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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1711 by gezelter, Sat May 19 02:58:35 2012 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]  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"
#	Line 46 | Line 47
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()){
#	Line 58 | Line 61 | namespace oopse {
61		Globals* simParams = info->getSimParams();
62		needCompression_ = simParams->getCompressDumpFile();
63		needForceVector_ = simParams->getOutputForceVector();
64	<
64	>	needParticlePot_ = simParams->getOutputParticlePotential();
65	>	cerr << "DW npp = " << needParticlePot_ << "\n";
66	>	createDumpFile_ = true;
67		#ifdef HAVE_LIBZ
68		if (needCompression_) {
69	<	filename_ += ".gz";
70	<	eorFilename_ += ".gz";
69	>	filename_ += ".gz";
70	>	eorFilename_ += ".gz";
71		}
72		#endif
73
74		#ifdef IS_MPI
75
76	<	if (worldRank == 0) {
76	>	if (worldRank == 0) {
77		#endif // is_mpi
78	+
79	+	dumpFile_ = createOStream(filename_);
80
81	+	if (!dumpFile_) {
82	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
83	+	filename_.c_str());
84	+	painCave.isFatal = 1;
85	+	simError();
86	+	}
87
75	–	dumpFile_ = createOStream(filename_);
76	–
77	–	if (!dumpFile_) {
78	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
79	–	filename_.c_str());
80	–	painCave.isFatal = 1;
81	–	simError();
82	–	}
83	–
88		#ifdef IS_MPI
89
90	<	}
90	>	}
91
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
92		#endif // is_mpi
93
94	<	}
94	>	}
95
96
97		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 101 | Line 102 | namespace oopse {
102
103		needCompression_ = simParams->getCompressDumpFile();
104		needForceVector_ = simParams->getOutputForceVector();
105	<
105	>	createDumpFile_ = true;
106		#ifdef HAVE_LIBZ
107		if (needCompression_) {
108	<	filename_ += ".gz";
109	<	eorFilename_ += ".gz";
108	>	filename_ += ".gz";
109	>	eorFilename_ += ".gz";
110		}
111		#endif
112
113		#ifdef IS_MPI
114
115	<	if (worldRank == 0) {
115	>	if (worldRank == 0) {
116		#endif // is_mpi
117
118	+
119	+	dumpFile_ = createOStream(filename_);
120
121	<	dumpFile_ = createOStream(filename_);
121	>	if (!dumpFile_) {
122	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
123	>	filename_.c_str());
124	>	painCave.isFatal = 1;
125	>	simError();
126	>	}
127
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	–
128		#ifdef IS_MPI
129
130	<	}
130	>	}
131
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
132		#endif // is_mpi
133
134	+	}
135	+
136	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
137	+	: info_(info), filename_(filename){
138	+
139	+	Globals* simParams = info->getSimParams();
140	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
141	+
142	+	needCompression_ = simParams->getCompressDumpFile();
143	+	needForceVector_ = simParams->getOutputForceVector();
144	+	needParticlePot_ = simParams->getOutputParticlePotential();
145	+
146	+	#ifdef HAVE_LIBZ
147	+	if (needCompression_) {
148	+	filename_ += ".gz";
149	+	eorFilename_ += ".gz";
150		}
151	+	#endif
152	+
153	+	#ifdef IS_MPI
154	+
155	+	if (worldRank == 0) {
156	+	#endif // is_mpi
157	+
158	+	createDumpFile_ = writeDumpFile;
159	+	if (createDumpFile_) {
160	+	dumpFile_ = createOStream(filename_);
161	+
162	+	if (!dumpFile_) {
163	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
164	+	filename_.c_str());
165	+	painCave.isFatal = 1;
166	+	simError();
167	+	}
168	+	}
169	+	#ifdef IS_MPI
170	+
171	+	}
172
173	+
174	+	#endif // is_mpi
175	+
176	+	}
177	+
178		DumpWriter::~DumpWriter() {
179
180		#ifdef IS_MPI
181
182		if (worldRank == 0) {
183		#endif // is_mpi
184	<
185	<	delete dumpFile_;
186	<
184	>	if (createDumpFile_){
185	>	writeClosing(*dumpFile_);
186	>	delete dumpFile_;
187	>	}
188		#ifdef IS_MPI
189
190		}
#	Line 152 | Line 193 | namespace oopse {
193
194		}
195
196	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
