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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 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 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)
67		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
68
69		Globals* simParams = info->getSimParams();
70	<	needCompression_ = simParams->getCompressDumpFile();
71	<	needForceVector_ = simParams->getOutputForceVector();
70	>	needCompression_   = simParams->getCompressDumpFile();
71	>	needForceVector_   = simParams->getOutputForceVector();
72	>	needParticlePot_   = simParams->getOutputParticlePotential();
73	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
74	>	needElectricField_ = simParams->getOutputElectricField();
75	>
76	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
77	>	doSiteData_ = true;
78	>	} else {
79	>	doSiteData_ = false;
80	>	}
81	>
82		createDumpFile_ = true;
83		#ifdef HAVE_LIBZ
84		if (needCompression_) {
85	<	filename_ += ".gz";
86	<	eorFilename_ += ".gz";
85	>	filename_ += ".gz";
86	>	eorFilename_ += ".gz";
87		}
88		#endif
89
90		#ifdef IS_MPI
91
92	<	if (worldRank == 0) {
92	>	if (worldRank == 0) {
93		#endif // is_mpi
73	–
94
95	<	dumpFile_ = createOStream(filename_);
95	>	dumpFile_ = createOStream(filename_);
96
97	<	if (!dumpFile_) {
98	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
99	<	filename_.c_str());
100	<	painCave.isFatal = 1;
101	<	simError();
102	<	}
97	>	if (!dumpFile_) {
98	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
99	>	filename_.c_str());
100	>	painCave.isFatal = 1;
101	>	simError();
102	>	}
103
104		#ifdef IS_MPI
105
106	<	}
106	>	}
107
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
108		#endif // is_mpi
109
110	<	}
110	>	}
111
112
113		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 99 | Line 116 | namespace oopse {
116		Globals* simParams = info->getSimParams();
117		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
118
119	<	needCompression_ = simParams->getCompressDumpFile();
120	<	needForceVector_ = simParams->getOutputForceVector();
119	>	needCompression_   = simParams->getCompressDumpFile();
120	>	needForceVector_   = simParams->getOutputForceVector();
121	>	needParticlePot_   = simParams->getOutputParticlePotential();
122	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
123	>	needElectricField_ = simParams->getOutputElectricField();
124	>
125	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
126	>	doSiteData_ = true;
127	>	} else {
128	>	doSiteData_ = false;
129	>	}
130	>
131		createDumpFile_ = true;
132		#ifdef HAVE_LIBZ
133		if (needCompression_) {
134	<	filename_ += ".gz";
135	<	eorFilename_ += ".gz";
134	>	filename_ += ".gz";
135	>	eorFilename_ += ".gz";
136		}
137		#endif
138
139		#ifdef IS_MPI
140
141	<	if (worldRank == 0) {
141	>	if (worldRank == 0) {
142		#endif // is_mpi
143
144
145	<	dumpFile_ = createOStream(filename_);
145	>	dumpFile_ = createOStream(filename_);
146
147	<	if (!dumpFile_) {
148	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
149	<	filename_.c_str());
150	<	painCave.isFatal = 1;
151	<	simError();
152	<	}
147	>	if (!dumpFile_) {
148	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
149	>	filename_.c_str());
150	>	painCave.isFatal = 1;
151	>	simError();
152	>	}
153
154		#ifdef IS_MPI
155
156	<	}
156	>	}
157
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
158		#endif // is_mpi
159
160	<	}
160	>	}
161
162		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
163	<	: info_(info), filename_(filename){
163	>	: info_(info), filename_(filename){
164
165		Globals* simParams = info->getSimParams();
166		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
167
168	<	needCompression_ = simParams->getCompressDumpFile();
169	<	needForceVector_ = simParams->getOutputForceVector();
170	<
168	>	needCompression_   = simParams->getCompressDumpFile();
169	>	needForceVector_   = simParams->getOutputForceVector();
170	>	needParticlePot_   = simParams->getOutputParticlePotential();
171	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
172	>	needElectricField_ = simParams->getOutputElectricField();
173	>
174	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
175	>	doSiteData_ = true;
176	>	} else {
177	>	doSiteData_ = false;
178	>	}
179	>
180		#ifdef HAVE_LIBZ
181		if (needCompression_) {
182		filename_ += ".gz";
#	Line 170 | Line 203 | namespace oopse {
203		#ifdef IS_MPI
204
205		}
206	+
207
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
208		#endif // is_mpi
209
210		}
180	–
181	–
182	–
183	–
184	–
211
212		DumpWriter::~DumpWriter() {
213
#	Line 190 | Line 216 | namespace oopse {
216		if (worldRank == 0) {
217		#endif // is_mpi
218		if (createDumpFile_){
219	+	writeClosing(*dumpFile_);
220		delete dumpFile_;
221		}
222		#ifdef IS_MPI
#	Line 200 | Line 227 | namespace oopse {
227
228		}
229
230	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
230	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
231
232	<	RealType currentTime;
233	<	Mat3x3d hmat;
234	<	RealType chi;
235	<	RealType integralOfChiDt;
236	<	Mat3x3d eta;
237	<
238	<	currentTime = s->getTime();
232	>	char buffer[1024];
233	>
234	>	os << "    <FrameData>\n";
235	>
236	>	RealType currentTime = s->getTime();
237	>
238	>	if (isinf(currentTime) || isnan(currentTime)) {
239	>	sprintf( painCave.errMsg,
240	>	"DumpWriter detected a numerical error writing the time");
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>
245	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
246	>	os << buffer;
247	>
248	>	Mat3x3d hmat;
249		hmat = s->getHmat();
250	<	chi = s->getChi();
251	<	integralOfChiDt = s->getIntegralOfChiDt();
252	<	eta = s->getEta();
250	>
251	>	for (unsigned int i = 0; i < 3; i++) {
252	>	for (unsigned int j = 0; j < 3; j++) {
253	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
254	>	sprintf( painCave.errMsg,
255	>	"DumpWriter detected a numerical error writing the box");
256	>	painCave.isFatal = 1;
257	>	simError();
258	>	}
259	>	}
260	>	}
261
262	<	os << currentTime << ";\t"
263	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
264	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
265	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
262	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
263	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
264	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
265	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
266	>	os << buffer;
267
268	<	//write out additional parameters, such as chi and eta
268	>	pair<RealType, RealType> thermostat = s->getThermostat();
269
270	<	os << chi << "\t" << integralOfChiDt << ";\t";
270	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
271	>	isinf(thermostat.second) || isnan(thermostat.second)) {
272	>	sprintf( painCave.errMsg,
273	>	"DumpWriter detected a numerical error writing the thermostat");
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
278	>	thermostat.second);
279	>	os << buffer;
280
281	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
282	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
283	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
284	<
285	<	os << "\n";
281	>	Mat3x3d eta;
282	>	eta = s->getBarostat();
283	>
284	>	for (unsigned int i = 0; i < 3; i++) {
285	>	for (unsigned int j = 0; j < 3; j++) {
286	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
287	>	sprintf( painCave.errMsg,
288	>	"DumpWriter detected a numerical error writing the barostat");
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292	>	}
293	>	}
294	>
295	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
296	>	eta(0, 0), eta(1, 0), eta(2, 0),
297	>	eta(0, 1), eta(1, 1), eta(2, 1),
298	>	eta(0, 2), eta(1, 2), eta(2, 2));
299	>	os << buffer;
300	>
301	>	os << "    </FrameData>\n";
302		}
303
304		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
305
306	<	char tempBuffer[BUFFERSIZE];
307	<	char writeLine[BUFFERSIZE];
306	>	#ifdef IS_MPI
307	>	MPI_Status* istatus;
308	>	#endif
309
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
310		Molecule* mol;
311	<	StuntDouble* integrableObject;
311	>	StuntDouble* sd;
312		SimInfo::MoleculeIterator mi;
313		Molecule::IntegrableObjectIterator ii;
314	<
252	<	int nTotObjects;
253	<	nTotObjects = info_->getNGlobalIntegrableObjects();
314	>	RigidBody::AtomIterator ai;
315
316		#ifndef IS_MPI
317	+	os << "  <Snapshot>\n";
318	+
319	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320
321	+	os << "    <StuntDoubles>\n";
322	+	for (mol = info_->beginMolecule(mi); mol != NULL;
323	+	mol = info_->nextMolecule(mi)) {
324	+
325	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
326	+	sd = mol->nextIntegrableObject(ii)) {
327	+	os << prepareDumpLine(sd);
328	+
329	+	}
330	+	}
331	+	os << "    </StuntDoubles>\n";
332
333	<	os << nTotObjects << "\n";
334	<
335	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
333	>	if (doSiteData_) {
334	>	os << "    <SiteData>\n";
335	>	for (mol = info_->beginMolecule(mi); mol != NULL;
336	>	mol = info_->nextMolecule(mi)) {
337	>
338	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
339	>	sd = mol->nextIntegrableObject(ii)) {
340
341	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
341	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
342	>	// do one for the IO itself
343	>	os << prepareSiteLine(sd, ioIndex, 0);
344
345	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
346	<	integrableObject = mol->nextIntegrableObject(ii)) {
347	<
345	>	if (sd->isRigidBody()) {
346	>
347	>	RigidBody* rb = static_cast<RigidBody*>(sd);
348	>	int siteIndex = 0;
349	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
350	>	atom = rb->nextAtom(ai)) {
351	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
352	>	siteIndex++;
353	>	}
354	>	}
355	>	}
356	>	}
357	>	os << "    </SiteData>\n";
358	>	}
359	>	os << "  </Snapshot>\n";
360
361	<	pos = integrableObject->getPos();
362	<	vel = integrableObject->getVel();
361	>	os.flush();
362	>	#else
363
364	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
365	<	integrableObject->getType().c_str(),
366	<	pos[0], pos[1], pos[2],
274	<	vel[0], vel[1], vel[2]);
364	>	const int masterNode = 0;
365	>	int worldRank;
366	>	int nProc;
367
368	<	strcpy(writeLine, tempBuffer);
368	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
369	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
370
278	–	if (integrableObject->isDirectional()) {
279	–	q = integrableObject->getQ();
280	–	ji = integrableObject->getJ();
371
372	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
373	<	q[0], q[1], q[2], q[3],
374	<	ji[0], ji[1], ji[2]);
375	<	strcat(writeLine, tempBuffer);
376	<	} else {
377	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
288	<	}
372	>	if (worldRank == masterNode) {
373	>	os << "  <Snapshot>\n";
374	>	writeFrameProperties(os,
375	>	info_->getSnapshotManager()->getCurrentSnapshot());
376	>	os << "    <StuntDoubles>\n";
377	>	}
378
379	<	if (needForceVector_) {
380	<	frc = integrableObject->getFrc();
381	<	trq = integrableObject->getTrq();
382	<
383	<	sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
384	<	frc[0], frc[1], frc[2],
385	<	trq[0], trq[1], trq[2]);
297	<	strcat(writeLine, tempBuffer);
298	<	}
299	<
300	<	strcat(writeLine, "\n");
301	<	os << writeLine;
302	<
379	>	//every node prepares the dump lines for integrable objects belong to itself
380	>	std::string buffer;
381	>	for (mol = info_->beginMolecule(mi); mol != NULL;
382	>	mol = info_->nextMolecule(mi)) {
383	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
384	>	sd = mol->nextIntegrableObject(ii)) {
385	>	buffer += prepareDumpLine(sd);
386		}
387		}
305	–
306	–	os.flush();
307	–	#else // is_mpi
308	–	/*********************************************************************
309	–	* Documentation?  You want DOCUMENTATION?
310	–	*
311	–	* Why all the potatoes below?
312	–	*
313	–	* To make a long story short, the original version of DumpWriter
314	–	* worked in the most inefficient way possible.  Node 0 would
315	–	* poke each of the node for an individual atom's formatted data
316	–	* as node 0 worked its way down the global index. This was particularly
317	–	* inefficient since the method blocked all processors at every atom
318	–	* (and did it twice!).
319	–	*
320	–	* An intermediate version of DumpWriter could be described from Node
321	–	* zero's perspective as follows:
322	–	*
323	–	*  1) Have 100 of your friends stand in a circle.
324	–	*  2) When you say go, have all of them start tossing potatoes at
325	–	*     you (one at a time).
326	–	*  3) Catch the potatoes.
327	–	*
328	–	* It was an improvement, but MPI has buffers and caches that could
329	–	* best be described in this analogy as "potato nets", so there's no
330	–	* need to block the processors atom-by-atom.
331	–	*
332	–	* This new and improved DumpWriter works in an even more efficient
333	–	* way:
334	–	*
335	–	*  1) Have 100 of your friend stand in a circle.
336	–	*  2) When you say go, have them start tossing 5-pound bags of
337	–	*     potatoes at you.
338	–	*  3) Once you've caught a friend's bag of potatoes,
339	–	*     toss them a spud to let them know they can toss another bag.
340	–	*
341	–	* How's THAT for documentation?
342	–	*
343	–	*********************************************************************/
344	–	const int masterNode = 0;
345	–
346	–	int * potatoes;
347	–	int myPotato;
348	–	int nProc;
349	–	int which_node;
350	–	RealType atomData[19];
351	–	int isDirectional;
352	–	char MPIatomTypeString[MINIBUFFERSIZE];
353	–	int msgLen; // the length of message actually recieved at master nodes
354	–	int haveError;
355	–	MPI_Status istatus;
356	–	int nCurObj;
388
389	<	// code to find maximum tag value
390	<	int * tagub;
391	<	int flag;
392	<	int MAXTAG;
393	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
389	>	if (worldRank == masterNode) {
390	>	os << buffer;
391	>
392	>	for (int i = 1; i < nProc; ++i) {
393	>	// tell processor i to start sending us data:
394	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
395
396	<	if (flag) {
397	<	MAXTAG = *tagub;
396	>	// receive the length of the string buffer that was
397	>	// prepared by processor i:
398	>	int recvLength;
399	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
400	>	istatus);
401	>
402	>	// create a buffer to receive the data
403	>	char* recvBuffer = new char[recvLength];
404	>	if (recvBuffer == NULL) {
405	>	} else {
406	>	// receive the data:
407	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
408	>	MPI_ANY_TAG, MPI_COMM_WORLD, istatus);
409	>	// send it to the file:
410	>	os << recvBuffer;
411	>	// get rid of the receive buffer:
412	>	delete [] recvBuffer;
413	>	}
414	>	}
415		} else {
416	<	MAXTAG = 32767;
417	<	}
416	>	int sendBufferLength = buffer.size() + 1;
417	>	int myturn = 0;
418	>	for (int i = 1; i < nProc; ++i){
419	>	// wait for the master node to call our number:
420	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
421	>	if (myturn == worldRank){
422	>	// send the length of our buffer:
423	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
424
425	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
425	>	// send our buffer:
426	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
427	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
428
429	<	// Node 0 needs a list of the magic potatoes for each processor;
429	>	}
430	>	}
431	>	}
432	>
433	>	if (worldRank == masterNode) {
434	>	os << "    </StuntDoubles>\n";
435	>	}
436
437	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
438	<	potatoes = new int[nProc];
437	>	if (doSiteData_) {
438	>	if (worldRank == masterNode) {
439	>	os << "    <SiteData>\n";
440	>	}
441	>	buffer.clear();
442	>	for (mol = info_->beginMolecule(mi); mol != NULL;
443	>	mol = info_->nextMolecule(mi)) {
444	>
445	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
446	>	sd = mol->nextIntegrableObject(ii)) {
447	>
448	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
449	>	// do one for the IO itself
450	>	buffer += prepareSiteLine(sd, ioIndex, 0);
451
452	<	//write out the comment lines
453	<	for(int i = 0; i < nProc; i++) {
454	<	potatoes[i] = 0;
452	>	if (sd->isRigidBody()) {
453	>
454	>	RigidBody* rb = static_cast<RigidBody*>(sd);
455	>	int siteIndex = 0;
456	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
457	>	atom = rb->nextAtom(ai)) {
458	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
459	>	siteIndex++;
460	>	}
461	>	}
462	>	}
463		}
464
465	+	if (worldRank == masterNode) {
466	+	os << buffer;
467	+
468	+	for (int i = 1; i < nProc; ++i) {
469	+
470	+	// tell processor i to start sending us data:
471	+	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
472	+
473	+	// receive the length of the string buffer that was
474	+	// prepared by processor i:
475	+	int recvLength;
476	+	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
477	+	istatus);
478	+
479	+	// create a buffer to receive the data
480	+	char* recvBuffer = new char[recvLength];
481	+	if (recvBuffer == NULL) {
482	+	} else {
483	+	// receive the data:
484	+	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
485	+	MPI_ANY_TAG, MPI_COMM_WORLD, istatus);
486	+	// send it to the file:
487	+	os << recvBuffer;
488	+	// get rid of the receive buffer:
489	+	delete [] recvBuffer;
490	+	}
491	+	}
492	+	} else {
493	+	int sendBufferLength = buffer.size() + 1;
494	+	int myturn = 0;
495	+	for (int i = 1; i < nProc; ++i){
496	+	// wait for the master node to call our number:
497	+	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
498	+	if (myturn == worldRank){
499	+	// send the length of our buffer:
500	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
501	+	// send our buffer:
502	+	MPI_Send((void *)buffer.c_str(), sendBufferLength,
503	+	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
504	+	}
505	+	}
506	+	}
507	+
508	+	if (worldRank == masterNode) {
509	+	os << "    </SiteData>\n";
510	+	}
511	+	}
512	+
513	+	if (worldRank == masterNode) {
514	+	os << "  </Snapshot>\n";
515	+	os.flush();
516	+	}
517	+
518	+	#endif // is_mpi
519	+
520	+	}
521
522	<	os << nTotObjects << "\n";
523	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
522	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
523	>
524	>	int index = sd->getGlobalIntegrableObjectIndex();
525	>	std::string type("pv");
526	>	std::string line;
527	>	char tempBuffer[4096];
528
529	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
529	>	Vector3d pos;
530	>	Vector3d vel;
531	>	pos = sd->getPos();
532
533	<	// Get the Node number which has this atom;
533	>	if (isinf(pos[0]) || isnan(pos[0]) ||
534	>	isinf(pos[1]) || isnan(pos[1]) ||
535	>	isinf(pos[2]) || isnan(pos[2]) ) {
536	>	sprintf( painCave.errMsg,
537	>	"DumpWriter detected a numerical error writing the position"
538	>	" for object %d", index);
539	>	painCave.isFatal = 1;
540	>	simError();
541	>	}
542
543	<	which_node = info_->getMolToProc(i);
543	>	vel = sd->getVel();
544
545	<	if (which_node != masterNode) { //current molecule is in slave node
546	<	if (potatoes[which_node] + 1 >= MAXTAG) {
547	<	// The potato was going to exceed the maximum value,
548	<	// so wrap this processor potato back to 0:
545	>	if (isinf(vel[0]) || isnan(vel[0]) ||
546	>	isinf(vel[1]) || isnan(vel[1]) ||
547	>	isinf(vel[2]) || isnan(vel[2]) ) {
548	>	sprintf( painCave.errMsg,
549	>	"DumpWriter detected a numerical error writing the velocity"
550	>	" for object %d", index);
551	>	painCave.isFatal = 1;
552	>	simError();
553	>	}
554
555	<	potatoes[which_node] = 0;
556	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
557	<	MPI_COMM_WORLD);
558	<	}
555	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
556	>	pos[0], pos[1], pos[2],
557	>	vel[0], vel[1], vel[2]);
558	>	line += tempBuffer;
559
560	<	myPotato = potatoes[which_node];
560	>	if (sd->isDirectional()) {
561	>	type += "qj";
562	>	Quat4d q;
563	>	Vector3d ji;
564	>	q = sd->getQ();
565
566	<	//recieve the number of integrableObject in current molecule
567	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
568	<	MPI_COMM_WORLD, &istatus);
569	<	myPotato++;
566	>	if (isinf(q[0]) || isnan(q[0]) ||
567	>	isinf(q[1]) || isnan(q[1]) ||
568	>	isinf(q[2]) || isnan(q[2]) ||
569	>	isinf(q[3]) || isnan(q[3]) ) {
570	>	sprintf( painCave.errMsg,
571	>	"DumpWriter detected a numerical error writing the quaternion"
572	>	" for object %d", index);
573	>	painCave.isFatal = 1;
574	>	simError();
575	>	}
576
577	<	for(int l = 0; l < nCurObj; l++) {
410	<	if (potatoes[which_node] + 2 >= MAXTAG) {
411	<	// The potato was going to exceed the maximum value,
412	<	// so wrap this processor potato back to 0:
577	>	ji = sd->getJ();
578
579	<	potatoes[which_node] = 0;
580	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
581	<	0, MPI_COMM_WORLD);
582	<	}
579	>	if (isinf(ji[0]) || isnan(ji[0]) ||
580	>	isinf(ji[1]) || isnan(ji[1]) ||
581	>	isinf(ji[2]) || isnan(ji[2]) ) {
582	>	sprintf( painCave.errMsg,
583	>	"DumpWriter detected a numerical error writing the angular"
584	>	" momentum for object %d", index);
585	>	painCave.isFatal = 1;
586	>	simError();
587	>	}
588
589	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
590	<	which_node, myPotato, MPI_COMM_WORLD,
591	<	&istatus);
589	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
590	>	q[0], q[1], q[2], q[3],
591	>	ji[0], ji[1], ji[2]);
592	>	line += tempBuffer;
593	>	}
594
595	<	myPotato++;
595	>	if (needForceVector_) {
596	>	type += "f";
597	>	Vector3d frc = sd->getFrc();
598	>	if (isinf(frc[0]) || isnan(frc[0]) ||
599	>	isinf(frc[1]) || isnan(frc[1]) ||
600	>	isinf(frc[2]) || isnan(frc[2]) ) {
601	>	sprintf( painCave.errMsg,
602	>	"DumpWriter detected a numerical error writing the force"
603	>	" for object %d", index);
604	>	painCave.isFatal = 1;
605	>	simError();
606	>	}
607	>	sprintf(tempBuffer, " %13e %13e %13e",
608	>	frc[0], frc[1], frc[2]);
609	>	line += tempBuffer;
610	>
611	>	if (sd->isDirectional()) {
612	>	type += "t";
613	>	Vector3d trq = sd->getTrq();
614	>	if (isinf(trq[0]) || isnan(trq[0]) ||
615	>	isinf(trq[1]) || isnan(trq[1]) ||
616	>	isinf(trq[2]) || isnan(trq[2]) ) {
617	>	sprintf( painCave.errMsg,
618	>	"DumpWriter detected a numerical error writing the torque"
619	>	" for object %d", index);
620	>	painCave.isFatal = 1;
621	>	simError();
622	>	}
623	>	sprintf(tempBuffer, " %13e %13e %13e",
624	>	trq[0], trq[1], trq[2]);
625	>	line += tempBuffer;
626	>	}
627	>	}
628
629	<	MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
630	<	MPI_COMM_WORLD, &istatus);
631	<	myPotato++;
629	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
