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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 966 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 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, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "io/DumpWriter.hpp"
#	Line 46 | Line 46
46		#include "io/gzstream.hpp"
47		#include "io/Globals.hpp"
48
49	+
50		#ifdef IS_MPI
51		#include <mpi.h>
52		#endif //is_mpi
53
54	<	namespace oopse {
54	>	using namespace std;
55	>	namespace OpenMD {
56
57		DumpWriter::DumpWriter(SimInfo* info)
58		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
#	Line 58 | Line 60 | namespace oopse {
60		Globals* simParams = info->getSimParams();
61		needCompression_ = simParams->getCompressDumpFile();
62		needForceVector_ = simParams->getOutputForceVector();
63	+	needParticlePot_ = simParams->getOutputParticlePotential();
64		createDumpFile_ = true;
65		#ifdef HAVE_LIBZ
66		if (needCompression_) {
67	<	filename_ += ".gz";
68	<	eorFilename_ += ".gz";
67	>	filename_ += ".gz";
68	>	eorFilename_ += ".gz";
69		}
70		#endif
71
72		#ifdef IS_MPI
73
74	<	if (worldRank == 0) {
74	>	if (worldRank == 0) {
75		#endif // is_mpi
73	–
76
77	<	dumpFile_ = createOStream(filename_);
77	>	dumpFile_ = createOStream(filename_);
78
79	<	if (!dumpFile_) {
80	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
81	<	filename_.c_str());
82	<	painCave.isFatal = 1;
83	<	simError();
84	<	}
79	>	if (!dumpFile_) {
80	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
81	>	filename_.c_str());
82	>	painCave.isFatal = 1;
83	>	simError();
84	>	}
85
86		#ifdef IS_MPI
87
88	<	}
88	>	}
89
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
90		#endif // is_mpi
91
92	<	}
92	>	}
93
94
95		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 104 | Line 103 | namespace oopse {
103		createDumpFile_ = true;
104		#ifdef HAVE_LIBZ
105		if (needCompression_) {
106	<	filename_ += ".gz";
107	<	eorFilename_ += ".gz";
106	>	filename_ += ".gz";
107	>	eorFilename_ += ".gz";
108		}
109		#endif
110
111		#ifdef IS_MPI
112
113	<	if (worldRank == 0) {
113	>	if (worldRank == 0) {
114		#endif // is_mpi
115
116
117	<	dumpFile_ = createOStream(filename_);
117	>	dumpFile_ = createOStream(filename_);
118
119	<	if (!dumpFile_) {
120	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
121	<	filename_.c_str());
122	<	painCave.isFatal = 1;
123	<	simError();
124	<	}
119	>	if (!dumpFile_) {
120	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
121	>	filename_.c_str());
122	>	painCave.isFatal = 1;
123	>	simError();
124	>	}
125
126		#ifdef IS_MPI
127
128	<	}
128	>	}
129
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
130		#endif // is_mpi
131
132	<	}
132	>	}
133
134		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
135	<	: info_(info), filename_(filename){
135	>	: info_(info), filename_(filename){
136
137		Globals* simParams = info->getSimParams();
138		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
139
140		needCompression_ = simParams->getCompressDumpFile();
141		needForceVector_ = simParams->getOutputForceVector();
142	+	needParticlePot_ = simParams->getOutputParticlePotential();
143
144		#ifdef HAVE_LIBZ
145		if (needCompression_) {
#	Line 170 | Line 167 | namespace oopse {
167		#ifdef IS_MPI
168
169		}
170	+
171
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
172		#endif // is_mpi
173
174		}
180	–
181	–
182	–
183	–
184	–
175
176		DumpWriter::~DumpWriter() {
177
#	Line 190 | Line 180 | namespace oopse {
180		if (worldRank == 0) {
181		#endif // is_mpi
182		if (createDumpFile_){
183	+	writeClosing(*dumpFile_);
184		delete dumpFile_;
185		}
186		#ifdef IS_MPI
#	Line 200 | Line 191 | namespace oopse {
191
192		}
193
