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trunk/src/io/DumpWriter.cpp (file contents), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1878 by gezelter, Thu Jun 13 14:26:09 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	<
322	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
323	<	integrableObject = mol->nextIntegrableObject(ii)) {
324	<	os << prepareDumpLine(integrableObject);
325	<
320	>	for (mol = info_->beginMolecule(mi); mol != NULL;
321	>	mol = info_->nextMolecule(mi)) {
322	>
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
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
361	+
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,
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; mol = info_->nextMolecule(mi)) {
376	<
377	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
378	<	integrableObject = mol->nextIntegrableObject(ii)) {
379	<	buffer += prepareDumpLine(integrableObject);
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
265	–	const int masterNode = 0;
266	–
383		if (worldRank == masterNode) {
268	–	os << "  <Snapshot>\n";
269	–	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270	–	os << "    <StuntDoubles>\n";
271	–
384		os << buffer;
385	<
274	<	int nProc;
275	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
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
280	<
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		}
291	–	os << "    </StuntDoubles>\n";
292	–
293	–	os << "  </Snapshot>\n";
294	–	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	+
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	+	if (sd->isRigidBody()) {
447	+
448	+	RigidBody* rb = static_cast<RigidBody*>(sd);
449	+	int siteIndex = 0;
450	+	for (Atom* 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	+	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* integrableObject) {
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();
526	<	vel = integrableObject->getVel();
525	>	pos = sd->getPos();
526	>
527	>	if (isinf(pos[0]) || isnan(pos[0]) ||
528	>	isinf(pos[1]) || isnan(pos[1]) ||
529	>	isinf(pos[2]) || isnan(pos[2]) ) {
530	>	sprintf( painCave.errMsg,
531	>	"DumpWriter detected a numerical error writing the position"
532	>	" for object %d", index);
533	>	painCave.isFatal = 1;
534	>	simError();
535	>	}
536	>
537	>	vel = sd->getVel();
538	>
539	>	if (isinf(vel[0]) || isnan(vel[0]) ||
540	>	isinf(vel[1]) || isnan(vel[1]) ||
541	>	isinf(vel[2]) || isnan(vel[2]) ) {
542	>	sprintf( painCave.errMsg,
543	>	"DumpWriter detected a numerical error writing the velocity"
544	>	" for object %d", index);
545	>	painCave.isFatal = 1;
546	>	simError();
547	>	}
548	>
549		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
550		pos[0], pos[1], pos[2],
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();
559	<	ji = integrableObject->getJ();
558	>	q = sd->getQ();
559	>
560	>	if (isinf(q[0]) || isnan(q[0]) ||
561	>	isinf(q[1]) || isnan(q[1]) ||
562	>	isinf(q[2]) || isnan(q[2]) ||
563	>	isinf(q[3]) || isnan(q[3]) ) {
564	>	sprintf( painCave.errMsg,
565	>	"DumpWriter detected a numerical error writing the quaternion"
566	>	" for object %d", index);
567	>	painCave.isFatal = 1;
568	>	simError();
569	>	}
570	>
571	>	ji = sd->getJ();
572	>
573	>	if (isinf(ji[0]) || isnan(ji[0]) ||
574	>	isinf(ji[1]) || isnan(ji[1]) ||
575	>	isinf(ji[2]) || isnan(ji[2]) ) {
576	>	sprintf( painCave.errMsg,
577	>	"DumpWriter detected a numerical error writing the angular"
578	>	" momentum for object %d", index);
579	>	painCave.isFatal = 1;
580	>	simError();
581	>	}
582	>
583		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
584		q[0], q[1], q[2], q[3],
585		ji[0], ji[1], ji[2]);
#	Line 331 | Line 587 | namespace oopse {
587		}
588
589		if (needForceVector_) {
590	<	type += "ft";
591	<	Vector3d frc;
592	<	Vector3d trq;
593	<	frc = integrableObject->getFrc();
594	<	trq = integrableObject->getTrq();
595	<
596	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
597	<	frc[0], frc[1], frc[2],
598	<	trq[0], trq[1], trq[2]);
590	>	type += "f";
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]) ) {
595	>	sprintf( painCave.errMsg,
596	>	"DumpWriter detected a numerical error writing the force"
597	>	" for object %d", index);
598	>	painCave.isFatal = 1;
599	>	simError();
600	>	}
601	>	sprintf(tempBuffer, " %13e %13e %13e",
602	>	frc[0], frc[1], frc[2]);
603		line += tempBuffer;
604	+
605	+	if (sd->isDirectional()) {
606	+	type += "t";
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]) ) {
611	+	sprintf( painCave.errMsg,
612	+	"DumpWriter detected a numerical error writing the torque"