630	>	return std::string(tempBuffer);
631	>	}
632
633	<	MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
633	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
634	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
635
636	<	if (msgLen == 13 || msgLen == 19)
637	<	isDirectional = 1;
638	<	else
639	<	isDirectional = 0;
636	>	std::string id;
637	>	std::string type;
638	>	std::string line;
639	>	char tempBuffer[4096];
640
641	<	// If we've survived to here, format the line:
641	>	if (sd->isRigidBody()) {
642	>	sprintf(tempBuffer, "%10d           ", ioIndex);
643	>	id = std::string(tempBuffer);
644	>	} else {
645	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
646	>	id = std::string(tempBuffer);
647	>	}
648	>
649	>	if (needFlucQ_) {
650	>	if (storageLayout & DataStorage::dslFlucQPosition) {
651	>	type += "c";
652	>	RealType fqPos = sd->getFlucQPos();
653	>	if (isinf(fqPos) || isnan(fqPos) ) {
654	>	sprintf( painCave.errMsg,
655	>	"DumpWriter detected a numerical error writing the"
656	>	" fluctuating charge for object %s", id.c_str());
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660	>	sprintf(tempBuffer, " %13e ", fqPos);
661	>	line += tempBuffer;
662	>	}
663
664	<	if (!isDirectional) {
665	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
666	<	MPIatomTypeString, atomData[0],
667	<	atomData[1], atomData[2],
668	<	atomData[3], atomData[4],
669	<	atomData[5]);
664	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
665	>	type += "w";
666	>	RealType fqVel = sd->getFlucQVel();
667	>	if (isinf(fqVel) || isnan(fqVel) ) {
668	>	sprintf( painCave.errMsg,
669	>	"DumpWriter detected a numerical error writing the"
670	>	" fluctuating charge velocity for object %s", id.c_str());
671	>	painCave.isFatal = 1;
672	>	simError();
673	>	}
674	>	sprintf(tempBuffer, " %13e ", fqVel);
675	>	line += tempBuffer;
676	>	}
677
678	<	strcat(writeLine,
679	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
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",
683	<	MPIatomTypeString,
684	<	atomData[0],
685	<	atomData[1],
686	<	atomData[2],
687	<	atomData[3],
688	<	atomData[4],
689	<	atomData[5],
690	<	atomData[6],
691	<	atomData[7],
692	<	atomData[8],
693	<	atomData[9],
694	<	atomData[10],
695	<	atomData[11],
696	<	atomData[12]);
697	<	}
698	<
699	<	if (needForceVector_) {
700	<	if (!isDirectional) {
701	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
702	<	atomData[6],
703	<	atomData[7],
704	<	atomData[8],
705	<	atomData[9],
706	<	atomData[10],
707	<	atomData[11]);
708	<	} else {
709	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
710	<	atomData[13],
711	<	atomData[14],
712	<	atomData[15],
480	<	atomData[16],
481	<	atomData[17],
482	<	atomData[18]);
483	<	}
484	<	}
678	>	if (needForceVector_) {
679	>	if (storageLayout & DataStorage::dslFlucQForce) {
680	>	type += "g";
681	>	RealType fqFrc = sd->getFlucQFrc();
682	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
683	>	sprintf( painCave.errMsg,
684	>	"DumpWriter detected a numerical error writing the"
685	>	" fluctuating charge force for object %s", id.c_str());
686	>	painCave.isFatal = 1;
687	>	simError();
688	>	}
689	>	sprintf(tempBuffer, " %13e ", fqFrc);
690	>	line += tempBuffer;
691	>	}
692	>	}
693	>	}
694	>
695	>	if (needElectricField_) {
696	>	if (storageLayout & DataStorage::dslElectricField) {
697	>	type += "e";
698	>	Vector3d eField= sd->getElectricField();
699	>	if (isinf(eField[0]) || isnan(eField[0]) ||
700	>	isinf(eField[1]) || isnan(eField[1]) ||
701	>	isinf(eField[2]) || isnan(eField[2]) ) {
702	>	sprintf( painCave.errMsg,
703	>	"DumpWriter detected a numerical error writing the electric"
704	>	" field for object %s", id.c_str());
705	>	painCave.isFatal = 1;
706	>	simError();
707	>	}
708	>	sprintf(tempBuffer, " %13e %13e %13e",
709	>	eField[0], eField[1], eField[2]);
710	>	line += tempBuffer;
711	>	}
712	>	}
713
486	–	sprintf(writeLine, "\n");
487	–	os << writeLine;
714
715	<	} // end for(int l =0)
716	<
717	<	potatoes[which_node] = myPotato;
718	<	} else { //master node has current molecule
719	<
720	<	mol = info_->getMoleculeByGlobalIndex(i);
721	<
722	<	if (mol == NULL) {
723	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
724	<	painCave.isFatal = 1;
725	<	simError();
726	<	}
727	<
502	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
503	<	integrableObject = mol->nextIntegrableObject(ii)) {
504	<
505	<	pos = integrableObject->getPos();
506	<	vel = integrableObject->getVel();
507	<
508	<	atomData[0] = pos[0];
509	<	atomData[1] = pos[1];
