ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 395 by tim, Thu Mar 3 14:40:20 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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	<
172	<	int nTotObjects;
173	<	nTotObjects = info_->getNGlobalIntegrableObjects();
312	>	RigidBody::AtomIterator ai;
313
314		#ifndef IS_MPI
315	+	os << "  <Snapshot>\n";
316	+
317	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318
319	+	os << "    <StuntDoubles>\n";
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	<	os << nTotObjects << "\n";
332	<
333	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
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	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	>	// do one for the IO itself
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
344	<	integrableObject = mol->nextIntegrableObject(ii)) {
345	<
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	<	pos = integrableObject->getPos();
360	<	vel = integrableObject->getVel();
359	>	os.flush();
360	>	#else
361
362	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
363	<	integrableObject->getType().c_str(),
364	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
362	>	const int masterNode = 0;
363	>	int worldRank = MPI::COMM_WORLD.Get_rank();
364	>	int nProc = MPI::COMM_WORLD.Get_size();
365
366	<	strcpy(writeLine, tempBuffer);
366	>	if (worldRank == masterNode) {
367	>	os << "  <Snapshot>\n";
368	>	writeFrameProperties(os,
369	>	info_->getSnapshotManager()->getCurrentSnapshot());
370	>	os << "    <StuntDoubles>\n";
371	>	}
372
373	<	if (integrableObject->isDirectional()) {
374	<	q = integrableObject->getQ();
375	<	ji = integrableObject->getJ();
373	>	//every node prepares the dump lines for integrable objects belong to itself
374	>	std::string buffer;
375	>	for (mol = info_->beginMolecule(mi); mol != NULL;
376	>	mol = info_->nextMolecule(mi)) {
377	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
378	>	sd = mol->nextIntegrableObject(ii)) {
379	>	buffer += prepareDumpLine(sd);
380	>	}
381	>	}
382	>
383	>	if (worldRank == masterNode) {
384	>	os << buffer;
385	>
386	>	for (int i = 1; i < nProc; ++i) {
387	>	// tell processor i to start sending us data:
388	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
389
390	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
391	<	q[0], q[1], q[2], q[3],
392	<	ji[0], ji[1], ji[2]);
393	<	strcat(writeLine, tempBuffer);
394	<	} else {
207	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208	<	}
390	>	// receive the length of the string buffer that was
391	>	// prepared by processor i:
392	>	int recvLength;
393	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
394	>	istatus);
395
396	<	os << writeLine;
396	>	// create a buffer to receive the data
397	>	char* recvBuffer = new char[recvLength];
398	>	if (recvBuffer == NULL) {
399	>	} else {
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	>	// get rid of the receive buffer:
406	>	delete [] recvBuffer;
407	>	}
408	>	}
409	>	} else {
410	>	int sendBufferLength = buffer.size() + 1;
411	>	int myturn = 0;
412	>	for (int i = 1; i < nProc; ++i){
413	>	// wait for the master node to call our number:
414	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
415	>	if (myturn == worldRank){
416	>	// send the length of our buffer:
417	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
418
419	+	// send our buffer:
420	+	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
421	+	MPI::CHAR, masterNode, 0);
422		}
423	+	}
424		}
425	+
426	+	if (worldRank == masterNode) {
427	+	os << "    </StuntDoubles>\n";
428	+	}
429
430	<	os.flush();
431	<	#else // is_mpi
432	<	/*********************************************************************
433	<	* Documentation?  You want DOCUMENTATION?
434	<	*
435	<	* Why all the potatoes below?
436	<	*
437	<	* To make a long story short, the original version of DumpWriter
438	<	* worked in the most inefficient way possible.  Node 0 would
439	<	* poke each of the node for an individual atom's formatted data
440	<	* as node 0 worked its way down the global index. This was particularly
441	<	* inefficient since the method blocked all processors at every atom
442	<	* (and did it twice!).
