_LIBZ |
| 131 |
|
if (needCompression_) { |
| 163 |
|
Globals* simParams = info->getSimParams(); |
| 164 |
|
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
| 165 |
|
|
| 166 |
< |
needCompression_ = simParams->getCompressDumpFile(); |
| 167 |
< |
needForceVector_ = simParams->getOutputForceVector(); |
| 168 |
< |
|
| 166 |
> |
needCompression_ = simParams->getCompressDumpFile(); |
| 167 |
> |
needForceVector_ = simParams->getOutputForceVector(); |
| 168 |
> |
needParticlePot_ = simParams->getOutputParticlePotential(); |
| 169 |
> |
needFlucQ_ = simParams->getOutputFluctuatingCharges(); |
| 170 |
> |
needElectricField_ = simParams->getOutputElectricField(); |
| 171 |
> |
|
| 172 |
> |
if (needParticlePot_ || needFlucQ_ || needElectricField_) { |
| 173 |
> |
doSiteData_ = true; |
| 174 |
> |
} else { |
| 175 |
> |
doSiteData_ = false; |
| 176 |
> |
} |
| 177 |
> |
|
| 178 |
|
#ifdef HAVE_LIBZ |
| 179 |
|
if (needCompression_) { |
| 180 |
|
filename_ += ".gz"; |
| 263 |
|
hmat(0, 2), hmat(1, 2), hmat(2, 2)); |
| 264 |
|
os << buffer; |
| 265 |
|
|
| 266 |
< |
RealType chi = s->getChi(); |
| 267 |
< |
RealType integralOfChiDt = s->getIntegralOfChiDt(); |
| 268 |
< |
if (isinf(chi) || isnan(chi) || |
| 269 |
< |
isinf(integralOfChiDt) || isnan(integralOfChiDt)) { |
| 266 |
> |
pair<RealType, RealType> thermostat = s->getThermostat(); |
| 267 |
> |
|
| 268 |
> |
if (isinf(thermostat.first) || isnan(thermostat.first) || |
| 269 |
> |
isinf(thermostat.second) || isnan(thermostat.second)) { |
| 270 |
|
sprintf( painCave.errMsg, |
| 271 |
|
"DumpWriter detected a numerical error writing the thermostat"); |
| 272 |
|
painCave.isFatal = 1; |
| 273 |
|
simError(); |
| 274 |
|
} |
| 275 |
< |
sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
| 275 |
> |
sprintf(buffer, " Thermostat: %.10g , %.10g\n", thermostat.first, |
| 276 |
> |
thermostat.second); |
| 277 |
|
os << buffer; |
| 278 |
|
|
| 279 |
|
Mat3x3d eta; |
| 280 |
< |
eta = s->getEta(); |
| 280 |
> |
eta = s->getBarostat(); |
| 281 |
|
|
| 282 |
|
for (unsigned int i = 0; i < 3; i++) { |
| 283 |
|
for (unsigned int j = 0; j < 3; j++) { |
| 302 |
|
void DumpWriter::writeFrame(std::ostream& os) { |
| 303 |
|
|
| 304 |
|
#ifdef IS_MPI |
| 305 |
< |
MPI_Status istatus; |
| 305 |
> |
MPI::Status istatus; |
| 306 |
|
#endif |
| 307 |
|
|
| 308 |
|
Molecule* mol; |
| 309 |
< |
StuntDouble* integrableObject; |
| 309 |
> |
StuntDouble* sd; |
| 310 |
|
SimInfo::MoleculeIterator mi; |
| 311 |
|
Molecule::IntegrableObjectIterator ii; |
| 312 |
+ |
RigidBody::AtomIterator ai; |
| 313 |
|
|
| 314 |
|
#ifndef IS_MPI |
| 315 |
|
os << " <Snapshot>\n"; |
| 317 |
|
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 318 |
|
|
| 319 |
|
os << " <StuntDoubles>\n"; |
| 320 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 321 |
< |
|
| 320 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 321 |
> |
mol = info_->nextMolecule(mi)) { |
| 322 |
|
|
| 323 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 324 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 325 |
< |
os << prepareDumpLine(integrableObject); |
