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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 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.
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 IS_MPI
54	<	#include <mpi.h>
55	<	#endif //is_mpi
53	>	#ifdef HAVE_ZLIB
54	>	#include "io/gzstream.hpp"
55	>	#endif
56	>	#include "io/Globals.hpp"
57
58	<	namespace oopse {
58	>	#ifdef _MSC_VER
59	>	#define isnan(x) _isnan((x))
60	>	#define isinf(x) (!_finite(x) && !_isnan(x))
61	>	#endif
62
63	+	using namespace std;
64	+	namespace OpenMD {
65	+
66		DumpWriter::DumpWriter(SimInfo* info)
67	<	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
68	<	#ifdef IS_MPI
67	>	: info_(info), filename_(info->getDumpFileName()),
68	>	eorFilename_(info->getFinalConfigFileName()){
69
70	<	if (worldRank == 0) {
71	<	#endif // is_mpi
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	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
78	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
79	>	needSitePotential_) {
80	>	doSiteData_ = true;
81	>	} else {
82	>	doSiteData_ = false;
83	>	}
84
85	<	if (!dumpFile_) {
86	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
87	<	filename_.c_str());
88	<	painCave.isFatal = 1;
89	<	simError();
90	<	}
91	<
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	+	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
107	<	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	<	MPIcheckPoint();
107	>	#ifdef IS_MPI
108
109	+	}
110	+
111		#endif // is_mpi
112
113	<	}
113	>	}
114
115
116		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
117		: info_(info), filename_(filename){
82	–	#ifdef IS_MPI
118
119	<	if (worldRank == 0) {
120	<	#endif // is_mpi
119	>	Globals* simParams = info->getSimParams();
120	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
121
122	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
123	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
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 (!dumpFile_) {
130	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
131	<	filename_.c_str());
132	<	painCave.isFatal = 1;
133	<	simError();
134	<	}
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	+
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	<	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	<	MPIcheckPoint();
159	>	#ifdef IS_MPI
160
161	+	}
162	+
163		#endif // is_mpi
164
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	+	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
181	+	needSitePotential_) {
182	+	doSiteData_ = true;
183	+	} else {
184	+	doSiteData_ = false;
185		}
186
187	+	#ifdef HAVE_LIBZ
188	+	if (needCompression_) {
189	+	filename_ += ".gz";
190	+	eorFilename_ += ".gz";
191	+	}
192	+	#endif
193	+
194	+	#ifdef IS_MPI
195	+
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	+
215	+	#endif // is_mpi
216	+
217	+	}
218	+
219		DumpWriter::~DumpWriter() {
220
221		#ifdef IS_MPI
222
223		if (worldRank == 0) {
224		#endif // is_mpi
225	<
226	<	dumpFile_.close();
227	<
225	>	if (createDumpFile_){
226	>	writeClosing(*dumpFile_);
227	>	delete dumpFile_;
228	>	}
229		#ifdef IS_MPI
230
231		}
#	Line 122 | Line 234 | namespace oopse {
234
235		}
236
237	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
237	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
238
239	<	double currentTime;
240	<	Mat3x3d hmat;
241	<	double chi;
242	<	double integralOfChiDt;
243	<	Mat3x3d eta;
239	>	char buffer[1024];
240	>
241	>	os << "    <FrameData>\n";
242	>
243	>	RealType currentTime = s->getTime();
244	>
245	>	if (isinf(currentTime) || isnan(currentTime)) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the time");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251
252	<	currentTime = s->getTime();
252	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
253	>	os << buffer;
254	>
255	>	Mat3x3d hmat;
256		hmat = s->getHmat();
257	<	chi = s->getChi();
258	<	integralOfChiDt = s->getIntegralOfChiDt();
259	<	eta = s->getEta();
257	>
258	>	for (unsigned int i = 0; i < 3; i++) {
259	>	for (unsigned int j = 0; j < 3; j++) {
260	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
261	>	sprintf( painCave.errMsg,
262	>	"DumpWriter detected a numerical error writing the box");
263	>	painCave.isFatal = 1;
264	>	simError();
265	>	}
266	>	}
267	>	}
268
269	<	os << currentTime << ";\t"
270	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
271	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
272	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
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	<	//write out additional parameters, such as chi and eta
275	>	pair<RealType, RealType> thermostat = s->getThermostat();
276
277	<	os << chi << "\t" << integralOfChiDt << "\t;";
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	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
289	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
290	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
291	<
292	<	os << "\n";
288	>	Mat3x3d eta;
289	>	eta = s->getBarostat();
290	>
291	>	for (unsigned int i = 0; i < 3; i++) {
292	>	for (unsigned int j = 0; j < 3; j++) {
293	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
294	>	sprintf( painCave.errMsg,
295	>	"DumpWriter detected a numerical error writing the barostat");
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}
300	>	}
301	>
302	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
303	>	eta(0, 0), eta(1, 0), eta(2, 0),
304	>	eta(0, 1), eta(1, 1), eta(2, 1),
305	>	eta(0, 2), eta(1, 2), eta(2, 2));
306	>	os << buffer;
307	>
308	>	os << "    </FrameData>\n";
309		}
310
311		void DumpWriter::writeFrame(std::ostream& os) {
156	–	const int BUFFERSIZE = 2000;
157	–	const int MINIBUFFERSIZE = 100;
312
313	<	char tempBuffer[BUFFERSIZE];
314	<	char writeLine[BUFFERSIZE];
313	>	#ifdef IS_MPI
314	>	MPI_Status istatus;
315	>	#endif
316
162	–	Quat4d q;
163	–	Vector3d ji;
164	–	Vector3d pos;
165	–	Vector3d vel;
166	–
317		Molecule* mol;
318	<	StuntDouble* integrableObject;
318	>	StuntDouble* sd;
319		SimInfo::MoleculeIterator mi;
320		Molecule::IntegrableObjectIterator ii;
321	<
172	<	int nTotObjects;
173	<	nTotObjects = info_->getNGlobalIntegrableObjects();
321	>	RigidBody::AtomIterator ai;
322
323		#ifndef IS_MPI
324	+	os << "  <Snapshot>\n";
325	+
326	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327
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	<	os << nTotObjects << "\n";
341	<
342	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
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	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
348	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
349	>	// do one for the IO itself
350	>	os << prepareSiteLine(sd, ioIndex, 0);
351
352	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
353	<	integrableObject = mol->nextIntegrableObject(ii)) {
354	<
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	<	pos = integrableObject->getPos();
369	<	vel = integrableObject->getVel();
368	>	os.flush();
369	>	#else
370
371	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
372	<	integrableObject->getType().c_str(),
373	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
371	>	const int masterNode = 0;
372	>	int worldRank;
373	>	int nProc;
374
375	<	strcpy(writeLine, tempBuffer);
375	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
376	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
377
198	–	if (integrableObject->isDirectional()) {
199	–	q = integrableObject->getQ();
200	–	ji = integrableObject->getJ();
378
379	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
380	<	q[0], q[1], q[2], q[3],
381	<	ji[0], ji[1], ji[2]);
382	<	strcat(writeLine, tempBuffer);
383	<	} else {
384	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208	<	}
379	>	if (worldRank == masterNode) {
380	>	os << "  <Snapshot>\n";
381	>	writeFrameProperties(os,
382	>	info_->getSnapshotManager()->getCurrentSnapshot());
383	>	os << "    <StuntDoubles>\n";
384	>	}
385
386	<	os << writeLine;
387	<
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		}
214	–
215	–	os.flush();
216	–	#else // is_mpi
217	–	/*********************************************************************
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	–	*********************************************************************/
253	–	const int masterNode = 0;
254	–
255	–	int * potatoes;
256	–	int myPotato;
257	–	int nProc;
258	–	int which_node;
259	–	double atomData[13];
260	–	int isDirectional;
261	–	char MPIatomTypeString[MINIBUFFERSIZE];
262	–	int msgLen; // the length of message actually recieved at master nodes
263	–	int haveError;
264	–	MPI_Status istatus;
265	–	int nCurObj;
395
396	<	// code to find maximum tag value
397	<	int * tagub;
398	<	int flag;
399	<	int MAXTAG;
400	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
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	<	if (flag) {
404	<	MAXTAG = *tagub;
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	>	// 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	<	MAXTAG = 32767;
424	<	}
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	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
432	>	// send our buffer:
433	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
434	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
435
436	<	// Node 0 needs a list of the magic potatoes for each processor;
282	<
283	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
284	<	potatoes = new int[nProc];
285	<
286	<	//write out the comment lines
287	<	for(int i = 0; i < nProc; i++) {
288	<	potatoes[i] = 0;