443	<	*
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	<	*********************************************************************/
253	<	const int masterNode = 0;
430	>	if (doSiteData_) {
431	>	if (worldRank == masterNode) {
432	>	os << "    <SiteData>\n";
433	>	}
434	>	buffer.clear();
435	>	for (mol = info_->beginMolecule(mi); mol != NULL;
436	>	mol = info_->nextMolecule(mi)) {
437	>
438	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
439	>	sd = mol->nextIntegrableObject(ii)) {
440	>
441	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
442	>	// do one for the IO itself
443	>	buffer += prepareSiteLine(sd, ioIndex, 0);
444
445	<	int * potatoes;
446	<	int myPotato;
447	<	int nProc;
448	<	int which_node;
449	<	double atomData[13];
450	<	int isDirectional;
451	<	char MPIatomTypeString[MINIBUFFERSIZE];
452	<	int msgLen; // the length of message actually recieved at master nodes
453	<	int haveError;
454	<	MPI_Status istatus;
455	<	int nCurObj;
456	<
267	<	// code to find maximum tag value
268	<	int * tagub;
269	<	int flag;
270	<	int MAXTAG;
271	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
445	>	if (sd->isRigidBody()) {
446	>
447	>	RigidBody* rb = static_cast<RigidBody*>(sd);
448	>	int siteIndex = 0;
449	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
450	>	atom = rb->nextAtom(ai)) {
451	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
452	>	siteIndex++;
453	>	}
454	>	}
455	>	}
456	>	}
457
458	<	if (flag) {
459	<	MAXTAG = *tagub;
460	<	} else {
461	<	MAXTAG = 32767;
458	>	if (worldRank == masterNode) {
459	>	os << buffer;
460	>
461	>	for (int i = 1; i < nProc; ++i) {
462	>
463	>	// tell processor i to start sending us data:
464	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
465	>
466	>	// receive the length of the string buffer that was
467	>	// prepared by processor i:
468	>	int recvLength;
469	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
470	>	istatus);
471	>
472	>	// create a buffer to receive the data
473	>	char* recvBuffer = new char[recvLength];
474	>	if (recvBuffer == NULL) {
475	>	} else {
476	>	// receive the data:
477	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
478	>	MPI::ANY_TAG, istatus);
479	>	// send it to the file:
480	>	os << recvBuffer;
481	>	// get rid of the receive buffer:
482	>	delete [] recvBuffer;
483	>	}
484	>	}
485	>	} else {
486	>	int sendBufferLength = buffer.size() + 1;
487	>	int myturn = 0;
488	>	for (int i = 1; i < nProc; ++i){
489	>	// wait for the master node to call our number:
490	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
491	>	if (myturn == worldRank){
492	>	// send the length of our buffer:
493	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
494	>	// send our buffer:
495	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
496	>	MPI::CHAR, masterNode, 0);
497	>	}
498	>	}
499	>	}
500	>
501	>	if (worldRank == masterNode) {
502	>	os << "    </SiteData>\n";
503	>	}
504		}
505	+
506	+	if (worldRank == masterNode) {
507	+	os << "  </Snapshot>\n";
508	+	os.flush();
509	+	}
510	+
511	+	#endif // is_mpi
512	+
513	+	}
514
515	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
515	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
516	>
517	>	int index = sd->getGlobalIntegrableObjectIndex();
518	>	std::string type("pv");
519	>	std::string line;
520	>	char tempBuffer[4096];
521
522	<	// Node 0 needs a list of the magic potatoes for each processor;
522	>	Vector3d pos;
523	>	Vector3d vel;
524	>	pos = sd->getPos();
525
526	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
527	<	potatoes = new int[nProc];
526	>	if (isinf(pos[0]) || isnan(pos[0]) ||
527	>	isinf(pos[1]) || isnan(pos[1]) ||
528	>	isinf(pos[2]) || isnan(pos[2]) ) {
529	>	sprintf( painCave.errMsg,
530	>	"DumpWriter detected a numerical error writing the position"
531	>	" for object %d", index);
532	>	painCave.isFatal = 1;
533	>	simError();
