[ViewVC] Diff of: OpenMD/branches/development/src/io/DumpWriter.cpp

Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 35 \| Line 35
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).
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		*/
#	Line 302 \| Line 302 \| namespace OpenMD {
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	–	Atom* atom;
313
314		#ifndef IS_MPI
315		os << " <Snapshot>\n";
#	Line 318 \| Line 317 \| namespace OpenMD {
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		}
#	Line 331 \| Line 330 \| namespace OpenMD {
330
331		if (doSiteData_) {
332		os << " <SiteData>\n";
333	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
333	>	for (mol = info_->beginMolecule(mi); mol != NULL;
334	>	mol = info_->nextMolecule(mi)) {
335
336	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
337	<	integrableObject = mol->nextIntegrableObject(ii)) {
336	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
337	>	sd = mol->nextIntegrableObject(ii)) {
338
339	<	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340		// do one for the IO itself
341	<	os << prepareSiteLine(integrableObject, ioIndex, 0);
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	if (integrableObject->isRigidBody()) {
343	>	if (sd->isRigidBody()) {
344
345	<	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
345	>	RigidBody* rb = static_cast<RigidBody*>(sd);
346		int siteIndex = 0;
347	<	for (atom = rb->beginAtom(ai); atom != NULL;
347	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
348		atom = rb->nextAtom(ai)) {
349		os << prepareSiteLine(atom, ioIndex, siteIndex);
350		siteIndex++;
#	Line 358 \| Line 358 \| namespace OpenMD {
358
359		os.flush();
360		#else
361	–	//every node prepares the dump lines for integrable objects belong to itself
362	–	std::string buffer;
363	–	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
361
362	+	const int masterNode = 0;
363	+	int worldRank = MPI::COMM_WORLD.Get_rank();
364	+	int nProc = MPI::COMM_WORLD.Get_size();
365
366	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
367	<	integrableObject = mol->nextIntegrableObject(ii)) {
368	<	buffer += prepareDumpLine(integrableObject);
366	>	if (worldRank == masterNode) {
367	>	os << " <Snapshot>\n";
368	>	writeFrameProperties(os,
369	>	info_->getSnapshotManager()->getCurrentSnapshot());
370	>	os << " <StuntDoubles>\n";
371	>	}
372	>
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
372	–	const int masterNode = 0;
373	–	int nProc;
374	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
383		if (worldRank == masterNode) {
376	–	os << " <Snapshot>\n";
377	–	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
378	–	os << " <StuntDoubles>\n";
379	–
384		os << buffer;
385	<
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
386	<
387	<	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
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		}
398	–	os << " </StuntDoubles>\n";
399	–
400	–	os << " </Snapshot>\n";
401	–	os.flush();
409		} else {
410		int sendBufferLength = buffer.size() + 1;
411		int myturn = 0;
412		for (int i = 1; i < nProc; ++i){
413	<	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
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	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
417	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
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	<	}
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	<	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
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* 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]) \|\|
#	Line 436 \| Line 533 \| namespace OpenMD {
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]) \|\|
#	Line 453 \| Line 550 \| namespace OpenMD {
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]) \|\|
#	Line 470 \| Line 567 \| namespace OpenMD {
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]) \|\|
#	Line 490 \| Line 587 \| namespace OpenMD {
587
588		if (needForceVector_) {
589		type += "f";
590	<	Vector3d frc = integrableObject->getFrc();
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]) ) {
#	Line 504 \| Line 601 \| namespace OpenMD {
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 = integrableObject->getTrq();
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]) ) {
#	Line 526 \| Line 623 \| namespace OpenMD {
623		return std::string(tempBuffer);
624		}
625
626	<	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
626	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
627
628
629		std::string id;
#	Line 534 \| Line 631 \| namespace OpenMD {
631		std::string line;
632		char tempBuffer[4096];
633
634	<	if (integrableObject->isRigidBody()) {
634	>	if (sd->isRigidBody()) {
635		sprintf(tempBuffer, "%10d ", ioIndex);
636		id = std::string(tempBuffer);
637		} else {
#	Line 544 \| Line 641 \| namespace OpenMD {
641
642		if (needFlucQ_) {
643		type += "cw";
644	<	RealType fqPos = integrableObject->getFlucQPos();
644	>	RealType fqPos = sd->getFlucQPos();
645		if (isinf(fqPos) \|\| isnan(fqPos) ) {
646		sprintf( painCave.errMsg,
647		"DumpWriter detected a numerical error writing the"
#	Line 555 \| Line 652 \| namespace OpenMD {
652		sprintf(tempBuffer, " %13e ", fqPos);
653		line += tempBuffer;
654
655	<	RealType fqVel = integrableObject->getFlucQVel();
655	>	RealType fqVel = sd->getFlucQVel();
656		if (isinf(fqVel) \|\| isnan(fqVel) ) {
657		sprintf( painCave.errMsg,
658		"DumpWriter detected a numerical error writing the"
#	Line 568 \| Line 665 \| namespace OpenMD {
665
666		if (needForceVector_) {
667		type += "g";
668	<	RealType fqFrc = integrableObject->getFlucQFrc();
668	>	RealType fqFrc = sd->getFlucQFrc();
669		if (isinf(fqFrc) \|\| isnan(fqFrc) ) {
670		sprintf( painCave.errMsg,
671		"DumpWriter detected a numerical error writing the"
#	Line 583 \| Line 680 \| namespace OpenMD {
680
681		if (needElectricField_) {
682		type += "e";
683	<	Vector3d eField= integrableObject->getElectricField();
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]) ) {
#	Line 601 \| Line 698 \| namespace OpenMD {
698
699		if (needParticlePot_) {
700		type += "u";
701	<	RealType particlePot = integrableObject->getParticlePot();
701	>	RealType particlePot = sd->getParticlePot();
702		if (isinf(particlePot) \|\| isnan(particlePot)) {
703		sprintf( painCave.errMsg,
704		"DumpWriter detected a numerical error writing the particle "
#	Line 628 \| Line 725 \| namespace OpenMD {
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		}
636	–	#endif // is_mpi
637	–
638	–	writeFrame(*eorStream);
639	–
640	–	#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

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Comparing branches/development/src/io/DumpWriter.cpp (file contents): Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs. Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

Diff Legend

Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC