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

Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 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 44 \| Line 44
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 {
#	Line 257 \| Line 263 \| namespace OpenMD {
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++) {
#	Line 295 \| 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;
#	Line 314 \| Line 321 \| namespace OpenMD {
321		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
322
323
324	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
325	<	integrableObject = mol->nextIntegrableObject(ii)) {
326	<	os << prepareDumpLine(integrableObject);
324	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
325	>	sd = mol->nextIntegrableObject(ii)) {
326	>	os << prepareDumpLine(sd);
327
328		}
329		}
#	Line 324 \| Line 331 \| namespace OpenMD {
331
332		if (doSiteData_) {
333		os << " <SiteData>\n";
334	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
334	>	for (mol = info_->beginMolecule(mi); mol != NULL;
335	>	mol = info_->nextMolecule(mi)) {
336
337	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
338	<	integrableObject = mol->nextIntegrableObject(ii)) {
337	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
338	>	sd = mol->nextIntegrableObject(ii)) {
339
340	<	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
340	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
341		// do one for the IO itself
342	<	os << prepareSiteLine(integrableObject, ioIndex, 0);
342	>	os << prepareSiteLine(sd, ioIndex, 0);
343
344	<	if (integrableObject->isRigidBody()) {
344	>	if (sd->isRigidBody()) {
345
346	<	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
346	>	RigidBody* rb = static_cast<RigidBody*>(sd);
347		int siteIndex = 0;
348		for (atom = rb->beginAtom(ai); atom != NULL;
349		atom = rb->nextAtom(ai)) {
#	Line 351 \| Line 359 \| namespace OpenMD {
359
360		os.flush();
361		#else
354	–	//every node prepares the dump lines for integrable objects belong to itself
355	–	std::string buffer;
356	–	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
362
358	–
359	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
360	–	integrableObject = mol->nextIntegrableObject(ii)) {
361	–	buffer += prepareDumpLine(integrableObject);
362	–	}
363	–	}
364	–
363		const int masterNode = 0;
364	<	int nProc;
365	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
364	>	int worldRank = MPI::COMM_WORLD.Get_rank();
365	>	int nProc = MPI::COMM_WORLD.Get_size();
366	>
367		if (worldRank == masterNode) {
368		os << " <Snapshot>\n";
369	<	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
369	>	writeFrameProperties(os,
370	>	info_->getSnapshotManager()->getCurrentSnapshot());
371		os << " <StuntDoubles>\n";
372	<
373	<	os << buffer;
372	>	}
373
374	+	//every node prepares the dump lines for integrable objects belong to itself
375	+	std::string buffer;
376	+	for (mol = info_->beginMolecule(mi); mol != NULL;
377	+	mol = info_->nextMolecule(mi)) {
378	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
379	+	sd = mol->nextIntegrableObject(ii)) {
380	+	buffer += prepareDumpLine(sd);
381	+	}
382	+	}
383	+
384	+	if (worldRank == masterNode) {
385	+	os << buffer;
386	+
387		for (int i = 1; i < nProc; ++i) {
388	+	// tell processor i to start sending us data:
389	+	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
390
391		// receive the length of the string buffer that was
392	<	// prepared by processor i
379	<
380	<	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
392	>	// prepared by processor i:
393		int recvLength;
394	<	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
394	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
395	>	istatus);
396	>
397	>	// create a buffer to receive the data
398		char* recvBuffer = new char[recvLength];
399		if (recvBuffer == NULL) {
400		} else {
401	<	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
401	>	// receive the data:
402	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
403	>	MPI::ANY_TAG, istatus);
404	>	// send it to the file:
405		os << recvBuffer;
406	+	// get rid of the receive buffer:
407		delete [] recvBuffer;
408		}
409		}
391	–	os << " </StuntDoubles>\n";
392	–
393	–	os << " </Snapshot>\n";
394	–	os.flush();
410		} else {
411		int sendBufferLength = buffer.size() + 1;
412		int myturn = 0;
413		for (int i = 1; i < nProc; ++i){
414	<	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
414	>	// wait for the master node to call our number:
415	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
416		if (myturn == worldRank){
417	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
418	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
417	>	// send the length of our buffer:
418	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
419	>
420	>	// send our buffer:
421	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
422	>	MPI::CHAR, masterNode, 0);
423		}
424		}
425		}
426	+
427	+	if (worldRank == masterNode) {
428	+	os << " </StuntDoubles>\n";
429	+	}
430
431	<	#endif // is_mpi
431	>	if (doSiteData_) {
432	>	if (worldRank == masterNode) {
433	>	os << " <SiteData>\n";
434	>	}
435	>	buffer.clear();
436	>	for (mol = info_->beginMolecule(mi); mol != NULL;
437	>	mol = info_->nextMolecule(mi)) {
438	>
439	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
440	>	sd = mol->nextIntegrableObject(ii)) {
441	>
442	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
443	>	// do one for the IO itself
444	>	buffer += prepareSiteLine(sd, ioIndex, 0);
445
446	<	}
446	>	if (sd->isRigidBody()) {
447	>
448	>	RigidBody* rb = static_cast<RigidBody*>(sd);
449	>	int siteIndex = 0;
450	>	for (atom = rb->beginAtom(ai); atom != NULL;
451	>	atom = rb->nextAtom(ai)) {
452	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
453	>	siteIndex++;
454	>	}
455	>	}
456	>	}
457	>	}
458
459	<	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
459	>	if (worldRank == masterNode) {
460	>	os << buffer;
461	>
462	>	for (int i = 1; i < nProc; ++i) {
463	>
464	>	// tell processor i to start sending us data:
465	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
466	>
467	>	// receive the length of the string buffer that was
468	>	// prepared by processor i:
469	>	int recvLength;
470	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
471	>	istatus);
472	>
473	>	// create a buffer to receive the data
474	>	char* recvBuffer = new char[recvLength];
475	>	if (recvBuffer == NULL) {
476	>	} else {
477	>	// receive the data:
478	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
479	>	MPI::ANY_TAG, istatus);
480	>	// send it to the file:
481	>	os << recvBuffer;
482	>	// get rid of the receive buffer:
483	>	delete [] recvBuffer;
484	>	}
485	>	}
486	>	} else {
487	>	int sendBufferLength = buffer.size() + 1;
488	>	int myturn = 0;
489	>	for (int i = 1; i < nProc; ++i){
490	>	// wait for the master node to call our number:
491	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
492	>	if (myturn == worldRank){
493	>	// send the length of our buffer:
494	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
495	>	// send our buffer:
496	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
497	>	MPI::CHAR, masterNode, 0);
498	>	}
499	>	}
500	>	}
501	>
502	>	if (worldRank == masterNode) {
503	>	os << " </SiteData>\n";
504	>	}
505	>	}
506	>
507	>	if (worldRank == masterNode) {
508	>	os << " </Snapshot>\n";
509	>	os.flush();
510	>	}
511	>
512	>	#endif // is_mpi
513	>
514	>	}
515	>
516	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
517
518	<	int index = integrableObject->getGlobalIntegrableObjectIndex();
518	>	int index = sd->getGlobalIntegrableObjectIndex();
519		std::string type("pv");
520		std::string line;
521		char tempBuffer[4096];
522
523		Vector3d pos;
524		Vector3d vel;
525	<	pos = integrableObject->getPos();
525	>	pos = sd->getPos();
526
527		if (isinf(pos[0]) \|\| isnan(pos[0]) \|\|
528		isinf(pos[1]) \|\| isnan(pos[1]) \|\|
#	Line 429 \| Line 534 \| namespace OpenMD {
534		simError();
535		}
536
537	<	vel = integrableObject->getVel();
537	>	vel = sd->getVel();
538
539		if (isinf(vel[0]) \|\| isnan(vel[0]) \|\|
540		isinf(vel[1]) \|\| isnan(vel[1]) \|\|
#	Line 446 \| Line 551 \| namespace OpenMD {
551		vel[0], vel[1], vel[2]);
552		line += tempBuffer;
553
554	<	if (integrableObject->isDirectional()) {
554	>	if (sd->isDirectional()) {
555		type += "qj";
556		Quat4d q;
557		Vector3d ji;
558	<	q = integrableObject->getQ();
558	>	q = sd->getQ();
559
560		if (isinf(q[0]) \|\| isnan(q[0]) \|\|
561		isinf(q[1]) \|\| isnan(q[1]) \|\|
#	Line 463 \| Line 568 \| namespace OpenMD {
568		simError();
569		}
570
571	<	ji = integrableObject->getJ();
571	>	ji = sd->getJ();
572
573		if (isinf(ji[0]) \|\| isnan(ji[0]) \|\|
574		isinf(ji[1]) \|\| isnan(ji[1]) \|\|
#	Line 483 \| Line 588 \| namespace OpenMD {
588
589		if (needForceVector_) {
590		type += "f";
591	<	Vector3d frc = integrableObject->getFrc();
591	>	Vector3d frc = sd->getFrc();
592		if (isinf(frc[0]) \|\| isnan(frc[0]) \|\|
593		isinf(frc[1]) \|\| isnan(frc[1]) \|\|
594		isinf(frc[2]) \|\| isnan(frc[2]) ) {
#	Line 497 \| Line 602 \| namespace OpenMD {
602		frc[0], frc[1], frc[2]);
603		line += tempBuffer;
604
605	<	if (integrableObject->isDirectional()) {
605	>	if (sd->isDirectional()) {
606		type += "t";
607	<	Vector3d trq = integrableObject->getTrq();
607	>	Vector3d trq = sd->getTrq();
608		if (isinf(trq[0]) \|\| isnan(trq[0]) \|\|
609		isinf(trq[1]) \|\| isnan(trq[1]) \|\|
610		isinf(trq[2]) \|\| isnan(trq[2]) ) {
#	Line 519 \| Line 624 \| namespace OpenMD {
624		return std::string(tempBuffer);
625		}
626
627	<	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
627	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
628
629
630		std::string id;
#	Line 527 \| Line 632 \| namespace OpenMD {
632		std::string line;
633		char tempBuffer[4096];
634
635	<	if (integrableObject->isRigidBody()) {
635	>	if (sd->isRigidBody()) {
636		sprintf(tempBuffer, "%10d ", ioIndex);
637		id = std::string(tempBuffer);
638		} else {
#	Line 537 \| Line 642 \| namespace OpenMD {
642
643		if (needFlucQ_) {
644		type += "cw";
645	<	RealType fqPos = integrableObject->getFlucQPos();
645	>	RealType fqPos = sd->getFlucQPos();
646		if (isinf(fqPos) \|\| isnan(fqPos) ) {
647		sprintf( painCave.errMsg,
648		"DumpWriter detected a numerical error writing the"
#	Line 548 \| Line 653 \| namespace OpenMD {
653		sprintf(tempBuffer, " %13e ", fqPos);
654		line += tempBuffer;
655
656	<	RealType fqVel = integrableObject->getFlucQVel();
656	>	RealType fqVel = sd->getFlucQVel();
657		if (isinf(fqVel) \|\| isnan(fqVel) ) {
658		sprintf( painCave.errMsg,
659		"DumpWriter detected a numerical error writing the"
#	Line 561 \| Line 666 \| namespace OpenMD {
666
667		if (needForceVector_) {
668		type += "g";
669	<	RealType fqFrc = integrableObject->getFlucQFrc();
669	>	RealType fqFrc = sd->getFlucQFrc();
670		if (isinf(fqFrc) \|\| isnan(fqFrc) ) {
671		sprintf( painCave.errMsg,
672		"DumpWriter detected a numerical error writing the"
#	Line 576 \| Line 681 \| namespace OpenMD {
681
682		if (needElectricField_) {
683		type += "e";
684	<	Vector3d eField= integrableObject->getElectricField();
684	>	Vector3d eField= sd->getElectricField();
685		if (isinf(eField[0]) \|\| isnan(eField[0]) \|\|
686		isinf(eField[1]) \|\| isnan(eField[1]) \|\|
687		isinf(eField[2]) \|\| isnan(eField[2]) ) {
#	Line 594 \| Line 699 \| namespace OpenMD {
699
700		if (needParticlePot_) {
701		type += "u";
702	<	RealType particlePot = integrableObject->getParticlePot();
702	>	RealType particlePot = sd->getParticlePot();
703		if (isinf(particlePot) \|\| isnan(particlePot)) {
704		sprintf( painCave.errMsg,
705		"DumpWriter detected a numerical error writing the particle "
#	Line 621 \| Line 726 \| namespace OpenMD {
726		#ifdef IS_MPI
727		if (worldRank == 0) {
728		#endif // is_mpi
729	<
729	>
730		eorStream = createOStream(eorFilename_);
731	<
731	>	writeFrame(*eorStream);
732	>
733		#ifdef IS_MPI
734		}
629	–	#endif // is_mpi
630	–
631	–	writeFrame(*eorStream);
632	–
633	–	#ifdef IS_MPI
735		if (worldRank == 0) {
736		#endif // is_mpi
737	+
738		writeClosing(*eorStream);
739		delete eorStream;
740	+
741		#ifdef IS_MPI
742		}
743		#endif // is_mpi
#	Line 678 \| Line 781 \| namespace OpenMD {
781		std::ostream* DumpWriter::createOStream(const std::string& filename) {
782
783		std::ostream* newOStream;
784	<	#ifdef HAVE_LIBZ
784	>	#ifdef HAVE_ZLIB
785		if (needCompression_) {
786		newOStream = new ogzstream(filename.c_str());
787		} else {

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Comparing branches/development/src/io/DumpWriter.cpp (file contents): Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC vs. Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

Diff Legend

Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC