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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 2020 by gezelter, Mon Sep 22 19:18:35 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	+	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	<
350	<	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 (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
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	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
369	<	integrableObject = mol->nextIntegrableObject(ii)) {
186	<
368	>	os.flush();
369	>	#else
370
371	<	pos = integrableObject->getPos();
372	<	vel = integrableObject->getVel();
371	>	const int masterNode = 0;
372	>	int worldRank;
373	>	int nProc;
374
375	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
376	<	integrableObject->getType().c_str(),
193	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
375	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
376	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
377
196	–	strcpy(writeLine, tempBuffer);
378
379	<	if (integrableObject->isDirectional()) {
380	<	q = integrableObject->getQ();
381	<	ji = integrableObject->getJ();
379	>	if (worldRank == masterNode) {
380	>	os << "  <Snapshot>\n";
381	>	writeFrameProperties(os,
382	>	info_->getSnapshotManager()->getCurrentSnapshot());
383	>	os << "    <StuntDoubles>\n";
384	>	}
385
386	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
387	<	q[0], q[1], q[2], q[3],
388	<	ji[0], ji[1], ji[2]);
389	<	strcat(writeLine, tempBuffer);
390	<	} else {
391	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
392	<	}
209	<
210	<	os << writeLine;
211	<
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
402	<	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;
402	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
403
404	<	int * potatoes;
405	<	int myPotato;
406	<	int nProc;
407	<	int which_node;
408	<	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;
266	<
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);
404	>	// receive the length of the string buffer that was
405	>	// prepared by processor i:
406	>	int recvLength;
407	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
408	>	&istatus);
409
410	<	if (flag) {
411	<	MAXTAG = *tagub;
410	>	// create a buffer to receive the data
411	>	char* recvBuffer = new char[recvLength];
412	>	if (recvBuffer == NULL) {
413	>	} else {
414	>	// receive the data:
415	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
416	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
417	>	// send it to the file:
418	>	os << recvBuffer;
419	>	// get rid of the receive buffer:
420	>	delete [] recvBuffer;
421	>	}
422	>	}
423		} else {
424	<	MAXTAG = 32767;
425	<	}
424	>	int sendBufferLength = buffer.size() + 1;
425	>	int myturn = 0;
426	>	for (int i = 1; i < nProc; ++i){
427	>	// wait for the master node to call our number:
428	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
429	>	if (myturn == worldRank){
430	>	// send the length of our buffer:
431
432	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
432	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
433
434	<	// Node 0 needs a list of the magic potatoes for each processor;
434	>	// send our buffer:
435	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
436	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
437
438	<	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;
438	>	}
439		}
440	+	}
441	+
442	+	if (worldRank == masterNode) {
443	+	os << "    </StuntDoubles>\n";
444	+	}
445
446	<
447	<	os << nTotObjects << "\n";
448	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
449	<
450	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
451	<
452	<	// Get the Node number which has this atom;
453	<
454	<	which_node = info_->getMolToProc(i);
455	<
456	<	if (which_node != masterNode) { //current molecule is in slave node
457	<	if (potatoes[which_node] + 1 >= MAXTAG) {
458	<	// The potato was going to exceed the maximum value,
459	<	// 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);
446	>	if (doSiteData_) {
447	>	if (worldRank == masterNode) {
448	>	os << "    <SiteData>\n";
449	>	}
450	>	buffer.clear();
451	>	for (mol = info_->beginMolecule(mi); mol != NULL;
452	>	mol = info_->nextMolecule(mi)) {
453	>
454	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
455	>	sd = mol->nextIntegrableObject(ii)) {
456	>
457	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
458	>	// do one for the IO itself
459	>	buffer += prepareSiteLine(sd, ioIndex, 0);
460
461	<	if (mol == NULL) {
462	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
463	<	painCave.isFatal = 1;
464	<	simError();
465	<	}
466	<
467	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
468	<	integrableObject = mol->nextIntegrableObject(ii)) {
461	>	if (sd->isRigidBody()) {
462	>
463	>	RigidBody* rb = static_cast<RigidBody*>(sd);
464	>	int siteIndex = 0;
465	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
466	>	atom = rb->nextAtom(ai)) {
467	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
468	>	siteIndex++;
469	>	}
470	>	}
471	>	}
472	>	}
473
474	<	pos = integrableObject->getPos();
475	<	vel = integrableObject->getVel();
474	>	if (worldRank == masterNode) {
475	>	os << buffer;
476	>
477	>	for (int i = 1; i < nProc; ++i) {
478	>
479	>	// tell processor i to start sending us data:
480	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
481	>
482	>	// receive the length of the string buffer that was
483	>	// prepared by processor i:
484	>	int recvLength;
485	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
486	>	&istatus);
487	>
488	>	// create a buffer to receive the data
489	>	char* recvBuffer = new char[recvLength];
490	>	if (recvBuffer == NULL) {
491	>	} else {
492	>	// receive the data:
493	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
494	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
495	>	// send it to the file:
496	>	os << recvBuffer;
497	>	// get rid of the receive buffer:
498	>	delete [] recvBuffer;
499	>	}
500	>	}
501	>	} else {
502	>	int sendBufferLength = buffer.size() + 1;
503	>	int myturn = 0;
504	>	for (int i = 1; i < nProc; ++i){
505	>	// wait for the master node to call our number:
506	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
507	>	if (myturn == worldRank){
508	>	// send the length of our buffer:
509	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
510	>	// send our buffer:
511	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
512	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
513	>	}
514	>	}
515	>	}
516	>
517	>	if (worldRank == masterNode) {
518	>	os << "    </SiteData>\n";
519	>	}
520	>	}
521	>
522	>	if (worldRank == masterNode) {
523	>	os << "  </Snapshot>\n";
524	>	os.flush();
525	>	}
526	>
527	>	#endif // is_mpi
528	>
529	>	}
530
531	<	atomData[0] = pos[0];
532	<	atomData[1] = pos[1];
533	<	atomData[2] = pos[2];
531	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
532	>
533	>	int index = sd->getGlobalIntegrableObjectIndex();
534	>	std::string type("pv");
535	>	std::string line;
536	>	char tempBuffer[4096];
537
538	<	atomData[3] = vel[0];
539	<	atomData[4] = vel[1];
540	<	atomData[5] = vel[2];
538	>	Vector3d pos;
539	>	Vector3d vel;
540	>	pos = sd->getPos();
541
542	<	isDirectional = 0;
542	>	if (isinf(pos[0]) || isnan(pos[0]) ||
543	>	isinf(pos[1]) || isnan(pos[1]) ||
544	>	isinf(pos[2]) || isnan(pos[2]) ) {
545	>	sprintf( painCave.errMsg,
546	>	"DumpWriter detected a numerical error writing the position"
547	>	" for object %d", index);
548	>	painCave.isFatal = 1;
549	>	simError();
550	>	}
551
552	<	if (integrableObject->isDirectional()) {
407	<	isDirectional = 1;
552	>	vel = sd->getVel();
553
554	<	q = integrableObject->getQ();
555	<	ji = integrableObject->getJ();
554	>	if (isinf(vel[0]) || isnan(vel[0]) ||
555	>	isinf(vel[1]) || isnan(vel[1]) ||
556	>	isinf(vel[2]) || isnan(vel[2]) ) {
557	>	sprintf( painCave.errMsg,
558	>	"DumpWriter detected a numerical error writing the velocity"
559	>	" for object %d", index);
560	>	painCave.isFatal = 1;
561	>	simError();
562	>	}
563
564	<	for(int j = 0; j < 6; j++) {
565	<	atomData[j] = atomData[j];
566	<	}
564	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
565	>	pos[0], pos[1], pos[2],
566	>	vel[0], vel[1], vel[2]);
567	>	line += tempBuffer;
568
569	<	atomData[6] = q[0];
570	<	atomData[7] = q[1];
571	<	atomData[8] = q[2];
572	<	atomData[9] = q[3];
569	>	if (sd->isDirectional()) {
570	>	type += "qj";
571	>	Quat4d q;
572	>	Vector3d ji;
573	>	q = sd->getQ();
574
575	<	atomData[10] = ji[0];
576	<	atomData[11] = ji[1];
577	<	atomData[12] = ji[2];
578	<	}
575	>	if (isinf(q[0]) || isnan(q[0]) ||
576	>	isinf(q[1]) || isnan(q[1]) ||
577	>	isinf(q[2]) || isnan(q[2]) ||
578	>	isinf(q[3]) || isnan(q[3]) ) {
579	>	sprintf( painCave.errMsg,
580	>	"DumpWriter detected a numerical error writing the quaternion"
581	>	" for object %d", index);
582	>	painCave.isFatal = 1;
583	>	simError();
584	>	}
585
586	<	// If we've survived to here, format the line:
586	>	ji = sd->getJ();
587
588	<	if (!isDirectional) {
589	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
590	<	integrableObject->getType().c_str(), atomData[0],
591	<	atomData[1], atomData[2],
592	<	atomData[3], atomData[4],
593	<	atomData[5]);
588	>	if (isinf(ji[0]) || isnan(ji[0]) ||
589	>	isinf(ji[1]) || isnan(ji[1]) ||
590	>	isinf(ji[2]) || isnan(ji[2]) ) {
591	>	sprintf( painCave.errMsg,
592	>	"DumpWriter detected a numerical error writing the angular"
593	>	" momentum for object %d", index);
594	>	painCave.isFatal = 1;
595	>	simError();
596	>	}
597
598	<	strcat(writeLine,
599	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
600	<	} else {
601	<	sprintf(writeLine,
602	<	"%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	<	}
598	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
599	>	q[0], q[1], q[2], q[3],
600	>	ji[0], ji[1], ji[2]);
601	>	line += tempBuffer;
602	>	}
603
604	+	if (needForceVector_) {
605	+	type += "f";
606	+	Vector3d frc = sd->getFrc();
607	+	if (isinf(frc[0]) || isnan(frc[0]) ||
608	+	isinf(frc[1]) || isnan(frc[1]) ||
609	+	isinf(frc[2]) || isnan(frc[2]) ) {
610	+	sprintf( painCave.errMsg,
611	+	"DumpWriter detected a numerical error writing the force"
612	+	" for object %d", index);
613	+	painCave.isFatal = 1;
614	+	simError();
615	+	}
616	+	sprintf(tempBuffer, " %13e %13e %13e",
617	+	frc[0], frc[1], frc[2]);
618	+	line += tempBuffer;
619	+
620	+	if (sd->isDirectional()) {
621	+	type += "t";
622	+	Vector3d trq = sd->getTrq();
623	+	if (isinf(trq[0]) || isnan(trq[0]) ||
624	+	isinf(trq[1]) || isnan(trq[1]) ||
625	+	isinf(trq[2]) || isnan(trq[2]) ) {
626	+	sprintf( painCave.errMsg,
627	+	"DumpWriter detected a numerical error writing the torque"
628	+	" for object %d", index);
629	+	painCave.isFatal = 1;
630	+	simError();
631	+	}
632	+	sprintf(tempBuffer, " %13e %13e %13e",
633	+	trq[0], trq[1], trq[2]);
634	+	line += tempBuffer;
635	+	}
636	+	}
637
638	<	os << writeLine;
638	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
639	>	return std::string(tempBuffer);
640	>	}
641
642	<	} //end for(iter = integrableObject.begin())
643	<	}
461	<	} //end for(i = 0; i < mpiSim->getNmol())
642	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
643	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
644
645	<	os.flush();
646	<
647	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
648	<	MPIcheckPoint();
645	>	std::string id;
646	>	std::string type;
647	>	std::string line;
648	>	char tempBuffer[4096];
649
650	<	delete [] potatoes;
650	>	if (sd->isRigidBody()) {
651	>	sprintf(tempBuffer, "%10d           ", ioIndex);
652	>	id = std::string(tempBuffer);
653		} else {
654	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
655	+	id = std::string(tempBuffer);
656	+	}
657	+
658	+	if (needFlucQ_) {
659	+	if (storageLayout & DataStorage::dslFlucQPosition) {
660	+	type += "c";
661	+	RealType fqPos = sd->getFlucQPos();
662	+	if (isinf(fqPos) || isnan(fqPos) ) {
663	+	sprintf( painCave.errMsg,
664	+	"DumpWriter detected a numerical error writing the"
665	+	" fluctuating charge for object %s", id.c_str());
666	+	painCave.isFatal = 1;
667	+	simError();
668	+	}
669	+	sprintf(tempBuffer, " %13e ", fqPos);
670	+	line += tempBuffer;
671	+	}
672
673	<	// worldRank != 0, so I'm a remote node.
