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root/OpenMD/branches/development/src/io/DumpWriter.cpp

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trunk/src/io/DumpWriter.cpp (file contents), Revision 1217 by xsun, Wed Jan 23 21:23:02 2008 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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, 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	<	namespace oopse {
61	>	using namespace std;
62	>	namespace OpenMD {
63
64		DumpWriter::DumpWriter(SimInfo* info)
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_) {
#	Line 95 | Line 114 | namespace oopse {
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_) {
#	Line 134 | Line 163 | namespace oopse {
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";
#	Line 194 | Line 232 | namespace oopse {
232		os << "    <FrameData>\n";
233
234		RealType currentTime = s->getTime();
235	+
236	+	if (isinf(currentTime) || isnan(currentTime)) {
237	+	sprintf( painCave.errMsg,
238	+	"DumpWriter detected a numerical error writing the time");
239	+	painCave.isFatal = 1;
240	+	simError();
241	+	}
242	+
243		sprintf(buffer, "        Time: %.10g\n", currentTime);
244		os << buffer;
245
246		Mat3x3d hmat;
247		hmat = s->getHmat();
248	+
249	+	for (unsigned int i = 0; i < 3; i++) {
250	+	for (unsigned int j = 0; j < 3; j++) {
251	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
252	+	sprintf( painCave.errMsg,
253	+	"DumpWriter detected a numerical error writing the box");
254	+	painCave.isFatal = 1;
255	+	simError();
256	+	}
257	+	}
258	+	}
259	+
260		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261		hmat(0, 0), hmat(1, 0), hmat(2, 0),
262		hmat(0, 1), hmat(1, 1), hmat(2, 1),
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	<	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, 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", 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++) {
284	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
285	>	sprintf( painCave.errMsg,
286	>	"DumpWriter detected a numerical error writing the barostat");
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>	}
291	>	}
292	>
293		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
294		eta(0, 0), eta(1, 0), eta(2, 0),
295		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 224 | Line 302 | namespace oopse {
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";
#	Line 238 | Line 317 | namespace oopse {
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
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)) {
361
260	–
261	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
262	–	integrableObject = mol->nextIntegrableObject(ii)) {
263	–	buffer += prepareDumpLine(integrableObject);
264	–	}
265	–	}
266	–
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	<
274	<	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
282	<
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	<	delete recvBuffer;
405	>	// get rid of the receive buffer:
406	>	delete [] recvBuffer;
407		}
408		}
293	–	os << "    </StuntDoubles>\n";
294	–
295	–	os << "  </Snapshot>\n";
296	–	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	<	}
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();
525	<	vel = integrableObject->getVel();
524	>	pos = sd->getPos();
525	>
526	>	if (isinf(pos[0]) || isnan(pos[0]) ||
527	>	isinf(pos[1]) || isnan(pos[1]) ||
528	>	isinf(pos[2]) || isnan(pos[2]) ) {
529	>	sprintf( painCave.errMsg,
530	>	"DumpWriter detected a numerical error writing the position"
531	>	" for object %d", index);
532	>	painCave.isFatal = 1;
533	>	simError();
534	>	}
535	>
536	>	vel = sd->getVel();
537	>
538	>	if (isinf(vel[0]) || isnan(vel[0]) ||
539	>	isinf(vel[1]) || isnan(vel[1]) ||
540	>	isinf(vel[2]) || isnan(vel[2]) ) {
541	>	sprintf( painCave.errMsg,
542	>	"DumpWriter detected a numerical error writing the velocity"
543	>	" for object %d", index);
544	>	painCave.isFatal = 1;
545	>	simError();
546	>	}
547	>
548		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
549		pos[0], pos[1], pos[2],
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();
558	<	ji = integrableObject->getJ();
557	>	q = sd->getQ();
558	>
559	>	if (isinf(q[0]) || isnan(q[0]) ||
560	>	isinf(q[1]) || isnan(q[1]) ||
561	>	isinf(q[2]) || isnan(q[2]) ||
562	>	isinf(q[3]) || isnan(q[3]) ) {
563	>	sprintf( painCave.errMsg,
564	>	"DumpWriter detected a numerical error writing the quaternion"
565	>	" for object %d", index);
566	>	painCave.isFatal = 1;
567	>	simError();
568	>	}
569	>
570	>	ji = sd->getJ();
571	>
572	>	if (isinf(ji[0]) || isnan(ji[0]) ||
573	>	isinf(ji[1]) || isnan(ji[1]) ||
574	>	isinf(ji[2]) || isnan(ji[2]) ) {
575	>	sprintf( painCave.errMsg,
576	>	"DumpWriter detected a numerical error writing the angular"
577	>	" momentum for object %d", index);
578	>	painCave.isFatal = 1;
579	>	simError();
580	>	}
581	>
582		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
583		q[0], q[1], q[2], q[3],
584		ji[0], ji[1], ji[2]);
#	Line 333 | Line 586 | namespace oopse {
586		}
587
588		if (needForceVector_) {
589	<	type += "ft";
590	<	Vector3d frc;
591	<	Vector3d trq;
592	<	frc = integrableObject->getFrc();
593	<	trq = integrableObject->getTrq();
594	<
595	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
596	<	frc[0], frc[1], frc[2],
597	<	trq[0], trq[1], trq[2]);
589	>	type += "f";
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]) ) {
594	>	sprintf( painCave.errMsg,
595	>	"DumpWriter detected a numerical error writing the force"
596	>	" for object %d", index);
597	>	painCave.isFatal = 1;
598	>	simError();
599	>	}
600	>	sprintf(tempBuffer, " %13e %13e %13e",
601	>	frc[0], frc[1], frc[2]);
602		line += tempBuffer;
603	+
604	+	if (sd->isDirectional()) {
605	+	type += "t";
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]) ) {
610	+	sprintf( painCave.errMsg,
611	+	"DumpWriter detected a numerical error writing the torque"
612	+	" for object %d", index);
613	+	painCave.isFatal = 1;
614	+	simError();
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	+
718		void DumpWriter::writeDump() {
719		writeFrame(*dumpFile_);
720		}
#	Line 359 | Line 725 | namespace oopse {
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		}
367	–	#endif // is_mpi
368	–
369	–	writeFrame(*eorStream);
370	–
371	–	#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
#	Line 416 | Line 780 | namespace oopse {
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 {
#	Line 426 | Line 790 | namespace oopse {
790		newOStream = new std::ofstream(filename.c_str());
791		#endif
792		//write out MetaData first
793	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
793	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
794		(*newOStream) << "  <MetaData>" << std::endl;
795		(*newOStream) << info_->getRawMetaData();
796		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 435 | Line 799 | namespace oopse {
799
800		void DumpWriter::writeClosing(std::ostream& os) {
801
802	<	os << "</OOPSE>\n";
802	>	os << "</OpenMD>\n";
803		os.flush();
804		}
805
806	<	}//end namespace oopse
806	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1217 by xsun, Wed Jan 23 21:23:02 2008 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 0 | Line 1
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