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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 376 by tim, Thu Feb 24 20:55:07 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include "io/DumpWriter.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46		#include "io/basic_teebuf.hpp"
47	+	#include "io/gzstream.hpp"
48	+	#include "io/Globals.hpp"
49	+
50	+
51		#ifdef IS_MPI
52		#include <mpi.h>
53		#endif //is_mpi
54
55	<	namespace oopse {
55	>	using namespace std;
56	>	namespace OpenMD {
57
58	<	DumpWriter::DumpWriter(SimInfo* info)
59	<	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
58	>	DumpWriter::DumpWriter(SimInfo* info)
59	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
60	>
61	>	Globals* simParams = info->getSimParams();
62	>	needCompression_ = simParams->getCompressDumpFile();
63	>	needForceVector_ = simParams->getOutputForceVector();
64	>	needParticlePot_ = simParams->getOutputParticlePotential();
65	>	createDumpFile_ = true;
66	>	#ifdef HAVE_LIBZ
67	>	if (needCompression_) {
68	>	filename_ += ".gz";
69	>	eorFilename_ += ".gz";
70	>	}
71	>	#endif
72	>
73		#ifdef IS_MPI
74
75		if (worldRank == 0) {
76		#endif // is_mpi
77	+
78	+	dumpFile_ = createOStream(filename_);
79
80	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
80	>	if (!dumpFile_) {
81	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
82	>	filename_.c_str());
83	>	painCave.isFatal = 1;
84	>	simError();
85	>	}
86
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	–
87		#ifdef IS_MPI
88
89		}
90
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
91		#endif // is_mpi
92
93	<	}
93	>	}
94
95
96	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
97	<	: info_(info), filename_(filename){
96	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
97	>	: info_(info), filename_(filename){
98	>
99	>	Globals* simParams = info->getSimParams();
100	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
101	>
102	>	needCompression_ = simParams->getCompressDumpFile();
103	>	needForceVector_ = simParams->getOutputForceVector();
104	>	createDumpFile_ = true;
105	>	#ifdef HAVE_LIBZ
106	>	if (needCompression_) {
107	>	filename_ += ".gz";
108	>	eorFilename_ += ".gz";
109	>	}
110	>	#endif
111	>
112		#ifdef IS_MPI
113
114		if (worldRank == 0) {
115		#endif // is_mpi
116
117	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
118	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
117	>
118	>	dumpFile_ = createOStream(filename_);
119
120	<	if (!dumpFile_) {
121	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
122	<	filename_.c_str());
123	<	painCave.isFatal = 1;
124	<	simError();
125	<	}
120	>	if (!dumpFile_) {
121	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
122	>	filename_.c_str());
123	>	painCave.isFatal = 1;
124	>	simError();
125	>	}
126
127		#ifdef IS_MPI
128
129		}
130
131	<	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	<	MPIcheckPoint();
131	>	#endif // is_mpi
132
133	+	}
134	+
135	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
136	+	: info_(info), filename_(filename){
137	+
138	+	Globals* simParams = info->getSimParams();
139	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
140	+
141	+	needCompression_ = simParams->getCompressDumpFile();
142	+	needForceVector_ = simParams->getOutputForceVector();
143	+	needParticlePot_ = simParams->getOutputParticlePotential();
144	+
145	+	#ifdef HAVE_LIBZ
146	+	if (needCompression_) {
147	+	filename_ += ".gz";
148	+	eorFilename_ += ".gz";
149	+	}
150	+	#endif
151	+
152	+	#ifdef IS_MPI
153	+
154	+	if (worldRank == 0) {
155		#endif // is_mpi
156	+
157	+	createDumpFile_ = writeDumpFile;
158	+	if (createDumpFile_) {
159	+	dumpFile_ = createOStream(filename_);
160	+
161	+	if (!dumpFile_) {
162	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
163	+	filename_.c_str());
164	+	painCave.isFatal = 1;
165	+	simError();
166	+	}
167	+	}
168	+	#ifdef IS_MPI
169	+
170	+	}
171
172	<	}
172	>
173	>	#endif // is_mpi
174	>
175	>	}
176
