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root/OpenMD/trunk/src/io/DumpWriter.cpp

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 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).
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 IS_MPI
59	<	#include <mpi.h>
60	<	#endif //is_mpi
58	>	#ifdef _MSC_VER
59	>	#define isnan(x) _isnan((x))
60	>	#define isinf(x) (!_finite(x) && !_isnan(x))
61	>	#endif
62
63	+	using namespace std;
64		namespace OpenMD {
65
66		DumpWriter::DumpWriter(SimInfo* info)
67		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
68
69		Globals* simParams = info->getSimParams();
70	<	needCompression_ = simParams->getCompressDumpFile();
71	<	needForceVector_ = simParams->getOutputForceVector();
70	>	needCompression_   = simParams->getCompressDumpFile();
71	>	needForceVector_   = simParams->getOutputForceVector();
72	>	needParticlePot_   = simParams->getOutputParticlePotential();
73	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
74	>	needElectricField_ = simParams->getOutputElectricField();
75	>
76	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
77	>	doSiteData_ = true;
78	>	} else {
79	>	doSiteData_ = false;
80	>	}
81	>
82		createDumpFile_ = true;
83		#ifdef HAVE_LIBZ
84		if (needCompression_) {
#	Line 95 | Line 116 | namespace OpenMD {
116		Globals* simParams = info->getSimParams();
117		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
118
119	<	needCompression_ = simParams->getCompressDumpFile();
120	<	needForceVector_ = simParams->getOutputForceVector();
119	>	needCompression_   = simParams->getCompressDumpFile();
120	>	needForceVector_   = simParams->getOutputForceVector();
121	>	needParticlePot_   = simParams->getOutputParticlePotential();
122	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
123	>	needElectricField_ = simParams->getOutputElectricField();
124	>
125	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
126	>	doSiteData_ = true;
127	>	} else {
128	>	doSiteData_ = false;
129	>	}
130	>
131		createDumpFile_ = true;
132		#ifdef HAVE_LIBZ
133		if (needCompression_) {
#	Line 134 | Line 165 | namespace OpenMD {
165		Globals* simParams = info->getSimParams();
166		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
167
168	<	needCompression_ = simParams->getCompressDumpFile();
169	<	needForceVector_ = simParams->getOutputForceVector();
170	<
168	>	needCompression_   = simParams->getCompressDumpFile();
169	>	needForceVector_   = simParams->getOutputForceVector();
170	>	needParticlePot_   = simParams->getOutputParticlePotential();
171	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
172	>	needElectricField_ = simParams->getOutputElectricField();
173	>
174	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
175	>	doSiteData_ = true;
176	>	} else {
177	>	doSiteData_ = false;
178	>	}
179	>
180		#ifdef HAVE_LIBZ
181		if (needCompression_) {
182		filename_ += ".gz";
#	Line 194 | Line 234 | namespace OpenMD {
234		os << "    <FrameData>\n";
235
236		RealType currentTime = s->getTime();
237	+
238	+	if (isinf(currentTime) || isnan(currentTime)) {
239	+	sprintf( painCave.errMsg,
240	+	"DumpWriter detected a numerical error writing the time");
241	+	painCave.isFatal = 1;
242	+	simError();
243	+	}
244	+
245		sprintf(buffer, "        Time: %.10g\n", currentTime);
246		os << buffer;
247
248		Mat3x3d hmat;
249		hmat = s->getHmat();
250	+
251	+	for (unsigned int i = 0; i < 3; i++) {
252	+	for (unsigned int j = 0; j < 3; j++) {
253	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
254	+	sprintf( painCave.errMsg,
255	+	"DumpWriter detected a numerical error writing the box");
256	+	painCave.isFatal = 1;
257	+	simError();
258	+	}
259	+	}
260	+	}
261	+
262		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
263		hmat(0, 0), hmat(1, 0), hmat(2, 0),
264		hmat(0, 1), hmat(1, 1), hmat(2, 1),
265		hmat(0, 2), hmat(1, 2), hmat(2, 2));
266		os << buffer;
267
268	<	RealType chi = s->getChi();
269	<	RealType integralOfChiDt = s->getIntegralOfChiDt();
270	<	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
268	>	pair<RealType, RealType> thermostat = s->getThermostat();
269	>
270	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
271	>	isinf(thermostat.second) || isnan(thermostat.second)) {
272	>	sprintf( painCave.errMsg,
273	>	"DumpWriter detected a numerical error writing the thermostat");
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
278	>	thermostat.second);
279		os << buffer;
280
281		Mat3x3d eta;
282	<	eta = s->getEta();
282	>	eta = s->getBarostat();
283	>
284	>	for (unsigned int i = 0; i < 3; i++) {
285	>	for (unsigned int j = 0; j < 3; j++) {
286	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
287	>	sprintf( painCave.errMsg,
288	>	"DumpWriter detected a numerical error writing the barostat");
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292	>	}
293	>	}
294	>
295		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
296		eta(0, 0), eta(1, 0), eta(2, 0),
297		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 228 | Line 308 | namespace OpenMD {
308		#endif
309
310		Molecule* mol;
311	<	StuntDouble* integrableObject;
311	>	StuntDouble* sd;
312		SimInfo::MoleculeIterator mi;
313		Molecule::IntegrableObjectIterator ii;
314	+	RigidBody::AtomIterator ai;
315
316		#ifndef IS_MPI
317		os << "  <Snapshot>\n";
#	Line 238 | Line 319 | namespace OpenMD {
319		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320
321		os << "    <StuntDoubles>\n";
322	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
323	<
322	>	for (mol = info_->beginMolecule(mi); mol != NULL;
323	>	mol = info_->nextMolecule(mi)) {
324
325	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
326	<	integrableObject = mol->nextIntegrableObject(ii)) {
327	<	os << prepareDumpLine(integrableObject);
325	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
326	>	sd = mol->nextIntegrableObject(ii)) {
327	>	os << prepareDumpLine(sd);
328
329		}
330		}
331		os << "    </StuntDoubles>\n";
332	<
332	>
333	>	if (doSiteData_) {
334	>	os << "    <SiteData>\n";
335	>	for (mol = info_->beginMolecule(mi); mol != NULL;
336	>	mol = info_->nextMolecule(mi)) {
337	>
338	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
339	>	sd = mol->nextIntegrableObject(ii)) {
340	>
341	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
342	>	// do one for the IO itself
343	>	os << prepareSiteLine(sd, ioIndex, 0);
344	>
345	>	if (sd->isRigidBody()) {
346	>
347	>	RigidBody* rb = static_cast<RigidBody*>(sd);
348	>	int siteIndex = 0;
349	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
350	>	atom = rb->nextAtom(ai)) {
351	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
352	>	siteIndex++;
353	>	}
354	>	}
355	>	}
356	>	}
357	>	os << "    </SiteData>\n";
358	>	}
359		os << "  </Snapshot>\n";
360
361		os.flush();
362		#else
256	–	//every node prepares the dump lines for integrable objects belong to itself
257	–	std::string buffer;
258	–	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
363
260	–
261	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
262	–	integrableObject = mol->nextIntegrableObject(ii)) {
263	–	buffer += prepareDumpLine(integrableObject);
264	–	}
265	–	}
266	–
364		const int masterNode = 0;
365	+	int worldRank;
366	+	int nProc;
367
368	+	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
369	+	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
370	+
371	+
372		if (worldRank == masterNode) {
373		os << "  <Snapshot>\n";
374	<	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
374	>	writeFrameProperties(os,
375	>	info_->getSnapshotManager()->getCurrentSnapshot());
376		os << "    <StuntDoubles>\n";
377	<
274	<	os << buffer;
377	>	}
378
379	<	int nProc;
380	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
379	>	//every node prepares the dump lines for integrable objects belong to itself
380	>	std::string buffer;
381	>	for (mol = info_->beginMolecule(mi); mol != NULL;
382	>	mol = info_->nextMolecule(mi)) {
383	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
384	>	sd = mol->nextIntegrableObject(ii)) {
385	>	buffer += prepareDumpLine(sd);
386	>	}
387	>	}
388	>
389	>	if (worldRank == masterNode) {
390	>	os << buffer;
391	>
392		for (int i = 1; i < nProc; ++i) {
393	+	// tell processor i to start sending us data:
394	+	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
395
396		// receive the length of the string buffer that was
397	<	// prepared by processor i
282	<
397	>	// prepared by processor i:
398		int recvLength;
399	<	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
399	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
400	>	&istatus);
401	>
402	>	// create a buffer to receive the data
403		char* recvBuffer = new char[recvLength];
404		if (recvBuffer == NULL) {
405		} else {
406	<	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
406	>	// receive the data:
407	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
408	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
409	>	// send it to the file:
410		os << recvBuffer;
411	+	// get rid of the receive buffer:
412		delete [] recvBuffer;
413		}
414		}
293	–	os << "    </StuntDoubles>\n";
294	–
295	–	os << "  </Snapshot>\n";
296	–	os.flush();
415		} else {
416		int sendBufferLength = buffer.size() + 1;
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	>	int myturn = 0;
418	>	for (int i = 1; i < nProc; ++i){
419	>	// wait for the master node to call our number:
420	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
421	>	if (myturn == worldRank){
422	>	// send the length of our buffer:
423	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
424	>
425	>	// send our buffer:
426	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
427	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
428	>
429	>	}
430	>	}
431		}
432	+
433	+	if (worldRank == masterNode) {
434	+	os << "    </StuntDoubles>\n";
435	+	}
436
437	<	#endif // is_mpi
437	>	if (doSiteData_) {
438	>	if (worldRank == masterNode) {
439	>	os << "    <SiteData>\n";
440	>	}
441	>	buffer.clear();
442	>	for (mol = info_->beginMolecule(mi); mol != NULL;
443	>	mol = info_->nextMolecule(mi)) {
444	>
445	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
446	>	sd = mol->nextIntegrableObject(ii)) {
447	>
448	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
449	>	// do one for the IO itself
450	>	buffer += prepareSiteLine(sd, ioIndex, 0);
451
452	<	}
452	>	if (sd->isRigidBody()) {
453	>
454	>	RigidBody* rb = static_cast<RigidBody*>(sd);
455	>	int siteIndex = 0;
456	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
457	>	atom = rb->nextAtom(ai)) {
458	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
459	>	siteIndex++;
460	>	}
461	>	}
462	>	}
463	>	}
464
465	<	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
465	>	if (worldRank == masterNode) {
466	>	os << buffer;
467	>
468	>	for (int i = 1; i < nProc; ++i) {
469	>
470	>	// tell processor i to start sending us data:
471	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
472	>
473	>	// receive the length of the string buffer that was
474	>	// prepared by processor i:
475	>	int recvLength;
476	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
477	>	&istatus);
478	>
479	>	// create a buffer to receive the data
480	>	char* recvBuffer = new char[recvLength];
481	>	if (recvBuffer == NULL) {
482	>	} else {
483	>	// receive the data:
484	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
485	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
486	>	// send it to the file:
487	>	os << recvBuffer;
488	>	// get rid of the receive buffer:
489	>	delete [] recvBuffer;
490	>	}
491	>	}
492	>	} else {
493	>	int sendBufferLength = buffer.size() + 1;
494	>	int myturn = 0;
495	>	for (int i = 1; i < nProc; ++i){
496	>	// wait for the master node to call our number:
497	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
498	>	if (myturn == worldRank){
499	>	// send the length of our buffer:
500	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
501	>	// send our buffer:
502	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
503	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
504	>	}
505	>	}
506	>	}
507	>
508	>	if (worldRank == masterNode) {
509	>	os << "    </SiteData>\n";
510	>	}
511	>	}
512	>
513	>	if (worldRank == masterNode) {
514	>	os << "  </Snapshot>\n";
515	>	os.flush();
516	>	}
517	>
518	>	#endif // is_mpi
519	>
520	>	}
521	>
522	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
523
524	<	int index = integrableObject->getGlobalIntegrableObjectIndex();
524	>	int index = sd->getGlobalIntegrableObjectIndex();
525		std::string type("pv");
526		std::string line;
527		char tempBuffer[4096];
528
529		Vector3d pos;
530		Vector3d vel;
531	<	pos = integrableObject->getPos();
532	<	vel = integrableObject->getVel();
531	>	pos = sd->getPos();
532	>
533	>	if (isinf(pos[0]) || isnan(pos[0]) ||
534	>	isinf(pos[1]) || isnan(pos[1]) ||
535	>	isinf(pos[2]) || isnan(pos[2]) ) {
536	>	sprintf( painCave.errMsg,
537	>	"DumpWriter detected a numerical error writing the position"
538	>	" for object %d", index);
539	>	painCave.isFatal = 1;
540	>	simError();
541	>	}
542	>
543	>	vel = sd->getVel();
544	>
545	>	if (isinf(vel[0]) || isnan(vel[0]) ||
546	>	isinf(vel[1]) || isnan(vel[1]) ||
547	>	isinf(vel[2]) || isnan(vel[2]) ) {
548	>	sprintf( painCave.errMsg,
549	>	"DumpWriter detected a numerical error writing the velocity"
550	>	" for object %d", index);
551	>	painCave.isFatal = 1;
552	>	simError();
553	>	}
554	>
555		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
556		pos[0], pos[1], pos[2],
557		vel[0], vel[1], vel[2]);
558		line += tempBuffer;
559
560	<	if (integrableObject->isDirectional()) {
560	>	if (sd->isDirectional()) {
561		type += "qj";
562		Quat4d q;
563		Vector3d ji;
564	<	q = integrableObject->getQ();
565	<	ji = integrableObject->getJ();
564	>	q = sd->getQ();
565	>
566	>	if (isinf(q[0]) || isnan(q[0]) ||
567	>	isinf(q[1]) || isnan(q[1]) ||
568	>	isinf(q[2]) || isnan(q[2]) ||
569	>	isinf(q[3]) || isnan(q[3]) ) {
570	>	sprintf( painCave.errMsg,
571	>	"DumpWriter detected a numerical error writing the quaternion"
572	>	" for object %d", index);
573	>	painCave.isFatal = 1;
574	>	simError();
575	>	}
576	>
577	>	ji = sd->getJ();
578	>
579	>	if (isinf(ji[0]) || isnan(ji[0]) ||
580	>	isinf(ji[1]) || isnan(ji[1]) ||
581	>	isinf(ji[2]) || isnan(ji[2]) ) {
582	>	sprintf( painCave.errMsg,
583	>	"DumpWriter detected a numerical error writing the angular"
584	>	" momentum for object %d", index);
585	>	painCave.isFatal = 1;
586	>	simError();
587	>	}
588	>
589		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
590		q[0], q[1], q[2], q[3],
591		ji[0], ji[1], ji[2]);
#	Line 333 | Line 593 | namespace OpenMD {
593		}
594
595		if (needForceVector_) {
596	<	type += "ft";
597	<	Vector3d frc;
598	<	Vector3d trq;
599	<	frc = integrableObject->getFrc();
600	<	trq = integrableObject->getTrq();
601	<
602	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
603	<	frc[0], frc[1], frc[2],
604	<	trq[0], trq[1], trq[2]);
596	>	type += "f";
597	>	Vector3d frc = sd->getFrc();
598	>	if (isinf(frc[0]) || isnan(frc[0]) ||
599	>	isinf(frc[1]) || isnan(frc[1]) ||
600	>	isinf(frc[2]) || isnan(frc[2]) ) {
601	>	sprintf( painCave.errMsg,
602	>	"DumpWriter detected a numerical error writing the force"
603	>	" for object %d", index);
604	>	painCave.isFatal = 1;
605	>	simError();
606	>	}
607	>	sprintf(tempBuffer, " %13e %13e %13e",
608	>	frc[0], frc[1], frc[2]);
609		line += tempBuffer;
610	+
611	+	if (sd->isDirectional()) {
612	+	type += "t";
613	+	Vector3d trq = sd->getTrq();
614	+	if (isinf(trq[0]) || isnan(trq[0]) ||
615	+	isinf(trq[1]) || isnan(trq[1]) ||
616	+	isinf(trq[2]) || isnan(trq[2]) ) {
617	+	sprintf( painCave.errMsg,
618	+	"DumpWriter detected a numerical error writing the torque"
619	+	" for object %d", index);
620	+	painCave.isFatal = 1;
621	+	simError();
622	+	}
623	+	sprintf(tempBuffer, " %13e %13e %13e",
624	+	trq[0], trq[1], trq[2]);
625	+	line += tempBuffer;
626	+	}
627		}
628	<
628	>
629		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
630		return std::string(tempBuffer);
631		}
632
633	+	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
634	+	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
635	+
636	+	std::string id;
637	+	std::string type;
638	+	std::string line;
639	+	char tempBuffer[4096];
640	+
641	+	if (sd->isRigidBody()) {
642	+	sprintf(tempBuffer, "%10d           ", ioIndex);
643	+	id = std::string(tempBuffer);
644	+	} else {
645	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
646	+	id = std::string(tempBuffer);
647	+	}
648	+
649	+	if (needFlucQ_) {
650	+	if (storageLayout & DataStorage::dslFlucQPosition) {
651	+	type += "c";
652	+	RealType fqPos = sd->getFlucQPos();
653	+	if (isinf(fqPos) || isnan(fqPos) ) {
654	+	sprintf( painCave.errMsg,
655	+	"DumpWriter detected a numerical error writing the"
656	+	" fluctuating charge for object %s", id.c_str());
657	+	painCave.isFatal = 1;
658	+	simError();
659	+	}
660	+	sprintf(tempBuffer, " %13e ", fqPos);
661	+	line += tempBuffer;
662	+	}
663	+
664	+	if (storageLayout & DataStorage::dslFlucQVelocity) {
665	+	type += "w";
666	+	RealType fqVel = sd->getFlucQVel();
667	+	if (isinf(fqVel) || isnan(fqVel) ) {
668	+	sprintf( painCave.errMsg,
669	+	"DumpWriter detected a numerical error writing the"
670	+	" fluctuating charge velocity for object %s", id.c_str());
671	+	painCave.isFatal = 1;
672	+	simError();
673	+	}
674	+	sprintf(tempBuffer, " %13e ", fqVel);
675	+	line += tempBuffer;
676	+	}
677	+
678	+	if (needForceVector_) {
679	+	if (storageLayout & DataStorage::dslFlucQForce) {
680	+	type += "g";
681	+	RealType fqFrc = sd->getFlucQFrc();
682	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
683	+	sprintf( painCave.errMsg,
684	+	"DumpWriter detected a numerical error writing the"
685	+	" fluctuating charge force for object %s", id.c_str());
686	+	painCave.isFatal = 1;
687	+	simError();
688	+	}
689	+	sprintf(tempBuffer, " %13e ", fqFrc);
690	+	line += tempBuffer;
691	+	}
692	+	}
693	+	}
694	+
695	+	if (needElectricField_) {
696	+	if (storageLayout & DataStorage::dslElectricField) {
697	+	type += "e";
698	+	Vector3d eField= sd->getElectricField();
699	+	if (isinf(eField[0]) || isnan(eField[0]) ||
700	+	isinf(eField[1]) || isnan(eField[1]) ||
701	+	isinf(eField[2]) || isnan(eField[2]) ) {
702	+	sprintf( painCave.errMsg,
703	+	"DumpWriter detected a numerical error writing the electric"
704	+	" field for object %s", id.c_str());
705	+	painCave.isFatal = 1;
706	+	simError();
707	+	}
708	+	sprintf(tempBuffer, " %13e %13e %13e",
709	+	eField[0], eField[1], eField[2]);
710	+	line += tempBuffer;
711	+	}
712	+	}
713	+
714	+
715	+	if (needParticlePot_) {
716	+	if (storageLayout & DataStorage::dslParticlePot) {
717	+	type += "u";
718	+	RealType particlePot = sd->getParticlePot();
719	+	if (isinf(particlePot) || isnan(particlePot)) {
720	+	sprintf( painCave.errMsg,
721	+	"DumpWriter detected a numerical error writing the particle "
722	+	" potential for object %s", id.c_str());
723	+	painCave.isFatal = 1;
724	+	simError();
725	+	}
726	+	sprintf(tempBuffer, " %13e", particlePot);
727	+	line += tempBuffer;
728	+	}
729	+	}
730	+
731	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
732	+	return std::string(tempBuffer);
733	+	}
734	+
735		void DumpWriter::writeDump() {
736		writeFrame(*dumpFile_);
737		}
738
739		void DumpWriter::writeEor() {
740	<	std::ostream* eorStream;
741	<
740	>
741	>	std::ostream* eorStream = NULL;
742	>
743		#ifdef IS_MPI
744		if (worldRank == 0) {
745		#endif // is_mpi
746	<
746	>
747		eorStream = createOStream(eorFilename_);
748
749		#ifdef IS_MPI
750		}
751	<	#endif // is_mpi
752	<
751	>	#endif
752	>
753		writeFrame(*eorStream);
754	<
754	>
755		#ifdef IS_MPI
756		if (worldRank == 0) {
757	<	#endif // is_mpi
757	>	#endif
758	>
759		writeClosing(*eorStream);
760		delete eorStream;
761	+
762		#ifdef IS_MPI
763		}
764		#endif // is_mpi
#	Line 386 | Line 772 | namespace OpenMD {
772		#ifdef IS_MPI
773		if (worldRank == 0) {
774		#endif // is_mpi
389	–
775		buffers.push_back(dumpFile_->rdbuf());
391	–
776		eorStream = createOStream(eorFilename_);
393	–
777		buffers.push_back(eorStream->rdbuf());
395	–
778		#ifdef IS_MPI
779		}
780		#endif // is_mpi
781
782		TeeBuf tbuf(buffers.begin(), buffers.end());
783		std::ostream os(&tbuf);
402	–
784		writeFrame(os);
785
786		#ifdef IS_MPI
#	Line 409 | Line 790 | namespace OpenMD {
790		delete eorStream;
791		#ifdef IS_MPI
792		}
793	<	#endif // is_mpi
413	<
793	>	#endif // is_mpi
794		}
795
796		std::ostream* DumpWriter::createOStream(const std::string& filename) {
797
798		std::ostream* newOStream;
799	<	#ifdef HAVE_LIBZ
799	>	#ifdef HAVE_ZLIB
800		if (needCompression_) {
801		newOStream = new ogzstream(filename.c_str());
802		} else {
#	Line 426 | Line 806 | namespace OpenMD {
806		newOStream = new std::ofstream(filename.c_str());
807		#endif
808		//write out MetaData first
809	<	(*newOStream) << "<OpenMD version=1>" << std::endl;
809	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
810		(*newOStream) << "  <MetaData>" << std::endl;
811		(*newOStream) << info_->getRawMetaData();
812		(*newOStream) << "  </MetaData>" << std::endl;

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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