674	<
675	<	// Set my magic potato to 0:
673	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
674	>	type += "w";
675	>	RealType fqVel = sd->getFlucQVel();
676	>	if (isinf(fqVel) || isnan(fqVel) ) {
677	>	sprintf( painCave.errMsg,
678	>	"DumpWriter detected a numerical error writing the"
679	>	" fluctuating charge velocity for object %s", id.c_str());
680	>	painCave.isFatal = 1;
681	>	simError();
682	>	}
683	>	sprintf(tempBuffer, " %13e ", fqVel);
684	>	line += tempBuffer;
685	>	}
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:
699	<
700	<	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	<
687	>	if (needForceVector_) {
688	>	if (storageLayout & DataStorage::dslFlucQForce) {
689	>	type += "g";
690	>	RealType fqFrc = sd->getFlucQFrc();
691	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
692	>	sprintf( painCave.errMsg,
693	>	"DumpWriter detected a numerical error writing the"
694	>	" fluctuating charge force for object %s", id.c_str());
695	>	painCave.isFatal = 1;
696	>	simError();
697	>	}
698	>	sprintf(tempBuffer, " %13e ", fqFrc);
699	>	line += tempBuffer;
700	>	}
701		}
566	–	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
567	–	MPIcheckPoint();
702		}
703	+
704	+	if (needElectricField_) {
705	+	if (storageLayout & DataStorage::dslElectricField) {
706	+	type += "e";
707	+	Vector3d eField= sd->getElectricField();
708	+	if (isinf(eField[0]) || isnan(eField[0]) ||
709	+	isinf(eField[1]) || isnan(eField[1]) ||
710	+	isinf(eField[2]) || isnan(eField[2]) ) {
711	+	sprintf( painCave.errMsg,
712	+	"DumpWriter detected a numerical error writing the electric"
713	+	" field for object %s", id.c_str());
714	+	painCave.isFatal = 1;
715	+	simError();
716	+	}
717	+	sprintf(tempBuffer, " %13e %13e %13e",
718	+	eField[0], eField[1], eField[2]);
719	+	line += tempBuffer;
720	+	}
721	+	}
722
723	<	#endif // is_mpi
724	<
723	>	if (needSitePotential_) {
724	>	if (storageLayout & DataStorage::dslSitePotential) {
725	>	type += "s";
726	>	RealType sPot = sd->getSitePotential();
727	>	if (isinf(sPot) || isnan(sPot) ) {
728	>	sprintf( painCave.errMsg,
729	>	"DumpWriter detected a numerical error writing the"
730	>	" site potential for object %s", id.c_str());
731	>	painCave.isFatal = 1;
732	>	simError();
733	>	}
734	>	sprintf(tempBuffer, " %13e ", sPot);
735	>	line += tempBuffer;
736	>	}
737	>	}
738	>
739	>	if (needParticlePot_) {
740	>	if (storageLayout & DataStorage::dslParticlePot) {
741	>	type += "u";
742	>	RealType particlePot = sd->getParticlePot();
743	>	if (isinf(particlePot) || isnan(particlePot)) {
744	>	sprintf( painCave.errMsg,
745	>	"DumpWriter detected a numerical error writing the particle "
746	>	" potential for object %s", id.c_str());
747	>	painCave.isFatal = 1;
748	>	simError();
749	>	}
750	>	sprintf(tempBuffer, " %13e", particlePot);
751	>	line += tempBuffer;
752	>	}
753	>	}
754	>
755	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
756	>	return std::string(tempBuffer);
757		}
758
759		void DumpWriter::writeDump() {
760	<	writeFrame(dumpFile_);
576	<
760	>	writeFrame(*dumpFile_);
761		}
762
763		void DumpWriter::writeEor() {
764	<	std::ofstream eorStream;
765	<
764	>
765	>	std::ostream* eorStream = NULL;
766	>
767		#ifdef IS_MPI
768		if (worldRank == 0) {
769		#endif // is_mpi
770	+
771	+	eorStream = createOStream(eorFilename_);
772
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	–
773		#ifdef IS_MPI
774		}
775	<	#endif // is_mpi
775	>	#endif
776	>
777	>	writeFrame(*eorStream);
778	>
779	>	#ifdef IS_MPI
780	>	if (worldRank == 0) {
781	>	#endif
782	>
783	>	writeClosing(*eorStream);
784	>	delete eorStream;
785	>
786	>	#ifdef IS_MPI
787	>	}
788	>	#endif // is_mpi
789
598	–	writeFrame(eorStream);
790		}
791
792
793		void DumpWriter::writeDumpAndEor() {
603	–	std::ofstream eorStream;
794		std::vector<std::streambuf*> buffers;
795	+	std::ostream* eorStream;
796		#ifdef IS_MPI
797		if (worldRank == 0) {
798		#endif // is_mpi
799	<
800	<	buffers.push_back(dumpFile_.rdbuf());
801	<
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	<
799	>	buffers.push_back(dumpFile_->rdbuf());
800	>	eorStream = createOStream(eorFilename_);
801	>	buffers.push_back(eorStream->rdbuf());
802		#ifdef IS_MPI
803		}
804		#endif // is_mpi
805
806		TeeBuf tbuf(buffers.begin(), buffers.end());
807		std::ostream os(&tbuf);
627	–
808		writeFrame(os);
809	<
809	>
810	>	#ifdef IS_MPI
811	>	if (worldRank == 0) {
812	>	#endif // is_mpi
813	>	writeClosing(*eorStream);
814	>	delete eorStream;
815	>	#ifdef IS_MPI
816	>	}
817	>	#endif // is_mpi
818		}
819
820	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
821
822	+	std::ostream* newOStream;
823	+	#ifdef HAVE_ZLIB
824	+	if (needCompression_) {
825	+	newOStream = new ogzstream(filename.c_str());
826	+	} else {
827	+	newOStream = new std::ofstream(filename.c_str());
828	+	}
829	+	#else
830	+	newOStream = new std::ofstream(filename.c_str());
831	+	#endif
832	+	//write out MetaData first
833	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
834	+	(*newOStream) << "  <MetaData>" << std::endl;
835	+	(*newOStream) << info_->getRawMetaData();
836	+	(*newOStream) << "  </MetaData>" << std::endl;
837	+	return newOStream;
838	+	}
839
840	<	}//end namespace oopse
840	>	void DumpWriter::writeClosing(std::ostream& os) {
841	>
842	>	os << "</OpenMD>\n";
843	>	os.flush();
844	>	}
845	>
846	>	}//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 2020 by gezelter, Mon Sep 22 19:18:35 2014 UTC

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