613	+	" for object %d", index);
614	+	painCave.isFatal = 1;
615	+	simError();
616	+	}
617	+	sprintf(tempBuffer, " %13e %13e %13e",
618	+	trq[0], trq[1], trq[2]);
619	+	line += tempBuffer;
620	+	}
621		}
622	<
622	>
623		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
624		return std::string(tempBuffer);
625		}
626
627	+	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
628	+
629	+
630	+	std::string id;
631	+	std::string type;
632	+	std::string line;
633	+	char tempBuffer[4096];
634	+
635	+	if (sd->isRigidBody()) {
636	+	sprintf(tempBuffer, "%10d           ", ioIndex);
637	+	id = std::string(tempBuffer);
638	+	} else {
639	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
640	+	id = std::string(tempBuffer);
641	+	}
642	+
643	+	if (needFlucQ_) {
644	+	type += "cw";
645	+	RealType fqPos = sd->getFlucQPos();
646	+	if (isinf(fqPos) || isnan(fqPos) ) {
647	+	sprintf( painCave.errMsg,
648	+	"DumpWriter detected a numerical error writing the"
649	+	" fluctuating charge for object %s", id.c_str());
650	+	painCave.isFatal = 1;
651	+	simError();
652	+	}
653	+	sprintf(tempBuffer, " %13e ", fqPos);
654	+	line += tempBuffer;
655	+
656	+	RealType fqVel = sd->getFlucQVel();
657	+	if (isinf(fqVel) || isnan(fqVel) ) {
658	+	sprintf( painCave.errMsg,
659	+	"DumpWriter detected a numerical error writing the"
660	+	" fluctuating charge velocity for object %s", id.c_str());
661	+	painCave.isFatal = 1;
662	+	simError();
663	+	}
664	+	sprintf(tempBuffer, " %13e ", fqVel);
665	+	line += tempBuffer;
666	+
667	+	if (needForceVector_) {
668	+	type += "g";
669	+	RealType fqFrc = sd->getFlucQFrc();
670	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
671	+	sprintf( painCave.errMsg,
672	+	"DumpWriter detected a numerical error writing the"
673	+	" fluctuating charge force for object %s", id.c_str());
674	+	painCave.isFatal = 1;
675	+	simError();
676	+	}
677	+	sprintf(tempBuffer, " %13e ", fqFrc);
678	+	line += tempBuffer;
679	+	}
680	+	}
681	+
682	+	if (needElectricField_) {
683	+	type += "e";
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]) ) {
688	+	sprintf( painCave.errMsg,
689	+	"DumpWriter detected a numerical error writing the electric"
690	+	" field for object %s", id.c_str());
691	+	painCave.isFatal = 1;
692	+	simError();
693	+	}
694	+	sprintf(tempBuffer, " %13e %13e %13e",
695	+	eField[0], eField[1], eField[2]);
696	+	line += tempBuffer;
697	+	}
698	+
699	+
700	+	if (needParticlePot_) {
701	+	type += "u";
702	+	RealType particlePot = sd->getParticlePot();
703	+	if (isinf(particlePot) || isnan(particlePot)) {
704	+	sprintf( painCave.errMsg,
705	+	"DumpWriter detected a numerical error writing the particle "
706	+	" potential for object %s", id.c_str());
707	+	painCave.isFatal = 1;
708	+	simError();
709	+	}
710	+	sprintf(tempBuffer, " %13e", particlePot);
711	+	line += tempBuffer;
712	+	}
713	+
714	+
715	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
716	+	return std::string(tempBuffer);
717	+	}
718	+
719		void DumpWriter::writeDump() {
720		writeFrame(*dumpFile_);
721		}
#	Line 357 | Line 726 | namespace oopse {
726		#ifdef IS_MPI
727		if (worldRank == 0) {
728		#endif // is_mpi
729	<
729	>
730		eorStream = createOStream(eorFilename_);
731
732		#ifdef IS_MPI
733		}
734	<	#endif // is_mpi
735	<
734	>	#endif
735	>
736		writeFrame(*eorStream);
737	<
737	>
738		#ifdef IS_MPI
739		if (worldRank == 0) {
740	<	#endif // is_mpi
740	>	#endif
741	>
742		writeClosing(*eorStream);
743		delete eorStream;
744	+
745		#ifdef IS_MPI
746		}
747		#endif // is_mpi
#	Line 414 | Line 785 | namespace oopse {
785		std::ostream* DumpWriter::createOStream(const std::string& filename) {
786
787		std::ostream* newOStream;
788	<	#ifdef HAVE_LIBZ
788	>	#ifdef HAVE_ZLIB
789		if (needCompression_) {
790		newOStream = new ogzstream(filename.c_str());
791		} else {
#	Line 424 | Line 795 | namespace oopse {
795		newOStream = new std::ofstream(filename.c_str());
796		#endif
797		//write out MetaData first
798	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
798	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
799		(*newOStream) << "  <MetaData>" << std::endl;
800		(*newOStream) << info_->getRawMetaData();
801		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 804 | namespace oopse {
804
805		void DumpWriter::writeClosing(std::ostream& os) {
806
807	<	os << "</OOPSE>\n";
807	>	os << "</OpenMD>\n";
808		os.flush();
809		}
810
811	<	}//end namespace oopse
811	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1878 by gezelter, Thu Jun 13 14:26:09 2013 UTC

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