177	<	DumpWriter::~DumpWriter() {
177	>	DumpWriter::~DumpWriter() {
178
179		#ifdef IS_MPI
180
181		if (worldRank == 0) {
182		#endif // is_mpi
183	<
184	<	dumpFile_.close();
185	<
183	>	if (createDumpFile_){
184	>	writeClosing(*dumpFile_);
185	>	delete dumpFile_;
186	>	}
187		#ifdef IS_MPI
188
189		}
190
191		#endif // is_mpi
192
193	<	}
193	>	}
194
195	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
195	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
196
197	<	double currentTime;
198	<	Mat3x3d hmat;
199	<	double chi;
200	<	double integralOfChiDt;
201	<	Mat3x3d eta;
197	>	char buffer[1024];
198	>
199	>	os << "    <FrameData>\n";
200	>
201	>	RealType currentTime = s->getTime();
202	>
203	>	if (isinf(currentTime) || isnan(currentTime)) {
204	>	sprintf( painCave.errMsg,
205	>	"DumpWriter detected a numerical error writing the time");
206	>	painCave.isFatal = 1;
207	>	simError();
208	>	}
209
210	<	currentTime = s->getTime();
210	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
211	>	os << buffer;
212	>
213	>	Mat3x3d hmat;
214		hmat = s->getHmat();
215	<	chi = s->getChi();
216	<	integralOfChiDt = s->getIntegralOfChiDt();
217	<	eta = s->getEta();
215	>
216	>	for (unsigned int i = 0; i < 3; i++) {
217	>	for (unsigned int j = 0; j < 3; j++) {
218	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
219	>	sprintf( painCave.errMsg,
220	>	"DumpWriter detected a numerical error writing the box");
221	>	painCave.isFatal = 1;
222	>	simError();
223	>	}
224	>	}
225	>	}
226
227	<	os << currentTime << ";\t"
228	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
229	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
230	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
227	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
228	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
229	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
230	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
231	>	os << buffer;
232
233	<	//write out additional parameters, such as chi and eta
233	>	RealType chi = s->getChi();
234	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
235	>	if (isinf(chi) || isnan(chi) ||
236	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
237	>	sprintf( painCave.errMsg,
238	>	"DumpWriter detected a numerical error writing the thermostat");
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
243	>	os << buffer;
244
245	<	os << chi << "\t" << integralOfChiDt << "\t;";
245	>	Mat3x3d eta;
246	>	eta = s->getEta();
247
248	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
249	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
250	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
251	<
252	<	os << "\n";
253	<	}
248	>	for (unsigned int i = 0; i < 3; i++) {
249	>	for (unsigned int j = 0; j < 3; j++) {
250	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
251	>	sprintf( painCave.errMsg,
252	>	"DumpWriter detected a numerical error writing the barostat");
253	>	painCave.isFatal = 1;
254	>	simError();
255	>	}
256	>	}
257	>	}
258
259	<	void DumpWriter::writeFrame(std::ostream& os) {
260	<	const int BUFFERSIZE = 2000;
261	<	const int MINIBUFFERSIZE = 100;
259	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
260	>	eta(0, 0), eta(1, 0), eta(2, 0),
261	>	eta(0, 1), eta(1, 1), eta(2, 1),
262	>	eta(0, 2), eta(1, 2), eta(2, 2));
263	>	os << buffer;
264
265	<	char tempBuffer[BUFFERSIZE];
266	<	char writeLine[BUFFERSIZE];
265	>	os << "    </FrameData>\n";
266	>	}
267
268	<	Quat4d q;
163	<	Vector3d ji;
164	<	Vector3d pos;
165	<	Vector3d vel;
268	>	void DumpWriter::writeFrame(std::ostream& os) {
269
270	+	#ifdef IS_MPI
271	+	MPI_Status istatus;
272	+	#endif
273	+
274		Molecule* mol;
275		StuntDouble* integrableObject;
276		SimInfo::MoleculeIterator mi;
277		Molecule::IntegrableObjectIterator ii;
171	–
172	–	int nTotObjects;
173	–	nTotObjects = info_->getNGlobalIntegrableObjects();
278
279		#ifndef IS_MPI
280	+	os << "  <Snapshot>\n";
281	+
282	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
283
284	+	os << "    <StuntDoubles>\n";
285	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
286
287	<	os << nTotObjects << "\n";
288	<
289	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
287	>
288	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
289	>	integrableObject = mol->nextIntegrableObject(ii)) {
290	>	os << prepareDumpLine(integrableObject);
291	>
292	>	}
293	>	}
294	>	os << "    </StuntDoubles>\n";
295	>
296	>	os << "  </Snapshot>\n";
297
298	+	os.flush();
299	+	#else
300	+	//every node prepares the dump lines for integrable objects belong to itself
301	+	std::string buffer;
302		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
303
184	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
185	–	integrableObject = mol->nextIntegrableObject(ii)) {
186	–
304
305	<	pos = integrableObject->getPos();
306	<	vel = integrableObject->getVel();
305	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
306	>	integrableObject = mol->nextIntegrableObject(ii)) {
307	>	buffer += prepareDumpLine(integrableObject);
308	>	}
309	>	}
310	>
311	>	const int masterNode = 0;
312	>	int nProc;
313	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
314	>	if (worldRank == masterNode) {
315	>	os << "  <Snapshot>\n";
316	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
317	>	os << "    <StuntDoubles>\n";
318	>
319	>	os << buffer;
320
321	<	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]);
321	>	for (int i = 1; i < nProc; ++i) {
322
323	<	strcpy(writeLine, tempBuffer);
323	>	// receive the length of the string buffer that was
324	>	// prepared by processor i
325
326	<	if (integrableObject->isDirectional()) {
327	<	q = integrableObject->getQ();
328	<	ji = integrableObject->getJ();
326	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
327	>	int recvLength;
328	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
329	>	char* recvBuffer = new char[recvLength];
330	>	if (recvBuffer == NULL) {
331	>	} else {
332	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
333	>	os << recvBuffer;
334	>	delete [] recvBuffer;
335	>	}
336	>	}
337	>	os << "    </StuntDoubles>\n";
338	>
339	>	os << "  </Snapshot>\n";
340	>	os.flush();
341	>	} else {
342	>	int sendBufferLength = buffer.size() + 1;
343	>	int myturn = 0;
344	>	for (int i = 1; i < nProc; ++i){
345	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
346	>	if (myturn == worldRank){
347	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
348	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
349	>	}
350	>	}
351	>	}
352
353	<	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	<	}
353	>	#endif // is_mpi
354
355	<	os << writeLine;
355	>	}
356
357	<	}
358	<	}
357	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
358	>
359	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
360	>	std::string type("pv");
361	>	std::string line;
362	>	char tempBuffer[4096];
363
364	<	os.flush();
365	<	#else // is_mpi
366	<	/*********************************************************************
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;
364	>	Vector3d pos;
365	>	Vector3d vel;
366	>	pos = integrableObject->getPos();
367
368	<	int * potatoes;
369	<	int myPotato;
370	<	int nProc;
371	<	int which_node;
372	<	double atomData[13];
373	<	int isDirectional;
374	<	const char * atomTypeString;
375	<	char MPIatomTypeString[MINIBUFFERSIZE];
376	<	int msgLen; // the length of message actually recieved at master nodes
264	<	int haveError;
265	<	MPI_Status istatus;
266	<	int nCurObj;
267	<
268	<	// code to find maximum tag value
269	<	int * tagub;
270	<	int flag;
271	<	int MAXTAG;
272	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
368	>	if (isinf(pos[0]) || isnan(pos[0]) ||
369	>	isinf(pos[1]) || isnan(pos[1]) ||
370	>	isinf(pos[2]) || isnan(pos[2]) ) {
371	>	sprintf( painCave.errMsg,
372	>	"DumpWriter detected a numerical error writing the position"
373	>	" for object %d", index);
374	>	painCave.isFatal = 1;
