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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 395 by tim, Thu Mar 3 14:40:20 2005 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.
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "io/DumpWriter.hpp"
43		#include "primitives/Molecule.hpp"
44		#include "utils/simError.h"
45		#include "io/basic_teebuf.hpp"
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()){
57	>	DumpWriter::DumpWriter(SimInfo* info)
58	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
59	>
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";
69	>	}
70	>	#endif
71	>
72		#ifdef IS_MPI
73
74		if (worldRank == 0) {
75		#endif // is_mpi
76	+
77	+	dumpFile_ = createOStream(filename_);
78
79	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
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
61	–	if (!dumpFile_) {
62	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
63	–	filename_.c_str());
64	–	painCave.isFatal = 1;
65	–	simError();
66	–	}
67	–
86		#ifdef IS_MPI
87
88		}
89
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
90		#endif // is_mpi
91
92	<	}
92	>	}
93
94
95	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
96	<	: info_(info), filename_(filename){
95	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
96	>	: info_(info), filename_(filename){
97	>
98	>	Globals* simParams = info->getSimParams();
99	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
100	>
101	>	needCompression_ = simParams->getCompressDumpFile();
102	>	needForceVector_ = simParams->getOutputForceVector();
103	>	createDumpFile_ = true;
104	>	#ifdef HAVE_LIBZ
105	>	if (needCompression_) {
106	>	filename_ += ".gz";
107	>	eorFilename_ += ".gz";
108	>	}
109	>	#endif
110	>
111		#ifdef IS_MPI
112
113		if (worldRank == 0) {
114		#endif // is_mpi
115
116	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
117	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
116	>
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		}
129
130	<	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	<	MPIcheckPoint();
130	>	#endif // is_mpi
131
132	+	}
133	+
134	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
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_) {
146	+	filename_ += ".gz";
147	+	eorFilename_ += ".gz";
148	+	}
149	+	#endif
150	+
151	+	#ifdef IS_MPI
152	+
153	+	if (worldRank == 0) {
154		#endif // is_mpi
155	+
156	+	createDumpFile_ = writeDumpFile;
157	+	if (createDumpFile_) {
158	+	dumpFile_ = createOStream(filename_);
159	+
160	+	if (!dumpFile_) {
161	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
162	+	filename_.c_str());
163	+	painCave.isFatal = 1;
164	+	simError();
165	+	}
166	+	}
167	+	#ifdef IS_MPI
168	+
169	+	}
170
171	<	}
171	>
172	>	#endif // is_mpi
173	>
174	>	}
175
176	<	DumpWriter::~DumpWriter() {
176	>	DumpWriter::~DumpWriter() {
177
178		#ifdef IS_MPI
179
180		if (worldRank == 0) {
181		#endif // is_mpi
182	<
183	<	dumpFile_.close();
184	<
182	>	if (createDumpFile_){
183	>	writeClosing(*dumpFile_);
184	>	delete dumpFile_;
185	>	}
186		#ifdef IS_MPI
187
188		}
189
190		#endif // is_mpi
191
192	<	}
192	>	}
193
194	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
194	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
195
196	<	double currentTime;
197	<	Mat3x3d hmat;
198	<	double chi;
199	<	double integralOfChiDt;
200	<	Mat3x3d eta;
196	>	char buffer[1024];
197	>
198	>	os << "    <FrameData>\n";
199	>
200	>	RealType currentTime = s->getTime();
201	>
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	<	currentTime = s->getTime();
209	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
210	>	os << buffer;
211	>
212	>	Mat3x3d hmat;
213		hmat = s->getHmat();
214	<	chi = s->getChi();
215	<	integralOfChiDt = s->getIntegralOfChiDt();
216	<	eta = s->getEta();
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	<	os << currentTime << ";\t"
227	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
228	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
229	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
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	<	//write out additional parameters, such as chi and eta
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	<	os << chi << "\t" << integralOfChiDt << "\t;";
244	>	Mat3x3d eta;
245	>	eta = s->getEta();
246
247	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
248	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
249	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
250	<
251	<	os << "\n";
252	<	}
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	<	void DumpWriter::writeFrame(std::ostream& os) {
259	<	const int BUFFERSIZE = 2000;
260	<	const int MINIBUFFERSIZE = 100;
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	<	char tempBuffer[BUFFERSIZE];
265	<	char writeLine[BUFFERSIZE];
264	>	os << "    </FrameData>\n";
265	>	}
266
267	<	Quat4d q;
163	<	Vector3d ji;
164	<	Vector3d pos;
165	<	Vector3d vel;
267	>	void DumpWriter::writeFrame(std::ostream& os) {
268
269	+	#ifdef IS_MPI
270	+	MPI_Status istatus;
271	+	#endif
272	+
273		Molecule* mol;
274		StuntDouble* integrableObject;
275		SimInfo::MoleculeIterator mi;
276		Molecule::IntegrableObjectIterator ii;
171	–
172	–	int nTotObjects;
173	–	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
184	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
185	–	integrableObject = mol->nextIntegrableObject(ii)) {
186	–
303
304	<	pos = integrableObject->getPos();
305	<	vel = integrableObject->getVel();
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, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
192	<	integrableObject->getType().c_str(),
193	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
320	>	for (int i = 1; i < nProc; ++i) {
321
322	<	strcpy(writeLine, tempBuffer);
322	>	// receive the length of the string buffer that was
323	>	// prepared by processor i
324
325	<	if (integrableObject->isDirectional()) {
326	<	q = integrableObject->getQ();
327	<	ji = integrableObject->getJ();
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	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
203	<	q[0], q[1], q[2], q[3],
204	<	ji[0], ji[1], ji[2]);
205	<	strcat(writeLine, tempBuffer);
206	<	} else {
207	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208	<	}
352	>	#endif // is_mpi
353
354	<	os << writeLine;
354	>	}
355
356	<	}
357	<	}
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	<	os.flush();
364	<	#else // is_mpi
365	<	/*********************************************************************
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;
363	>	Vector3d pos;
364	>	Vector3d vel;
365	>	pos = integrableObject->getPos();
366
367	<	int * potatoes;
368	<	int myPotato;
369	<	int nProc;
370	<	int which_node;
371	<	double atomData[13];
372	<	int isDirectional;
373	<	char MPIatomTypeString[MINIBUFFERSIZE];
374	<	int msgLen; // the length of message actually recieved at master nodes
375	<	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);
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 (flag) {
378	<	MAXTAG = *tagub;
379	<	} else {
380	<	MAXTAG = 32767;
377	>	vel = integrableObject->getVel();
378	>
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	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
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	<	// Node 0 needs a list of the magic potatoes for each processor;
394	>	if (integrableObject->isDirectional()) {
395	>	type += "qj";
396	>	Quat4d q;
397	>	Vector3d ji;
398	>	q = integrableObject->getQ();
399
400	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
401	<	potatoes = new int[nProc];
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	<	//write out the comment lines
287	<	for(int i = 0; i < nProc; i++) {
288	<	potatoes[i] = 0;
289	<	}
411	>	ji = integrableObject->getJ();
412
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	<	os << nTotObjects << "\n";
424	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
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	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
429	>	if (needForceVector_) {
430	>	type += "f";
431	>	Vector3d frc;
432
433	<	// Get the Node number which has this atom;
433	>	frc = integrableObject->getFrc();
434
435	<	which_node = info_->getMolToProc(i);
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	<	if (which_node != masterNode) { //current molecule is in slave node
302	<	if (potatoes[which_node] + 1 >= MAXTAG) {
303	<	// The potato was going to exceed the maximum value,
304	<	// so wrap this processor potato back to 0:
473	>	particlePot = integrableObject->getParticlePot();
474
475	<	potatoes[which_node] = 0;
476	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
477	<	MPI_COMM_WORLD);
478	<	}
479	<
480	<	myPotato = potatoes[which_node];
481	<
482	<	//recieve the number of integrableObject in current molecule
483	<	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);
383	<
384	<	if (mol == NULL) {
385	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<
390	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	<
393	<	pos = integrableObject->getPos();
394	<	vel = integrableObject->getVel();
395	<
396	<	atomData[0] = pos[0];
397	<	atomData[1] = pos[1];
398	<	atomData[2] = pos[2];
399	<
400	<	atomData[3] = vel[0];
401	<	atomData[4] = vel[1];
402	<	atomData[5] = vel[2];
403	<
404	<	isDirectional = 0;
405	<
406	<	if (integrableObject->isDirectional()) {
407	<	isDirectional = 1;
408	<
409	<	q = integrableObject->getQ();
410	<	ji = integrableObject->getJ();
411	<
412	<	for(int j = 0; j < 6; j++) {
413	<	atomData[j] = atomData[j];
414	<	}
415	<
416	<	atomData[6] = q[0];
417	<	atomData[7] = q[1];
418	<	atomData[8] = q[2];
419	<	atomData[9] = q[3];
420	<
421	<	atomData[10] = ji[0];
422	<	atomData[11] = ji[1];
423	<	atomData[12] = ji[2];
424	<	}
425	<
426	<	// If we've survived to here, format the line:
427	<
428	<	if (!isDirectional) {
429	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
430	<	integrableObject->getType().c_str(), atomData[0],
431	<	atomData[1], atomData[2],
432	<	atomData[3], atomData[4],
433	<	atomData[5]);
434	<
435	<	strcat(writeLine,
436	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
437	<	} else {
438	<	sprintf(writeLine,
439	<	"%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	<	}
455	<
456	<
457	<	os << writeLine;
458	<
459	<	} //end for(iter = integrableObject.begin())
460	<	}
461	<	} //end for(i = 0; i < mpiSim->getNmol())
462	<
463	<	os.flush();
464	<
465	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
466	<	MPIcheckPoint();
467	<
468	<	delete [] potatoes;
469	<	} else {
470	<
471	<	// worldRank != 0, so I'm a remote node.
472	<
473	<	// Set my magic potato to 0:
474	<
475	<	myPotato = 0;
476	<
477	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
478	<
479	<	// Am I the node which has this integrableObject?
480	<	int whichNode = info_->getMolToProc(i);
481	<	if (whichNode == worldRank) {
482	<	if (myPotato + 1 >= MAXTAG) {
483	<
484	<	// The potato was going to exceed the maximum value,
485	<	// so wrap this processor potato back to 0 (and block until
486	<	// node 0 says we can go:
487	<
488	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
489	<	&istatus);
490	<	}
491	<
492	<	mol = info_->getMoleculeByGlobalIndex(i);
493	<
494	<
495	<	nCurObj = mol->getNIntegrableObjects();
496	<
497	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
498	<	myPotato++;
499	<
500	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
501	<	integrableObject = mol->nextIntegrableObject(ii)) {
502	<
503	<	if (myPotato + 2 >= MAXTAG) {
504	<
505	<	// The potato was going to exceed the maximum value,
506	<	// so wrap this processor potato back to 0 (and block until
507	<	// node 0 says we can go:
508	<
509	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
510	<	&istatus);
511	<	}
512	<
513	<	pos = integrableObject->getPos();
514	<	vel = integrableObject->getVel();
515	<
516	<	atomData[0] = pos[0];
517	<	atomData[1] = pos[1];
518	<	atomData[2] = pos[2];
519	<
520	<	atomData[3] = vel[0];
521	<	atomData[4] = vel[1];
522	<	atomData[5] = vel[2];
523	<
524	<	isDirectional = 0;
525	<
526	<	if (integrableObject->isDirectional()) {
527	<	isDirectional = 1;
528	<
529	<	q = integrableObject->getQ();
530	<	ji = integrableObject->getJ();
531	<
532	<	atomData[6] = q[0];
533	<	atomData[7] = q[1];
534	<	atomData[8] = q[2];
535	<	atomData[9] = q[3];
536	<
537	<	atomData[10] = ji[0];
538	<	atomData[11] = ji[1];
539	<	atomData[12] = ji[2];
540	<	}
541	<
542	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
543	<
544	<	// null terminate the  std::string before sending (just in case):
545	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
546	<
547	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
548	<	myPotato, MPI_COMM_WORLD);
549	<
550	<	myPotato++;
551	<
552	<	if (isDirectional) {
553	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
554	<	MPI_COMM_WORLD);
555	<	} else {
556	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
557	<	MPI_COMM_WORLD);
558	<	}
559	<
560	<	myPotato++;
561	<	}
562	<
563	<	}
564	<
565	<	}
566	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
567	<	MPIcheckPoint();
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(tempBuffer, " %13e", particlePot);
483	>	line += tempBuffer;
484		}
485	+
486	+	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
487	+	return std::string(tempBuffer);
488	+	}
489
490	<	#endif // is_mpi
490	>	void DumpWriter::writeDump() {
491	>	writeFrame(*dumpFile_);
492	>	}
493
494	<	}
495	<
574	<	void DumpWriter::writeDump() {
575	<	writeFrame(dumpFile_);
576	<
577	<	}
578	<
579	<	void DumpWriter::writeEor() {
580	<	std::ofstream eorStream;
494	>	void DumpWriter::writeEor() {
495	>	std::ostream* eorStream;
496
497		#ifdef IS_MPI
498		if (worldRank == 0) {
499		#endif // is_mpi
500
501	<	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	<	}
501	>	eorStream = createOStream(eorFilename_);
502
503		#ifdef IS_MPI
504		}
505		#endif // is_mpi
506
507	<	writeFrame(eorStream);
599	<	}
507	>	writeFrame(*eorStream);
508
509	+	#ifdef IS_MPI
510	+	if (worldRank == 0) {
511	+	#endif // is_mpi
512	+	writeClosing(*eorStream);
513	+	delete eorStream;
514	+	#ifdef IS_MPI
515	+	}
516	+	#endif // is_mpi
517
518	<	void DumpWriter::writeDumpAndEor() {
519	<	std::ofstream eorStream;
518	>	}
519	>
520	>
521	>	void DumpWriter::writeDumpAndEor() {
522		std::vector<std::streambuf*> buffers;
523	+	std::ostream* eorStream;
524		#ifdef IS_MPI
525		if (worldRank == 0) {
526		#endif // is_mpi
527
528	<	buffers.push_back(dumpFile_.rdbuf());
528	>	buffers.push_back(dumpFile_->rdbuf());
529
530	<	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	<	}
530	>	eorStream = createOStream(eorFilename_);
531
532	<	buffers.push_back(eorStream.rdbuf());
532	>	buffers.push_back(eorStream->rdbuf());
533
534		#ifdef IS_MPI
535		}
#	Line 626 | Line 539 | void DumpWriter::writeDumpAndEor() {
539		std::ostream os(&tbuf);
540
541		writeFrame(os);
542	+
543	+	#ifdef IS_MPI
544	+	if (worldRank == 0) {
545	+	#endif // is_mpi
546	+	writeClosing(*eorStream);
547	+	delete eorStream;
548	+	#ifdef IS_MPI
549	+	}
550	+	#endif // is_mpi
551
552	<	}
552	>	}
553
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());
560	+	} else {
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	+	}
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 395 by tim, Thu Mar 3 14:40:20 2005 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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