510	<	atomData[2] = pos[2];
511	<
512	<	atomData[3] = vel[0];
513	<	atomData[4] = vel[1];
514	<	atomData[5] = vel[2];
515	<
516	<	isDirectional = 0;
517	<
518	<	if (integrableObject->isDirectional()) {
519	<	isDirectional = 1;
520	<
521	<	q = integrableObject->getQ();
522	<	ji = integrableObject->getJ();
523	<
524	<	for(int j = 0; j < 6; j++) {
525	<	atomData[j] = atomData[j];
526	<	}
527	<
528	<	atomData[6] = q[0];
529	<	atomData[7] = q[1];
530	<	atomData[8] = q[2];
531	<	atomData[9] = q[3];
532	<
533	<	atomData[10] = ji[0];
534	<	atomData[11] = ji[1];
535	<	atomData[12] = ji[2];
536	<	}
537	<
538	<	if (needForceVector_) {
539	<	frc = integrableObject->getFrc();
540	<	trq = integrableObject->getTrq();
541	<
542	<	if (!isDirectional) {
543	<	atomData[6] = frc[0];
544	<	atomData[7] = frc[1];
545	<	atomData[8] = frc[2];
546	<	atomData[9] = trq[0];
547	<	atomData[10] = trq[1];
548	<	atomData[11] = trq[2];
549	<	} else {
550	<	atomData[13] = frc[0];
551	<	atomData[14] = frc[1];
552	<	atomData[15] = frc[2];
553	<	atomData[16] = trq[0];
554	<	atomData[17] = trq[1];
555	<	atomData[18] = trq[2];
556	<	}
557	<	}
558	<
559	<	// If we've survived to here, format the line:
560	<
561	<	if (!isDirectional) {
562	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563	<	integrableObject->getType().c_str(), atomData[0],
564	<	atomData[1], atomData[2],
565	<	atomData[3], atomData[4],
566	<	atomData[5]);
567	<
568	<	strcat(writeLine,
569	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
570	<	} else {
571	<	sprintf(writeLine,
572	<	"%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",
573	<	integrableObject->getType().c_str(),
574	<	atomData[0],
575	<	atomData[1],
576	<	atomData[2],
577	<	atomData[3],
578	<	atomData[4],
579	<	atomData[5],
580	<	atomData[6],
581	<	atomData[7],
582	<	atomData[8],
583	<	atomData[9],
584	<	atomData[10],
585	<	atomData[11],
586	<	atomData[12]);
587	<	}
588	<
589	<	if (needForceVector_) {
590	<	if (!isDirectional) {
591	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
592	<	atomData[6],
593	<	atomData[7],
594	<	atomData[8],
595	<	atomData[9],
596	<	atomData[10],
597	<	atomData[11]);
598	<	} else {
599	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
600	<	atomData[13],
601	<	atomData[14],
602	<	atomData[15],
603	<	atomData[16],
604	<	atomData[17],
605	<	atomData[18]);
606	<	}
607	<	}
608	<
609	<	sprintf(writeLine, "\n");
610	<	os << writeLine;
611	<
612	<	} //end for(iter = integrableObject.begin())
613	<	}
614	<	} //end for(i = 0; i < mpiSim->getNmol())
615	<
616	<	os.flush();
617	<
618	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
619	<	MPIcheckPoint();
620	<
621	<	delete [] potatoes;
622	<	} else {
623	<
624	<	// worldRank != 0, so I'm a remote node.
625	<
626	<	// Set my magic potato to 0:
627	<
628	<	myPotato = 0;
629	<
630	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
631	<
632	<	// Am I the node which has this integrableObject?
633	<	int whichNode = info_->getMolToProc(i);
634	<	if (whichNode == worldRank) {
635	<	if (myPotato + 1 >= MAXTAG) {
636	<
637	<	// The potato was going to exceed the maximum value,
638	<	// so wrap this processor potato back to 0 (and block until
639	<	// node 0 says we can go:
640	<
641	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
642	<	&istatus);
643	<	}
644	<
645	<	mol = info_->getMoleculeByGlobalIndex(i);
646	<
647	<
648	<	nCurObj = mol->getNIntegrableObjects();
649	<
650	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
651	<	myPotato++;
652	<
653	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
654	<	integrableObject = mol->nextIntegrableObject(ii)) {
655	<
656	<	if (myPotato + 2 >= MAXTAG) {
657	<
658	<	// The potato was going to exceed the maximum value,
659	<	// so wrap this processor potato back to 0 (and block until
660	<	// node 0 says we can go:
661	<
662	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
663	<	&istatus);
664	<	}
665	<
666	<	pos = integrableObject->getPos();
667	<	vel = integrableObject->getVel();
668	<
669	<	atomData[0] = pos[0];
670	<	atomData[1] = pos[1];
671	<	atomData[2] = pos[2];
672	<
673	<	atomData[3] = vel[0];
674	<	atomData[4] = vel[1];
675	<	atomData[5] = vel[2];
676	<
677	<	isDirectional = 0;
678	<
679	<	if (integrableObject->isDirectional()) {
680	<	isDirectional = 1;
681	<
682	<	q = integrableObject->getQ();
683	<	ji = integrableObject->getJ();
684	<
685	<	atomData[6] = q[0];
686	<	atomData[7] = q[1];
687	<	atomData[8] = q[2];
688	<	atomData[9] = q[3];
689	<
