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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 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"
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()){
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) {
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	<	}
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){
97	+
98	+	Globals* simParams = info->getSimParams();
99	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
100	+
101	+	needCompression_ = simParams->getCompressDumpFile();
102	+	needForceVector_ = simParams->getOutputForceVector();
103	+	needParticlePot_ = simParams->getOutputParticlePotential();
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) {
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	<	}
129	>	}
130
101	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	–	MPIcheckPoint();
103	–
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	+
173	+	#endif // is_mpi
174	+
175	+	}
176	+
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		}
#	Line 122 | Line 192 | namespace oopse {
192
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";
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	>	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	>	os << "    </FrameData>\n";
266		}
267
268		void DumpWriter::writeFrame(std::ostream& os) {
156	–	const int BUFFERSIZE = 2000;
157	–	const int MINIBUFFERSIZE = 100;
269
270	<	char tempBuffer[BUFFERSIZE];
271	<	char writeLine[BUFFERSIZE];
270	>	#ifdef IS_MPI
271	>	MPI_Status istatus;
272	>	#endif
273
162	–	Quat4d q;
163	–	Vector3d ji;
164	–	Vector3d pos;
165	–	Vector3d vel;
166	–
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
304	+
305		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
306	<	integrableObject = mol->nextIntegrableObject(ii)) {
307	<
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	<	pos = integrableObject->getPos();
322	<	vel = integrableObject->getVel();
321	>
322	>	for (int i = 1; i < nProc; ++i) {
323
324	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
325	<	integrableObject->getType().c_str(),
326	<	pos[0], pos[1], pos[2],
327	<	vel[0], vel[1], vel[2]);
324	>	// receive the length of the string buffer that was
325	>	// prepared by processor i
326	>
327	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
328	>	int recvLength;
329	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
330	>	char* recvBuffer = new char[recvLength];
331	>	if (recvBuffer == NULL) {
332	>	} else {
333	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
334	>	os << recvBuffer;
335	>	delete [] recvBuffer;
336	>	}
337	>	}
338	>	os << "    </StuntDoubles>\n";
339	>
340	>	os << "  </Snapshot>\n";
341	>	os.flush();
342	>	} else {
343	>	int sendBufferLength = buffer.size() + 1;
344	>	int myturn = 0;
345	>	for (int i = 1; i < nProc; ++i){
346	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
347	>	if (myturn == worldRank){
348	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
349	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
350	>	}
351	>	}
352	>	}
353
354	<	strcpy(writeLine, tempBuffer);
354	>	#endif // is_mpi
355
356	<	if (integrableObject->isDirectional()) {
199	<	q = integrableObject->getQ();
200	<	ji = integrableObject->getJ();
356	>	}
357
358	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
359	<	q[0], q[1], q[2], q[3],
360	<	ji[0], ji[1], ji[2]);
361	<	strcat(writeLine, tempBuffer);
362	<	} else {
363	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208	<	}
358	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
359	>
360	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
361	>	std::string type("pv");
362	>	std::string line;
363	>	char tempBuffer[4096];
364
365	<	os << writeLine;
365	>	Vector3d pos;
366	>	Vector3d vel;
367	>	pos = integrableObject->getPos();
368
369	<	}
369	>	if (isinf(pos[0]) || isnan(pos[0]) ||
370	>	isinf(pos[1]) || isnan(pos[1]) ||
371	>	isinf(pos[2]) || isnan(pos[2]) ) {
372	>	sprintf( painCave.errMsg,
373	>	"DumpWriter detected a numerical error writing the position"
374	>	" for object %d", index);
375	>	painCave.isFatal = 1;
376	>	simError();
377		}
378
379	<	os.flush();
216	<	#else // is_mpi
217	<	/*********************************************************************
218	<	* Documentation?  You want DOCUMENTATION?
219	<	*
220	<	* Why all the potatoes below?
221	<	*
222	<	* To make a long story short, the original version of DumpWriter
223	<	* worked in the most inefficient way possible.  Node 0 would
224	<	* poke each of the node for an individual atom's formatted data
225	<	* as node 0 worked its way down the global index. This was particularly
226	<	* inefficient since the method blocked all processors at every atom
227	<	* (and did it twice!).
228	<	*
229	<	* An intermediate version of DumpWriter could be described from Node
230	<	* zero's perspective as follows:
231	<	*
232	<	*  1) Have 100 of your friends stand in a circle.
233	<	*  2) When you say go, have all of them start tossing potatoes at
234	<	*     you (one at a time).
235	<	*  3) Catch the potatoes.
236	<	*
237	<	* It was an improvement, but MPI has buffers and caches that could
238	<	* best be described in this analogy as "potato nets", so there's no
239	<	* need to block the processors atom-by-atom.
240	<	*
241	<	* This new and improved DumpWriter works in an even more efficient
242	<	* way:
243	<	*
244	<	*  1) Have 100 of your friend stand in a circle.
245	<	*  2) When you say go, have them start tossing 5-pound bags of
246	<	*     potatoes at you.
247	<	*  3) Once you've caught a friend's bag of potatoes,
248	<	*     toss them a spud to let them know they can toss another bag.
249	<	*
250	<	* How's THAT for documentation?
251	<	*
252	<	*********************************************************************/
253	<	const int masterNode = 0;
379	>	vel = integrableObject->getVel();
380
381	<	int * potatoes;
382	<	int myPotato;
383	<	int nProc;
384	<	int which_node;
385	<	double atomData[13];
386	<	int isDirectional;
387	<	char MPIatomTypeString[MINIBUFFERSIZE];
388	<	int msgLen; // the length of message actually recieved at master nodes
263	<	int haveError;
264	<	MPI_Status istatus;
265	<	int nCurObj;
266	<
267	<	// code to find maximum tag value
268	<	int * tagub;
269	<	int flag;
270	<	int MAXTAG;
271	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
272	<
273	<	if (flag) {
274	<	MAXTAG = *tagub;
275	<	} else {
276	<	MAXTAG = 32767;
381	>	if (isinf(vel[0]) || isnan(vel[0]) ||
382	>	isinf(vel[1]) || isnan(vel[1]) ||
383	>	isinf(vel[2]) || isnan(vel[2]) ) {
384	>	sprintf( painCave.errMsg,
385	>	"DumpWriter detected a numerical error writing the velocity"
386	>	" for object %d", index);
387	>	painCave.isFatal = 1;
388	>	simError();
389		}
390
391	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
391	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
392	>	pos[0], pos[1], pos[2],
393	>	vel[0], vel[1], vel[2]);
394	>	line += tempBuffer;
395
396	<	// Node 0 needs a list of the magic potatoes for each processor;
396	>	if (integrableObject->isDirectional()) {
397	>	type += "qj";
398	>	Quat4d q;
399	>	Vector3d ji;
400	>	q = integrableObject->getQ();
401
402	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
403	<	potatoes = new int[nProc];
404	<
405	<	//write out the comment lines
406	<	for(int i = 0; i < nProc; i++) {
407	<	potatoes[i] = 0;
402	>	if (isinf(q[0]) || isnan(q[0]) ||
403	>	isinf(q[1]) || isnan(q[1]) ||
404	>	isinf(q[2]) || isnan(q[2]) ||
405	>	isinf(q[3]) || isnan(q[3]) ) {
406	>	sprintf( painCave.errMsg,
407	>	"DumpWriter detected a numerical error writing the quaternion"
408	>	" for object %d", index);
409	>	painCave.isFatal = 1;
410	>	simError();
411		}
412
413	+	ji = integrableObject->getJ();
414
415	<	os << nTotObjects << "\n";
416	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
415	>	if (isinf(ji[0]) || isnan(ji[0]) ||
416	>	isinf(ji[1]) || isnan(ji[1]) ||
417	>	isinf(ji[2]) || isnan(ji[2]) ) {
418	>	sprintf( painCave.errMsg,
419	>	"DumpWriter detected a numerical error writing the angular"
420	>	" momentum for object %d", index);
421	>	painCave.isFatal = 1;
422	>	simError();
423	>	}
424
425	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
425	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
426	>	q[0], q[1], q[2], q[3],
427	>	ji[0], ji[1], ji[2]);
428	>	line += tempBuffer;
429	>	}
430
431	<	// Get the Node number which has this atom;
431	>	if (needForceVector_) {
432	>	type += "f";
433	>	Vector3d frc;
434
435	<	which_node = info_->getMolToProc(i);
435	>	frc = integrableObject->getFrc();
436
437	<	if (which_node != masterNode) { //current molecule is in slave node
438	<	if (potatoes[which_node] + 1 >= MAXTAG) {
439	<	// The potato was going to exceed the maximum value,
440	<	// so wrap this processor potato back to 0:
441	<
442	<	potatoes[which_node] = 0;
443	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
444	<	MPI_COMM_WORLD);
445	<	}
446	<
447	<	myPotato = potatoes[which_node];
448	<
449	<	//recieve the number of integrableObject in current molecule
450	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
451	<	MPI_COMM_WORLD, &istatus);
452	<	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();
437	>	if (isinf(frc[0]) || isnan(frc[0]) ||
438	>	isinf(frc[1]) || isnan(frc[1]) ||
439	>	isinf(frc[2]) || isnan(frc[2]) ) {
440	>	sprintf( painCave.errMsg,
441	>	"DumpWriter detected a numerical error writing the force"
442	>	" for object %d", index);
443	>	painCave.isFatal = 1;
444	>	simError();
445	>	}
446	>	sprintf(tempBuffer, " %13e %13e %13e",
447	>	frc[0], frc[1], frc[2]);
448	>	line += tempBuffer;
449	>
450	>	if (integrableObject->isDirectional()) {
451	>	type += "t";
452	>	Vector3d trq;
453
454	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
455	<	MPIcheckPoint();
456	<
457	<	delete [] potatoes;
458	<	} else {
454	>	trq = integrableObject->getTrq();
455	>
456	>	if (isinf(trq[0]) || isnan(trq[0]) ||
457	>	isinf(trq[1]) || isnan(trq[1]) ||
458	>	isinf(trq[2]) || isnan(trq[2]) ) {
459	>	sprintf( painCave.errMsg,
460	>	"DumpWriter detected a numerical error writing the torque"
461	>	" for object %d", index);
462	>	painCave.isFatal = 1;
463	>	simError();
464	>	}
465	>
466	>	sprintf(tempBuffer, " %13e %13e %13e",
467	>	trq[0], trq[1], trq[2]);
468	>	line += tempBuffer;
469	>	}
470	>	}
471	>	if (needParticlePot_) {
472	>	type += "u";
473	>	RealType particlePot;
474
475	<	// worldRank != 0, so I'm a remote node.
