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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 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 "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	<	namespace oopse {
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 oopse {
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 oopse {
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 oopse {
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 224 | Line 304 | namespace oopse {
304		void DumpWriter::writeFrame(std::ostream& os) {
305
306		#ifdef IS_MPI
307	<	MPI_Status istatus;
307	>	MPI::Status istatus;
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 oopse {
319		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320
321		os << "    <StuntDoubles>\n";
322	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
323	<
324	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
325	<	integrableObject = mol->nextIntegrableObject(ii)) {
326	<	os << prepareDumpLine(integrableObject);
327	<
322	>	for (mol = info_->beginMolecule(mi); mol != NULL;
323	>	mol = info_->nextMolecule(mi)) {
324	>
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
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
363	+
364	+	const int masterNode = 0;
365	+	int worldRank = MPI::COMM_WORLD.Get_rank();
366	+	int nProc = MPI::COMM_WORLD.Get_size();
367	+
368	+	if (worldRank == masterNode) {
369	+	os << "  <Snapshot>\n";
370	+	writeFrameProperties(os,
371	+	info_->getSnapshotManager()->getCurrentSnapshot());
372	+	os << "    <StuntDoubles>\n";
373	+	}
374	+
375		//every node prepares the dump lines for integrable objects belong to itself
376		std::string buffer;
377	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
378	<
379	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
380	<	integrableObject = mol->nextIntegrableObject(ii)) {
381	<	buffer += prepareDumpLine(integrableObject);
377	>	for (mol = info_->beginMolecule(mi); mol != NULL;
378	>	mol = info_->nextMolecule(mi)) {
379	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
380	>	sd = mol->nextIntegrableObject(ii)) {
381	>	buffer += prepareDumpLine(sd);
382		}
383		}
384
265	–	const int masterNode = 0;
266	–
385		if (worldRank == masterNode) {
268	–	os << "  <Snapshot>\n";
269	–	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270	–	os << "    <StuntDoubles>\n";
271	–
386		os << buffer;
387	<
274	<	int nProc;
275	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
387	>
388		for (int i = 1; i < nProc; ++i) {
389	+	// tell processor i to start sending us data:
390	+	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
391
392		// receive the length of the string buffer that was
393	<	// prepared by processor i
280	<
393	>	// prepared by processor i:
394		int recvLength;
395	<	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
395	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
396	>	istatus);
397	>
398	>	// create a buffer to receive the data
399		char* recvBuffer = new char[recvLength];
400		if (recvBuffer == NULL) {
401		} else {
402	<	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
402	>	// receive the data:
403	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
404	>	MPI::ANY_TAG, istatus);
405	>	// send it to the file:
406		os << recvBuffer;
407	<	delete recvBuffer;
407	>	// get rid of the receive buffer:
408	>	delete [] recvBuffer;
409		}
410		}
291	–	os << "    </StuntDoubles>\n";
292	–
293	–	os << "  </Snapshot>\n";
294	–	os.flush();
411		} else {
412		int sendBufferLength = buffer.size() + 1;
413	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
414	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
413	>	int myturn = 0;
414	>	for (int i = 1; i < nProc; ++i){
415	>	// wait for the master node to call our number:
416	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
417	>	if (myturn == worldRank){
418	>	// send the length of our buffer:
419	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
420	>
421	>	// send our buffer:
422	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
423	>	MPI::CHAR, masterNode, 0);
424	>
425	>	}
426	>	}
427		}
428	+
429	+	if (worldRank == masterNode) {
430	+	os << "    </StuntDoubles>\n";
431	+	}
432
433	<	#endif // is_mpi
433	>	if (doSiteData_) {
434	>	if (worldRank == masterNode) {
435	>	os << "    <SiteData>\n";
436	>	}
437	>	buffer.clear();
438	>	for (mol = info_->beginMolecule(mi); mol != NULL;
439	>	mol = info_->nextMolecule(mi)) {
440	>
441	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
442	>	sd = mol->nextIntegrableObject(ii)) {
443	>
444	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
445	>	// do one for the IO itself
446	>	buffer += prepareSiteLine(sd, ioIndex, 0);
447
448	<	}
448	>	if (sd->isRigidBody()) {
449	>
450	>	RigidBody* rb = static_cast<RigidBody*>(sd);
451	>	int siteIndex = 0;
452	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
453	>	atom = rb->nextAtom(ai)) {
454	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
455	>	siteIndex++;
456	>	}
457	>	}
458	>	}
459	>	}
460
461	<	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
461	>	if (worldRank == masterNode) {
462	>	os << buffer;
463	>
464	>	for (int i = 1; i < nProc; ++i) {
465	>
466	>	// tell processor i to start sending us data:
467	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
468	>
469	>	// receive the length of the string buffer that was
470	>	// prepared by processor i:
471	>	int recvLength;
472	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
473	>	istatus);
474	>
475	>	// create a buffer to receive the data
476	>	char* recvBuffer = new char[recvLength];
477	>	if (recvBuffer == NULL) {
478	>	} else {
479	>	// receive the data:
480	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
481	>	MPI::ANY_TAG, istatus);
482	>	// send it to the file:
483	>	os << recvBuffer;
484	>	// get rid of the receive buffer:
485	>	delete [] recvBuffer;
486	>	}
487	>	}
488	>	} else {
489	>	int sendBufferLength = buffer.size() + 1;
490	>	int myturn = 0;
491	>	for (int i = 1; i < nProc; ++i){
492	>	// wait for the master node to call our number:
493	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
494	>	if (myturn == worldRank){
495	>	// send the length of our buffer:
496	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
497	>	// send our buffer:
498	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
499	>	MPI::CHAR, masterNode, 0);
500	>	}
501	>	}
502	>	}
503	>
504	>	if (worldRank == masterNode) {
505	>	os << "    </SiteData>\n";
506	>	}
507	>	}
508	>
509	>	if (worldRank == masterNode) {
510	>	os << "  </Snapshot>\n";
511	>	os.flush();
512	>	}
513	>
514	>	#endif // is_mpi
515	>
516	>	}
517	>
518	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
519
520	<	int index = integrableObject->getGlobalIntegrableObjectIndex();
520	>	int index = sd->getGlobalIntegrableObjectIndex();
521		std::string type("pv");
522		std::string line;
523		char tempBuffer[4096];
524
525		Vector3d pos;
526		Vector3d vel;
527	<	pos = integrableObject->getPos();
528	<	vel = integrableObject->getVel();
527	>	pos = sd->getPos();
528	>
529	>	if (isinf(pos[0]) || isnan(pos[0]) ||
530	>	isinf(pos[1]) || isnan(pos[1]) ||
531	>	isinf(pos[2]) || isnan(pos[2]) ) {
532	>	sprintf( painCave.errMsg,
533	>	"DumpWriter detected a numerical error writing the position"
534	>	" for object %d", index);
535	>	painCave.isFatal = 1;
536	>	simError();
537	>	}
538	>
539	>	vel = sd->getVel();
540	>
541	>	if (isinf(vel[0]) || isnan(vel[0]) ||
542	>	isinf(vel[1]) || isnan(vel[1]) ||
543	>	isinf(vel[2]) || isnan(vel[2]) ) {
544	>	sprintf( painCave.errMsg,
545	>	"DumpWriter detected a numerical error writing the velocity"
546	>	" for object %d", index);
547	>	painCave.isFatal = 1;
548	>	simError();
549	>	}
550	>
551		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
552		pos[0], pos[1], pos[2],
553		vel[0], vel[1], vel[2]);
554		line += tempBuffer;
555
556	<	if (integrableObject->isDirectional()) {
556	>	if (sd->isDirectional()) {
557		type += "qj";
558		Quat4d q;
559		Vector3d ji;
560	<	q = integrableObject->getQ();
561	<	ji = integrableObject->getJ();
560	>	q = sd->getQ();
561	>
562	>	if (isinf(q[0]) || isnan(q[0]) ||
563	>	isinf(q[1]) || isnan(q[1]) ||
564	>	isinf(q[2]) || isnan(q[2]) ||
565	>	isinf(q[3]) || isnan(q[3]) ) {
566	>	sprintf( painCave.errMsg,
567	>	"DumpWriter detected a numerical error writing the quaternion"
568	>	" for object %d", index);
569	>	painCave.isFatal = 1;
570	>	simError();
571	>	}
572	>
573	>	ji = sd->getJ();
574	>
575	>	if (isinf(ji[0]) || isnan(ji[0]) ||
576	>	isinf(ji[1]) || isnan(ji[1]) ||
577	>	isinf(ji[2]) || isnan(ji[2]) ) {
578	>	sprintf( painCave.errMsg,
579	>	"DumpWriter detected a numerical error writing the angular"
580	>	" momentum for object %d", index);
581	>	painCave.isFatal = 1;
582	>	simError();
583	>	}
584	>
585		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
586		q[0], q[1], q[2], q[3],
587		ji[0], ji[1], ji[2]);
#	Line 331 | Line 589 | namespace oopse {
589		}
590
591		if (needForceVector_) {
592	<	type += "ft";
593	<	Vector3d frc;
594	<	Vector3d trq;
595	<	frc = integrableObject->getFrc();
596	<	trq = integrableObject->getTrq();
597	<
598	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
599	<	frc[0], frc[1], frc[2],
600	<	trq[0], trq[1], trq[2]);
592	>	type += "f";
593	>	Vector3d frc = sd->getFrc();
594	>	if (isinf(frc[0]) || isnan(frc[0]) ||
595	>	isinf(frc[1]) || isnan(frc[1]) ||
596	>	isinf(frc[2]) || isnan(frc[2]) ) {
597	>	sprintf( painCave.errMsg,
598	>	"DumpWriter detected a numerical error writing the force"
599	>	" for object %d", index);
600	>	painCave.isFatal = 1;
601	>	simError();
602	>	}
603	>	sprintf(tempBuffer, " %13e %13e %13e",
604	>	frc[0], frc[1], frc[2]);
605		line += tempBuffer;
606	+
607	+	if (sd->isDirectional()) {
608	+	type += "t";
609	+	Vector3d trq = sd->getTrq();
610	+	if (isinf(trq[0]) || isnan(trq[0]) ||
611	+	isinf(trq[1]) || isnan(trq[1]) ||
612	+	isinf(trq[2]) || isnan(trq[2]) ) {
613	+	sprintf( painCave.errMsg,
614	+	"DumpWriter detected a numerical error writing the torque"
615	+	" for object %d", index);
616	+	painCave.isFatal = 1;
617	+	simError();
618	+	}
619	+	sprintf(tempBuffer, " %13e %13e %13e",
620	+	trq[0], trq[1], trq[2]);
621	+	line += tempBuffer;
622	+	}
623		}
624	<
624	>
625		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
626		return std::string(tempBuffer);
627		}
628
629	+	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
630	+	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
631	+
632	+	std::string id;
633	+	std::string type;
634	+	std::string line;
635	+	char tempBuffer[4096];
636	+
637	+	if (sd->isRigidBody()) {
638	+	sprintf(tempBuffer, "%10d           ", ioIndex);
639	+	id = std::string(tempBuffer);
640	+	} else {
641	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
642	+	id = std::string(tempBuffer);
643	+	}
644	+
645	+	if (needFlucQ_) {
646	+	if (storageLayout & DataStorage::dslFlucQPosition) {
647	+	type += "c";
648	+	RealType fqPos = sd->getFlucQPos();
649	+	if (isinf(fqPos) || isnan(fqPos) ) {
650	+	sprintf( painCave.errMsg,
651	+	"DumpWriter detected a numerical error writing the"
652	+	" fluctuating charge for object %s", id.c_str());
653	+	painCave.isFatal = 1;
654	+	simError();
655	+	}
656	+	sprintf(tempBuffer, " %13e ", fqPos);
657	+	line += tempBuffer;
658	+	}
659	+
660	+	if (storageLayout & DataStorage::dslFlucQVelocity) {
661	+	type += "w";
662	+	RealType fqVel = sd->getFlucQVel();
663	+	if (isinf(fqVel) || isnan(fqVel) ) {
664	+	sprintf( painCave.errMsg,
665	+	"DumpWriter detected a numerical error writing the"
666	+	" fluctuating charge velocity for object %s", id.c_str());
667	+	painCave.isFatal = 1;
668	+	simError();
669	+	}
670	+	sprintf(tempBuffer, " %13e ", fqVel);
671	+	line += tempBuffer;
672	+	}
673	+
674	+	if (needForceVector_) {
675	+	if (storageLayout & DataStorage::dslFlucQForce) {
676	+	type += "g";
677	+	RealType fqFrc = sd->getFlucQFrc();
678	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
679	+	sprintf( painCave.errMsg,
680	+	"DumpWriter detected a numerical error writing the"
681	+	" fluctuating charge force for object %s", id.c_str());
682	+	painCave.isFatal = 1;
683	+	simError();
684	+	}
685	+	sprintf(tempBuffer, " %13e ", fqFrc);
686	+	line += tempBuffer;
687	+	}
688	+	}
689	+	}
690	+
691	+	if (needElectricField_) {
692	+	if (storageLayout & DataStorage::dslElectricField) {
693	+	type += "e";
694	+	Vector3d eField= sd->getElectricField();
695	+	if (isinf(eField[0]) || isnan(eField[0]) ||
696	+	isinf(eField[1]) || isnan(eField[1]) ||
697	+	isinf(eField[2]) || isnan(eField[2]) ) {
698	+	sprintf( painCave.errMsg,
699	+	"DumpWriter detected a numerical error writing the electric"
700	+	" field for object %s", id.c_str());
701	+	painCave.isFatal = 1;
702	+	simError();
703	+	}
704	+	sprintf(tempBuffer, " %13e %13e %13e",
705	+	eField[0], eField[1], eField[2]);
706	+	line += tempBuffer;
707	+	}
708	+	}
709	+
710	+
711	+	if (needParticlePot_) {
712	+	if (storageLayout & DataStorage::dslParticlePot) {
713	+	type += "u";
714	+	RealType particlePot = sd->getParticlePot();
715	+	if (isinf(particlePot) || isnan(particlePot)) {
716	+	sprintf( painCave.errMsg,
717	+	"DumpWriter detected a numerical error writing the particle "
718	+	" potential for object %s", id.c_str());
719	+	painCave.isFatal = 1;
720	+	simError();
721	+	}
722	+	sprintf(tempBuffer, " %13e", particlePot);
723	+	line += tempBuffer;
724	+	}
725	+	}
726	+
727	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
728	+	return std::string(tempBuffer);
729	+	}
730	+
731		void DumpWriter::writeDump() {
732		writeFrame(*dumpFile_);
733		}
#	Line 357 | Line 738 | namespace oopse {
738		#ifdef IS_MPI
739		if (worldRank == 0) {
740		#endif // is_mpi
741	<
741	>
742		eorStream = createOStream(eorFilename_);
743
744		#ifdef IS_MPI
745		}
746	<	#endif // is_mpi
747	<
746	>	#endif
747	>
748		writeFrame(*eorStream);
749	<
749	>
750		#ifdef IS_MPI
751		if (worldRank == 0) {
752	<	#endif // is_mpi
752	>	#endif
753	>
754		writeClosing(*eorStream);
755		delete eorStream;
756	+
757		#ifdef IS_MPI
758		}
759		#endif // is_mpi
#	Line 414 | Line 797 | namespace oopse {
797		std::ostream* DumpWriter::createOStream(const std::string& filename) {
798
799		std::ostream* newOStream;
800	<	#ifdef HAVE_LIBZ
800	>	#ifdef HAVE_ZLIB
801		if (needCompression_) {
802		newOStream = new ogzstream(filename.c_str());
803		} else {
#	Line 424 | Line 807 | namespace oopse {
807		newOStream = new std::ofstream(filename.c_str());
808		#endif
809		//write out MetaData first
810	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
810	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
811		(*newOStream) << "  <MetaData>" << std::endl;
812		(*newOStream) << info_->getRawMetaData();
813		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 816 | namespace oopse {
816
817		void DumpWriter::writeClosing(std::ostream& os) {
818
819	<	os << "</OOPSE>\n";
819	>	os << "</OpenMD>\n";
820		os.flush();
821		}
822
823	<	}//end namespace oopse
823	>	}//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.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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

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