436	>	}
437		}
438	+	}
439	+
440	+	if (worldRank == masterNode) {
441	+	os << "    </StuntDoubles>\n";
442	+	}
443
444	<
445	<	os << nTotObjects << "\n";
446	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
447	<
448	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
449	<
450	<	// Get the Node number which has this atom;
451	<
452	<	which_node = info_->getMolToProc(i);
453	<
454	<	if (which_node != masterNode) { //current molecule is in slave node
455	<	if (potatoes[which_node] + 1 >= MAXTAG) {
456	<	// The potato was going to exceed the maximum value,
457	<	// so wrap this processor potato back to 0:
305	<
306	<	potatoes[which_node] = 0;
307	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
308	<	MPI_COMM_WORLD);
309	<	}
310	<
311	<	myPotato = potatoes[which_node];
312	<
313	<	//recieve the number of integrableObject in current molecule
314	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
315	<	MPI_COMM_WORLD, &istatus);
316	<	myPotato++;
317	<
318	<	for(int l = 0; l < nCurObj; l++) {
319	<	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:
322	<
323	<	potatoes[which_node] = 0;
324	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
325	<	0, MPI_COMM_WORLD);
326	<	}
327	<
328	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
329	<	which_node, myPotato, MPI_COMM_WORLD,
330	<	&istatus);
331	<
332	<	myPotato++;
333	<
334	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
335	<	MPI_COMM_WORLD, &istatus);
336	<	myPotato++;
337	<
338	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
339	<
340	<	if (msgLen == 13)
341	<	isDirectional = 1;
342	<	else
343	<	isDirectional = 0;
344	<
345	<	// If we've survived to here, format the line:
346	<
347	<	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);
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	<	if (mol == NULL) {
460	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
461	<	painCave.isFatal = 1;
462	<	simError();
463	<	}
464	<
465	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
466	<	integrableObject = mol->nextIntegrableObject(ii)) {
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	<	pos = integrableObject->getPos();
473	<	vel = integrableObject->getVel();
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	<	atomData[0] = pos[0];
530	<	atomData[1] = pos[1];
531	<	atomData[2] = pos[2];
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	<	atomData[3] = vel[0];
537	<	atomData[4] = vel[1];
538	<	atomData[5] = vel[2];
536	>	Vector3d pos;
537	>	Vector3d vel;
538	>	pos = sd->getPos();
539
540	<	isDirectional = 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	<	if (integrableObject->isDirectional()) {
407	<	isDirectional = 1;
550	>	vel = sd->getVel();
551
552	<	q = integrableObject->getQ();
553	<	ji = integrableObject->getJ();
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	<	for(int j = 0; j < 6; j++) {
563	<	atomData[j] = atomData[j];
564	<	}
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	<	atomData[6] = q[0];
568	<	atomData[7] = q[1];
569	<	atomData[8] = q[2];
570	<	atomData[9] = q[3];
567	>	if (sd->isDirectional()) {
568	>	type += "qj";
569	>	Quat4d q;
570	>	Vector3d ji;
571	>	q = sd->getQ();
572
573	<	atomData[10] = ji[0];
574	<	atomData[11] = ji[1];
575	<	atomData[12] = ji[2];
576	<	}
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	<	// If we've survived to here, format the line:
584	>	ji = sd->getJ();
585
586	<	if (!isDirectional) {
587	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
588	<	integrableObject->getType().c_str(), atomData[0],
589	<	atomData[1], atomData[2],
590	<	atomData[3], atomData[4],
591	<	atomData[5]);
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	<	strcat(writeLine,
597	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
598	<	} else {
599	<	sprintf(writeLine,
600	<	"%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	<	}
596	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
597	>	q[0], q[1], q[2], q[3],
598	>	ji[0], ji[1], ji[2]);
599	>	line += tempBuffer;
600	>	}
601
602	+	if (needForceVector_) {
603	+	type += "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	<	os << writeLine;
636	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
637	>	return std::string(tempBuffer);
638	>	}
639
640	<	} //end for(iter = integrableObject.begin())
641	<	}
461	<	} //end for(i = 0; i < mpiSim->getNmol())
640	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
641	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
642
643	<	os.flush();
644	<
645	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
646	<	MPIcheckPoint();
643	>	std::string id;
644	>	std::string type;
645	>	std::string line;
646	>	char tempBuffer[4096];
647
648	<	delete [] potatoes;
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	<	// worldRank != 0, so I'm a remote node.
