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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 324 by tim, Sun Feb 13 19:10:25 2005 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.
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 "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, const std::string& filename)
67	<	: info_(info), filename_(filename){
66	>	DumpWriter::DumpWriter(SimInfo* info)
67	>	: info_(info), filename_(info->getDumpFileName()),
68	>	eorFilename_(info->getFinalConfigFileName()){
69	>
70	>	Globals* simParams = info->getSimParams();
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_) {
88	>	filename_ += ".gz";
89	>	eorFilename_ += ".gz";
90	>	}
91	>	#endif
92	>
93		#ifdef IS_MPI
94
95		if (worldRank == 0) {
96		#endif // is_mpi
97	+
98	+	dumpFile_ = createOStream(filename_);
99
100	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
100	>	if (!dumpFile_) {
101	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
102	>	filename_.c_str());
103	>	painCave.isFatal = 1;
104	>	simError();
105	>	}
106
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	–
107		#ifdef IS_MPI
108
109		}
110
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
111		#endif // is_mpi
112
113	<	}
113	>	}
114
79	–	DumpWriter::~DumpWriter() {
115
116	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
117	+	: info_(info), filename_(filename){
118	+
119	+	Globals* simParams = info->getSimParams();
120	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
121	+
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_) {
139	+	filename_ += ".gz";
140	+	eorFilename_ += ".gz";
141	+	}
142	+	#endif
143	+
144		#ifdef IS_MPI
145
146		if (worldRank == 0) {
147		#endif // is_mpi
148
149	<	dumpFile_.close();
149	>
150	>	dumpFile_ = createOStream(filename_);
151
152	+	if (!dumpFile_) {
153	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
154	+	filename_.c_str());
155	+	painCave.isFatal = 1;
156	+	simError();
157	+	}
158	+
159		#ifdef IS_MPI
160
161		}
162
163		#endif // is_mpi
164
165	<	}
165	>	}
166	>
167	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
168	>	: info_(info), filename_(filename){
169	>
170	>	Globals* simParams = info->getSimParams();
171	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
172	>
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	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
180	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
181	>	needSitePotential_) {
182	>	doSiteData_ = true;
183	>	} else {
184	>	doSiteData_ = false;
185	>	}
186
187	<	double currentTime;
188	<	Mat3x3d hmat;
189	<	double chi;
190	<	double integralOfChiDt;
191	<	Mat3x3d eta;
187	>	#ifdef HAVE_LIBZ
188	>	if (needCompression_) {
189	>	filename_ += ".gz";
190	>	eorFilename_ += ".gz";
191	>	}
192	>	#endif
193
194	<	currentTime = s->getTime();
105	<	hmat = s->getHmat();
106	<	chi = s->getChi();
107	<	integralOfChiDt = s->getIntegralOfChiDt();
108	<	eta = s->getEta();
194	>	#ifdef IS_MPI
195
196	<	os << currentTime << ";\t"
197	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
198	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
199	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
196	>	if (worldRank == 0) {
197	>	#endif // is_mpi
198	>
199	>	createDumpFile_ = writeDumpFile;
200	>	if (createDumpFile_) {
201	>	dumpFile_ = createOStream(filename_);
202	>
203	>	if (!dumpFile_) {
204	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
205	>	filename_.c_str());
206	>	painCave.isFatal = 1;
207	>	simError();
208	>	}
209	>	}
210	>	#ifdef IS_MPI
211	>
212	>	}
213
214	<	//write out additional parameters, such as chi and eta
214	>
215	>	#endif // is_mpi
216	>
217	>	}
218
219	<	os << chi << "\t" << integralOfChiDt << "\t;";
219	>	DumpWriter::~DumpWriter() {
220
221	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
120	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