475	>	particlePot = integrableObject->getParticlePot();
476
477	<	// Set my magic potato to 0:
478	<
479	<	myPotato = 0;
480	<
481	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
482	<
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	<
477	>	if (isinf(particlePot) || isnan(particlePot)) {
478	>	sprintf( painCave.errMsg,
479	>	"DumpWriter detected a numerical error writing the particle "
480	>	" potential for object %d", index);
481	>	painCave.isFatal = 1;
482	>	simError();
483		}
484	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
485	<	MPIcheckPoint();
484	>	sprintf(tempBuffer, " %13e", particlePot);
485	>	line += tempBuffer;
486		}
487	<
488	<	#endif // is_mpi
489	<
487	>
488	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
489	>	return std::string(tempBuffer);
490		}
491
492		void DumpWriter::writeDump() {
493	<	writeFrame(dumpFile_);
576	<
493	>	writeFrame(*dumpFile_);
494		}
495
496		void DumpWriter::writeEor() {
497	<	std::ofstream eorStream;
497	>	std::ostream* eorStream;
498
499		#ifdef IS_MPI
500		if (worldRank == 0) {
501		#endif // is_mpi
502
503	<	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	<	}
503	>	eorStream = createOStream(eorFilename_);
504
505		#ifdef IS_MPI
506		}
507		#endif // is_mpi
508
509	<	writeFrame(eorStream);
509	>	writeFrame(*eorStream);
510	>
511	>	#ifdef IS_MPI
512	>	if (worldRank == 0) {
513	>	#endif // is_mpi
514	>	writeClosing(*eorStream);
515	>	delete eorStream;
516	>	#ifdef IS_MPI
517	>	}
518	>	#endif // is_mpi
519	>
520		}
521
522
523		void DumpWriter::writeDumpAndEor() {
603	–	std::ofstream eorStream;
524		std::vector<std::streambuf*> buffers;
525	+	std::ostream* eorStream;
526		#ifdef IS_MPI
527		if (worldRank == 0) {
528		#endif // is_mpi
529
530	<	buffers.push_back(dumpFile_.rdbuf());
530	>	buffers.push_back(dumpFile_->rdbuf());
531
532	<	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	<	}
532	>	eorStream = createOStream(eorFilename_);
533
534	<	buffers.push_back(eorStream.rdbuf());
534	>	buffers.push_back(eorStream->rdbuf());
535
536		#ifdef IS_MPI
537		}
#	Line 626 | Line 541 | namespace oopse {
541		std::ostream os(&tbuf);
542
543		writeFrame(os);
544	+
545	+	#ifdef IS_MPI
546	+	if (worldRank == 0) {
547	+	#endif // is_mpi
548	+	writeClosing(*eorStream);
549	+	delete eorStream;
550	+	#ifdef IS_MPI
551	+	}
552	+	#endif // is_mpi
553
554		}
555
556	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
557
558	+	std::ostream* newOStream;
559	+	#ifdef HAVE_LIBZ
560	+	if (needCompression_) {
561	+	newOStream = new ogzstream(filename.c_str());
562	+	} else {
563	+	newOStream = new std::ofstream(filename.c_str());
564	+	}
565	+	#else
566	+	newOStream = new std::ofstream(filename.c_str());
567	+	#endif
568	+	//write out MetaData first
569	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
570	+	(*newOStream) << "  <MetaData>" << std::endl;
571	+	(*newOStream) << info_->getRawMetaData();
572	+	(*newOStream) << "  </MetaData>" << std::endl;
573	+	return newOStream;
574	+	}
575
576	<	}//end namespace oopse
576	>	void DumpWriter::writeClosing(std::ostream& os) {
577	>
578	>	os << "</OpenMD>\n";
579	>	os.flush();
580	>	}
581	>
582	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC

#	Line 0 | Line 1
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