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	<	// Set my magic potato to 0:
686	<
687	<	myPotato = 0;
688	<
689	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
690	<
691	<	// Am I the node which has this integrableObject?
692	<	int whichNode = info_->getMolToProc(i);
693	<	if (whichNode == worldRank) {
694	<	if (myPotato + 1 >= MAXTAG) {
695	<
696	<	// The potato was going to exceed the maximum value,
697	<	// so wrap this processor potato back to 0 (and block until
698	<	// 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	<
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		}
566	–	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
567	–	MPIcheckPoint();
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	<	#endif // is_mpi
722	<
721	>	if (needSitePotential_) {
722	>	if (storageLayout & DataStorage::dslSitePotential) {
723	>	type += "s";
724	>	RealType sPot = sd->getSitePotential();
725	>	if (isinf(sPot) || isnan(sPot) ) {
726	>	sprintf( painCave.errMsg,
727	>	"DumpWriter detected a numerical error writing the"
728	>	" site potential for object %s", id.c_str());
729	>	painCave.isFatal = 1;
730	>	simError();
731	>	}
732	>	sprintf(tempBuffer, " %13e ", sPot);
733	>	line += tempBuffer;
734	>	}
735	>	}
736	>
737	>	if (needParticlePot_) {
738	>	if (storageLayout & DataStorage::dslParticlePot) {
739	>	type += "u";
740	>	RealType particlePot = sd->getParticlePot();
741	>	if (isinf(particlePot) || isnan(particlePot)) {
742	>	sprintf( painCave.errMsg,
743	>	"DumpWriter detected a numerical error writing the particle "
744	>	" potential for object %s", id.c_str());
745	>	painCave.isFatal = 1;
746	>	simError();
747	>	}
748	>	sprintf(tempBuffer, " %13e", particlePot);
749	>	line += tempBuffer;
750	>	}
751	>	}
752	>
753	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
754	>	return std::string(tempBuffer);
755		}
756
757		void DumpWriter::writeDump() {
758	<	writeFrame(dumpFile_);
576	<
758	>	writeFrame(*dumpFile_);
759		}
760
761		void DumpWriter::writeEor() {
762	<	std::ofstream eorStream;
763	<
762	>
763	>	std::ostream* eorStream = NULL;
764	>
765		#ifdef IS_MPI
766		if (worldRank == 0) {
767		#endif // is_mpi
768	+
769	+	eorStream = createOStream(eorFilename_);
770
586	–	eorStream.open(eorFilename_.c_str());
587	–	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	–	}
593	–
771		#ifdef IS_MPI
772		}
773	<	#endif // is_mpi
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
598	–	writeFrame(eorStream);
788		}
789
790
791		void DumpWriter::writeDumpAndEor() {
603	–	std::ofstream eorStream;
792		std::vector<std::streambuf*> buffers;
793	+	std::ostream* eorStream;
794		#ifdef IS_MPI
795		if (worldRank == 0) {
796		#endif // is_mpi
797	<
798	<	buffers.push_back(dumpFile_.rdbuf());
799	<
611	<	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	<	}
618	<
619	<	buffers.push_back(eorStream.rdbuf());
620	<
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		TeeBuf tbuf(buffers.begin(), buffers.end());
805		std::ostream os(&tbuf);
627	–
806		writeFrame(os);
807	<
807	>
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	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
819
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	<	}//end namespace oopse
838	>	void DumpWriter::writeClosing(std::ostream& os) {
839	>
840	>	os << "</OpenMD>\n";
841	>	os.flush();
842	>	}
843	>
844	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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