690	<	atomData[10] = ji[0];
691	<	atomData[11] = ji[1];
692	<	atomData[12] = ji[2];
693	<	}
694	<
695	<	if (needForceVector_) {
696	<	frc = integrableObject->getFrc();
697	<	trq = integrableObject->getTrq();
698	<
699	<	if (!isDirectional) {
700	<	atomData[6] = frc[0];
701	<	atomData[7] = frc[1];
702	<	atomData[8] = frc[2];
703	<
704	<	atomData[9] = trq[0];
705	<	atomData[10] = trq[1];
706	<	atomData[11] = trq[2];
707	<	} else {
708	<	atomData[13] = frc[0];
709	<	atomData[14] = frc[1];
710	<	atomData[15] = frc[2];
711	<
712	<	atomData[16] = trq[0];
713	<	atomData[17] = trq[1];
714	<	atomData[18] = trq[2];
715	<	}
716	<	}
717	<
718	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
719	<
720	<	// null terminate the  std::string before sending (just in case):
721	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
722	<
723	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
724	<	myPotato, MPI_COMM_WORLD);
725	<
726	<	myPotato++;
727	<
728	<	if (isDirectional && needForceVector_) {
729	<	MPI_Send(atomData, 19, MPI_REALTYPE, 0, myPotato,
730	<	MPI_COMM_WORLD);
731	<	} else if (isDirectional) {
732	<	MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
733	<	MPI_COMM_WORLD);
734	<	} else if (needForceVector_) {
735	<	MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
736	<	MPI_COMM_WORLD);
737	<	} else {
738	<	MPI_Send(atomData, 6, MPI_REALTYPE, 0, myPotato,
739	<	MPI_COMM_WORLD);
740	<	}
741	<
742	<	myPotato++;
743	<	}
744	<
745	<	}
746	<
715	>	if (needParticlePot_) {
716	>	if (storageLayout & DataStorage::dslParticlePot) {
717	>	type += "u";
718	>	RealType particlePot = sd->getParticlePot();
719	>	if (isinf(particlePot) || isnan(particlePot)) {
720	>	sprintf( painCave.errMsg,
721	>	"DumpWriter detected a numerical error writing the particle "
722	>	" potential for object %s", id.c_str());
723	>	painCave.isFatal = 1;
724	>	simError();
725	>	}
726	>	sprintf(tempBuffer, " %13e", particlePot);
727	>	line += tempBuffer;
728		}
748	–	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
749	–	MPIcheckPoint();
729		}
730	<
731	<	#endif // is_mpi
732	<
730	>
731	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
732	>	return std::string(tempBuffer);
733		}
734
735		void DumpWriter::writeDump() {
#	Line 763 | Line 742 | namespace oopse {
742		#ifdef IS_MPI
743		if (worldRank == 0) {
744		#endif // is_mpi
745	<
745	>
746		eorStream = createOStream(eorFilename_);
747
748		#ifdef IS_MPI
749		}
750	<	#endif // is_mpi
751	<
750	>	#endif
751	>
752		writeFrame(*eorStream);
753	<
753	>
754		#ifdef IS_MPI
755		if (worldRank == 0) {
756	<	#endif // is_mpi
757	<	delete eorStream;
758	<
756	>	#endif
757	>
758	>	writeClosing(*eorStream);
759	>	delete eorStream;
760	>
761		#ifdef IS_MPI
762		}
763		#endif // is_mpi
#	Line 790 | Line 771 | namespace oopse {
771		#ifdef IS_MPI
772		if (worldRank == 0) {
773		#endif // is_mpi
793	–
774		buffers.push_back(dumpFile_->rdbuf());
795	–
775		eorStream = createOStream(eorFilename_);
797	–
776		buffers.push_back(eorStream->rdbuf());
799	–
777		#ifdef IS_MPI
778		}
779		#endif // is_mpi
780
781		TeeBuf tbuf(buffers.begin(), buffers.end());
782		std::ostream os(&tbuf);
806	–
783		writeFrame(os);
784
785		#ifdef IS_MPI
786		if (worldRank == 0) {
787		#endif // is_mpi
788	<	delete eorStream;
789	<
788	>	writeClosing(*eorStream);
789	>	delete eorStream;
790		#ifdef IS_MPI
791		}
792	<	#endif // is_mpi
817	<
792	>	#endif // is_mpi
793		}
794
795	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
795	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
796
797		std::ostream* newOStream;
798	<	#ifdef HAVE_LIBZ
798	>	#ifdef HAVE_ZLIB
799		if (needCompression_) {
800	<	newOStream = new ogzstream(filename.c_str());
800	>	newOStream = new ogzstream(filename.c_str());
801		} else {
802	<	newOStream = new std::ofstream(filename.c_str());
802	>	newOStream = new std::ofstream(filename.c_str());
803		}
804		#else
805		newOStream = new std::ofstream(filename.c_str());
806		#endif
807	+	//write out MetaData first
808	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
809	+	(*newOStream) << "  <MetaData>" << std::endl;
810	+	(*newOStream) << info_->getRawMetaData();
811	+	(*newOStream) << "  </MetaData>" << std::endl;
812		return newOStream;
813	<	}
813	>	}
814
815	<	}//end namespace oopse
815	>	void DumpWriter::writeClosing(std::ostream& os) {
816	>
817	>	os << "</OpenMD>\n";
818	>	os.flush();
819	>	}
820	>
821	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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