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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 376 by tim, Thu Feb 24 20:55:07 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
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()){
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();
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_) {
83	>	filename_ += ".gz";
84	>	eorFilename_ += ".gz";
85	>	}
86	>	#endif
87	>
88		#ifdef IS_MPI
89
90		if (worldRank == 0) {
91		#endif // is_mpi
92	+
93	+	dumpFile_ = createOStream(filename_);
94
95	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
95	>	if (!dumpFile_) {
96	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
97	>	filename_.c_str());
98	>	painCave.isFatal = 1;
99	>	simError();
100	>	}
101
61	–	if (!dumpFile_) {
62	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
63	–	filename_.c_str());
64	–	painCave.isFatal = 1;
65	–	simError();
66	–	}
67	–
102		#ifdef IS_MPI
103
104		}
105
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
106		#endif // is_mpi
107
108	<	}
108	>	}
109
110
111	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
112	<	: info_(info), filename_(filename){
111	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
112	>	: info_(info), filename_(filename){
113	>
114	>	Globals* simParams = info->getSimParams();
115	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
116	>
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_) {
132	>	filename_ += ".gz";
133	>	eorFilename_ += ".gz";
134	>	}
135	>	#endif
136	>
137		#ifdef IS_MPI
138
139		if (worldRank == 0) {
140		#endif // is_mpi
141
142	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
143	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
142	>
143	>	dumpFile_ = createOStream(filename_);
144
145	<	if (!dumpFile_) {
146	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	<	filename_.c_str());
148	<	painCave.isFatal = 1;
149	<	simError();
150	<	}
145	>	if (!dumpFile_) {
146	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	>	filename_.c_str());
148	>	painCave.isFatal = 1;
149	>	simError();
150	>	}
151
152		#ifdef IS_MPI
153
154		}
155
101	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	–	MPIcheckPoint();
103	–
156		#endif // is_mpi
157
158	<	}
158	>	}
159	>
160	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
161	>	: info_(info), filename_(filename){
162	>
163	>	Globals* simParams = info->getSimParams();
164	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
165	>
166	>	needCompression_   = simParams->getCompressDumpFile();
167	>	needForceVector_   = simParams->getOutputForceVector();
168	>	needParticlePot_   = simParams->getOutputParticlePotential();
169	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
170	>	needElectricField_ = simParams->getOutputElectricField();
171
172	<	DumpWriter::~DumpWriter() {
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";
181	+	eorFilename_ += ".gz";
182	+	}
183	+	#endif
184	+
185		#ifdef IS_MPI
186	<
186	>
187		if (worldRank == 0) {
188		#endif // is_mpi
189	+
190	+	createDumpFile_ = writeDumpFile;
191	+	if (createDumpFile_) {
192	+	dumpFile_ = createOStream(filename_);
193	+
194	+	if (!dumpFile_) {
195	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
196	+	filename_.c_str());
197	+	painCave.isFatal = 1;
198	+	simError();
199	+	}
200	+	}
201	+	#ifdef IS_MPI
202	+
203	+	}
204
205	<	dumpFile_.close();
205	>
206	>	#endif // is_mpi
207	>
208	>	}
209
210	+	DumpWriter::~DumpWriter() {
211	+
212		#ifdef IS_MPI
213
214	+	if (worldRank == 0) {
215	+	#endif // is_mpi
216	+	if (createDumpFile_){
217	+	writeClosing(*dumpFile_);
218	+	delete dumpFile_;
219	+	}
220	+	#ifdef IS_MPI
221	+
222		}
223
224		#endif // is_mpi
225
226	<	}
226	>	}
227
228	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
228	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
229
230	<	double currentTime;
231	<	Mat3x3d hmat;
232	<	double chi;
233	<	double integralOfChiDt;
234	<	Mat3x3d eta;
230	>	char buffer[1024];
231	>
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	<	currentTime = s->getTime();
243	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
244	>	os << buffer;
245	>
246	>	Mat3x3d hmat;
247		hmat = s->getHmat();
248	<	chi = s->getChi();
249	<	integralOfChiDt = s->getIntegralOfChiDt();
250	<	eta = s->getEta();
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	<	os << currentTime << ";\t"
261	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