375	>	simError();
376	>	}
377
378	<	if (flag) {
379	<	MAXTAG = *tagub;
380	<	} else {
381	<	MAXTAG = 32767;
378	>	vel = integrableObject->getVel();
379	>
380	>	if (isinf(vel[0]) || isnan(vel[0]) ||
381	>	isinf(vel[1]) || isnan(vel[1]) ||
382	>	isinf(vel[2]) || isnan(vel[2]) ) {
383	>	sprintf( painCave.errMsg,
384	>	"DumpWriter detected a numerical error writing the velocity"
385	>	" for object %d", index);
386	>	painCave.isFatal = 1;
387	>	simError();
388		}
389
390	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
390	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
391	>	pos[0], pos[1], pos[2],
392	>	vel[0], vel[1], vel[2]);
393	>	line += tempBuffer;
394
395	<	// Node 0 needs a list of the magic potatoes for each processor;
395	>	if (integrableObject->isDirectional()) {
396	>	type += "qj";
397	>	Quat4d q;
398	>	Vector3d ji;
399	>	q = integrableObject->getQ();
400
401	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
402	<	potatoes = new int[nProc];
401	>	if (isinf(q[0]) || isnan(q[0]) ||
402	>	isinf(q[1]) || isnan(q[1]) ||
403	>	isinf(q[2]) || isnan(q[2]) ||
404	>	isinf(q[3]) || isnan(q[3]) ) {
405	>	sprintf( painCave.errMsg,
406	>	"DumpWriter detected a numerical error writing the quaternion"
407	>	" for object %d", index);
408	>	painCave.isFatal = 1;
409	>	simError();
410	>	}
411	>
412	>	ji = integrableObject->getJ();
413
414	<	//write out the comment lines
415	<	for(int i = 0; i < nProc; i++) {
416	<	potatoes[i] = 0;
417	<	}
414	>	if (isinf(ji[0]) || isnan(ji[0]) ||
415	>	isinf(ji[1]) || isnan(ji[1]) ||
416	>	isinf(ji[2]) || isnan(ji[2]) ) {
417	>	sprintf( painCave.errMsg,
418	>	"DumpWriter detected a numerical error writing the angular"
419	>	" momentum for object %d", index);
420	>	painCave.isFatal = 1;
421	>	simError();
422	>	}
423
424	+	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
425	+	q[0], q[1], q[2], q[3],
426	+	ji[0], ji[1], ji[2]);
427	+	line += tempBuffer;
428	+	}
429
430	<	os << nTotObjects << "\n";
431	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
430	>	if (needForceVector_) {
431	>	type += "f";
432	>	Vector3d frc;
433
434	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
434	>	frc = integrableObject->getFrc();
435
436	<	// Get the Node number which has this atom;
436	>	if (isinf(frc[0]) || isnan(frc[0]) ||
437	>	isinf(frc[1]) || isnan(frc[1]) ||
438	>	isinf(frc[2]) || isnan(frc[2]) ) {
439	>	sprintf( painCave.errMsg,
440	>	"DumpWriter detected a numerical error writing the force"
441	>	" for object %d", index);
442	>	painCave.isFatal = 1;
443	>	simError();
444	>	}
445	>	sprintf(tempBuffer, " %13e %13e %13e",
446	>	frc[0], frc[1], frc[2]);
447	>	line += tempBuffer;
448	>
449	>	if (integrableObject->isDirectional()) {
450	>	type += "t";
451	>	Vector3d trq;
452	>
453	>	trq = integrableObject->getTrq();
454	>
455	>	if (isinf(trq[0]) || isnan(trq[0]) ||
456	>	isinf(trq[1]) || isnan(trq[1]) ||
457	>	isinf(trq[2]) || isnan(trq[2]) ) {
458	>	sprintf( painCave.errMsg,
459	>	"DumpWriter detected a numerical error writing the torque"
460	>	" for object %d", index);
461	>	painCave.isFatal = 1;
462	>	simError();
463	>	}
464	>
465	>	sprintf(tempBuffer, " %13e %13e %13e",
466	>	trq[0], trq[1], trq[2]);
467	>	line += tempBuffer;
468	>	}
469	>	}
470	>	if (needParticlePot_) {
471	>	type += "u";
472	>	RealType particlePot;
473
474	<	which_node = info_->getMolToProc(i);
474	>	particlePot = integrableObject->getParticlePot();
475
476	<	if (which_node != masterNode) { //current molecule is in slave node
477	<	if (potatoes[which_node] + 1 >= MAXTAG) {
478	<	// The potato was going to exceed the maximum value,
479	<	// so wrap this processor potato back to 0:
480	<
481	<	potatoes[which_node] = 0;
482	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
483	<	MPI_COMM_WORLD);
484	<	}
311	<
312	<	myPotato = potatoes[which_node];
313	<
314	<	//recieve the number of integrableObject in current molecule
315	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
316	<	MPI_COMM_WORLD, &istatus);