196	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
197
198	<	double currentTime;
199	<	Mat3x3d hmat;
200	<	double chi;
201	<	double integralOfChiDt;
202	<	Mat3x3d eta;
198	>	char buffer[1024];
199	>
200	>	os << "    <FrameData>\n";
201	>
202	>	RealType currentTime = s->getTime();
203	>
204	>	if (isinf(currentTime) || isnan(currentTime)) {
205	>	sprintf( painCave.errMsg,
206	>	"DumpWriter detected a numerical error writing the time");
207	>	painCave.isFatal = 1;
208	>	simError();
209	>	}
210
211	<	currentTime = s->getTime();
211	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
212	>	os << buffer;
213	>
214	>	Mat3x3d hmat;
215		hmat = s->getHmat();
216	<	chi = s->getChi();
217	<	integralOfChiDt = s->getIntegralOfChiDt();
218	<	eta = s->getEta();
216	>
217	>	for (unsigned int i = 0; i < 3; i++) {
218	>	for (unsigned int j = 0; j < 3; j++) {
219	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
220	>	sprintf( painCave.errMsg,
221	>	"DumpWriter detected a numerical error writing the box");
222	>	painCave.isFatal = 1;
223	>	simError();
224	>	}
225	>	}
226	>	}
227
228	<	os << currentTime << ";\t"
229	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
230	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
231	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
228	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
229	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
230	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
231	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
232	>	os << buffer;
233
234	<	//write out additional parameters, such as chi and eta
234	>	RealType chi = s->getChi();
235	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
236	>	if (isinf(chi) || isnan(chi) ||
237	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
238	>	sprintf( painCave.errMsg,
239	>	"DumpWriter detected a numerical error writing the thermostat");
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
244	>	os << buffer;
245
246	<	os << chi << "\t" << integralOfChiDt << "\t;";
246	>	Mat3x3d eta;
247	>	eta = s->getEta();
248
249	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
250	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
251	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
252	<
253	<	os << "\n";
249	>	for (unsigned int i = 0; i < 3; i++) {
250	>	for (unsigned int j = 0; j < 3; j++) {
251	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
252	>	sprintf( painCave.errMsg,
253	>	"DumpWriter detected a numerical error writing the barostat");
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257	>	}
258	>	}
259	>
260	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261	>	eta(0, 0), eta(1, 0), eta(2, 0),
262	>	eta(0, 1), eta(1, 1), eta(2, 1),
263	>	eta(0, 2), eta(1, 2), eta(2, 2));
264	>	os << buffer;
265	>
266	>	os << "    </FrameData>\n";
267		}
268
269		void DumpWriter::writeFrame(std::ostream& os) {
186	–	const int BUFFERSIZE = 2000;
187	–	const int MINIBUFFERSIZE = 100;
270
271	<	char tempBuffer[BUFFERSIZE];
272	<	char writeLine[BUFFERSIZE];
271	>	#ifdef IS_MPI
272	>	MPI_Status istatus;
273	>	#endif
274
192	–	Quat4d q;
193	–	Vector3d ji;
194	–	Vector3d pos;
195	–	Vector3d vel;
196	–	Vector3d frc;
197	–	Vector3d trq;
198	–
275		Molecule* mol;
276		StuntDouble* integrableObject;
277		SimInfo::MoleculeIterator mi;
278		Molecule::IntegrableObjectIterator ii;
203	–
204	–	int nTotObjects;
205	–	nTotObjects = info_->getNGlobalIntegrableObjects();
279
280		#ifndef IS_MPI
281	+	os << "  <Snapshot>\n";
282	+
283	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
284
285	+	os << "    <StuntDoubles>\n";
286	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
287
288	<	os << nTotObjects << "\n";
289	<
290	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
288	>
289	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
290	>	integrableObject = mol->nextIntegrableObject(ii)) {
291	>	os << prepareDumpLine(integrableObject);
292	>
293	>	}
294	>	}
295	>	os << "    </StuntDoubles>\n";
296	>
297	>	os << "  </Snapshot>\n";
298
299	+	os.flush();
300	+	#else
301	+	//every node prepares the dump lines for integrable objects belong to itself
302	+	std::string buffer;
303		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
304
305	+
306		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
307	<	integrableObject = mol->nextIntegrableObject(ii)) {
308	<
307	>	integrableObject = mol->nextIntegrableObject(ii)) {
308	>	buffer += prepareDumpLine(integrableObject);
309	>	}
310	>	}
311	>
312	>	const int masterNode = 0;
313	>	int nProc;
314	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
315	>	if (worldRank == masterNode) {
316	>	os << "  <Snapshot>\n";
317	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318	>	os << "    <StuntDoubles>\n";
319	>
320	>	os << buffer;
321
322	<	pos = integrableObject->getPos();
221	<	vel = integrableObject->getVel();
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(),
225	<	pos[0], pos[1], pos[2],
226	<	vel[0], vel[1], vel[2]);
324	>	// receive the length of the string buffer that was
325	>	// prepared by processor i
326
327	<	strcpy(writeLine, tempBuffer);
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	<	if (integrableObject->isDirectional()) {
231	<	q = integrableObject->getQ();
232	<	ji = integrableObject->getJ();
354	>	#endif // is_mpi
355
356	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
235	<	q[0], q[1], q[2], q[3],
236	<	ji[0], ji[1], ji[2]);
237	<	strcat(writeLine, tempBuffer);
238	<	} else {
239	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
240	<	}
356	>	}
357
358	<	if (needForceVector_) {
243	<	frc = integrableObject->getFrc();
244	<	trq = integrableObject->getTrq();
245	<
246	<	sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
247	<	frc[0], frc[1], frc[2],
248	<	trq[0], trq[1], trq[2]);
249	<	strcat(writeLine, tempBuffer);
250	<	}
358	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
359
360	<	strcat(writeLine, "\n");
361	<	os << writeLine;
360	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
361	>	std::string type("pv");
362	>	std::string line;
363	>	char tempBuffer[4096];
364
365	<	}
365	>	Vector3d pos;
366	>	Vector3d vel;
367	>	pos = integrableObject->getPos();
368	>
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();
259	<	#else // is_mpi
260	<	/*********************************************************************
261	<	* Documentation?  You want DOCUMENTATION?
262	<	*
263	<	* Why all the potatoes below?
264	<	*
265	<	* To make a long story short, the original version of DumpWriter
266	<	* worked in the most inefficient way possible.  Node 0 would
267	<	* poke each of the node for an individual atom's formatted data
268	<	* as node 0 worked its way down the global index. This was particularly
269	<	* inefficient since the method blocked all processors at every atom
270	<	* (and did it twice!).
271	<	*
272	<	* An intermediate version of DumpWriter could be described from Node
273	<	* zero's perspective as follows:
274	<	*
275	<	*  1) Have 100 of your friends stand in a circle.
276	<	*  2) When you say go, have all of them start tossing potatoes at
277	<	*     you (one at a time).
278	<	*  3) Catch the potatoes.
279	<	*
280	<	* It was an improvement, but MPI has buffers and caches that could
281	<	* best be described in this analogy as "potato nets", so there's no
282	<	* need to block the processors atom-by-atom.
283	<	*
284	<	* This new and improved DumpWriter works in an even more efficient
285	<	* way:
286	<	*
287	<	*  1) Have 100 of your friend stand in a circle.
288	<	*  2) When you say go, have them start tossing 5-pound bags of
289	<	*     potatoes at you.
290	<	*  3) Once you've caught a friend's bag of potatoes,
291	<	*     toss them a spud to let them know they can toss another bag.
292	<	*
293	<	* How's THAT for documentation?