| 323 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 324 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 325 |
> |
os << prepareDumpLine(sd); |
| 326 |
|
|
| 327 |
|
} |
| 328 |
|
} |
| 329 |
|
os << " </StuntDoubles>\n"; |
| 330 |
< |
|
| 330 |
> |
|
| 331 |
> |
if (doSiteData_) { |
| 332 |
> |
os << " <SiteData>\n"; |
| 333 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 334 |
> |
mol = info_->nextMolecule(mi)) { |
| 335 |
> |
|
| 336 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 337 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 338 |
> |
|
| 339 |
> |
int ioIndex = sd->getGlobalIntegrableObjectIndex(); |
| 340 |
> |
// do one for the IO itself |
| 341 |
> |
os << prepareSiteLine(sd, ioIndex, 0); |
| 342 |
> |
|
| 343 |
> |
if (sd->isRigidBody()) { |
| 344 |
> |
|
| 345 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 346 |
> |
int siteIndex = 0; |
| 347 |
> |
for (Atom* atom = rb->beginAtom(ai); atom != NULL; |
| 348 |
> |
atom = rb->nextAtom(ai)) { |
| 349 |
> |
os << prepareSiteLine(atom, ioIndex, siteIndex); |
| 350 |
> |
siteIndex++; |
| 351 |
> |
} |
| 352 |
> |
} |
| 353 |
> |
} |
| 354 |
> |
} |
| 355 |
> |
os << " </SiteData>\n"; |
| 356 |
> |
} |
| 357 |
|
os << " </Snapshot>\n"; |
| 358 |
|
|
| 359 |
|
os.flush(); |
| 360 |
|
#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)) { |
| 361 |
|
|
| 301 |
– |
|
| 302 |
– |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 303 |
– |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 304 |
– |
buffer += prepareDumpLine(integrableObject); |
| 305 |
– |
} |
| 306 |
– |
} |
| 307 |
– |
|
| 362 |
|
const int masterNode = 0; |
| 363 |
+ |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 364 |
+ |
int nProc = MPI::COMM_WORLD.Get_size(); |
| 365 |
|
|
| 366 |
|
if (worldRank == masterNode) { |
| 367 |
|
os << " <Snapshot>\n"; |
| 368 |
< |
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 368 |
> |
writeFrameProperties(os, |
| 369 |
> |
info_->getSnapshotManager()->getCurrentSnapshot()); |
| 370 |
|
os << " <StuntDoubles>\n"; |
| 371 |
< |
|
| 315 |
< |
os << buffer; |
| 371 |
> |
} |
| 372 |
|
|
| 373 |
< |
int nProc; |
| 374 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 373 |
> |
//every node prepares the dump lines for integrable objects belong to itself |
| 374 |
> |
std::string buffer; |
| 375 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 376 |
> |
mol = info_->nextMolecule(mi)) { |
| 377 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 378 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 379 |
> |
buffer += prepareDumpLine(sd); |
| 380 |
> |
} |
| 381 |
> |
} |
| 382 |
> |
|
| 383 |
> |
if (worldRank == masterNode) { |
| 384 |
> |
os << buffer; |
| 385 |
> |
|
| 386 |
|
for (int i = 1; i < nProc; ++i) { |
| 387 |
+ |
// tell processor i to start sending us data: |
| 388 |
+ |
MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode); |
| 389 |
|
|
| 390 |
|
// receive the length of the string buffer that was |
| 391 |
< |
// prepared by processor i |
| 323 |
< |
|
| 391 |
> |
// prepared by processor i: |
| 392 |
|
int recvLength; |
| 393 |
< |
MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
| 393 |
> |
MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG, |
| 394 |
> |
istatus); |
| 395 |
> |
|
| 396 |
> |
// create a buffer to receive the data |
| 397 |
|
char* recvBuffer = new char[recvLength]; |
| 398 |
|
if (recvBuffer == NULL) { |
| 399 |
|
} else { |
| 400 |
< |
MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
| 400 |
> |
// receive the data: |
| 401 |
> |
MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i, |
| 402 |
> |
MPI::ANY_TAG, istatus); |
| 403 |
> |
// send it to the file: |
| 404 |
|
os << recvBuffer; |
| 405 |
+ |
// get rid of the receive buffer: |
| 406 |
|
delete [] recvBuffer; |
| 407 |
|
} |
| 408 |
|
} |
| 334 |
– |
os << " </StuntDoubles>\n"; |
| 335 |
– |
|
| 336 |
– |
os << " </Snapshot>\n"; |
| 337 |
– |
os.flush(); |
| 409 |
|
} else { |
| 410 |
|
int sendBufferLength = buffer.size() + 1; |
| 411 |
< |
MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 412 |
< |
MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
| 411 |
> |
int myturn = 0; |
| 412 |
> |
for (int i = 1; i < nProc; ++i){ |
| 413 |
> |
// wait for the master node to call our number: |
| 414 |
> |
MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode); |
| 415 |
> |
if (myturn == worldRank){ |
| 416 |
> |
// send the length of our buffer: |
| 417 |
> |
MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0); |
| 418 |
> |
|
| 419 |
> |
// send our buffer: |
| 420 |
> |
MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength, |
| 421 |
> |
MPI::CHAR, masterNode, 0); |
| 422 |
> |
} |
| 423 |
> |
} |
| 424 |
|
} |
| 425 |
+ |
|
| 426 |
+ |
if (worldRank == masterNode) { |
| 427 |
+ |
os << " </StuntDoubles>\n"; |
| 428 |
+ |
} |
| 429 |
|
|
| 430 |
< |
#endif // is_mpi |
| 430 |
> |
if (doSiteData_) { |
| 431 |
> |
if (worldRank == masterNode) { |
| 432 |
> |
os << " <SiteData>\n"; |
| 433 |
> |
} |
| 434 |
> |
buffer.clear(); |
| 435 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 436 |
> |
mol = info_->nextMolecule(mi)) { |
| 437 |
> |
|
| 438 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 439 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 440 |
> |
|
| 441 |
> |
int ioIndex = sd->getGlobalIntegrableObjectIndex(); |
| 442 |
> |
// do one for the IO itself |
| 443 |
> |
buffer += prepareSiteLine(sd, ioIndex, 0); |
| 444 |
> |
|
| 445 |
> |
if (sd->isRigidBody()) { |
| 446 |
> |
|
| 447 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 448 |
> |
int siteIndex = 0; |
| 449 |
> |
for (Atom* atom = rb->beginAtom(ai); atom != NULL; |
| 450 |
> |
atom = rb->nextAtom(ai)) { |
| 451 |
> |
buffer += prepareSiteLine(atom, ioIndex, siteIndex); |
| 452 |
> |
siteIndex++; |
| 453 |
> |
} |
| 454 |
> |
} |
| 455 |
> |
} |
| 456 |
> |
} |
| 457 |
|
|
| 458 |
+ |
if (worldRank == masterNode) { |
| 459 |
+ |
os << buffer; |
| 460 |
+ |
|
| 461 |
+ |
for (int i = 1; i < nProc; ++i) { |
| 462 |
+ |
|
| 463 |
+ |
// tell processor i to start sending us data: |
| 464 |
+ |
MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode); |
| 465 |
+ |
|
| 466 |
+ |
// receive the length of the string buffer that was |