262	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
263	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
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	<	//write out additional parameters, such as chi and eta
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267
268	<	os << chi << "\t" << integralOfChiDt << "\t;";
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	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
280	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
150	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
151	<
152	<	os << "\n";
153	<	}
279	>	Mat3x3d eta;
280	>	eta = s->getBarostat();
281
282	<	void DumpWriter::writeFrame(std::ostream& os) {
283	<	const int BUFFERSIZE = 2000;
284	<	const int MINIBUFFERSIZE = 100;
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	<	char tempBuffer[BUFFERSIZE];
294	<	char writeLine[BUFFERSIZE];
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),
296	>	eta(0, 2), eta(1, 2), eta(2, 2));
297	>	os << buffer;
298
299	<	Quat4d q;
300	<	Vector3d ji;
164	<	Vector3d pos;
165	<	Vector3d vel;
299	>	os << "    </FrameData>\n";
300	>	}
301
302	+	void DumpWriter::writeFrame(std::ostream& os) {
303	+
304	+	#ifdef IS_MPI
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	<
313	<	int nTotObjects;
173	<	nTotObjects = info_->getNGlobalIntegrableObjects();
312	>	RigidBody::AtomIterator ai;
313	>	Atom* atom;
314
315		#ifndef IS_MPI
316	<
317	<
318	<	os << nTotObjects << "\n";
319	<
320	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
181	<
316	>	os << "  <Snapshot>\n";
317	>
318	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
319	>
320	>	os << "    <StuntDoubles>\n";
321		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
322
323	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
324	<	integrableObject = mol->nextIntegrableObject(ii)) {
325	<
323	>
324	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
325	>	sd = mol->nextIntegrableObject(ii)) {
326	>	os << prepareDumpLine(sd);
327	>
328	>	}
329	>	}
330	>	os << "    </StuntDoubles>\n";
331
332	<	pos = integrableObject->getPos();
333	<	vel = integrableObject->getVel();
332	>	if (doSiteData_) {
333	>	os << "    <SiteData>\n";
334	>	for (mol = info_->beginMolecule(mi); mol != NULL;
335	>	mol = info_->nextMolecule(mi)) {
336	>
337	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
338	>	sd = mol->nextIntegrableObject(ii)) {
339
340	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
341	<	integrableObject->getType().c_str(),
342	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
340	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
341	>	// do one for the IO itself
342	>	os << prepareSiteLine(sd, ioIndex, 0);
343
344	<	strcpy(writeLine, tempBuffer);
345	<
346	<	if (integrableObject->isDirectional()) {
347	<	q = integrableObject->getQ();
348	<	ji = integrableObject->getJ();
349	<
350	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
351	<	q[0], q[1], q[2], q[3],
204	<	ji[0], ji[1], ji[2]);
205	<	strcat(writeLine, tempBuffer);
206	<	} else {
207	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
344	>	if (sd->isRigidBody()) {
345	>
346	>	RigidBody* rb = static_cast<RigidBody*>(sd);
347	>	int siteIndex = 0;
348	>	for (atom = rb->beginAtom(ai); atom != NULL;
349	>	atom = rb->nextAtom(ai)) {
350	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
351	>	siteIndex++;
352		}
353	<
210	<	os << writeLine;
211	<
353	>	}
354		}
355	+	}
356	+	os << "    </SiteData>\n";
357		}
358	+	os << "  </Snapshot>\n";
359
360		os.flush();
361	<	#else // is_mpi
362	<	/*********************************************************************
218	<	* Documentation?  You want DOCUMENTATION?
219	<	*
220	<	* Why all the potatoes below?
221	<	*
222	<	* To make a long story short, the original version of DumpWriter
223	<	* worked in the most inefficient way possible.  Node 0 would
224	<	* poke each of the node for an individual atom's formatted data
225	<	* as node 0 worked its way down the global index. This was particularly
226	<	* inefficient since the method blocked all processors at every atom
227	<	* (and did it twice!).
228	<	*
229	<	* An intermediate version of DumpWriter could be described from Node
230	<	* zero's perspective as follows:
231	<	*
232	<	*  1) Have 100 of your friends stand in a circle.
233	<	*  2) When you say go, have all of them start tossing potatoes at
234	<	*     you (one at a time).