194	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
194	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
195
196	<	RealType currentTime;
206	<	Mat3x3d hmat;
207	<	RealType chi;
208	<	RealType integralOfChiDt;
209	<	Mat3x3d eta;
210	<
211	<	currentTime = s->getTime();
212	<	hmat = s->getHmat();
213	<	chi = s->getChi();
214	<	integralOfChiDt = s->getIntegralOfChiDt();
215	<	eta = s->getEta();
216	<
217	<	os << currentTime << ";\t"
218	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
219	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
220	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
196	>	char buffer[1024];
197
198	<	//write out additional parameters, such as chi and eta
198	>	os << "    <FrameData>\n";
199
200	<	os << chi << "\t" << integralOfChiDt << ";\t";
200	>	RealType currentTime = s->getTime();
201
202	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
203	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
204	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
205	<
206	<	os << "\n";
202	>	if (isinf(currentTime) || isnan(currentTime)) {
203	>	sprintf( painCave.errMsg,
204	>	"DumpWriter detected a numerical error writing the time");
205	>	painCave.isFatal = 1;
206	>	simError();
207	>	}
208	>
209	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
210	>	os << buffer;
211	>
212	>	Mat3x3d hmat;
213	>	hmat = s->getHmat();
214	>
215	>	for (unsigned int i = 0; i < 3; i++) {
216	>	for (unsigned int j = 0; j < 3; j++) {
217	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
218	>	sprintf( painCave.errMsg,
219	>	"DumpWriter detected a numerical error writing the box");
220	>	painCave.isFatal = 1;
221	>	simError();
222	>	}
223	>	}
224	>	}
225	>
226	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
227	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
228	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
229	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
230	>	os << buffer;
231	>
232	>	RealType chi = s->getChi();
233	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
234	>	if (isinf(chi) || isnan(chi) ||
235	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
236	>	sprintf( painCave.errMsg,
237	>	"DumpWriter detected a numerical error writing the thermostat");
238	>	painCave.isFatal = 1;
239	>	simError();
240	>	}
241	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
242	>	os << buffer;
243	>
244	>	Mat3x3d eta;
245	>	eta = s->getEta();
246	>
247	>	for (unsigned int i = 0; i < 3; i++) {
248	>	for (unsigned int j = 0; j < 3; j++) {
249	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
250	>	sprintf( painCave.errMsg,
251	>	"DumpWriter detected a numerical error writing the barostat");
252	>	painCave.isFatal = 1;
253	>	simError();
254	>	}
255	>	}
256	>	}
257	>
258	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
259	>	eta(0, 0), eta(1, 0), eta(2, 0),
260	>	eta(0, 1), eta(1, 1), eta(2, 1),
261	>	eta(0, 2), eta(1, 2), eta(2, 2));
262	>	os << buffer;
263	>
264	>	os << "    </FrameData>\n";
265		}
266
267		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
268
269	<	char tempBuffer[BUFFERSIZE];
270	<	char writeLine[BUFFERSIZE];
269	>	#ifdef IS_MPI
270	>	MPI_Status istatus;
271	>	#endif
272
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
273		Molecule* mol;
274		StuntDouble* integrableObject;
275		SimInfo::MoleculeIterator mi;
276		Molecule::IntegrableObjectIterator ii;
251	–
252	–	int nTotObjects;
253	–	nTotObjects = info_->getNGlobalIntegrableObjects();
277
278		#ifndef IS_MPI
279	+	os << "  <Snapshot>\n";
280	+
281	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
282
283	+	os << "    <StuntDoubles>\n";
284	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
285
286	<	os << nTotObjects << "\n";