294	<	*
295	<	*********************************************************************/
296	<	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[19];
386	<	int isDirectional;
387	<	char MPIatomTypeString[MINIBUFFERSIZE];
388	<	int msgLen; // the length of message actually recieved at master nodes
306	<	int haveError;
307	<	MPI_Status istatus;
308	<	int nCurObj;
309	<
310	<	// code to find maximum tag value
311	<	int * tagub;
312	<	int flag;
313	<	int MAXTAG;
314	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
315	<
316	<	if (flag) {
317	<	MAXTAG = *tagub;
318	<	} else {
319	<	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());
417	<
418	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
419	<
420	<	// Get the Node number which has this atom;
421	<
422	<	which_node = info_->getMolToProc(i);
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	<	if (which_node != masterNode) { //current molecule is in slave node
426	<	if (potatoes[which_node] + 1 >= MAXTAG) {
427	<	// The potato was going to exceed the maximum value,
428	<	// so wrap this processor potato back to 0:
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	<	potatoes[which_node] = 0;
432	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
433	<	MPI_COMM_WORLD);
352	<	}
431	>	if (needForceVector_) {
432	>	type += "f";
433	>	Vector3d frc;
434
435	<	myPotato = potatoes[which_node];
435	>	frc = integrableObject->getFrc();
436
437	<	//recieve the number of integrableObject in current molecule
438	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
439	<	MPI_COMM_WORLD, &istatus);
440	<	myPotato++;
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	>	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	<	for(int l = 0; l < nCurObj; l++) {
362	<	if (potatoes[which_node] + 2 >= MAXTAG) {
363	<	// The potato was going to exceed the maximum value,
364	<	// so wrap this processor potato back to 0:
475	>	particlePot = integrableObject->getParticlePot();
476
477	<	potatoes[which_node] = 0;
478	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
479	<	0, MPI_COMM_WORLD);
480	<	}
481	<
482	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
372	<	which_node, myPotato, MPI_COMM_WORLD,
373	<	&istatus);
374	<
375	<	myPotato++;
376	<
377	<	MPI_Recv(atomData, 19, MPI_DOUBLE, which_node, myPotato,
378	<	MPI_COMM_WORLD, &istatus);
379	<	myPotato++;
380	<
381	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
382	<
383	<	if (msgLen == 13 || msgLen == 19)
384	<	isDirectional = 1;
385	<	else
386	<	isDirectional = 0;
387	<
388	<	// If we've survived to here, format the line:
389	<
390	<	if (!isDirectional) {
391	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
392	<	MPIatomTypeString, atomData[0],
393	<	atomData[1], atomData[2],
394	<	atomData[3], atomData[4],
395	<	atomData[5]);
396	<
397	<	strcat(writeLine,
398	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
399	<	} else {
400	<	sprintf(writeLine,
401	<	"%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",
402	<	MPIatomTypeString,
403	<	atomData[0],
404	<	atomData[1],
405	<	atomData[2],
406	<	atomData[3],
407	<	atomData[4],
408	<	atomData[5],
409	<	atomData[6],
410	<	atomData[7],
411	<	atomData[8],
412	<	atomData[9],
413	<	atomData[10],
414	<	atomData[11],
415	<	atomData[12]);
416	<	}
417	<
418	<	if (needForceVector_) {
419	<	if (!isDirectional) {
420	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
421	<	atomData[6],
422	<	atomData[7],
423	<	atomData[8],
424	<	atomData[9],
425	<	atomData[10],
426	<	atomData[11]);
427	<	} else {
428	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
429	<	atomData[13],
430	<	atomData[14],
431	<	atomData[15],