235	<	*  3) Catch the potatoes.
236	<	*
237	<	* It was an improvement, but MPI has buffers and caches that could
238	<	* best be described in this analogy as "potato nets", so there's no
239	<	* need to block the processors atom-by-atom.
240	<	*
241	<	* This new and improved DumpWriter works in an even more efficient
242	<	* way:
243	<	*
244	<	*  1) Have 100 of your friend stand in a circle.
245	<	*  2) When you say go, have them start tossing 5-pound bags of
246	<	*     potatoes at you.
247	<	*  3) Once you've caught a friend's bag of potatoes,
248	<	*     toss them a spud to let them know they can toss another bag.
249	<	*
250	<	* How's THAT for documentation?
251	<	*
252	<	*********************************************************************/
361	>	#else
362	>
363		const int masterNode = 0;
364	+	int worldRank = MPI::COMM_WORLD.Get_rank();
365	+	int nProc = MPI::COMM_WORLD.Get_size();
366
367	<	int * potatoes;
368	<	int myPotato;
369	<	int nProc;
370	<	int which_node;
371	<	double atomData[13];
372	<	int isDirectional;
261	<	const char * atomTypeString;
262	<	char MPIatomTypeString[MINIBUFFERSIZE];
263	<	int msgLen; // the length of message actually recieved at master nodes
264	<	int haveError;
265	<	MPI_Status istatus;
266	<	int nCurObj;
267	<
268	<	// code to find maximum tag value
269	<	int * tagub;
270	<	int flag;
271	<	int MAXTAG;
272	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
367	>	if (worldRank == masterNode) {
368	>	os << "  <Snapshot>\n";
369	>	writeFrameProperties(os,
370	>	info_->getSnapshotManager()->getCurrentSnapshot());
371	>	os << "    <StuntDoubles>\n";
372	>	}
373
374	<	if (flag) {
375	<	MAXTAG = *tagub;
376	<	} else {
377	<	MAXTAG = 32767;
374	>	//every node prepares the dump lines for integrable objects belong to itself
375	>	std::string buffer;
376	>	for (mol = info_->beginMolecule(mi); mol != NULL;
377	>	mol = info_->nextMolecule(mi)) {
378	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
379	>	sd = mol->nextIntegrableObject(ii)) {
380	>	buffer += prepareDumpLine(sd);
381	>	}
382		}
383	+
384	+	if (worldRank == masterNode) {
385	+	os << buffer;
386	+
387	+	for (int i = 1; i < nProc; ++i) {
388	+	// tell processor i to start sending us data:
389	+	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
390
391	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
391	>	// receive the length of the string buffer that was
392	>	// prepared by processor i:
393	>	int recvLength;
394	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
395	>	istatus);
396
397	<	// Node 0 needs a list of the magic potatoes for each processor;
397	>	// create a buffer to receive the data
398	>	char* recvBuffer = new char[recvLength];
399	>	if (recvBuffer == NULL) {
400	>	} else {
401	>	// receive the data:
402	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
403	>	MPI::ANY_TAG, istatus);
404	>	// send it to the file:
405	>	os << recvBuffer;
406	>	// get rid of the receive buffer:
407	>	delete [] recvBuffer;
408	>	}
409	>	}
410	>	} else {
411	>	int sendBufferLength = buffer.size() + 1;
412	>	int myturn = 0;
413	>	for (int i = 1; i < nProc; ++i){
414	>	// wait for the master node to call our number:
415	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
416	>	if (myturn == worldRank){
417	>	// send the length of our buffer:
418	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
419
420	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
421	<	potatoes = new int[nProc];
422	<
287	<	//write out the comment lines
288	<	for(int i = 0; i < nProc; i++) {
289	<	potatoes[i] = 0;
420	>	// send our buffer:
421	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
422	>	MPI::CHAR, masterNode, 0);
423		}
424	+	}
425	+	}
426	+
427	+	if (worldRank == masterNode) {
428	+	os << "    </StuntDoubles>\n";
429	+	}
430
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	<	os << nTotObjects << "\n";
447	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
446	>	if (sd->isRigidBody()) {