287	<
288	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
286	>
287	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
288	>	integrableObject = mol->nextIntegrableObject(ii)) {
289	>	os << prepareDumpLine(integrableObject);
290	>
291	>	}
292	>	}
293	>	os << "    </StuntDoubles>\n";
294	>
295	>	os << "  </Snapshot>\n";
296
297	+	os.flush();
298	+	#else
299	+	//every node prepares the dump lines for integrable objects belong to itself
300	+	std::string buffer;
301		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
302
264	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
265	–	integrableObject = mol->nextIntegrableObject(ii)) {
266	–
303
304	<	pos = integrableObject->getPos();
305	<	vel = integrableObject->getVel();
306	<
307	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
308	<	integrableObject->getType().c_str(),
309	<	pos[0], pos[1], pos[2],
310	<	vel[0], vel[1], vel[2]);
311	<
312	<	strcpy(writeLine, tempBuffer);
313	<
314	<	if (integrableObject->isDirectional()) {
315	<	q = integrableObject->getQ();
316	<	ji = integrableObject->getJ();
304	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
305	>	integrableObject = mol->nextIntegrableObject(ii)) {
306	>	buffer += prepareDumpLine(integrableObject);
307	>	}
308	>	}
309	>
310	>	const int masterNode = 0;
311	>	int nProc;
312	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
313	>	if (worldRank == masterNode) {
314	>	os << "  <Snapshot>\n";
315	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
316	>	os << "    <StuntDoubles>\n";
317	>
318	>	os << buffer;
319
320	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
283	<	q[0], q[1], q[2], q[3],
284	<	ji[0], ji[1], ji[2]);
285	<	strcat(writeLine, tempBuffer);
286	<	} else {
287	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
288	<	}
320	>	for (int i = 1; i < nProc; ++i) {
321
322	<	if (needForceVector_) {
323	<	frc = integrableObject->getFrc();
292	<	trq = integrableObject->getTrq();
293	<
294	<	sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
295	<	frc[0], frc[1], frc[2],
296	<	trq[0], trq[1], trq[2]);
297	<	strcat(writeLine, tempBuffer);
298	<	}
299	<
300	<	strcat(writeLine, "\n");
301	<	os << writeLine;
322	>	// receive the length of the string buffer that was
323	>	// prepared by processor i
324
325	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
326	+	int recvLength;
327	+	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
328	+	char* recvBuffer = new char[recvLength];
329	+	if (recvBuffer == NULL) {
330	+	} else {
331	+	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
332	+	os << recvBuffer;
333	+	delete [] recvBuffer;
334	+	}
335	+	}
336	+	os << "    </StuntDoubles>\n";
337	+
338	+	os << "  </Snapshot>\n";
339	+	os.flush();
340	+	} else {
341	+	int sendBufferLength = buffer.size() + 1;
342	+	int myturn = 0;
343	+	for (int i = 1; i < nProc; ++i){
344	+	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
345	+	if (myturn == worldRank){
346	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
347	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
348	+	}
349		}
350		}
351
352	<	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;
352	>	#endif // is_mpi
353
354	<	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;
357	<
358	<	// code to find maximum tag value
359	<	int * tagub;
360	<	int flag;
361	<	int MAXTAG;
362	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
354	>	}
355
356	<	if (flag) {
357	<	MAXTAG = *tagub;
358	<	} else {
359	<	MAXTAG = 32767;
356	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
357	>
358	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
359	>	std::string type("pv");
360	>	std::string line;
361	>	char tempBuffer[4096];
362	>
363	>	Vector3d pos;
364	>	Vector3d vel;
365	>	pos = integrableObject->getPos();
366	>
367	>	if (isinf(pos[0]) || isnan(pos[0]) ||
368	>	isinf(pos[1]) || isnan(pos[1]) ||
369	>	isinf(pos[2]) || isnan(pos[2]) ) {
370	>	sprintf( painCave.errMsg,
371	>	"DumpWriter detected a numerical error writing the position"
372	>	" for object %d", index);
373	>	painCave.isFatal = 1;
374	>	simError();
375		}
376
377	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
377	>	vel = integrableObject->getVel();
378
379	<	// Node 0 needs a list of the magic potatoes for each processor;
379	>	if (isinf(vel[0]) || isnan(vel[0]) ||
380	>	isinf(vel[1]) || isnan(vel[1]) ||
381	>	isinf(vel[2]) || isnan(vel[2]) ) {
382	>	sprintf( painCave.errMsg,
383	>	"DumpWriter detected a numerical error writing the velocity"
384	>	" for object %d", index);
385	>	painCave.isFatal = 1;
386	>	simError();
387	>	}
388
389	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
390	<	potatoes = new int[nProc];
389	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
390	>	pos[0], pos[1], pos[2],
391	>	vel[0], vel[1], vel[2]);
392	>	line += tempBuffer;
393
394	<	//write out the comment lines
395	<	for(int i = 0; i < nProc; i++) {
396	<	potatoes[i] = 0;
394	>	if (integrableObject->isDirectional()) {
395	>	type += "qj";
396	>	Quat4d q;
397	>	Vector3d ji;
398	>	q = integrableObject->getQ();
399	>
400	>	if (isinf(q[0]) || isnan(q[0]) ||
401	>	isinf(q[1]) || isnan(q[1]) ||
402	>	isinf(q[2]) || isnan(q[2]) ||
403	>	isinf(q[3]) || isnan(q[3]) ) {
404	>	sprintf( painCave.errMsg,
405	>	"DumpWriter detected a numerical error writing the quaternion"
406	>	" for object %d", index);
407	>	painCave.isFatal = 1;
408	>	simError();
409		}
410
411	+	ji = integrableObject->getJ();
412
413	<	os << nTotObjects << "\n";
414	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
413	>	if (isinf(ji[0]) || isnan(ji[0]) ||
414	>	isinf(ji[1]) || isnan(ji[1]) ||
415	>	isinf(ji[2]) || isnan(ji[2]) ) {
416	>	sprintf( painCave.errMsg,
417	>	"DumpWriter detected a numerical error writing the angular"
418	>	" momentum for object %d", index);
419	>	painCave.isFatal = 1;
420	>	simError();
421	>	}
422
423	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
423	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
424	>	q[0], q[1], q[2], q[3],
425	>	ji[0], ji[1], ji[2]);
426	>	line += tempBuffer;
427	>	}
428
429	<	// Get the Node number which has this atom;
429	>	if (needForceVector_) {
430	>	type += "f";
431	>	Vector3d frc;
432
433	<	which_node = info_->getMolToProc(i);
433	>	frc = integrableObject->getFrc();
434
435	<	if (which_node != masterNode) { //current molecule is in slave node
436	<	if (potatoes[which_node] + 1 >= MAXTAG) {
437	<	// The potato was going to exceed the maximum value,
438	<	// so wrap this processor potato back to 0:
435	>	if (isinf(frc[0]) || isnan(frc[0]) ||
436	>	isinf(frc[1]) || isnan(frc[1]) ||
437	>	isinf(frc[2]) || isnan(frc[2]) ) {
438	>	sprintf( painCave.errMsg,
439	>	"DumpWriter detected a numerical error writing the force"
440	>	" for object %d", index);
441	>	painCave.isFatal = 1;
442	>	simError();
443	>	}
444	>	sprintf(tempBuffer, " %13e %13e %13e",
445	>	frc[0], frc[1], frc[2]);
446	>	line += tempBuffer;
447	>
448	>	if (integrableObject->isDirectional()) {
449	>	type += "t";
450	>	Vector3d trq;
451	>
452	>	trq = integrableObject->getTrq();
453	>
454	>	if (isinf(trq[0]) || isnan(trq[0]) ||
455	>	isinf(trq[1]) || isnan(trq[1]) ||
456	>	isinf(trq[2]) || isnan(trq[2]) ) {
457	>	sprintf( painCave.errMsg,
458	>	"DumpWriter detected a numerical error writing the torque"
459	>	" for object %d", index);
460	>	painCave.isFatal = 1;
461	>	simError();
462	>	}
463	>
464	>	sprintf(tempBuffer, " %13e %13e %13e",
465	>	trq[0], trq[1], trq[2]);