432	<	atomData[16],
433	<	atomData[17],
434	<	atomData[18]);
435	<	}
436	<	}
437	<
438	<	sprintf(writeLine, "\n");
439	<	os << writeLine;
440	<
441	<	} // end for(int l =0)
442	<
443	<	potatoes[which_node] = myPotato;
444	<	} else { //master node has current molecule
445	<
446	<	mol = info_->getMoleculeByGlobalIndex(i);
447	<
448	<	if (mol == NULL) {
449	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
450	<	painCave.isFatal = 1;
451	<	simError();
452	<	}
453	<
454	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
455	<	integrableObject = mol->nextIntegrableObject(ii)) {
456	<
457	<	pos = integrableObject->getPos();
458	<	vel = integrableObject->getVel();
459	<
460	<	atomData[0] = pos[0];
461	<	atomData[1] = pos[1];
462	<	atomData[2] = pos[2];
463	<
464	<	atomData[3] = vel[0];
465	<	atomData[4] = vel[1];
466	<	atomData[5] = vel[2];
467	<
468	<	isDirectional = 0;
469	<
470	<	if (integrableObject->isDirectional()) {
471	<	isDirectional = 1;
472	<
473	<	q = integrableObject->getQ();
474	<	ji = integrableObject->getJ();
475	<
476	<	for(int j = 0; j < 6; j++) {
477	<	atomData[j] = atomData[j];
478	<	}
479	<
480	<	atomData[6] = q[0];
481	<	atomData[7] = q[1];
482	<	atomData[8] = q[2];
483	<	atomData[9] = q[3];
484	<
485	<	atomData[10] = ji[0];
486	<	atomData[11] = ji[1];
487	<	atomData[12] = ji[2];
488	<	}
489	<
490	<	if (needForceVector_) {
491	<	frc = integrableObject->getFrc();
492	<	trq = integrableObject->getTrq();
493	<
494	<	if (!isDirectional) {
495	<	atomData[6] = frc[0];
496	<	atomData[7] = frc[1];
497	<	atomData[8] = frc[2];
498	<	atomData[9] = trq[0];
499	<	atomData[10] = trq[1];
500	<	atomData[11] = trq[2];
501	<	} else {
502	<	atomData[13] = frc[0];
503	<	atomData[14] = frc[1];
504	<	atomData[15] = frc[2];
505	<	atomData[16] = trq[0];
506	<	atomData[17] = trq[1];
507	<	atomData[18] = trq[2];
508	<	}
509	<	}
510	<
511	<	// If we've survived to here, format the line:
512	<
513	<	if (!isDirectional) {
514	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515	<	integrableObject->getType().c_str(), atomData[0],
516	<	atomData[1], atomData[2],
517	<	atomData[3], atomData[4],
518	<	atomData[5]);
519	<
520	<	strcat(writeLine,
521	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
522	<	} else {
523	<	sprintf(writeLine,
524	<	"%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",
525	<	integrableObject->getType().c_str(),
526	<	atomData[0],
527	<	atomData[1],
528	<	atomData[2],
529	<	atomData[3],
530	<	atomData[4],
531	<	atomData[5],
532	<	atomData[6],
533	<	atomData[7],
534	<	atomData[8],
535	<	atomData[9],
536	<	atomData[10],
537	<	atomData[11],
538	<	atomData[12]);
539	<	}
540	<
541	<	if (needForceVector_) {
542	<	if (!isDirectional) {
543	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
544	<	atomData[6],
545	<	atomData[7],
546	<	atomData[8],
547	<	atomData[9],
548	<	atomData[10],
549	<	atomData[11]);
550	<	} else {
551	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
552	<	atomData[13],
553	<	atomData[14],
554	<	atomData[15],
555	<	atomData[16],
556	<	atomData[17],
557	<	atomData[18]);
558	<	}
559	<	}
560	<
561	<	sprintf(writeLine, "\n");
562	<	os << writeLine;
563	<
564	<	} //end for(iter = integrableObject.begin())
565	<	}
566	<	} //end for(i = 0; i < mpiSim->getNmol())
567	<
568	<	os.flush();
569	<
570	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
571	<	MPIcheckPoint();
572	<
573	<	delete [] potatoes;
574	<	} else {
575	<
576	<	// worldRank != 0, so I'm a remote node.
577	<
578	<	// Set my magic potato to 0:
579	<
580	<	myPotato = 0;
581	<
582	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
583	<
584	<	// Am I the node which has this integrableObject?
585	<	int whichNode = info_->getMolToProc(i);
586	<	if (whichNode == worldRank) {
587	<	if (myPotato + 1 >= MAXTAG) {
588	<
589	<	// The potato was going to exceed the maximum value,
590	<	// so wrap this processor potato back to 0 (and block until
591	<	// node 0 says we can go:
592	<
593	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
594	<	&istatus);
595	<	}
596	<
597	<	mol = info_->getMoleculeByGlobalIndex(i);
598	<
599	<
600	<	nCurObj = mol->getNIntegrableObjects();
601	<
602	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
603	<	myPotato++;
604	<
605	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
606	<	integrableObject = mol->nextIntegrableObject(ii)) {
607	<
608	<	if (myPotato + 2 >= MAXTAG) {
609	<
610	<	// The potato was going to exceed the maximum value,
611	<	// so wrap this processor potato back to 0 (and block until
612	<	// node 0 says we can go:
613	<
614	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
615	<	&istatus);
616	<	}
617	<
618	<	pos = integrableObject->getPos();
619	<	vel = integrableObject->getVel();
620	<
621	<	atomData[0] = pos[0];
622	<	atomData[1] = pos[1];
623	<	atomData[2] = pos[2];
624	<
625	<	atomData[3] = vel[0];
626	<	atomData[4] = vel[1];
627	<	atomData[5] = vel[2];
628	<
629	<	isDirectional = 0;
630	<
631	<	if (integrableObject->isDirectional()) {
632	<	isDirectional = 1;
633	<
634	<	q = integrableObject->getQ();
635	<	ji = integrableObject->getJ();
636	<
637	<	atomData[6] = q[0];
638	<	atomData[7] = q[1];
639	<	atomData[8] = q[2];
640	<	atomData[9] = q[3];
641	<
642	<	atomData[10] = ji[0];
643	<	atomData[11] = ji[1];
644	<	atomData[12] = ji[2];
645	<	}
646	<
647	<	if (needForceVector_) {
648	<	frc = integrableObject->getFrc();
649	<	trq = integrableObject->getTrq();
650	<
651	<	if (!isDirectional) {
652	<	atomData[6] = frc[0];
653	<	atomData[7] = frc[1];
654	<	atomData[8] = frc[2];
655	<
656	<	atomData[9] = trq[0];
657	<	atomData[10] = trq[1];
658	<	atomData[11] = trq[2];
659	<	} else {
660	<	atomData[13] = frc[0];
661	<	atomData[14] = frc[1];
662	<	atomData[15] = frc[2];
663	<
664	<	atomData[16] = trq[0];
665	<	atomData[17] = trq[1];
666	<	atomData[18] = trq[2];
667	<	}
668	<	}
669	<
670	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
671	<
672	<	// null terminate the  std::string before sending (just in case):
673	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
674	<
675	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
676	<	myPotato, MPI_COMM_WORLD);
677	<
678	<	myPotato++;
679	<
680	<	if (isDirectional && needForceVector_) {
681	<	MPI_Send(atomData, 19, MPI_DOUBLE, 0, myPotato,
682	<	MPI_COMM_WORLD);
683	<	} else if (isDirectional) {
684	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
685	<	MPI_COMM_WORLD);
686	<	} else if (needForceVector_) {
687	<	MPI_Send(atomData, 12, MPI_DOUBLE, 0, myPotato,
688	<	MPI_COMM_WORLD);
689	<	} else {
690	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
691	<	MPI_COMM_WORLD);
692	<	}
693	<
694	<	myPotato++;
695	<	}
696	<
697	<	}
698	<
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() {
#	Line 727 | Line 511 | namespace oopse {
511		#ifdef IS_MPI
512		if (worldRank == 0) {
513		#endif // is_mpi
514	<	delete eorStream;
515	<
514	>	writeClosing(*eorStream);
515	>	delete eorStream;
516		#ifdef IS_MPI
517		}
518		#endif // is_mpi
#	Line 761 | Line 545 | namespace oopse {
545		#ifdef IS_MPI
546		if (worldRank == 0) {
547		#endif // is_mpi
548	<	delete eorStream;
549	<
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) {
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());
561	>	newOStream = new ogzstream(filename.c_str());
562		} else {
563	<	newOStream = new std::ofstream(filename.c_str());
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	<	}
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 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1711 by gezelter, Sat May 19 02:58:35 2012 UTC

#	Line 0 | Line 1
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