121	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
122	<
123	<	os << std::endl;
124	<	}
221	>	#ifdef IS_MPI
222
223	<	void DumpWriter::writeFrame(std::ostream& os) {
224	<	const int BUFFERSIZE = 2000;
225	<	const int MINIBUFFERSIZE = 100;
223	>	if (worldRank == 0) {
224	>	#endif // is_mpi
225	>	if (createDumpFile_){
226	>	writeClosing(*dumpFile_);
227	>	delete dumpFile_;
228	>	}
229	>	#ifdef IS_MPI
230
231	<	char tempBuffer[BUFFERSIZE];
131	<	char writeLine[BUFFERSIZE];
231	>	}
232
233	<	Quat4d q;
134	<	Vector3d ji;
135	<	Vector3d pos;
136	<	Vector3d vel;
233	>	#endif // is_mpi
234
235	<	Molecule* mol;
139	<	StuntDouble* integrableObject;
140	<	SimInfo::MoleculeIterator mi;
141	<	Molecule::IntegrableObjectIterator ii;
142	<
143	<	int nTotObjects;
144	<	nTotObjects = info_->getNGlobalIntegrableObjects();
235	>	}
236
237	<	#ifndef IS_MPI
237	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
238
239	+	char buffer[1024];
240
241	<	os << nTotObjects << "\n";
150	<
151	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
241	>	os << "    <FrameData>\n";
242
243	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
243	>	RealType currentTime = s->getTime();
244
245	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
246	<	integrableObject = mol->nextIntegrableObject(ii)) {
247	<
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	<	pos = integrableObject->getPos();
256	<	vel = integrableObject->getVel();
255	>	Mat3x3d hmat;
256	>	hmat = s->getHmat();
257
258	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
259	<	integrableObject->getType().c_str(),
260	<	pos[0], pos[1], pos[2],
261	<	vel[0], vel[1], vel[2]);
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	<	strcpy(writeLine, tempBuffer);
275	>	pair<RealType, RealType> thermostat = s->getThermostat();
276
277	<	if (integrableObject->isDirectional()) {
278	<	q = integrableObject->getQ();
279	<	ji = integrableObject->getJ();
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	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
289	<	q[0], q[1], q[2], q[3],
175	<	ji[0], ji[1], ji[2]);
176	<	strcat(writeLine, tempBuffer);
177	<	} else {
178	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
179	<	}
288	>	Mat3x3d eta;
289	>	eta = s->getBarostat();
290
291	<	os << writeLine;
292	<
293	<	}
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	<	os.flush();
303	<	#else // is_mpi
304	<	/*********************************************************************
305	<	* Documentation?  You want DOCUMENTATION?
306	<	*
191	<	* Why all the potatoes below?
192	<	*
193	<	* To make a long story short, the original version of DumpWriter
194	<	* worked in the most inefficient way possible.  Node 0 would
195	<	* poke each of the node for an individual atom's formatted data
196	<	* as node 0 worked its way down the global index. This was particularly
197	<	* inefficient since the method blocked all processors at every atom
198	<	* (and did it twice!).
199	<	*
200	<	* An intermediate version of DumpWriter could be described from Node
201	<	* zero's perspective as follows:
202	<	*
203	<	*  1) Have 100 of your friends stand in a circle.
204	<	*  2) When you say go, have all of them start tossing potatoes at
205	<	*     you (one at a time).
206	<	*  3) Catch the potatoes.
207	<	*
208	<	* It was an improvement, but MPI has buffers and caches that could
209	<	* best be described in this analogy as "potato nets", so there's no
210	<	* need to block the processors atom-by-atom.
211	<	*
212	<	* This new and improved DumpWriter works in an even more efficient
213	<	* way:
214	<	*
215	<	*  1) Have 100 of your friend stand in a circle.
216	<	*  2) When you say go, have them start tossing 5-pound bags of
217	<	*     potatoes at you.
218	<	*  3) Once you've caught a friend's bag of potatoes,
219	<	*     toss them a spud to let them know they can toss another bag.
220	<	*
221	<	* How's THAT for documentation?
222	<	*
223	<	*********************************************************************/
224	<	const int masterNode = 0;
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),
305	>	eta(0, 2), eta(1, 2), eta(2, 2));
306	>	os << buffer;
307
308	<	int * potatoes;
309	<	int myPotato;
228	<	int nProc;
229	<	int which_node;
230	<	double atomData[13];
231	<	int isDirectional;
232	<	const char * atomTypeString;
233	<	char MPIatomTypeString[MINIBUFFERSIZE];
234	<	int msgLen; // the length of message actually recieved at master nodes
235	<	int haveError;
236	<	MPI_Status istatus;
237	<	int nCurObj;
238	<
239	<	// code to find maximum tag value
240	<	int * tagub;
241	<	int flag;
242	<	int MAXTAG;
243	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
308	>	os << "    </FrameData>\n";
309	>	}
310
311	<	if (flag) {
246	<	MAXTAG = *tagub;
247	<	} else {
248	<	MAXTAG = 32767;
249	<	}
311	>	void DumpWriter::writeFrame(std::ostream& os) {
312
313	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
313	>	#ifdef IS_MPI
314	>	MPI_Status istatus;
315	>	#endif
316
317	<	// Node 0 needs a list of the magic potatoes for each processor;
317	>	Molecule* mol;
318	>	StuntDouble* sd;
319	>	SimInfo::MoleculeIterator mi;
320	>	Molecule::IntegrableObjectIterator ii;
321	>	RigidBody::AtomIterator ai;
322
323	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
324	<	potatoes = new int[nProc];
323	>	#ifndef IS_MPI
324	>	os << "  <Snapshot>\n";
325	>
326	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327
328	<	//write out the comment lines
329	<	for(int i = 0; i < nProc; i++) {
330	<	potatoes[i] = 0;
331	<	}
328	>	os << "    <StuntDoubles>\n";
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	<	os << nTotObjects << "\n";
349	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
348	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
349	>	// do one for the IO itself
350	>	os << prepareSiteLine(sd, ioIndex, 0);
351
352	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
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	<	// Get the Node number which has this atom;
368	>	os.flush();
369	>	#else
370
371	<	which_node = info_->getMolToProc(i);
371	>	const int masterNode = 0;
372	>	int worldRank;
373	>	int nProc;
374
375	<	if (which_node != masterNode) { //current molecule is in slave node
376	<	if (potatoes[which_node] + 1 >= MAXTAG) {
275	<	// The potato was going to exceed the maximum value,
276	<	// so wrap this processor potato back to 0:
375	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
376	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
377
278	–	potatoes[which_node] = 0;
279	–	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
280	–	MPI_COMM_WORLD);
281	–	}
378
379	<	myPotato = potatoes[which_node];
379	>	if (worldRank == masterNode) {
380	>	os << "  <Snapshot>\n";
381	>	writeFrameProperties(os,
382	>	info_->getSnapshotManager()->getCurrentSnapshot());
383	>	os << "    <StuntDoubles>\n";
384	>	}
385
386	<	//recieve the number of integrableObject in current molecule
387	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
388	<	MPI_COMM_WORLD, &istatus);
389	<	myPotato++;
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;
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	>
396	>	if (worldRank == masterNode) {
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	<	for(int l = 0; l < nCurObj; l++) {
404	<	if (potatoes[which_node] + 2 >= MAXTAG) {
405	<	// The potato was going to exceed the maximum value,
406	<	// so wrap this processor potato back to 0:
403	>	// receive the length of the string buffer that was
404	>	// prepared by processor i:
405	>	int recvLength;
406	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
407	>	&istatus);
408
409	<	potatoes[which_node] = 0;
410	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
411	<	0, MPI_COMM_WORLD);
412	<	}
409	>	// create a buffer to receive the data
410	>	char* recvBuffer = new char[recvLength];
411	>	if (recvBuffer == NULL) {
412	>	} else {
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	>	// get rid of the receive buffer:
419	>	delete [] recvBuffer;
420	>	}
421	>	}
422	>	} else {
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	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
433	<	which_node, myPotato, MPI_COMM_WORLD,
434	<	&istatus);
432	>	// send our buffer:
433	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
434	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
435
436	<	atomTypeString = MPIatomTypeString;
436	>	}
437	>	}
438	>	}
439	>
440	>	if (worldRank == masterNode) {
441	>	os << "    </StuntDoubles>\n";
442	>	}
443
444	<	myPotato++;
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	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
460	<	MPI_COMM_WORLD, &istatus);
461	<	myPotato++;
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	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
473	<
474	<	if (msgLen == 13)
475	<	isDirectional = 1;
476	<	else
477	<	isDirectional = 0;
478	<
479	<	// If we've survived to here, format the line:
480	<
481	<	if (!isDirectional) {
482	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
483	<	atomTypeString, atomData[0],
484	<	atomData[1], atomData[2],
485	<	atomData[3], atomData[4],
486	<	atomData[5]);
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	<	strcat(writeLine,
530	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
531	<	} else {
532	<	sprintf(writeLine,
533	<	"%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",
534	<	atomTypeString,
334	<	atomData[0],
335	<	atomData[1],
336	<	atomData[2],
337	<	atomData[3],
338	<	atomData[4],
339	<	atomData[5],
340	<	atomData[6],
341	<	atomData[7],
342	<	atomData[8],
343	<	atomData[9],
344	<	atomData[10],
345	<	atomData[11],
346	<	atomData[12]);
347	<	}
529	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
530	>
531	>	int index = sd->getGlobalIntegrableObjectIndex();
532	>	std::string type("pv");
533	>	std::string line;
534	>	char tempBuffer[4096];
535
536	<	os << writeLine;
536	>	Vector3d pos;
537	>	Vector3d vel;
538	>	pos = sd->getPos();
539
540	<	} // end for(int l =0)
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	<	potatoes[which_node] = myPotato;
354	<	} else { //master node has current molecule
550	>	vel = sd->getVel();
551
552	<	mol = info_->getMoleculeByGlobalIndex(i);
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	<	if (mol == NULL) {
563	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
564	<	painCave.isFatal = 1;
565	<	simError();
362	<	}
363	<
364	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
365	<	integrableObject = mol->nextIntegrableObject(ii)) {
366	<
367	<	atomTypeString = integrableObject->getType().c_str();
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	<	pos = integrableObject->getPos();
568	<	vel = integrableObject->getVel();
567	>	if (sd->isDirectional()) {
568	>	type += "qj";
569	>	Quat4d q;
570	>	Vector3d ji;
571	>	q = sd->getQ();
572
573	<	atomData[0] = pos[0];
574	<	atomData[1] = pos[1];
575	<	atomData[2] = pos[2];
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	<	atomData[3] = vel[0];
377	<	atomData[4] = vel[1];
378	<	atomData[5] = vel[2];
584	>	ji = sd->getJ();
585
586	<	isDirectional = 0;
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	<	if (integrableObject->isDirectional()) {
597	<	isDirectional = 1;
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	<	q = integrableObject->getQ();
603	<	ji = integrableObject->getJ();
602	>	if (needForceVector_) {
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	<	for(int j = 0; j < 6; j++) {
637	<	atomData[j] = atomData[j];
638	<	}
636	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
637	>	return std::string(tempBuffer);
638	>	}
639
640	<	atomData[6] = q[0];
641	<	atomData[7] = q[1];
394	<	atomData[8] = q[2];
395	<	atomData[9] = q[3];
640	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
641	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
642
643	<	atomData[10] = ji[0];
644	<	atomData[11] = ji[1];
645	<	atomData[12] = ji[2];
646	<	}
643	>	std::string id;
644	>	std::string type;
645	>	std::string line;
646	>	char tempBuffer[4096];
647
648	<	// If we've survived to here, format the line:
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 (!isDirectional) {
672	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
673	<	atomTypeString, atomData[0],
674	<	atomData[1], atomData[2],
675	<	atomData[3], atomData[4],
676	<	atomData[5]);
677	<
678	<	strcat(writeLine,
679	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
680	<	} else {
681	<	sprintf(writeLine,
682	<	"%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",
683	<	atomTypeString,
417	<	atomData[0],
418	<	atomData[1],
419	<	atomData[2],
420	<	atomData[3],
421	<	atomData[4],
422	<	atomData[5],
423	<	atomData[6],
424	<	atomData[7],
425	<	atomData[8],
426	<	atomData[9],
427	<	atomData[10],
428	<	atomData[11],
429	<	atomData[12]);
430	<	}
431	<
432	<
433	<	os << writeLine;
434	<
435	<	} //end for(iter = integrableObject.begin())
436	<	}
437	<	} //end for(i = 0; i < mpiSim->getNmol())
438	<
439	<	os.flush();
440	<
441	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
442	<	MPIcheckPoint();
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	<	delete [] potatoes;
686	<	} else {
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	<	// worldRank != 0, so I'm a remote node.
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	<	// Set my magic potato to 0:
757	>	void DumpWriter::writeDump() {
758	>	writeFrame(*dumpFile_);
759	>	}
760
761	<	myPotato = 0;
761	>	void DumpWriter::writeEor() {
762
763	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
763	>	std::ostream* eorStream = NULL;
764
765	<	// Am I the node which has this integrableObject?
766	<	int whichNode = info_->getMolToProc(i);
767	<	if (whichNode == worldRank) {
768	<	if (myPotato + 1 >= MAXTAG) {
765	>	#ifdef IS_MPI
766	>	if (worldRank == 0) {
767	>	#endif // is_mpi
768	>
769	>	eorStream = createOStream(eorFilename_);
770
771	<	// The potato was going to exceed the maximum value,
772	<	// so wrap this processor potato back to 0 (and block until
773	<	// node 0 says we can go:
771	>	#ifdef IS_MPI
772	>	}
773	>	#endif
774	>
775	>	writeFrame(*eorStream);
776	>
777	>	#ifdef IS_MPI
778	>	if (worldRank == 0) {
779	>	#endif
780	>
781	>	writeClosing(*eorStream);
782	>	delete eorStream;
783	>
784	>	#ifdef IS_MPI
785	>	}
786	>	#endif // is_mpi
787
788	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
465	<	&istatus);
466	<	}
788	>	}
789
468	–	mol = info_->getMoleculeByGlobalIndex(i);
790
791	<
792	<	nCurObj = mol->getNIntegrableObjects();
791	>	void DumpWriter::writeDumpAndEor() {
792	>	std::vector<std::streambuf*> buffers;
793	>	std::ostream* eorStream;
794	>	#ifdef IS_MPI
795	>	if (worldRank == 0) {
796	>	#endif // is_mpi
797	>	buffers.push_back(dumpFile_->rdbuf());
798	>	eorStream = createOStream(eorFilename_);
799	>	buffers.push_back(eorStream->rdbuf());
800	>	#ifdef IS_MPI
801	>	}
802	>	#endif // is_mpi
803
804	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
805	<	myPotato++;
804	>	TeeBuf tbuf(buffers.begin(), buffers.end());
805	>	std::ostream os(&tbuf);
806	>	writeFrame(os);
807
808	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
809	<	integrableObject = mol->nextIntegrableObject(ii)) {
808	>	#ifdef IS_MPI
809	>	if (worldRank == 0) {
810	>	#endif // is_mpi
811	>	writeClosing(*eorStream);
812	>	delete eorStream;
813	>	#ifdef IS_MPI
814	>	}
815	>	#endif // is_mpi
816	>	}
817
818	<	if (myPotato + 2 >= MAXTAG) {
818	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
819
820	<	// The potato was going to exceed the maximum value,
821	<	// so wrap this processor potato back to 0 (and block until
822	<	// node 0 says we can go:
823	<
824	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
825	<	&istatus);
487	<	}
488	<
489	<	atomTypeString = integrableObject->getType().c_str();
490	<
491	<	pos = integrableObject->getPos();
492	<	vel = integrableObject->getVel();
493	<
494	<	atomData[0] = pos[0];
495	<	atomData[1] = pos[1];
496	<	atomData[2] = pos[2];
497	<
498	<	atomData[3] = vel[0];
499	<	atomData[4] = vel[1];
500	<	atomData[5] = vel[2];
501	<
502	<	isDirectional = 0;
503	<
504	<	if (integrableObject->isDirectional()) {
505	<	isDirectional = 1;
506	<
507	<	q = integrableObject->getQ();
508	<	ji = integrableObject->getJ();
509	<
510	<	atomData[6] = q[0];
511	<	atomData[7] = q[1];
512	<	atomData[8] = q[2];
513	<	atomData[9] = q[3];
514	<
515	<	atomData[10] = ji[0];
516	<	atomData[11] = ji[1];
517	<	atomData[12] = ji[2];
518	<	}
519	<
520	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
521	<
522	<	// null terminate the  std::string before sending (just in case):
523	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
524	<
525	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
526	<	myPotato, MPI_COMM_WORLD);
527	<
528	<	myPotato++;
529	<
530	<	if (isDirectional) {
531	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
532	<	MPI_COMM_WORLD);
533	<	} else {
534	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
535	<	MPI_COMM_WORLD);
536	<	}
537	<
538	<	myPotato++;
539	<	}
540	<
541	<	}
542	<
543	<	}
544	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
545	<	MPIcheckPoint();
820	>	std::ostream* newOStream;
821	>	#ifdef HAVE_ZLIB
822	>	if (needCompression_) {
823	>	newOStream = new ogzstream(filename.c_str());
824	>	} else {
825	>	newOStream = new std::ofstream(filename.c_str());
826		}
827	+	#else
828	+	newOStream = new std::ofstream(filename.c_str());
829	+	#endif
830	+	//write out MetaData first
831	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
832	+	(*newOStream) << "  <MetaData>" << std::endl;
833	+	(*newOStream) << info_->getRawMetaData();
834	+	(*newOStream) << "  </MetaData>" << std::endl;
835	+	return newOStream;
836	+	}
837
838	<	#endif // is_mpi
838	>	void DumpWriter::writeClosing(std::ostream& os) {
839
840	<	}
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 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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