466	>	line += tempBuffer;
467	>	}
468	>	}
469	>	if (needParticlePot_) {
470	>	type += "u";
471	>	RealType particlePot;
472
473	<	potatoes[which_node] = 0;
398	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
399	<	MPI_COMM_WORLD);
400	<	}
473	>	particlePot = integrableObject->getParticlePot();
474
475	<	myPotato = potatoes[which_node];
476	<
477	<	//recieve the number of integrableObject in current molecule
478	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
479	<	MPI_COMM_WORLD, &istatus);
480	<	myPotato++;
408	<
409	<	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:
413	<
414	<	potatoes[which_node] = 0;
415	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416	<	0, MPI_COMM_WORLD);
417	<	}
418	<
419	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
420	<	which_node, myPotato, MPI_COMM_WORLD,
421	<	&istatus);
422	<
423	<	myPotato++;
424	<
425	<	MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
426	<	MPI_COMM_WORLD, &istatus);
427	<	myPotato++;
428	<
429	<	MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
430	<
431	<	if (msgLen == 13 || msgLen == 19)
432	<	isDirectional = 1;
433	<	else
434	<	isDirectional = 0;
435	<
436	<	// If we've survived to here, format the line:
437	<
438	<	if (!isDirectional) {
439	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
440	<	MPIatomTypeString, atomData[0],
441	<	atomData[1], atomData[2],
442	<	atomData[3], atomData[4],
443	<	atomData[5]);
444	<
445	<	strcat(writeLine,
446	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
447	<	} else {
448	<	sprintf(writeLine,
449	<	"%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",
450	<	MPIatomTypeString,
451	<	atomData[0],
452	<	atomData[1],
453	<	atomData[2],
454	<	atomData[3],
455	<	atomData[4],
456	<	atomData[5],
457	<	atomData[6],
458	<	atomData[7],
459	<	atomData[8],
460	<	atomData[9],
461	<	atomData[10],
462	<	atomData[11],
463	<	atomData[12]);
464	<	}
465	<
466	<	if (needForceVector_) {
467	<	if (!isDirectional) {
468	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
469	<	atomData[6],
470	<	atomData[7],
471	<	atomData[8],
472	<	atomData[9],
473	<	atomData[10],
474	<	atomData[11]);
475	<	} else {
476	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
477	<	atomData[13],
478	<	atomData[14],
479	<	atomData[15],
480	<	atomData[16],
481	<	atomData[17],
482	<	atomData[18]);
483	<	}
484	<	}
485	<
486	<	os << writeLine << "\n";
487	<
488	<	} // end for(int l =0)
489	<
490	<	potatoes[which_node] = myPotato;
491	<	} else { //master node has current molecule
492	<
493	<	mol = info_->getMoleculeByGlobalIndex(i);
494	<
495	<	if (mol == NULL) {
496	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
497	<	painCave.isFatal = 1;
498	<	simError();
499	<	}
500	<
501	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
502	<	integrableObject = mol->nextIntegrableObject(ii)) {
503	<
504	<	pos = integrableObject->getPos();
505	<	vel = integrableObject->getVel();
506	<
507	<	atomData[0] = pos[0];
508	<	atomData[1] = pos[1];
509	<	atomData[2] = pos[2];
510	<
511	<	atomData[3] = vel[0];
512	<	atomData[4] = vel[1];
513	<	atomData[5] = vel[2];
514	<
515	<	isDirectional = 0;
516	<
517	<	if (integrableObject->isDirectional()) {
518	<	isDirectional = 1;
519	<
520	<	q = integrableObject->getQ();
521	<	ji = integrableObject->getJ();
522	<
523	<	for(int j = 0; j < 6; j++) {
524	<	atomData[j] = atomData[j];
525	<	}
526	<
527	<	atomData[6] = q[0];
528	<	atomData[7] = q[1];
529	<	atomData[8] = q[2];
530	<	atomData[9] = q[3];
531	<
532	<	atomData[10] = ji[0];
533	<	atomData[11] = ji[1];
534	<	atomData[12] = ji[2];
535	<	}
536	<
537	<	if (needForceVector_) {
538	<	frc = integrableObject->getFrc();
539	<	trq = integrableObject->getTrq();
540	<