447	>
448	>	RigidBody* rb = static_cast<RigidBody*>(sd);
449	>	int siteIndex = 0;
450	>	for (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	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
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	<	// Get the Node number which has this atom;
516	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
517	>
518	>	int index = sd->getGlobalIntegrableObjectIndex();
519	>	std::string type("pv");
520	>	std::string line;
521	>	char tempBuffer[4096];
522
523	<	which_node = info_->getMolToProc(i);
523	>	Vector3d pos;
524	>	Vector3d vel;
525	>	pos = sd->getPos();
526
527	<	if (which_node != masterNode) { //current molecule is in slave node
528	<	if (potatoes[which_node] + 1 >= MAXTAG) {
529	<	// The potato was going to exceed the maximum value,
530	<	// so wrap this processor potato back to 0:
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	<	potatoes[which_node] = 0;
308	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
309	<	MPI_COMM_WORLD);
310	<	}
537	>	vel = sd->getVel();
538
539	<	myPotato = potatoes[which_node];
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	<	//recieve the number of integrableObject in current molecule
550	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
551	<	MPI_COMM_WORLD, &istatus);
552	<	myPotato++;
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	<	for(int l = 0; l < nCurObj; l++) {
555	<	if (potatoes[which_node] + 2 >= MAXTAG) {
556	<	// The potato was going to exceed the maximum value,
557	<	// so wrap this processor potato back to 0:
554	>	if (sd->isDirectional()) {
555	>	type += "qj";
556	>	Quat4d q;
557	>	Vector3d ji;
558	>	q = sd->getQ();
559
560	<	potatoes[which_node] = 0;
561	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
562	<	0, MPI_COMM_WORLD);
563	<	}
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	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
330	<	which_node, myPotato, MPI_COMM_WORLD,
331	<	&istatus);
571	>	ji = sd->getJ();
572
573	<	atomTypeString = MPIatomTypeString;
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	<	myPotato++;
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]);
586	>	line += tempBuffer;
587	>	}
588
589	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
590	<	MPI_COMM_WORLD, &istatus);
591	<	myPotato++;
589	>	if (needForceVector_) {
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
623	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
623	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
624	>	return std::string(tempBuffer);
625	>	}
626
627	<	if (msgLen == 13)
628	<	isDirectional = 1;
345	<	else
346	<	isDirectional = 0;
627	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
628	>
629
630	<	// If we've survived to here, format the line:
630	>	std::string id;
631	>	std::string type;
632	>	std::string line;
633	>	char tempBuffer[4096];
634
635	<	if (!isDirectional) {
636	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
637	<	atomTypeString, atomData[0],
638	<	atomData[1], atomData[2],
639	<	atomData[3], atomData[4],
640	<	atomData[5]);
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	<	strcat(writeLine,
668	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
669	<	} else {
670	<	sprintf(writeLine,
671	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
672	<	atomTypeString,
673	<	atomData[0],
674	<	atomData[1],
675	<	atomData[2],
676	<	atomData[3],
677	<	atomData[4],
678	<	atomData[5],
679	<	atomData[6],
680	<	atomData[7],
371	<	atomData[8],
372	<	atomData[9],
373	<	atomData[10],
374	<	atomData[11],
375	<	atomData[12]);
376	<	}
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	<	os << writeLine;
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
380	–	} // end for(int l =0)
699
700	<	potatoes[which_node] = myPotato;
701	<	} else { //master node has current molecule
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	<	mol = info_->getMoleculeByGlobalIndex(i);
716	<
717	<	if (mol == NULL) {
388	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
389	<	painCave.isFatal = 1;
390	<	simError();
391	<	}
392	<
393	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
394	<	integrableObject = mol->nextIntegrableObject(ii)) {
395	<
396	<	atomTypeString = integrableObject->getType().c_str();
397	<
398	<	pos = integrableObject->getPos();
399	<	vel = integrableObject->getVel();
400	<
401	<	atomData[0] = pos[0];
402	<	atomData[1] = pos[1];
403	<	atomData[2] = pos[2];
404	<
405	<	atomData[3] = vel[0];
406	<	atomData[4] = vel[1];
407	<	atomData[5] = vel[2];
408	<
409	<	isDirectional = 0;
410	<
411	<	if (integrableObject->isDirectional()) {
412	<	isDirectional = 1;
715	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
716	>	return std::string(tempBuffer);
717	>	}
718
719	<	q = integrableObject->getQ();
720	<	ji = integrableObject->getJ();
719	>	void DumpWriter::writeDump() {
720	>	writeFrame(*dumpFile_);
721	>	}
722
723	<	for(int j = 0; j < 6; j++) {
724	<	atomData[j] = atomData[j];
419	<	}
420	<
421	<	atomData[6] = q[0];
422	<	atomData[7] = q[1];
423	<	atomData[8] = q[2];
424	<	atomData[9] = q[3];
425	<
426	<	atomData[10] = ji[0];
427	<	atomData[11] = ji[1];
428	<	atomData[12] = ji[2];
429	<	}
430	<
431	<	// If we've survived to here, format the line:
432	<
433	<	if (!isDirectional) {
434	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
435	<	atomTypeString, atomData[0],
436	<	atomData[1], atomData[2],
437	<	atomData[3], atomData[4],
438	<	atomData[5]);
439	<
440	<	strcat(writeLine,
441	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
442	<	} else {
443	<	sprintf(writeLine,
444	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
445	<	atomTypeString,
446	<	atomData[0],
447	<	atomData[1],
448	<	atomData[2],
449	<	atomData[3],
450	<	atomData[4],
451	<	atomData[5],
452	<	atomData[6],
453	<	atomData[7],
454	<	atomData[8],
455	<	atomData[9],
456	<	atomData[10],
457	<	atomData[11],
458	<	atomData[12]);
459	<	}
460	<
461	<
462	<	os << writeLine;
463	<
464	<	} //end for(iter = integrableObject.begin())
465	<	}
466	<	} //end for(i = 0; i < mpiSim->getNmol())
467	<
468	<	os.flush();
469	<
470	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
471	<	MPIcheckPoint();
472	<
473	<	delete [] potatoes;
474	<	} else {
475	<
476	<	// worldRank != 0, so I'm a remote node.
477	<
478	<	// Set my magic potato to 0:
479	<
480	<	myPotato = 0;
481	<
482	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
483	<
484	<	// Am I the node which has this integrableObject?
485	<	int whichNode = info_->getMolToProc(i);
486	<	if (whichNode == worldRank) {
487	<	if (myPotato + 1 >= MAXTAG) {
488	<
489	<	// The potato was going to exceed the maximum value,
490	<	// so wrap this processor potato back to 0 (and block until
491	<	// node 0 says we can go:
492	<
493	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
494	<	&istatus);
495	<	}
496	<
497	<	mol = info_->getMoleculeByGlobalIndex(i);
498	<
499	<
500	<	nCurObj = mol->getNIntegrableObjects();
501	<
502	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
503	<	myPotato++;
504	<
505	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
506	<	integrableObject = mol->nextIntegrableObject(ii)) {
507	<
508	<	if (myPotato + 2 >= MAXTAG) {
509	<
510	<	// The potato was going to exceed the maximum value,
511	<	// so wrap this processor potato back to 0 (and block until
512	<	// node 0 says we can go:
513	<
514	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
515	<	&istatus);
516	<	}
517	<
518	<	atomTypeString = integrableObject->getType().c_str();
519	<
520	<	pos = integrableObject->getPos();
521	<	vel = integrableObject->getVel();
522	<
523	<	atomData[0] = pos[0];
524	<	atomData[1] = pos[1];
525	<	atomData[2] = pos[2];
526	<
527	<	atomData[3] = vel[0];
528	<	atomData[4] = vel[1];
529	<	atomData[5] = vel[2];
530	<
531	<	isDirectional = 0;
532	<
533	<	if (integrableObject->isDirectional()) {
534	<	isDirectional = 1;