317	<	myPotato++;
318	<
319	<	for(int l = 0; l < nCurObj; l++) {
320	<	if (potatoes[which_node] + 2 >= MAXTAG) {
321	<	// The potato was going to exceed the maximum value,
322	<	// so wrap this processor potato back to 0:
323	<
324	<	potatoes[which_node] = 0;
325	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
326	<	0, MPI_COMM_WORLD);
327	<	}
328	<
329	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
330	<	which_node, myPotato, MPI_COMM_WORLD,
331	<	&istatus);
332	<
333	<	atomTypeString = MPIatomTypeString;
334	<
335	<	myPotato++;
336	<
337	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
338	<	MPI_COMM_WORLD, &istatus);
339	<	myPotato++;
340	<
341	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
342	<
343	<	if (msgLen == 13)
344	<	isDirectional = 1;
345	<	else
346	<	isDirectional = 0;
347	<
348	<	// If we've survived to here, format the line:
349	<
350	<	if (!isDirectional) {
351	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
352	<	atomTypeString, atomData[0],
353	<	atomData[1], atomData[2],
354	<	atomData[3], atomData[4],
355	<	atomData[5]);
356	<
357	<	strcat(writeLine,
358	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
359	<	} else {
360	<	sprintf(writeLine,
361	<	"%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",
362	<	atomTypeString,
363	<	atomData[0],
364	<	atomData[1],
365	<	atomData[2],
366	<	atomData[3],
367	<	atomData[4],
368	<	atomData[5],
369	<	atomData[6],
370	<	atomData[7],
371	<	atomData[8],
372	<	atomData[9],
373	<	atomData[10],
374	<	atomData[11],
375	<	atomData[12]);
376	<	}
377	<
378	<	os << writeLine;
379	<
380	<	} // end for(int l =0)
381	<
382	<	potatoes[which_node] = myPotato;
383	<	} else { //master node has current molecule
384	<
385	<	mol = info_->getMoleculeByGlobalIndex(i);
386	<
387	<	if (mol == NULL) {
388	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
389	<	painCave.isFatal = 1;
390	<	simError();
391	<	}
392	<
393	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
394	<	integrableObject = mol->nextIntegrableObject(ii)) {
395	<
396	<	atomTypeString = integrableObject->getType().c_str();
397	<
398	<	pos = integrableObject->getPos();
399	<	vel = integrableObject->getVel();
400	<
401	<	atomData[0] = pos[0];
402	<	atomData[1] = pos[1];
403	<	atomData[2] = pos[2];
404	<
405	<	atomData[3] = vel[0];
406	<	atomData[4] = vel[1];
407	<	atomData[5] = vel[2];
408	<
409	<	isDirectional = 0;
410	<
411	<	if (integrableObject->isDirectional()) {
412	<	isDirectional = 1;
413	<
414	<	q = integrableObject->getQ();
415	<	ji = integrableObject->getJ();
416	<
417	<	for(int j = 0; j < 6; j++) {
418	<	atomData[j] = atomData[j];
419	<	}
420	<
421	<	atomData[6] = q[0];
422	<	atomData[7] = q[1];
423	<	atomData[8] = q[2];
424	<	atomData[9] = q[3];
425	<
426	<	atomData[10] = ji[0];
427	<	atomData[11] = ji[1];
428	<	atomData[12] = ji[2];
429	<	}
430	<
431	<	// If we've survived to here, format the line:
432	<
433	<	if (!isDirectional) {
434	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
435	<	atomTypeString, atomData[0],
436	<	atomData[1], atomData[2],
437	<	atomData[3], atomData[4],
438	<	atomData[5]);
439	<
440	<	strcat(writeLine,
441	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
442	<	} else {
443	<	sprintf(writeLine,
444	<	"%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",
445	<	atomTypeString,
446	<	atomData[0],
447	<	atomData[1],
448	<	atomData[2],
449	<	atomData[3],
450	<	atomData[4],
451	<	atomData[5],
452	<	atomData[6],
453	<	atomData[7],
454	<	atomData[8],
455	<	atomData[9],
456	<	atomData[10],
457	<	atomData[11],
458	<	atomData[12]);
459	<	}
460	<
461	<
462	<	os << writeLine;
463	<
464	<	} //end for(iter = integrableObject.begin())
465	<	}
466	<	} //end for(i = 0; i < mpiSim->getNmol())
467	<
468	<	os.flush();
469	<
470	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
471	<	MPIcheckPoint();
472	<
473	<	delete [] potatoes;
474	<	} else {
475	<
476	<	// worldRank != 0, so I'm a remote node.
477	<
478	<	// Set my magic potato to 0:
479	<
480	<	myPotato = 0;
481	<
482	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
483	<
484	<	// Am I the node which has this integrableObject?
485	<	int whichNode = info_->getMolToProc(i);
486	<	if (whichNode == worldRank) {
487	<	if (myPotato + 1 >= MAXTAG) {
488	<
489	<	// The potato was going to exceed the maximum value,
490	<	// so wrap this processor potato back to 0 (and block until
491	<	// node 0 says we can go:
492	<
493	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
494	<	&istatus);
495	<	}
496	<
497	<	mol = info_->getMoleculeByGlobalIndex(i);
498	<
499	<
500	<	nCurObj = mol->getNIntegrableObjects();
501	<
502	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
503	<	myPotato++;
504	<
505	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
506	<	integrableObject = mol->nextIntegrableObject(ii)) {
507	<
508	<	if (myPotato + 2 >= MAXTAG) {
509	<
510	<	// The potato was going to exceed the maximum value,
511	<	// so wrap this processor potato back to 0 (and block until
512	<	// node 0 says we can go:
513	<
514	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
515	<	&istatus);
516	<	}
517	<
518	<	atomTypeString = integrableObject->getType().c_str();
519	<
520	<	pos = integrableObject->getPos();
521	<	vel = integrableObject->getVel();
522	<
523	<	atomData[0] = pos[0];
524	<	atomData[1] = pos[1];
525	<	atomData[2] = pos[2];
526	<
527	<	atomData[3] = vel[0];
528	<	atomData[4] = vel[1];
529	<	atomData[5] = vel[2];
530	<
531	<	isDirectional = 0;
532	<
533	<	if (integrableObject->isDirectional()) {
534	<	isDirectional = 1;
535	<
536	<	q = integrableObject->getQ();
537	<	ji = integrableObject->getJ();
538	<
539	<	atomData[6] = q[0];
540	<	atomData[7] = q[1];
541	<	atomData[8] = q[2];
542	<	atomData[9] = q[3];
543	<
544	<	atomData[10] = ji[0];
545	<	atomData[11] = ji[1];
546	<	atomData[12] = ji[2];
547	<	}
548	<
549	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
550	<
551	<	// null terminate the  std::string before sending (just in case):
552	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
553	<
554	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
555	<	myPotato, MPI_COMM_WORLD);
556	<
557	<	myPotato++;
558	<
559	<	if (isDirectional) {
560	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
561	<	MPI_COMM_WORLD);
562	<	} else {
563	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
564	<	MPI_COMM_WORLD);
565	<	}
566	<
567	<	myPotato++;
568	<	}
569	<
570	<	}
571	<
572	<	}
573	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
574	<	MPIcheckPoint();
476	>	if (isinf(particlePot) || isnan(particlePot)) {
477	>	sprintf( painCave.errMsg,
478	>	"DumpWriter detected a numerical error writing the particle "
479	>	" potential for object %d", index);
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	}
483	>	sprintf(tempBuffer, " %13e", particlePot);
484	>	line += tempBuffer;
485		}
486	+
487	+	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
488	+	return std::string(tempBuffer);
489	+	}
490
491	<	#endif // is_mpi
491	>	void DumpWriter::writeDump() {
492	>	writeFrame(*dumpFile_);
493	>	}
494
495	<	}
496	<
581	<	void DumpWriter::writeDump() {
582	<	writeFrame(dumpFile_);
583	<
584	<	}
585	<
586	<	void DumpWriter::writeEor() {
587	<	std::ofstream eorStream;
495	>	void DumpWriter::writeEor() {
496	>	std::ostream* eorStream;
497
498		#ifdef IS_MPI
499		if (worldRank == 0) {
500		#endif // is_mpi
501
502	<	eorStream.open(eorFilename_.c_str());
594	<	if (!eorStream.is_open()) {
595	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
596	<	eorFilename_.c_str());
597	<	painCave.isFatal = 1;
598	<	simError();
599	<	}
502	>	eorStream = createOStream(eorFilename_);
503
504		#ifdef IS_MPI
505		}
506		#endif // is_mpi
507
508	<	writeFrame(eorStream);
606	<	}
508	>	writeFrame(*eorStream);
509
510	+	#ifdef IS_MPI
511	+	if (worldRank == 0) {
512	+	#endif // is_mpi
513	+	writeClosing(*eorStream);
514	+	delete eorStream;
515	+	#ifdef IS_MPI
516	+	}
517	+	#endif // is_mpi
518
519	<	void DumpWriter::writeDumpAndEor() {
520	<	std::ofstream eorStream;
519	>	}
520	>
521	>
522	>	void DumpWriter::writeDumpAndEor() {
523		std::vector<std::streambuf*> buffers;
524	+	std::ostream* eorStream;
525		#ifdef IS_MPI
526		if (worldRank == 0) {
527		#endif // is_mpi
528
529	<	buffers.push_back(dumpFile_.rdbuf());
529	>	buffers.push_back(dumpFile_->rdbuf());
530
531	<	eorStream.open(eorFilename_.c_str());
619	<	if (!eorStream.is_open()) {
620	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
621	<	eorFilename_.c_str());
622	<	painCave.isFatal = 1;
623	<	simError();
624	<	}
531	>	eorStream = createOStream(eorFilename_);
532
533	<	buffers.push_back(eorStream.rdbuf());
533	>	buffers.push_back(eorStream->rdbuf());
534
535		#ifdef IS_MPI
536		}
#	Line 633 | Line 540 | void DumpWriter::writeDumpAndEor() {
540		std::ostream os(&tbuf);
541
542		writeFrame(os);
543	+
544	+	#ifdef IS_MPI
545	+	if (worldRank == 0) {
546	+	#endif // is_mpi
547	+	writeClosing(*eorStream);
548	+	delete eorStream;
549	+	#ifdef IS_MPI
550	+	}
551	+	#endif // is_mpi
552
553	<	}
553	>	}
554
555	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
556
557	+	std::ostream* newOStream;
558	+	#ifdef HAVE_LIBZ
559	+	if (needCompression_) {
560	+	newOStream = new ogzstream(filename.c_str());
561	+	} else {
562	+	newOStream = new std::ofstream(filename.c_str());
563	+	}
564	+	#else
565	+	newOStream = new std::ofstream(filename.c_str());
566	+	#endif
567	+	//write out MetaData first
568	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
569	+	(*newOStream) << "  <MetaData>" << std::endl;
570	+	(*newOStream) << info_->getRawMetaData();
571	+	(*newOStream) << "  </MetaData>" << std::endl;
572	+	return newOStream;
573	+	}
574
575	<	}//end namespace oopse
575	>	void DumpWriter::writeClosing(std::ostream& os) {
576	>
577	>	os << "</OpenMD>\n";
578	>	os.flush();
579	>	}
580	>
581	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 376 by tim, Thu Feb 24 20:55:07 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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