541	<	if (!isDirectional) {
542	<	atomData[6] = frc[0];
543	<	atomData[7] = frc[1];
544	<	atomData[8] = frc[2];
545	<	atomData[9] = trq[0];
546	<	atomData[10] = trq[1];
547	<	atomData[11] = trq[2];
548	<	} else {
549	<	atomData[13] = frc[0];
550	<	atomData[14] = frc[1];
551	<	atomData[15] = frc[2];
552	<	atomData[16] = trq[0];
553	<	atomData[17] = trq[1];
554	<	atomData[18] = trq[2];
555	<	}
556	<	}
557	<
558	<	// If we've survived to here, format the line:
559	<
560	<	if (!isDirectional) {
561	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
562	<	integrableObject->getType().c_str(), atomData[0],
563	<	atomData[1], atomData[2],
564	<	atomData[3], atomData[4],
565	<	atomData[5]);
566	<
567	<	strcat(writeLine,
568	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
569	<	} else {
570	<	sprintf(writeLine,
571	<	"%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",
572	<	integrableObject->getType().c_str(),
573	<	atomData[0],
574	<	atomData[1],
575	<	atomData[2],
576	<	atomData[3],
577	<	atomData[4],
578	<	atomData[5],
579	<	atomData[6],
580	<	atomData[7],
581	<	atomData[8],
582	<	atomData[9],
583	<	atomData[10],
584	<	atomData[11],
585	<	atomData[12]);
586	<	}
587	<
588	<	if (needForceVector_) {
589	<	if (!isDirectional) {
590	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
591	<	atomData[6],
592	<	atomData[7],
593	<	atomData[8],
594	<	atomData[9],
595	<	atomData[10],
596	<	atomData[11]);
597	<	} else {
598	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
599	<	atomData[13],
600	<	atomData[14],
601	<	atomData[15],
602	<	atomData[16],
603	<	atomData[17],
604	<	atomData[18]);
605	<	}
606	<	}
607	<
608	<	os << writeLine << "\n";
609	<
610	<	} //end for(iter = integrableObject.begin())
611	<	}
612	<	} //end for(i = 0; i < mpiSim->getNmol())
613	<
614	<	os.flush();
615	<
616	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
617	<	MPIcheckPoint();
618	<
619	<	delete [] potatoes;
620	<	} else {
621	<
622	<	// worldRank != 0, so I'm a remote node.
623	<
624	<	// Set my magic potato to 0:
625	<
626	<	myPotato = 0;
627	<
628	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
629	<
630	<	// Am I the node which has this integrableObject?
631	<	int whichNode = info_->getMolToProc(i);
632	<	if (whichNode == worldRank) {
633	<	if (myPotato + 1 >= MAXTAG) {
634	<
635	<	// The potato was going to exceed the maximum value,
636	<	// so wrap this processor potato back to 0 (and block until
637	<	// node 0 says we can go:
638	<
639	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
640	<	&istatus);
641	<	}
642	<
643	<	mol = info_->getMoleculeByGlobalIndex(i);
644	<
645	<
646	<	nCurObj = mol->getNIntegrableObjects();
647	<
648	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
649	<	myPotato++;
650	<
651	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
652	<	integrableObject = mol->nextIntegrableObject(ii)) {
653	<
654	<	if (myPotato + 2 >= MAXTAG) {
655	<
656	<	// The potato was going to exceed the maximum value,
657	<	// so wrap this processor potato back to 0 (and block until
658	<	// node 0 says we can go:
659	<
660	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
661	<	&istatus);
662	<	}
663	<
664	<	pos = integrableObject->getPos();
665	<	vel = integrableObject->getVel();
666	<
667	<	atomData[0] = pos[0];
668	<	atomData[1] = pos[1];
669	<	atomData[2] = pos[2];
670	<
671	<	atomData[3] = vel[0];
672	<	atomData[4] = vel[1];
673	<	atomData[5] = vel[2];
674	<
675	<	isDirectional = 0;
676	<
677	<	if (integrableObject->isDirectional()) {
678	<	isDirectional = 1;
679	<
680	<	q = integrableObject->getQ();
681	<	ji = integrableObject->getJ();
682	<
683	<	atomData[6] = q[0];
684	<	atomData[7] = q[1];
685	<	atomData[8] = q[2];
686	<	atomData[9] = q[3];
687	<
688	<	atomData[10] = ji[0];
689	<	atomData[11] = ji[1];
690	<	atomData[12] = ji[2];
691	<	}
692	<
693	<	if (needForceVector_) {
694	<	frc = integrableObject->getFrc();
695	<	trq = integrableObject->getTrq();
696	<
697	<	if (!isDirectional) {
698	<	atomData[6] = frc[0];
699	<	atomData[7] = frc[1];
700	<	atomData[8] = frc[2];
701	<
702	<	atomData[9] = trq[0];
703	<	atomData[10] = trq[1];
704	<	atomData[11] = trq[2];
705	<	} else {
706	<	atomData[13] = frc[0];
707	<	atomData[14] = frc[1];
708	<	atomData[15] = frc[2];
709	<
710	<	atomData[16] = trq[0];
711	<	atomData[17] = trq[1];
712	<	atomData[18] = trq[2];
713	<	}
714	<	}
715	<
716	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
717	<
718	<	// null terminate the  std::string before sending (just in case):
719	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
720	<
721	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
722	<	myPotato, MPI_COMM_WORLD);
723	<
724	<	myPotato++;
725	<
726	<	if (isDirectional && needForceVector_) {
727	<	MPI_Send(atomData, 19, MPI_REALTYPE, 0, myPotato,
728	<	MPI_COMM_WORLD);
729	<	} else if (isDirectional) {
730	<	MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
731	<	MPI_COMM_WORLD);
732	<	} else if (needForceVector_) {
733	<	MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
734	<	MPI_COMM_WORLD);
735	<	} else {
736	<	MPI_Send(atomData, 6, MPI_REALTYPE, 0, myPotato,
737	<	MPI_COMM_WORLD);
738	<	}
739	<
740	<	myPotato++;
741	<	}
742	<
743	<	}
744	<
475	>	if (isinf(particlePot) || isnan(particlePot)) {
476	>	sprintf( painCave.errMsg,
477	>	"DumpWriter detected a numerical error writing the particle "
478	>	" potential for object %d", index);
479	>	painCave.isFatal = 1;
480	>	simError();
481		}
482	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
483	<	MPIcheckPoint();
482	>	sprintf(tempBuffer, " %13e", particlePot);
483	>	line += tempBuffer;
484		}
485	<
486	<	#endif // is_mpi
487	<
485	>
486	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
487	>	return std::string(tempBuffer);
488		}
489
490		void DumpWriter::writeDump() {
#	Line 773 | Line 509 | namespace oopse {
509		#ifdef IS_MPI
510		if (worldRank == 0) {
511		#endif // is_mpi
512	<	delete eorStream;
513	<
512	>	writeClosing(*eorStream);
513	>	delete eorStream;
514		#ifdef IS_MPI
515		}
516		#endif // is_mpi
#	Line 807 | Line 543 | namespace oopse {
543		#ifdef IS_MPI
544		if (worldRank == 0) {
545		#endif // is_mpi
546	<	delete eorStream;
547	<
546	>	writeClosing(*eorStream);
547	>	delete eorStream;
548		#ifdef IS_MPI
549		}
550		#endif // is_mpi
551
552		}
553
554	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
554	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
555
556		std::ostream* newOStream;
557		#ifdef HAVE_LIBZ
558		if (needCompression_) {
559	<	newOStream = new ogzstream(filename.c_str());
559	>	newOStream = new ogzstream(filename.c_str());
560		} else {
561	<	newOStream = new std::ofstream(filename.c_str());
561	>	newOStream = new std::ofstream(filename.c_str());
562		}
563		#else
564		newOStream = new std::ofstream(filename.c_str());
565		#endif
566	+	//write out MetaData first
567	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
568	+	(*newOStream) << "  <MetaData>" << std::endl;
569	+	(*newOStream) << info_->getRawMetaData();
570	+	(*newOStream) << "  </MetaData>" << std::endl;
571		return newOStream;
572	<	}
572	>	}
573
574	<	}//end namespace oopse
574	>	void DumpWriter::writeClosing(std::ostream& os) {
575	>
576	>	os << "</OpenMD>\n";
577	>	os.flush();
578	>	}
579	>
580	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 966 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

#	Line 0 | Line 1
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