| 467 |
+ |
// prepared by processor i: |
| 468 |
+ |
int recvLength; |
| 469 |
+ |
MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG, |
| 470 |
+ |
istatus); |
| 471 |
+ |
|
| 472 |
+ |
// create a buffer to receive the data |
| 473 |
+ |
char* recvBuffer = new char[recvLength]; |
| 474 |
+ |
if (recvBuffer == NULL) { |
| 475 |
+ |
} else { |
| 476 |
+ |
// receive the data: |
| 477 |
+ |
MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i, |
| 478 |
+ |
MPI::ANY_TAG, istatus); |
| 479 |
+ |
// send it to the file: |
| 480 |
+ |
os << recvBuffer; |
| 481 |
+ |
// get rid of the receive buffer: |
| 482 |
+ |
delete [] recvBuffer; |
| 483 |
+ |
} |
| 484 |
+ |
} |
| 485 |
+ |
} else { |
| 486 |
+ |
int sendBufferLength = buffer.size() + 1; |
| 487 |
+ |
int myturn = 0; |
| 488 |
+ |
for (int i = 1; i < nProc; ++i){ |
| 489 |
+ |
// wait for the master node to call our number: |
| 490 |
+ |
MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode); |
| 491 |
+ |
if (myturn == worldRank){ |
| 492 |
+ |
// send the length of our buffer: |
| 493 |
+ |
MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0); |
| 494 |
+ |
// send our buffer: |
| 495 |
+ |
MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength, |
| 496 |
+ |
MPI::CHAR, masterNode, 0); |
| 497 |
+ |
} |
| 498 |
+ |
} |
| 499 |
+ |
} |
| 500 |
+ |
|
| 501 |
+ |
if (worldRank == masterNode) { |
| 502 |
+ |
os << " </SiteData>\n"; |
| 503 |
+ |
} |
| 504 |
+ |
} |
| 505 |
+ |
|
| 506 |
+ |
if (worldRank == masterNode) { |
| 507 |
+ |
os << " </Snapshot>\n"; |
| 508 |
+ |
os.flush(); |
| 509 |
+ |
} |
| 510 |
+ |
|
| 511 |
+ |
#endif // is_mpi |
| 512 |
+ |
|
| 513 |
|
} |
| 514 |
|
|
| 515 |
< |
std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { |
| 515 |
> |
std::string DumpWriter::prepareDumpLine(StuntDouble* sd) { |
| 516 |
|
|
| 517 |
< |
int index = integrableObject->getGlobalIntegrableObjectIndex(); |
| 517 |
> |
int index = sd->getGlobalIntegrableObjectIndex(); |
| 518 |
|
std::string type("pv"); |
| 519 |
|
std::string line; |
| 520 |
|
char tempBuffer[4096]; |
| 521 |
|
|
| 522 |
|
Vector3d pos; |
| 523 |
|
Vector3d vel; |
| 524 |
< |
pos = integrableObject->getPos(); |
| 524 |
> |
pos = sd->getPos(); |
| 525 |
|
|
| 526 |
|
if (isinf(pos[0]) || isnan(pos[0]) || |
| 527 |
|
isinf(pos[1]) || isnan(pos[1]) || |
| 533 |
|
simError(); |
| 534 |
|
} |
| 535 |
|
|
| 536 |
< |
vel = integrableObject->getVel(); |
| 536 |
> |
vel = sd->getVel(); |
| 537 |
|
|
| 538 |
|
if (isinf(vel[0]) || isnan(vel[0]) || |
| 539 |
|
isinf(vel[1]) || isnan(vel[1]) || |
| 550 |
|
vel[0], vel[1], vel[2]); |
| 551 |
|
line += tempBuffer; |
| 552 |
|
|
| 553 |
< |
if (integrableObject->isDirectional()) { |
| 553 |
> |
if (sd->isDirectional()) { |
| 554 |
|
type += "qj"; |
| 555 |
|
Quat4d q; |
| 556 |
|
Vector3d ji; |
| 557 |
< |
q = integrableObject->getQ(); |
| 557 |
> |
q = sd->getQ(); |
| 558 |
|
|
| 559 |
|
if (isinf(q[0]) || isnan(q[0]) || |
| 560 |
|
isinf(q[1]) || isnan(q[1]) || |
| 567 |
|
simError(); |
| 568 |
|
} |
| 569 |
|
|
| 570 |
< |
ji = integrableObject->getJ(); |
| 570 |
> |
ji = sd->getJ(); |