534	>	}
535
536	<	//write out the comment lines
287	<	for(int i = 0; i < nProc; i++) {
288	<	potatoes[i] = 0;
289	<	}
536	>	vel = sd->getVel();
537
538	+	if (isinf(vel[0]) || isnan(vel[0]) ||
539	+	isinf(vel[1]) || isnan(vel[1]) ||
540	+	isinf(vel[2]) || isnan(vel[2]) ) {
541	+	sprintf( painCave.errMsg,
542	+	"DumpWriter detected a numerical error writing the velocity"
543	+	" for object %d", index);
544	+	painCave.isFatal = 1;
545	+	simError();
546	+	}
547
548	<	os << nTotObjects << "\n";
549	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
548	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
549	>	pos[0], pos[1], pos[2],
550	>	vel[0], vel[1], vel[2]);
551	>	line += tempBuffer;
552
553	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
553	>	if (sd->isDirectional()) {
554	>	type += "qj";
555	>	Quat4d q;
556	>	Vector3d ji;
557	>	q = sd->getQ();
558
559	<	// Get the Node number which has this atom;
559	>	if (isinf(q[0]) || isnan(q[0]) ||
560	>	isinf(q[1]) || isnan(q[1]) ||
561	>	isinf(q[2]) || isnan(q[2]) ||
562	>	isinf(q[3]) || isnan(q[3]) ) {
563	>	sprintf( painCave.errMsg,
564	>	"DumpWriter detected a numerical error writing the quaternion"
565	>	" for object %d", index);
566	>	painCave.isFatal = 1;
567	>	simError();
568	>	}
569
570	<	which_node = info_->getMolToProc(i);
570	>	ji = sd->getJ();
571
572	<	if (which_node != masterNode) { //current molecule is in slave node
573	<	if (potatoes[which_node] + 1 >= MAXTAG) {
574	<	// The potato was going to exceed the maximum value,
575	<	// so wrap this processor potato back to 0:
572	>	if (isinf(ji[0]) || isnan(ji[0]) ||
573	>	isinf(ji[1]) || isnan(ji[1]) ||
574	>	isinf(ji[2]) || isnan(ji[2]) ) {
575	>	sprintf( painCave.errMsg,
576	>	"DumpWriter detected a numerical error writing the angular"
577	>	" momentum for object %d", index);
578	>	painCave.isFatal = 1;
579	>	simError();
580	>	}
581
582	<	potatoes[which_node] = 0;
583	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
584	<	MPI_COMM_WORLD);
585	<	}
582	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
583	>	q[0], q[1], q[2], q[3],
584	>	ji[0], ji[1], ji[2]);
585	>	line += tempBuffer;
586	>	}
587
588	<	myPotato = potatoes[which_node];
588	>	if (needForceVector_) {
589	>	type += "f";
590	>	Vector3d frc = sd->getFrc();
591	>	if (isinf(frc[0]) || isnan(frc[0]) ||
592	>	isinf(frc[1]) || isnan(frc[1]) ||
593	>	isinf(frc[2]) || isnan(frc[2]) ) {
594	>	sprintf( painCave.errMsg,
595	>	"DumpWriter detected a numerical error writing the force"
596	>	" for object %d", index);
597	>	painCave.isFatal = 1;
598	>	simError();
599	>	}
600	>	sprintf(tempBuffer, " %13e %13e %13e",
601	>	frc[0], frc[1], frc[2]);
602	>	line += tempBuffer;
603	>
604	>	if (sd->isDirectional()) {
605	>	type += "t";
606	>	Vector3d trq = sd->getTrq();
607	>	if (isinf(trq[0]) || isnan(trq[0]) ||
608	>	isinf(trq[1]) || isnan(trq[1]) ||
609	>	isinf(trq[2]) || isnan(trq[2]) ) {
610	>	sprintf( painCave.errMsg,
611	>	"DumpWriter detected a numerical error writing the torque"
612	>	" for object %d", index);
613	>	painCave.isFatal = 1;
614	>	simError();
615	>	}
616	>	sprintf(tempBuffer, " %13e %13e %13e",
617	>	trq[0], trq[1], trq[2]);
618	>	line += tempBuffer;
619	>	}
620	>	}
621
622	<	//recieve the number of integrableObject in current molecule
623	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
624	<	MPI_COMM_WORLD, &istatus);
316	<	myPotato++;
622	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
623	>	return std::string(tempBuffer);
624	>	}
625
626	<	for(int l = 0; l < nCurObj; l++) {
627	<	if (potatoes[which_node] + 2 >= MAXTAG) {
320	<	// The potato was going to exceed the maximum value,
321	<	// so wrap this processor potato back to 0:
626	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
627	>
628
629	<	potatoes[which_node] = 0;
630	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
631	<	0, MPI_COMM_WORLD);
632	<	}
629	>	std::string id;
630	>	std::string type;
631	>	std::string line;
632	>	char tempBuffer[4096];
633
634	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
635	<	which_node, myPotato, MPI_COMM_WORLD,
636	<	&istatus);
634	>	if (sd->isRigidBody()) {
635	>	sprintf(tempBuffer, "%10d           ", ioIndex);
636	>	id = std::string(tempBuffer);
637	>	} else {
638	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
639	>	id = std::string(tempBuffer);
640	>	}
641	>
642	>	if (needFlucQ_) {
643	>	type += "cw";
644	>	RealType fqPos = sd->getFlucQPos();
645	>	if (isinf(fqPos) || isnan(fqPos) ) {
646	>	sprintf( painCave.errMsg,
647	>	"DumpWriter detected a numerical error writing the"
648	>	" fluctuating charge for object %s", id.c_str());
649	>	painCave.isFatal = 1;
650	>	simError();
651	>	}
652	>	sprintf(tempBuffer, " %13e ", fqPos);
653	>	line += tempBuffer;
654	>
655	>	RealType fqVel = sd->getFlucQVel();
656	>	if (isinf(fqVel) || isnan(fqVel) ) {
657	>	sprintf( painCave.errMsg,
658	>	"DumpWriter detected a numerical error writing the"
659	>	" fluctuating charge velocity for object %s", id.c_str());
660	>	painCave.isFatal = 1;
661	>	simError();
662	>	}
663	>	sprintf(tempBuffer, " %13e ", fqVel);
664	>	line += tempBuffer;
665
666	<	myPotato++;
666	>	if (needForceVector_) {
667	>	type += "g";
668	>	RealType fqFrc = sd->getFlucQFrc();
669	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
670	>	sprintf( painCave.errMsg,
671	>	"DumpWriter detected a numerical error writing the"
672	>	" fluctuating charge force for object %s", id.c_str());
673	>	painCave.isFatal = 1;
674	>	simError();
675	>	}
676	>	sprintf(tempBuffer, " %13e ", fqFrc);
677	>	line += tempBuffer;
678	>	}
679	>	}
680
681	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
682	<	MPI_COMM_WORLD, &istatus);
683	<	myPotato++;
681	>	if (needElectricField_) {
682	>	type += "e";
683	>	Vector3d eField= sd->getElectricField();
684	>	if (isinf(eField[0]) || isnan(eField[0]) ||
685	>	isinf(eField[1]) || isnan(eField[1]) ||
686	>	isinf(eField[2]) || isnan(eField[2]) ) {
687	>	sprintf( painCave.errMsg,
688	>	"DumpWriter detected a numerical error writing the electric"
689	>	" field for object %s", id.c_str());
690	>	painCave.isFatal = 1;
691	>	simError();
692	>	}
693	>	sprintf(tempBuffer, " %13e %13e %13e",
694	>	eField[0], eField[1], eField[2]);
695	>	line += tempBuffer;
696	>	}
697
338	–	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
698
699	<	if (msgLen == 13)
700	<	isDirectional = 1;
701	<	else
702	<	isDirectional = 0;
699	>	if (needParticlePot_) {
700	>	type += "u";
701	>	RealType particlePot = sd->getParticlePot();
702	>	if (isinf(particlePot) || isnan(particlePot)) {
703	>	sprintf( painCave.errMsg,
704	>	"DumpWriter detected a numerical error writing the particle "
705	>	" potential for object %s", id.c_str());
706	>	painCave.isFatal = 1;
707	>	simError();
708	>	}
709	>	sprintf(tempBuffer, " %13e", particlePot);
710	>	line += tempBuffer;
711	>	}
712	>
713
714	<	// If we've survived to here, format the line:
715	<
716	<	if (!isDirectional) {
348	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
349	<	MPIatomTypeString, atomData[0],
350	<	atomData[1], atomData[2],
351	<	atomData[3], atomData[4],
352	<	atomData[5]);
353	<
354	<	strcat(writeLine,
355	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
356	<	} else {
357	<	sprintf(writeLine,
358	<	"%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",
359	<	MPIatomTypeString,
360	<	atomData[0],
361	<	atomData[1],
362	<	atomData[2],
363	<	atomData[3],
364	<	atomData[4],
365	<	atomData[5],
366	<	atomData[6],
367	<	atomData[7],
368	<	atomData[8],
369	<	atomData[9],
370	<	atomData[10],
371	<	atomData[11],
372	<	atomData[12]);
373	<	}
374	<
375	<	os << writeLine;
376	<
377	<	} // end for(int l =0)
378	<
379	<	potatoes[which_node] = myPotato;
380	<	} else { //master node has current molecule
381	<
382	<	mol = info_->getMoleculeByGlobalIndex(i);
383	<
384	<	if (mol == NULL) {
385	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<
390	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	<
393	<	pos = integrableObject->getPos();
394	<	vel = integrableObject->getVel();
395	<
396	<	atomData[0] = pos[0];
397	<	atomData[1] = pos[1];
398	<	atomData[2] = pos[2];
399	<
400	<	atomData[3] = vel[0];
401	<	atomData[4] = vel[1];
402	<	atomData[5] = vel[2];
714	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
715	>	return std::string(tempBuffer);
716	>	}
717
718	<	isDirectional = 0;
718	>	void DumpWriter::writeDump() {
719	>	writeFrame(*dumpFile_);
720	>	}
721
722	<	if (integrableObject->isDirectional()) {
723	<	isDirectional = 1;
408	<
409	<	q = integrableObject->getQ();
410	<	ji = integrableObject->getJ();
411	<
412	<	for(int j = 0; j < 6; j++) {
413	<	atomData[j] = atomData[j];
414	<	}
415	<
416	<	atomData[6] = q[0];
417	<	atomData[7] = q[1];
418	<	atomData[8] = q[2];
419	<	atomData[9] = q[3];
420	<
421	<	atomData[10] = ji[0];
422	<	atomData[11] = ji[1];
423	<	atomData[12] = ji[2];
424	<	}
425	<
426	<	// If we've survived to here, format the line:
427	<
428	<	if (!isDirectional) {
429	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
430	<	integrableObject->getType().c_str(), atomData[0],
431	<	atomData[1], atomData[2],
432	<	atomData[3], atomData[4],
433	<	atomData[5]);
434	<
435	<	strcat(writeLine,
436	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
437	<	} else {
438	<	sprintf(writeLine,
439	<	"%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",
440	<	integrableObject->getType().c_str(),
441	<	atomData[0],
442	<	atomData[1],
443	<	atomData[2],
444	<	atomData[3],
445	<	atomData[4],
446	<	atomData[5],
447	<	atomData[6],
448	<	atomData[7],
449	<	atomData[8],
450	<	atomData[9],
451	<	atomData[10],
452	<	atomData[11],
453	<	atomData[12]);
454	<	}
455	<
456	<
457	<	os << writeLine;
458	<
459	<	} //end for(iter = integrableObject.begin())
460	<	}
461	<	} //end for(i = 0; i < mpiSim->getNmol())
462	<
463	<	os.flush();
464	<
465	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
466	<	MPIcheckPoint();
467	<
468	<	delete [] potatoes;
469	<	} else {
470	<
471	<	// worldRank != 0, so I'm a remote node.
472	<
473	<	// Set my magic potato to 0:
474	<
475	<	myPotato = 0;
476	<
477	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
478	<
479	<	// Am I the node which has this integrableObject?
480	<	int whichNode = info_->getMolToProc(i);
481	<	if (whichNode == worldRank) {
482	<	if (myPotato + 1 >= MAXTAG) {
483	<
484	<	// The potato was going to exceed the maximum value,
485	<	// so wrap this processor potato back to 0 (and block until
486	<	// node 0 says we can go:
487	<
488	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
489	<	&istatus);
490	<	}
491	<
492	<	mol = info_->getMoleculeByGlobalIndex(i);
493	<
494	<
495	<	nCurObj = mol->getNIntegrableObjects();
496	<
497	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
498	<	myPotato++;
499	<
500	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
501	<	integrableObject = mol->nextIntegrableObject(ii)) {
502	<
503	<	if (myPotato + 2 >= MAXTAG) {
504	<
505	<	// The potato was going to exceed the maximum value,
506	<	// so wrap this processor potato back to 0 (and block until
507	<	// node 0 says we can go:
508	<
509	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
510	<	&istatus);
511	<	}
512	<
513	<	pos = integrableObject->getPos();
514	<	vel = integrableObject->getVel();
515	<
516	<	atomData[0] = pos[0];
517	<	atomData[1] = pos[1];
518	<	atomData[2] = pos[2];
519	<
520	<	atomData[3] = vel[0];
521	<	atomData[4] = vel[1];
522	<	atomData[5] = vel[2];
523	<
524	<	isDirectional = 0;
525	<
526	<	if (integrableObject->isDirectional()) {
527	<	isDirectional = 1;
528	<
529	<	q = integrableObject->getQ();
530	<	ji = integrableObject->getJ();
531	<
532	<	atomData[6] = q[0];
533	<	atomData[7] = q[1];
534	<	atomData[8] = q[2];
535	<	atomData[9] = q[3];
536	<
537	<	atomData[10] = ji[0];
538	<	atomData[11] = ji[1];
539	<	atomData[12] = ji[2];
540	<	}
541	<
542	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
543	<
544	<	// null terminate the  std::string before sending (just in case):
545	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
546	<
547	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
548	<	myPotato, MPI_COMM_WORLD);
549	<
550	<	myPotato++;
551	<
552	<	if (isDirectional) {
553	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
554	<	MPI_COMM_WORLD);
555	<	} else {
556	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
557	<	MPI_COMM_WORLD);
558	<	}
559	<
560	<	myPotato++;
561	<	}
562	<
563	<	}
564	<
565	<	}
566	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
567	<	MPIcheckPoint();
568	<	}
569	<
570	<	#endif // is_mpi
571	<
572	<	}
573	<
574	<	void DumpWriter::writeDump() {
575	<	writeFrame(dumpFile_);
576	<
577	<	}
578	<
579	<	void DumpWriter::writeEor() {
580	<	std::ofstream eorStream;
722	>	void DumpWriter::writeEor() {
723	>	std::ostream* eorStream;
724
725		#ifdef IS_MPI
726		if (worldRank == 0) {
727		#endif // is_mpi
728	+
729	+	eorStream = createOStream(eorFilename_);
730	+	writeFrame(*eorStream);
731	+
732	+	#ifdef IS_MPI
733	+	}
734	+	if (worldRank == 0) {
735	+	#endif // is_mpi
736
737	<	eorStream.open(eorFilename_.c_str());
738	<	if (!eorStream.is_open()) {
588	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
589	<	eorFilename_.c_str());
590	<	painCave.isFatal = 1;
591	<	simError();
592	<	}
737	>	writeClosing(*eorStream);
738	>	delete eorStream;
739
740		#ifdef IS_MPI
741		}
742	<	#endif // is_mpi
742	>	#endif // is_mpi
743
744	<	writeFrame(eorStream);
599	<	}
744	>	}
745
746
747	<	void DumpWriter::writeDumpAndEor() {
603	<	std::ofstream eorStream;
747	>	void DumpWriter::writeDumpAndEor() {
748		std::vector<std::streambuf*> buffers;
749	+	std::ostream* eorStream;
750		#ifdef IS_MPI
751		if (worldRank == 0) {
752		#endif // is_mpi
753
754	<	buffers.push_back(dumpFile_.rdbuf());
754	>	buffers.push_back(dumpFile_->rdbuf());
755
756	<	eorStream.open(eorFilename_.c_str());
612	<	if (!eorStream.is_open()) {
613	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
614	<	eorFilename_.c_str());
615	<	painCave.isFatal = 1;
616	<	simError();
617	<	}
756	>	eorStream = createOStream(eorFilename_);
757
758	<	buffers.push_back(eorStream.rdbuf());
758	>	buffers.push_back(eorStream->rdbuf());
759
760		#ifdef IS_MPI
761		}
#	Line 626 | Line 765 | void DumpWriter::writeDumpAndEor() {
765		std::ostream os(&tbuf);
766
767		writeFrame(os);
768	+
769	+	#ifdef IS_MPI
770	+	if (worldRank == 0) {
771	+	#endif // is_mpi
772	+	writeClosing(*eorStream);
773	+	delete eorStream;
774	+	#ifdef IS_MPI
775	+	}
776	+	#endif // is_mpi
777
778	<	}
778	>	}
779
780	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
781
782	+	std::ostream* newOStream;
783	+	#ifdef HAVE_ZLIB
784	+	if (needCompression_) {
785	+	newOStream = new ogzstream(filename.c_str());
786	+	} else {
787	+	newOStream = new std::ofstream(filename.c_str());
788	+	}
789	+	#else
790	+	newOStream = new std::ofstream(filename.c_str());
791	+	#endif
792	+	//write out MetaData first
793	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
794	+	(*newOStream) << "  <MetaData>" << std::endl;
795	+	(*newOStream) << info_->getRawMetaData();
796	+	(*newOStream) << "  </MetaData>" << std::endl;
797	+	return newOStream;
798	+	}
799
800	<	}//end namespace oopse
800	>	void DumpWriter::writeClosing(std::ostream& os) {
801	>
802	>	os << "</OpenMD>\n";
803	>	os.flush();
804	>	}
805	>
806	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 395 by tim, Thu Mar 3 14:40:20 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines