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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 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()){
67	>	: info_(info), filename_(info->getDumpFileName()),
68	>	eorFilename_(info->getFinalConfigFileName()){
69
70		Globals* simParams = info->getSimParams();
71	<	needCompression_ = simParams->getCompressDumpFile();
72	<	needForceVector_ = simParams->getOutputForceVector();
71	>	needCompression_   = simParams->getCompressDumpFile();
72	>	needForceVector_   = simParams->getOutputForceVector();
73	>	needParticlePot_   = simParams->getOutputParticlePotential();
74	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
75	>	needElectricField_ = simParams->getOutputElectricField();
76	>	needSitePotential_ = simParams->getOutputSitePotential();
77	>
78	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
79	>	needSitePotential_) {
80	>	doSiteData_ = true;
81	>	} else {
82	>	doSiteData_ = false;
83	>	}
84	>
85		createDumpFile_ = true;
86		#ifdef HAVE_LIBZ
87		if (needCompression_) {
#	Line 95 | Line 119 | namespace oopse {
119		Globals* simParams = info->getSimParams();
120		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
121
122	<	needCompression_ = simParams->getCompressDumpFile();
123	<	needForceVector_ = simParams->getOutputForceVector();
122	>	needCompression_   = simParams->getCompressDumpFile();
123	>	needForceVector_   = simParams->getOutputForceVector();
124	>	needParticlePot_   = simParams->getOutputParticlePotential();
125	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
126	>	needElectricField_ = simParams->getOutputElectricField();
127	>	needSitePotential_ = simParams->getOutputSitePotential();
128	>
129	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
130	>	needSitePotential_) {
131	>	doSiteData_ = true;
132	>	} else {
133	>	doSiteData_ = false;
134	>	}
135	>
136		createDumpFile_ = true;
137		#ifdef HAVE_LIBZ
138		if (needCompression_) {
#	Line 134 | Line 170 | namespace oopse {
170		Globals* simParams = info->getSimParams();
171		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
172
173	<	needCompression_ = simParams->getCompressDumpFile();
174	<	needForceVector_ = simParams->getOutputForceVector();
175	<
173	>	needCompression_   = simParams->getCompressDumpFile();
174	>	needForceVector_   = simParams->getOutputForceVector();
175	>	needParticlePot_   = simParams->getOutputParticlePotential();
176	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
177	>	needElectricField_ = simParams->getOutputElectricField();
178	>	needSitePotential_ = simParams->getOutputSitePotential();
179	>
180	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
181	>	needSitePotential_) {
182	>	doSiteData_ = true;
183	>	} else {
184	>	doSiteData_ = false;
185	>	}
186	>
187		#ifdef HAVE_LIBZ
188		if (needCompression_) {
189		filename_ += ".gz";
#	Line 194 | Line 241 | namespace oopse {
241		os << "    <FrameData>\n";
242
243		RealType currentTime = s->getTime();
244	<	sprintf(buffer, "        Time: %.10g\n", time);
244	>
245	>	if (isinf(currentTime) || isnan(currentTime)) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the time");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>
252	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
253		os << buffer;
254
255		Mat3x3d hmat;
256		hmat = s->getHmat();
257	+
258	+	for (unsigned int i = 0; i < 3; i++) {
259	+	for (unsigned int j = 0; j < 3; j++) {
260	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
261	+	sprintf( painCave.errMsg,
262	+	"DumpWriter detected a numerical error writing the box");
263	+	painCave.isFatal = 1;
264	+	simError();
265	+	}
266	+	}
267	+	}
268	+
269		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