535	<
536	<	q = integrableObject->getQ();
537	<	ji = integrableObject->getJ();
538	<
539	<	atomData[6] = q[0];
540	<	atomData[7] = q[1];
541	<	atomData[8] = q[2];
542	<	atomData[9] = q[3];
543	<
544	<	atomData[10] = ji[0];
545	<	atomData[11] = ji[1];
546	<	atomData[12] = ji[2];
547	<	}
548	<
549	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
550	<
551	<	// null terminate the  std::string before sending (just in case):
552	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
553	<
554	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
555	<	myPotato, MPI_COMM_WORLD);
556	<
557	<	myPotato++;
558	<
559	<	if (isDirectional) {
560	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
561	<	MPI_COMM_WORLD);
562	<	} else {
563	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
564	<	MPI_COMM_WORLD);
565	<	}
566	<
567	<	myPotato++;
568	<	}
569	<
570	<	}
571	<
572	<	}
573	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
574	<	MPIcheckPoint();
575	<	}
576	<
577	<	#endif // is_mpi
578	<
579	<	}
580	<
581	<	void DumpWriter::writeDump() {
582	<	writeFrame(dumpFile_);
583	<
584	<	}
585	<
586	<	void DumpWriter::writeEor() {
587	<	std::ofstream eorStream;
723	>	void DumpWriter::writeEor() {
724	>	std::ostream* eorStream;
725
726		#ifdef IS_MPI
727		if (worldRank == 0) {
728		#endif // is_mpi
729	+
730	+	eorStream = createOStream(eorFilename_);
731	+	writeFrame(*eorStream);
732	+
733	+	#ifdef IS_MPI
734	+	}
735	+	if (worldRank == 0) {
736	+	#endif // is_mpi
737
738	<	eorStream.open(eorFilename_.c_str());
739	<	if (!eorStream.is_open()) {
595	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
596	<	eorFilename_.c_str());
597	<	painCave.isFatal = 1;
598	<	simError();
599	<	}
738	>	writeClosing(*eorStream);
739	>	delete eorStream;
740
741		#ifdef IS_MPI
742		}
743	<	#endif // is_mpi
743	>	#endif // is_mpi
744
745	<	writeFrame(eorStream);
606	<	}
745	>	}
746
747
748	<	void DumpWriter::writeDumpAndEor() {
610	<	std::ofstream eorStream;
748	>	void DumpWriter::writeDumpAndEor() {
749		std::vector<std::streambuf*> buffers;
750	+	std::ostream* eorStream;
751		#ifdef IS_MPI
752		if (worldRank == 0) {
753		#endif // is_mpi
754
755	<	buffers.push_back(dumpFile_.rdbuf());
755	>	buffers.push_back(dumpFile_->rdbuf());
756
757	<	eorStream.open(eorFilename_.c_str());
619	<	if (!eorStream.is_open()) {
620	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
621	<	eorFilename_.c_str());
622	<	painCave.isFatal = 1;
623	<	simError();
624	<	}
757	>	eorStream = createOStream(eorFilename_);
758
759	<	buffers.push_back(eorStream.rdbuf());
759	>	buffers.push_back(eorStream->rdbuf());
760
761		#ifdef IS_MPI
762		}
#	Line 633 | Line 766 | void DumpWriter::writeDumpAndEor() {
766		std::ostream os(&tbuf);
767
768		writeFrame(os);
769	+
770	+	#ifdef IS_MPI
771	+	if (worldRank == 0) {
772	+	#endif // is_mpi
773	+	writeClosing(*eorStream);
774	+	delete eorStream;
775	+	#ifdef IS_MPI
776	+	}
777	+	#endif // is_mpi
778
779	<	}
779	>	}
780
781	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
782
783	+	std::ostream* newOStream;
784	+	#ifdef HAVE_ZLIB
785	+	if (needCompression_) {
786	+	newOStream = new ogzstream(filename.c_str());
787	+	} else {
788	+	newOStream = new std::ofstream(filename.c_str());
789	+	}
790	+	#else
791	+	newOStream = new std::ofstream(filename.c_str());
792	+	#endif
793	+	//write out MetaData first
794	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
795	+	(*newOStream) << "  <MetaData>" << std::endl;
796	+	(*newOStream) << info_->getRawMetaData();
797	+	(*newOStream) << "  </MetaData>" << std::endl;
798	+	return newOStream;
799	+	}
800
801	<	}//end namespace oopse
801	>	void DumpWriter::writeClosing(std::ostream& os) {
802	>
803	>	os << "</OpenMD>\n";
804	>	os.flush();
805	>	}
806	>
807	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 376 by tim, Thu Feb 24 20:55:07 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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