| 571 |
|
|
| 572 |
|
if (isinf(ji[0]) || isnan(ji[0]) || |
| 573 |
|
isinf(ji[1]) || isnan(ji[1]) || |
| 587 |
|
|
| 588 |
|
if (needForceVector_) { |
| 589 |
|
type += "f"; |
| 590 |
< |
Vector3d frc; |
| 424 |
< |
|
| 425 |
< |
frc = integrableObject->getFrc(); |
| 426 |
< |
|
| 590 |
> |
Vector3d frc = sd->getFrc(); |
| 591 |
|
if (isinf(frc[0]) || isnan(frc[0]) || |
| 592 |
|
isinf(frc[1]) || isnan(frc[1]) || |
| 593 |
|
isinf(frc[2]) || isnan(frc[2]) ) { |
| 601 |
|
frc[0], frc[1], frc[2]); |
| 602 |
|
line += tempBuffer; |
| 603 |
|
|
| 604 |
< |
if (integrableObject->isDirectional()) { |
| 604 |
> |
if (sd->isDirectional()) { |
| 605 |
|
type += "t"; |
| 606 |
< |
Vector3d trq; |
| 443 |
< |
|
| 444 |
< |
trq = integrableObject->getTrq(); |
| 445 |
< |
|
| 606 |
> |
Vector3d trq = sd->getTrq(); |
| 607 |
|
if (isinf(trq[0]) || isnan(trq[0]) || |
| 608 |
|
isinf(trq[1]) || isnan(trq[1]) || |
| 609 |
|
isinf(trq[2]) || isnan(trq[2]) ) { |
| 612 |
|
" for object %d", index); |
| 613 |
|
painCave.isFatal = 1; |
| 614 |
|
simError(); |
| 615 |
< |
} |
| 455 |
< |
|
| 615 |
> |
} |
| 616 |
|
sprintf(tempBuffer, " %13e %13e %13e", |
| 617 |
|
trq[0], trq[1], trq[2]); |
| 618 |
|
line += tempBuffer; |
| 619 |
|
} |
| 620 |
|
} |
| 621 |
< |
|
| 621 |
> |
|
| 622 |
|
sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
| 623 |
+ |
return std::string(tempBuffer); |
| 624 |
+ |
} |
| 625 |
+ |
|
| 626 |
+ |
std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) { |
| 627 |
+ |
|
| 628 |
+ |
|
| 629 |
+ |
std::string id; |
| 630 |
+ |
std::string type; |
| 631 |
+ |
std::string line; |
| 632 |
+ |
char tempBuffer[4096]; |
| 633 |
+ |
|
| 634 |
+ |
if (sd->isRigidBody()) { |
| 635 |
+ |
sprintf(tempBuffer, "%10d ", ioIndex); |
| 636 |
+ |
id = std::string(tempBuffer); |
| 637 |
+ |
} else { |
| 638 |
+ |
sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex); |
| 639 |
+ |
id = std::string(tempBuffer); |
| 640 |
+ |
} |
| 641 |
+ |
|
| 642 |
+ |
if (needFlucQ_) { |
| 643 |
+ |
type += "cw"; |
| 644 |
+ |
RealType fqPos = sd->getFlucQPos(); |
| 645 |
+ |
if (isinf(fqPos) || isnan(fqPos) ) { |
| 646 |
+ |
sprintf( painCave.errMsg, |
| 647 |
+ |
"DumpWriter detected a numerical error writing the" |
| 648 |
+ |
" fluctuating charge for object %s", id.c_str()); |
| 649 |
+ |
painCave.isFatal = 1; |
| 650 |
+ |
simError(); |
| 651 |
+ |
} |
| 652 |
+ |
sprintf(tempBuffer, " %13e ", fqPos); |
| 653 |
+ |
line += tempBuffer; |
| 654 |
+ |
|
| 655 |
+ |
RealType fqVel = sd->getFlucQVel(); |
| 656 |
+ |
if (isinf(fqVel) || isnan(fqVel) ) { |
| 657 |
+ |
sprintf( painCave.errMsg, |
| 658 |
+ |
"DumpWriter detected a numerical error writing the" |
| 659 |
+ |
" fluctuating charge velocity for object %s", id.c_str()); |
| 660 |
+ |
painCave.isFatal = 1; |
| 661 |
+ |
simError(); |
| 662 |
+ |
} |
| 663 |
+ |
sprintf(tempBuffer, " %13e ", fqVel); |
| 664 |
+ |
line += tempBuffer; |
| 665 |
+ |
|
| 666 |
+ |
if (needForceVector_) { |
| 667 |
+ |
type += "g"; |
| 668 |
+ |
RealType fqFrc = sd->getFlucQFrc(); |
| 669 |
+ |
if (isinf(fqFrc) || isnan(fqFrc) ) { |
| 670 |
+ |
sprintf( painCave.errMsg, |
| 671 |
+ |
"DumpWriter detected a numerical error writing the" |
| 672 |
+ |
" fluctuating charge force for object %s", id.c_str()); |
| 673 |
+ |
painCave.isFatal = 1; |
| 674 |
+ |
simError(); |
| 675 |
+ |
} |
| 676 |
+ |
sprintf(tempBuffer, " %13e ", fqFrc); |
| 677 |
+ |
line += tempBuffer; |
| 678 |
+ |
} |
| 679 |
+ |
} |
| 680 |
+ |
|
| 681 |
+ |
if (needElectricField_) { |
| 682 |
+ |
type += "e"; |
| 683 |
+ |
Vector3d eField= sd->getElectricField(); |
| 684 |
+ |
if (isinf(eField[0]) || isnan(eField[0]) || |
| 685 |
+ |
isinf(eField[1]) || isnan(eField[1]) || |
| 686 |
+ |
isinf(eField[2]) || isnan(eField[2]) ) { |
| 687 |
+ |
sprintf( painCave.errMsg, |
| 688 |
+ |
"DumpWriter detected a numerical error writing the electric" |
| 689 |
+ |
" field for object %s", id.c_str()); |
| 690 |
+ |
painCave.isFatal = 1; |
| 691 |
+ |
simError(); |
| 692 |
+ |
} |
| 693 |
+ |
sprintf(tempBuffer, " %13e %13e %13e", |
| 694 |
+ |
eField[0], eField[1], eField[2]); |
| 695 |
+ |
line += tempBuffer; |
| 696 |
+ |
} |
| 697 |
+ |
|
| 698 |
+ |
|
| 699 |
+ |
if (needParticlePot_) { |
| 700 |
+ |
type += "u"; |
| 701 |
+ |
RealType particlePot = sd->getParticlePot(); |
| 702 |
+ |
if (isinf(particlePot) || isnan(particlePot)) { |
| 703 |
+ |
sprintf( painCave.errMsg, |
| 704 |
+ |
"DumpWriter detected a numerical error writing the particle " |
| 705 |
+ |
" potential for object %s", id.c_str()); |
| 706 |
+ |
painCave.isFatal = 1; |
| 707 |
+ |
simError(); |
| 708 |
+ |
} |
| 709 |
+ |
sprintf(tempBuffer, " %13e", particlePot); |
| 710 |
+ |
line += tempBuffer; |
| 711 |
+ |
} |
| 712 |
+ |
|
| 713 |
+ |
|
| 714 |
+ |
sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str()); |
| 715 |
|
return std::string(tempBuffer); |
| 716 |
|
} |
| 717 |
|
|
| 725 |
|
#ifdef IS_MPI |
| 726 |
|
if (worldRank == 0) { |
| 727 |
|
#endif // is_mpi |
| 728 |
< |
|
| 728 |
> |
|
| 729 |
|
eorStream = createOStream(eorFilename_); |
| 730 |
< |
|
| 730 |
> |
writeFrame(*eorStream); |
| 731 |
> |
|
| 732 |
|
#ifdef IS_MPI |
| 733 |
|
} |
| 481 |
– |
#endif // is_mpi |
| 482 |
– |
|
| 483 |
– |
writeFrame(*eorStream); |
| 484 |
– |
|
| 485 |
– |
#ifdef IS_MPI |
| 734 |
|
if (worldRank == 0) { |
| 735 |
|
#endif // is_mpi |
| 736 |
+ |
|
| 737 |
|
writeClosing(*eorStream); |
| 738 |
|
delete eorStream; |
| 739 |
+ |
|
| 740 |
|
#ifdef IS_MPI |
| 741 |
|
} |
| 742 |
|
#endif // is_mpi |
| 780 |
|
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
| 781 |
|
|
| 782 |
|
std::ostream* newOStream; |
| 783 |
< |
#ifdef HAVE_LIBZ |
| 783 |
> |
#ifdef HAVE_ZLIB |
| 784 |
|
if (needCompression_) { |
| 785 |
|
newOStream = new ogzstream(filename.c_str()); |
| 786 |
|
} else { |
| 790 |
|
newOStream = new std::ofstream(filename.c_str()); |
| 791 |
|
#endif |
| 792 |
|
//write out MetaData first |
| 793 |
< |
(*newOStream) << "<OpenMD version=1>" << std::endl; |
| 793 |
> |
(*newOStream) << "<OpenMD version=2>" << std::endl; |
| 794 |
|
(*newOStream) << " <MetaData>" << std::endl; |
| 795 |
|
(*newOStream) << info_->getRawMetaData(); |
| 796 |
|
(*newOStream) << " </MetaData>" << std::endl; |