270		hmat(0, 0), hmat(1, 0), hmat(2, 0),
271		hmat(0, 1), hmat(1, 1), hmat(2, 1),
272		hmat(0, 2), hmat(1, 2), hmat(2, 2));
273		os << buffer;
274
275	<	RealType chi = s->getChi();
276	<	RealType integralOfChiDt = s->getIntegralOfChiDt();
277	<	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
275	>	pair<RealType, RealType> thermostat = s->getThermostat();
276	>
277	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
278	>	isinf(thermostat.second) || isnan(thermostat.second)) {
279	>	sprintf( painCave.errMsg,
280	>	"DumpWriter detected a numerical error writing the thermostat");
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
285	>	thermostat.second);
286		os << buffer;
287
288		Mat3x3d eta;
289	<	eta = s->getEta();
289	>	eta = s->getBarostat();
290	>
291	>	for (unsigned int i = 0; i < 3; i++) {
292	>	for (unsigned int j = 0; j < 3; j++) {
293	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
294	>	sprintf( painCave.errMsg,
295	>	"DumpWriter detected a numerical error writing the barostat");
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}
300	>	}
301	>
302		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
303		eta(0, 0), eta(1, 0), eta(2, 0),
304		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 228 | Line 315 | namespace oopse {
315		#endif
316
317		Molecule* mol;
318	<	StuntDouble* integrableObject;
318	>	StuntDouble* sd;
319		SimInfo::MoleculeIterator mi;
320		Molecule::IntegrableObjectIterator ii;
321	+	RigidBody::AtomIterator ai;
322
323		#ifndef IS_MPI
324		os << "  <Snapshot>\n";
325	<
325	>
326		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327
328		os << "    <StuntDoubles>\n";
329	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
330	<
331	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
332	<	integrableObject = mol->nextIntegrableObject(ii)) {
333	<	os << prepareDumpLine(integrableObject);
334	<
329	>	for (mol = info_->beginMolecule(mi); mol != NULL;
330	>	mol = info_->nextMolecule(mi)) {
331	>
332	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
333	>	sd = mol->nextIntegrableObject(ii)) {
334	>	os << prepareDumpLine(sd);
335	>
336		}
337		}
338		os << "    </StuntDoubles>\n";
339
340	+	if (doSiteData_) {
341	+	os << "    <SiteData>\n";
342	+	for (mol = info_->beginMolecule(mi); mol != NULL;
343	+	mol = info_->nextMolecule(mi)) {
344	+
345	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
346	+	sd = mol->nextIntegrableObject(ii)) {
347	+
348	+	int ioIndex = sd->getGlobalIntegrableObjectIndex();
349	+	// do one for the IO itself
350	+	os << prepareSiteLine(sd, ioIndex, 0);
351	+
352	+	if (sd->isRigidBody()) {
353	+
354	+	RigidBody* rb = static_cast<RigidBody*>(sd);
355	+	int siteIndex = 0;
356	+	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
357	+	atom = rb->nextAtom(ai)) {
358	+	os << prepareSiteLine(atom, ioIndex, siteIndex);
359	+	siteIndex++;
360	+	}
361	+	}
362	+	}
363	+	}
364	+	os << "    </SiteData>\n";
365	+	}
366		os << "  </Snapshot>\n";
367
368		os.flush();
369		#else
370	+
371	+	const int masterNode = 0;
372	+	int worldRank;
373	+	int nProc;
374	+
375	+	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
376	+	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
377	+
378	+
379	+	if (worldRank == masterNode) {
380	+	os << "  <Snapshot>\n";
381	+	writeFrameProperties(os,
382	+	info_->getSnapshotManager()->getCurrentSnapshot());
383	+	os << "    <StuntDoubles>\n";
384	+	}
385	+
386		//every node prepares the dump lines for integrable objects belong to itself
387		std::string buffer;
388	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
389	<
390	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	<	buffer += prepareDumpLine(integrableObject);
388	>	for (mol = info_->beginMolecule(mi); mol != NULL;
389	>	mol = info_->nextMolecule(mi)) {
390	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
391	>	sd = mol->nextIntegrableObject(ii)) {
392	>	buffer += prepareDumpLine(sd);
393		}
394		}
395
265	–	const int masterNode = 0;
266	–
396		if (worldRank == masterNode) {
397	<	os << "  <Snapshot>\n";
398	<	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270	<	os << buffer;
271	<	os << "    <StuntDoubles>\n";
272	<
273	<	int nProc;
274	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
397	>	os << buffer;
398	>
399		for (int i = 1; i < nProc; ++i) {
400	+	// tell processor i to start sending us data:
401	+	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
402
403		// receive the length of the string buffer that was
404	<	// prepared by processor i
279	<
404	>	// prepared by processor i:
405		int recvLength;
406	<	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
406	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
407	>	&istatus);
408	>
409	>	// create a buffer to receive the data
410		char* recvBuffer = new char[recvLength];
411		if (recvBuffer == NULL) {
284	–
412		} else {
413	<	MPI_Recv(&recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
413	>	// receive the data:
414	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
415	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
416	>	// send it to the file:
417		os << recvBuffer;
418	<	delete recvBuffer;
418	>	// get rid of the receive buffer:
419	>	delete [] recvBuffer;
420		}
290	–
421		}
292	–	os << "    </StuntDoubles>\n";
293	–
294	–	os << "  </Snapshot>\n";
295	–	os.flush();
422		} else {
423	<	int sendBufferLength = buffer.size();
424	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
425	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
423	>	int sendBufferLength = buffer.size() + 1;
424	>	int myturn = 0;
425	>	for (int i = 1; i < nProc; ++i){
426	>	// wait for the master node to call our number:
427	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
428	>	if (myturn == worldRank){
429	>	// send the length of our buffer:
430	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
431	>
432	>	// send our buffer:
433	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
434	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
435	>
436	>	}
437	>	}
438		}
439	+
440	+	if (worldRank == masterNode) {
441	+	os << "    </StuntDoubles>\n";
442	+	}
443
444	<	#endif // is_mpi
444	>	if (doSiteData_) {
445	>	if (worldRank == masterNode) {
446	>	os << "    <SiteData>\n";
447	>	}
448	>	buffer.clear();
449	>	for (mol = info_->beginMolecule(mi); mol != NULL;
450	>	mol = info_->nextMolecule(mi)) {
451	>
452	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
453	>	sd = mol->nextIntegrableObject(ii)) {
454	>
455	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
456	>	// do one for the IO itself
457	>	buffer += prepareSiteLine(sd, ioIndex, 0);
458
459	<	}
459	>	if (sd->isRigidBody()) {
460	>
461	>	RigidBody* rb = static_cast<RigidBody*>(sd);
462	>	int siteIndex = 0;
463	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
464	>	atom = rb->nextAtom(ai)) {
465	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
466	>	siteIndex++;
467	>	}
468	>	}
469	>	}
470	>	}
471
472	<	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
472	>	if (worldRank == masterNode) {
473	>	os << buffer;
474	>
475	>	for (int i = 1; i < nProc; ++i) {
476	>
477	>	// tell processor i to start sending us data:
478	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
479	>
480	>	// receive the length of the string buffer that was
481	>	// prepared by processor i:
482	>	int recvLength;
483	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
484	>	&istatus);
485	>
486	>	// create a buffer to receive the data
487	>	char* recvBuffer = new char[recvLength];
488	>	if (recvBuffer == NULL) {
489	>	} else {
490	>	// receive the data:
491	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
492	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
493	>	// send it to the file:
494	>	os << recvBuffer;
495	>	// get rid of the receive buffer:
496	>	delete [] recvBuffer;
497	>	}
498	>	}
499	>	} else {
500	>	int sendBufferLength = buffer.size() + 1;
501	>	int myturn = 0;
502	>	for (int i = 1; i < nProc; ++i){
503	>	// wait for the master node to call our number:
504	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
505	>	if (myturn == worldRank){
506	>	// send the length of our buffer:
507	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
508	>	// send our buffer:
509	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
510	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
511	>	}
512	>	}
513	>	}
514	>
515	>	if (worldRank == masterNode) {
516	>	os << "    </SiteData>\n";
517	>	}
518	>	}
519	>
520	>	if (worldRank == masterNode) {
521	>	os << "  </Snapshot>\n";
522	>	os.flush();
523	>	}
524	>
525	>	#endif // is_mpi
526	>
527	>	}
528	>
529	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
530
531	<	int index = integrableObject->getGlobalIntegrableObjectIndex();
531	>	int index = sd->getGlobalIntegrableObjectIndex();
532		std::string type("pv");
533		std::string line;
534		char tempBuffer[4096];
535
536		Vector3d pos;
537		Vector3d vel;
538	<	pos = integrableObject->getPos();
539	<	vel = integrableObject->getVel();
540	<	sprintf(tempBuffer, "%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g",
538	>	pos = sd->getPos();
539	>
540	>	if (isinf(pos[0]) || isnan(pos[0]) ||
541	>	isinf(pos[1]) || isnan(pos[1]) ||
542	>	isinf(pos[2]) || isnan(pos[2]) ) {
543	>	sprintf( painCave.errMsg,
544	>	"DumpWriter detected a numerical error writing the position"
545	>	" for object %d", index);
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549	>
550	>	vel = sd->getVel();
551	>
552	>	if (isinf(vel[0]) || isnan(vel[0]) ||
553	>	isinf(vel[1]) || isnan(vel[1]) ||
554	>	isinf(vel[2]) || isnan(vel[2]) ) {
555	>	sprintf( painCave.errMsg,
556	>	"DumpWriter detected a numerical error writing the velocity"
557	>	" for object %d", index);
558	>	painCave.isFatal = 1;
559	>	simError();
560	>	}
561	>
562	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
563		pos[0], pos[1], pos[2],
564		vel[0], vel[1], vel[2]);
565		line += tempBuffer;
566
567	<	if (integrableObject->isDirectional()) {
567	>	if (sd->isDirectional()) {
568		type += "qj";
569		Quat4d q;
570		Vector3d ji;
571	<	q = integrableObject->getQ();
572	<	ji = integrableObject->getJ();
573	<	sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
571	>	q = sd->getQ();
572	>
573	>	if (isinf(q[0]) || isnan(q[0]) ||
574	>	isinf(q[1]) || isnan(q[1]) ||
575	>	isinf(q[2]) || isnan(q[2]) ||
576	>	isinf(q[3]) || isnan(q[3]) ) {
577	>	sprintf( painCave.errMsg,
578	>	"DumpWriter detected a numerical error writing the quaternion"
579	>	" for object %d", index);
580	>	painCave.isFatal = 1;
581	>	simError();
582	>	}
583	>
584	>	ji = sd->getJ();
585	>
586	>	if (isinf(ji[0]) || isnan(ji[0]) ||
587	>	isinf(ji[1]) || isnan(ji[1]) ||
588	>	isinf(ji[2]) || isnan(ji[2]) ) {
589	>	sprintf( painCave.errMsg,
590	>	"DumpWriter detected a numerical error writing the angular"
591	>	" momentum for object %d", index);
592	>	painCave.isFatal = 1;
593	>	simError();
594	>	}
595	>
596	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
597		q[0], q[1], q[2], q[3],
598		ji[0], ji[1], ji[2]);
599		line += tempBuffer;
600		}
601
602		if (needForceVector_) {
603	<	type += "ft";
604	<	Vector3d frc;
605	<	Vector3d trq;
606	<	frc = integrableObject->getFrc();
607	<	trq = integrableObject->getTrq();
608	<
609	<	sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
610	<	frc[0], frc[1], frc[2],
611	<	trq[0], trq[1], trq[2]);
603	>	type += "f";
604	>	Vector3d frc = sd->getFrc();
605	>	if (isinf(frc[0]) || isnan(frc[0]) ||
606	>	isinf(frc[1]) || isnan(frc[1]) ||
607	>	isinf(frc[2]) || isnan(frc[2]) ) {
608	>	sprintf( painCave.errMsg,
609	>	"DumpWriter detected a numerical error writing the force"
610	>	" for object %d", index);
611	>	painCave.isFatal = 1;
612	>	simError();
613	>	}
614	>	sprintf(tempBuffer, " %13e %13e %13e",
615	>	frc[0], frc[1], frc[2]);
616		line += tempBuffer;
617	+
618	+	if (sd->isDirectional()) {
619	+	type += "t";
620	+	Vector3d trq = sd->getTrq();
621	+	if (isinf(trq[0]) || isnan(trq[0]) ||
622	+	isinf(trq[1]) || isnan(trq[1]) ||
623	+	isinf(trq[2]) || isnan(trq[2]) ) {
624	+	sprintf( painCave.errMsg,
625	+	"DumpWriter detected a numerical error writing the torque"
626	+	" for object %d", index);
627	+	painCave.isFatal = 1;
628	+	simError();
629	+	}
630	+	sprintf(tempBuffer, " %13e %13e %13e",
631	+	trq[0], trq[1], trq[2]);
632	+	line += tempBuffer;
633	+	}
634		}
635	<
636	<	sprintf(tempBuffer, "%d\t%s\t%s\n", index, type.c_str(), line.c_str());
635	>
636	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
637		return std::string(tempBuffer);
638		}
639
640	+	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
641	+	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
642	+
643	+	std::string id;
644	+	std::string type;
645	+	std::string line;
646	+	char tempBuffer[4096];
647	+
648	+	if (sd->isRigidBody()) {
649	+	sprintf(tempBuffer, "%10d           ", ioIndex);
650	+	id = std::string(tempBuffer);
651	+	} else {
652	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
653	+	id = std::string(tempBuffer);
654	+	}
655	+
656	+	if (needFlucQ_) {
657	+	if (storageLayout & DataStorage::dslFlucQPosition) {
658	+	type += "c";
659	+	RealType fqPos = sd->getFlucQPos();
660	+	if (isinf(fqPos) || isnan(fqPos) ) {
661	+	sprintf( painCave.errMsg,
662	+	"DumpWriter detected a numerical error writing the"
663	+	" fluctuating charge for object %s", id.c_str());
664	+	painCave.isFatal = 1;
665	+	simError();
666	+	}
667	+	sprintf(tempBuffer, " %13e ", fqPos);
668	+	line += tempBuffer;
669	+	}
670	+
671	+	if (storageLayout & DataStorage::dslFlucQVelocity) {
672	+	type += "w";
673	+	RealType fqVel = sd->getFlucQVel();
674	+	if (isinf(fqVel) || isnan(fqVel) ) {
675	+	sprintf( painCave.errMsg,
676	+	"DumpWriter detected a numerical error writing the"
677	+	" fluctuating charge velocity for object %s", id.c_str());
678	+	painCave.isFatal = 1;
679	+	simError();
680	+	}
681	+	sprintf(tempBuffer, " %13e ", fqVel);
682	+	line += tempBuffer;
683	+	}
684	+
685	+	if (needForceVector_) {
686	+	if (storageLayout & DataStorage::dslFlucQForce) {
687	+	type += "g";
688	+	RealType fqFrc = sd->getFlucQFrc();
689	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
690	+	sprintf( painCave.errMsg,
691	+	"DumpWriter detected a numerical error writing the"
692	+	" fluctuating charge force for object %s", id.c_str());
693	+	painCave.isFatal = 1;
694	+	simError();
695	+	}
696	+	sprintf(tempBuffer, " %13e ", fqFrc);
697	+	line += tempBuffer;
698	+	}
699	+	}
700	+	}
701	+
702	+	if (needElectricField_) {
703	+	if (storageLayout & DataStorage::dslElectricField) {
704	+	type += "e";
705	+	Vector3d eField= sd->getElectricField();
706	+	if (isinf(eField[0]) || isnan(eField[0]) ||
707	+	isinf(eField[1]) || isnan(eField[1]) ||
708	+	isinf(eField[2]) || isnan(eField[2]) ) {
709	+	sprintf( painCave.errMsg,
710	+	"DumpWriter detected a numerical error writing the electric"
711	+	" field for object %s", id.c_str());
712	+	painCave.isFatal = 1;
713	+	simError();
714	+	}
715	+	sprintf(tempBuffer, " %13e %13e %13e",
716	+	eField[0], eField[1], eField[2]);
717	+	line += tempBuffer;
718	+	}
719	+	}
720	+
721	+	if (needSitePotential_) {
722	+	if (storageLayout & DataStorage::dslSitePotential) {
723	+	type += "s";
724	+	RealType sPot = sd->getSitePotential();
725	+	if (isinf(sPot) || isnan(sPot) ) {
726	+	sprintf( painCave.errMsg,
727	+	"DumpWriter detected a numerical error writing the"
728	+	" site potential for object %s", id.c_str());
729	+	painCave.isFatal = 1;
730	+	simError();
731	+	}
732	+	sprintf(tempBuffer, " %13e ", sPot);
733	+	line += tempBuffer;
734	+	}
735	+	}
736	+
737	+	if (needParticlePot_) {
738	+	if (storageLayout & DataStorage::dslParticlePot) {
739	+	type += "u";
740	+	RealType particlePot = sd->getParticlePot();
741	+	if (isinf(particlePot) || isnan(particlePot)) {
742	+	sprintf( painCave.errMsg,
743	+	"DumpWriter detected a numerical error writing the particle "
744	+	" potential for object %s", id.c_str());
745	+	painCave.isFatal = 1;
746	+	simError();
747	+	}
748	+	sprintf(tempBuffer, " %13e", particlePot);
749	+	line += tempBuffer;
750	+	}
751	+	}
752	+
753	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
754	+	return std::string(tempBuffer);
755	+	}
756	+
757		void DumpWriter::writeDump() {
758		writeFrame(*dumpFile_);
759		}
760
761		void DumpWriter::writeEor() {
762	<	std::ostream* eorStream;
763	<
762	>
763	>	std::ostream* eorStream = NULL;
764	>
765		#ifdef IS_MPI
766		if (worldRank == 0) {
767		#endif // is_mpi
768	<
768	>
769		eorStream = createOStream(eorFilename_);
770
771		#ifdef IS_MPI
772		}
773	<	#endif // is_mpi
774	<
773	>	#endif
774	>
775		writeFrame(*eorStream);
776	<
776	>
777		#ifdef IS_MPI
778		if (worldRank == 0) {
779	<	#endif // is_mpi
779	>	#endif
780	>
781		writeClosing(*eorStream);
782		delete eorStream;
783	+
784		#ifdef IS_MPI
785		}
786		#endif // is_mpi
#	Line 385 | Line 794 | namespace oopse {
794		#ifdef IS_MPI
795		if (worldRank == 0) {
796		#endif // is_mpi
388	–
797		buffers.push_back(dumpFile_->rdbuf());
390	–
798		eorStream = createOStream(eorFilename_);
392	–
799		buffers.push_back(eorStream->rdbuf());
394	–
800		#ifdef IS_MPI
801		}
802		#endif // is_mpi
803
804		TeeBuf tbuf(buffers.begin(), buffers.end());
805		std::ostream os(&tbuf);
401	–
806		writeFrame(os);
807
808		#ifdef IS_MPI
#	Line 408 | Line 812 | namespace oopse {
812		delete eorStream;
813		#ifdef IS_MPI
814		}
815	<	#endif // is_mpi
412	<
815	>	#endif // is_mpi
816		}
817
818		std::ostream* DumpWriter::createOStream(const std::string& filename) {
819
820		std::ostream* newOStream;
821	<	#ifdef HAVE_LIBZ
821	>	#ifdef HAVE_ZLIB
822		if (needCompression_) {
823		newOStream = new ogzstream(filename.c_str());
824		} else {
#	Line 425 | Line 828 | namespace oopse {
828		newOStream = new std::ofstream(filename.c_str());
829		#endif
830		//write out MetaData first
831	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
831	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
832		(*newOStream) << "  <MetaData>" << std::endl;
833		(*newOStream) << info_->getRawMetaData();
834		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 434 | Line 837 | namespace oopse {
837
838		void DumpWriter::writeClosing(std::ostream& os) {
839
840	<	os << "</OOPSE>\n";
840	>	os << "</OpenMD>\n";
841		os.flush();
842		}
843
844	<	}//end namespace oopse
844	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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

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