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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 1714 by gezelter, Sat May 19 18:12:46 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()){
60
61		Globals* simParams = info->getSimParams();
62	<	needCompression_ = simParams->getCompressDumpFile();
63	<	needForceVector_ = simParams->getOutputForceVector();
62	>	needCompression_   = simParams->getCompressDumpFile();
63	>	needForceVector_   = simParams->getOutputForceVector();
64	>	needParticlePot_   = simParams->getOutputParticlePotential();
65	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
66	>	needElectricField_ = simParams->getOutputElectricField();
67
68	+	createDumpFile_ = true;
69		#ifdef HAVE_LIBZ
70		if (needCompression_) {
71	<	filename_ += ".gz";
72	<	eorFilename_ += ".gz";
71	>	filename_ += ".gz";
72	>	eorFilename_ += ".gz";
73		}
74		#endif
75
76		#ifdef IS_MPI
77
78	<	if (worldRank == 0) {
78	>	if (worldRank == 0) {
79		#endif // is_mpi
80	+
81	+	dumpFile_ = createOStream(filename_);
82
83	+	if (!dumpFile_) {
84	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
85	+	filename_.c_str());
86	+	painCave.isFatal = 1;
87	+	simError();
88	+	}
89
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	–
90		#ifdef IS_MPI
91
92	<	}
92	>	}
93
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
94		#endif // is_mpi
95
96	<	}
96	>	}
97
98
99		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 99 | Line 102 | namespace oopse {
102		Globals* simParams = info->getSimParams();
103		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
104
105	<	needCompression_ = simParams->getCompressDumpFile();
106	<	needForceVector_ = simParams->getOutputForceVector();
105	>	needCompression_   = simParams->getCompressDumpFile();
106	>	needForceVector_   = simParams->getOutputForceVector();
107	>	needParticlePot_   = simParams->getOutputParticlePotential();
108	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
109	>	needElectricField_ = simParams->getOutputElectricField();
110
111	+	createDumpFile_ = true;
112		#ifdef HAVE_LIBZ
113		if (needCompression_) {
114	<	filename_ += ".gz";
115	<	eorFilename_ += ".gz";
114	>	filename_ += ".gz";
115	>	eorFilename_ += ".gz";
116		}
117		#endif
118
119		#ifdef IS_MPI
120
121	<	if (worldRank == 0) {
121	>	if (worldRank == 0) {
122		#endif // is_mpi
123
124	+
125	+	dumpFile_ = createOStream(filename_);
126
127	<	dumpFile_ = createOStream(filename_);
127	>	if (!dumpFile_) {
128	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
129	>	filename_.c_str());
130	>	painCave.isFatal = 1;
131	>	simError();
132	>	}
133
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	–
134		#ifdef IS_MPI
135
136	<	}
136	>	}
137
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
138		#endif // is_mpi
139
140	+	}
141	+
142	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
143	+	: info_(info), filename_(filename){
144	+
145	+	Globals* simParams = info->getSimParams();
146	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
147	+
148	+	needCompression_   = simParams->getCompressDumpFile();
149	+	needForceVector_   = simParams->getOutputForceVector();
150	+	needParticlePot_   = simParams->getOutputParticlePotential();
151	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
152	+	needElectricField_ = simParams->getOutputElectricField();
153	+
154	+	#ifdef HAVE_LIBZ
155	+	if (needCompression_) {
156	+	filename_ += ".gz";
157	+	eorFilename_ += ".gz";
158		}
159	+	#endif
160	+
161	+	#ifdef IS_MPI
162	+
163	+	if (worldRank == 0) {
164	+	#endif // is_mpi
165	+
166	+	createDumpFile_ = writeDumpFile;
167	+	if (createDumpFile_) {
168	+	dumpFile_ = createOStream(filename_);
169	+
170	+	if (!dumpFile_) {
171	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
172	+	filename_.c_str());
173	+	painCave.isFatal = 1;
174	+	simError();
175	+	}
176	+	}
177	+	#ifdef IS_MPI
178	+
179	+	}
180
181	+
182	+	#endif // is_mpi
183	+
184	+	}
185	+
186		DumpWriter::~DumpWriter() {
187
188		#ifdef IS_MPI
189
190		if (worldRank == 0) {
191		#endif // is_mpi
192	<
193	<	delete dumpFile_;
194	<
192	>	if (createDumpFile_){
193	>	writeClosing(*dumpFile_);
194	>	delete dumpFile_;
195	>	}
196		#ifdef IS_MPI
197
198		}
#	Line 152 | Line 201 | namespace oopse {
201
202		}
203
204	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
204	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
205
206	<	double currentTime;
207	<	Mat3x3d hmat;
208	<	double chi;
209	<	double integralOfChiDt;
210	<	Mat3x3d eta;
206	>	char buffer[1024];
207	>
208	>	os << "    <FrameData>\n";
209	>
210	>	RealType currentTime = s->getTime();
211	>
212	>	if (isinf(currentTime) || isnan(currentTime)) {
213	>	sprintf( painCave.errMsg,
214	>	"DumpWriter detected a numerical error writing the time");
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218
219	<	currentTime = s->getTime();
219	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
220	>	os << buffer;
221	>
222	>	Mat3x3d hmat;
223		hmat = s->getHmat();
224	<	chi = s->getChi();
225	<	integralOfChiDt = s->getIntegralOfChiDt();
226	<	eta = s->getEta();
224	>
225	>	for (unsigned int i = 0; i < 3; i++) {
226	>	for (unsigned int j = 0; j < 3; j++) {
227	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
228	>	sprintf( painCave.errMsg,
229	>	"DumpWriter detected a numerical error writing the box");
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	}
234	>	}
235
236	<	os << currentTime << ";\t"
237	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
238	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
239	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
236	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
237	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
238	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
239	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
240	>	os << buffer;
241
242	<	//write out additional parameters, such as chi and eta
242	>	RealType chi = s->getChi();
243	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
244	>	if (isinf(chi) || isnan(chi) ||
245	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the thermostat");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
252	>	os << buffer;
253
254	<	os << chi << "\t" << integralOfChiDt << "\t;";
254	>	Mat3x3d eta;
255	>	eta = s->getEta();
256
257	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
258	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
259	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
260	<
261	<	os << "\n";
257	>	for (unsigned int i = 0; i < 3; i++) {
258	>	for (unsigned int j = 0; j < 3; j++) {
259	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
260	>	sprintf( painCave.errMsg,
261	>	"DumpWriter detected a numerical error writing the barostat");
262	>	painCave.isFatal = 1;
263	>	simError();
264	>	}
265	>	}
266	>	}
267	>
268	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
269	>	eta(0, 0), eta(1, 0), eta(2, 0),
270	>	eta(0, 1), eta(1, 1), eta(2, 1),
271	>	eta(0, 2), eta(1, 2), eta(2, 2));
272	>	os << buffer;
273	>
274	>	os << "    </FrameData>\n";
275		}
276
277		void DumpWriter::writeFrame(std::ostream& os) {
186	–	const int BUFFERSIZE = 2000;
187	–	const int MINIBUFFERSIZE = 100;
278
279	<	char tempBuffer[BUFFERSIZE];
280	<	char writeLine[BUFFERSIZE];
279	>	#ifdef IS_MPI
280	>	MPI_Status istatus;
281	>	#endif
282
192	–	Quat4d q;
193	–	Vector3d ji;
194	–	Vector3d pos;
195	–	Vector3d vel;
196	–	Vector3d frc;
197	–	Vector3d trq;
198	–
283		Molecule* mol;
284		StuntDouble* integrableObject;
285		SimInfo::MoleculeIterator mi;
286		Molecule::IntegrableObjectIterator ii;
203	–
204	–	int nTotObjects;
205	–	nTotObjects = info_->getNGlobalIntegrableObjects();
287
288		#ifndef IS_MPI
289	+	os << "  <Snapshot>\n";
290	+
291	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
292
293	+	os << "    <StuntDoubles>\n";
294	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
295
296	<	os << nTotObjects << "\n";
297	<
298	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
296	>
297	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
298	>	integrableObject = mol->nextIntegrableObject(ii)) {
299	>	os << prepareDumpLine(integrableObject);
300	>
301	>	}
302	>	}
303	>	os << "    </StuntDoubles>\n";
304	>
305	>	os << "  </Snapshot>\n";
306
307	+	os.flush();
308	+	#else
309	+	//every node prepares the dump lines for integrable objects belong to itself
310	+	std::string buffer;
311		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
312
313	+
314		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
315	<	integrableObject = mol->nextIntegrableObject(ii)) {
316	<
315	>	integrableObject = mol->nextIntegrableObject(ii)) {
316	>	buffer += prepareDumpLine(integrableObject);
317	>	}
318	>	}
319	>
320	>	const int masterNode = 0;
321	>	int nProc;
322	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
323	>	if (worldRank == masterNode) {
324	>	os << "  <Snapshot>\n";
325	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
326	>	os << "    <StuntDoubles>\n";
327	>
328	>	os << buffer;
329
330	<	pos = integrableObject->getPos();
221	<	vel = integrableObject->getVel();
330	>	for (int i = 1; i < nProc; ++i) {
331
332	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
333	<	integrableObject->getType().c_str(),
225	<	pos[0], pos[1], pos[2],
226	<	vel[0], vel[1], vel[2]);
332	>	// receive the length of the string buffer that was
333	>	// prepared by processor i
334
335	<	strcpy(writeLine, tempBuffer);
335	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
336	>	int recvLength;
337	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
338	>	char* recvBuffer = new char[recvLength];
339	>	if (recvBuffer == NULL) {
340	>	} else {
341	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
342	>	os << recvBuffer;
343	>	delete [] recvBuffer;
344	>	}
345	>	}
346	>	os << "    </StuntDoubles>\n";
347	>
348	>	os << "  </Snapshot>\n";
349	>	os.flush();
350	>	} else {
351	>	int sendBufferLength = buffer.size() + 1;
352	>	int myturn = 0;
353	>	for (int i = 1; i < nProc; ++i){
354	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
355	>	if (myturn == worldRank){
356	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
357	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
358	>	}
359	>	}
360	>	}
361
362	<	if (integrableObject->isDirectional()) {
231	<	q = integrableObject->getQ();
232	<	ji = integrableObject->getJ();
362	>	#endif // is_mpi
363
364	<	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	<	}
364	>	}
365
366	<	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	<	}
366	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
367
368	<	strcat(writeLine, "\n");
369	<	os << writeLine;
368	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
369	>	std::string type("pv");
370	>	std::string line;
371	>	char tempBuffer[4096];
372
373	<	}
373	>	Vector3d pos;
374	>	Vector3d vel;
375	>	pos = integrableObject->getPos();
376	>
377	>	if (isinf(pos[0]) || isnan(pos[0]) ||
378	>	isinf(pos[1]) || isnan(pos[1]) ||
379	>	isinf(pos[2]) || isnan(pos[2]) ) {
380	>	sprintf( painCave.errMsg,
381	>	"DumpWriter detected a numerical error writing the position"
382	>	" for object %d", index);
383	>	painCave.isFatal = 1;
384	>	simError();
385		}
386
387	<	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;
387	>	vel = integrableObject->getVel();
388
389	<	int * potatoes;
390	<	int myPotato;
391	<	int nProc;
392	<	int which_node;
393	<	double atomData[19];
394	<	int isDirectional;
395	<	char MPIatomTypeString[MINIBUFFERSIZE];
396	<	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;
389	>	if (isinf(vel[0]) || isnan(vel[0]) ||
390	>	isinf(vel[1]) || isnan(vel[1]) ||
391	>	isinf(vel[2]) || isnan(vel[2]) ) {
392	>	sprintf( painCave.errMsg,
393	>	"DumpWriter detected a numerical error writing the velocity"
394	>	" for object %d", index);
395	>	painCave.isFatal = 1;
396	>	simError();
397		}
398
399	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
399	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
400	>	pos[0], pos[1], pos[2],
401	>	vel[0], vel[1], vel[2]);
402	>	line += tempBuffer;
403
404	<	// Node 0 needs a list of the magic potatoes for each processor;
404	>	if (integrableObject->isDirectional()) {
405	>	type += "qj";
406	>	Quat4d q;
407	>	Vector3d ji;
408	>	q = integrableObject->getQ();
409
410	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
411	<	potatoes = new int[nProc];
412	<
413	<	//write out the comment lines
414	<	for(int i = 0; i < nProc; i++) {
415	<	potatoes[i] = 0;
410	>	if (isinf(q[0]) || isnan(q[0]) ||
411	>	isinf(q[1]) || isnan(q[1]) ||
412	>	isinf(q[2]) || isnan(q[2]) ||
413	>	isinf(q[3]) || isnan(q[3]) ) {
414	>	sprintf( painCave.errMsg,
415	>	"DumpWriter detected a numerical error writing the quaternion"
416	>	" for object %d", index);
417	>	painCave.isFatal = 1;
418	>	simError();
419		}
420
421	+	ji = integrableObject->getJ();
422
423	<	os << nTotObjects << "\n";
424	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
423	>	if (isinf(ji[0]) || isnan(ji[0]) ||
424	>	isinf(ji[1]) || isnan(ji[1]) ||
425	>	isinf(ji[2]) || isnan(ji[2]) ) {
426	>	sprintf( painCave.errMsg,
427	>	"DumpWriter detected a numerical error writing the angular"
428	>	" momentum for object %d", index);
429	>	painCave.isFatal = 1;
430	>	simError();
431	>	}
432
433	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
433	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
434	>	q[0], q[1], q[2], q[3],
435	>	ji[0], ji[1], ji[2]);
436	>	line += tempBuffer;
437	>	}
438
439	<	// Get the Node number which has this atom;
440	<
441	<	which_node = info_->getMolToProc(i);
439	>	if (needForceVector_) {
440	>	type += "f";
441	>	Vector3d frc = integrableObject->getFrc();
442	>	if (isinf(frc[0]) || isnan(frc[0]) ||
443	>	isinf(frc[1]) || isnan(frc[1]) ||
444	>	isinf(frc[2]) || isnan(frc[2]) ) {
445	>	sprintf( painCave.errMsg,
446	>	"DumpWriter detected a numerical error writing the force"
447	>	" for object %d", index);
448	>	painCave.isFatal = 1;
449	>	simError();
450	>	}
451	>	sprintf(tempBuffer, " %13e %13e %13e",
452	>	frc[0], frc[1], frc[2]);
453	>	line += tempBuffer;
454	>
455	>	if (integrableObject->isDirectional()) {
456	>	type += "t";
457	>	Vector3d trq = integrableObject->getTrq();
458	>	if (isinf(trq[0]) || isnan(trq[0]) ||
459	>	isinf(trq[1]) || isnan(trq[1]) ||
460	>	isinf(trq[2]) || isnan(trq[2]) ) {
461	>	sprintf( painCave.errMsg,
462	>	"DumpWriter detected a numerical error writing the torque"
463	>	" for object %d", index);
464	>	painCave.isFatal = 1;
465	>	simError();
466	>	}
467	>	sprintf(tempBuffer, " %13e %13e %13e",
468	>	trq[0], trq[1], trq[2]);
469	>	line += tempBuffer;
470	>	}
471	>	}
472
473	<	if (which_node != masterNode) { //current molecule is in slave node
474	<	if (potatoes[which_node] + 1 >= MAXTAG) {
475	<	// The potato was going to exceed the maximum value,
476	<	// so wrap this processor potato back to 0:
473	>	if (needParticlePot_) {
474	>	type += "u";
475	>	RealType particlePot = integrableObject->getParticlePot();
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	>	if (needFlucQ_) {
488	>	type += "cw";
489	>	RealType fqPos = integrableObject->getFlucQPos();
490	>	if (isinf(fqPos) || isnan(fqPos) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the"
493	>	" fluctuating charge for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e ", fqPos);
498	>	line += tempBuffer;
499	>
500	>	RealType fqVel = integrableObject->getFlucQVel();
501	>	if (isinf(fqVel) || isnan(fqVel) ) {
502	>	sprintf( painCave.errMsg,
503	>	"DumpWriter detected a numerical error writing the"
504	>	" fluctuating charge velocity for object %d", index);
505	>	painCave.isFatal = 1;
506	>	simError();
507	>	}
508	>	sprintf(tempBuffer, " %13e ", fqVel);
509	>	line += tempBuffer;
510
511	<	potatoes[which_node] = 0;
512	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
513	<	MPI_COMM_WORLD);
514	<	}
515	<
516	<	myPotato = potatoes[which_node];
517	<
518	<	//recieve the number of integrableObject in current molecule
519	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
520	<	MPI_COMM_WORLD, &istatus);
521	<	myPotato++;
522	<
523	<	for(int l = 0; l < nCurObj; l++) {
524	<	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:
365	<
366	<	potatoes[which_node] = 0;
367	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
368	<	0, MPI_COMM_WORLD);
369	<	}
370	<
371	<	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]);
511	>	if (needForceVector_) {
512	>	type += "g";
513	>	RealType fqFrc = integrableObject->getFlucQFrc();
514	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
515	>	sprintf( painCave.errMsg,
516	>	"DumpWriter detected a numerical error writing the"
517	>	" fluctuating charge force for object %d", index);
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521	>	sprintf(tempBuffer, " %13e ", fqFrc);
522	>	line += tempBuffer;
523	>	}
524	>	}
525
526	<	strcat(writeLine,
527	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
528	<	} else {
529	<	sprintf(writeLine,
530	<	"%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",
531	<	integrableObject->getType().c_str(),
532	<	atomData[0],
533	<	atomData[1],
534	<	atomData[2],
535	<	atomData[3],
536	<	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	<
526	>	if (needElectricField_) {
527	>	type += "e";
528	>	Vector3d eField= integrableObject->getElectricField();
529	>	if (isinf(eField[0]) || isnan(eField[0]) ||
530	>	isinf(eField[1]) || isnan(eField[1]) ||
531	>	isinf(eField[2]) || isnan(eField[2]) ) {
532	>	sprintf( painCave.errMsg,
533	>	"DumpWriter detected a numerical error writing the electric"
534	>	" field for object %d", index);
535	>	painCave.isFatal = 1;
536	>	simError();
537		}
538	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
539	<	MPIcheckPoint();
538	>	sprintf(tempBuffer, " %13e %13e %13e",
539	>	eField[0], eField[1], eField[2]);
540	>	line += tempBuffer;
541		}
542
543	<	#endif // is_mpi
544	<
543	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
544	>	return std::string(tempBuffer);
545		}
546
547		void DumpWriter::writeDump() {
#	Line 727 | Line 566 | namespace oopse {
566		#ifdef IS_MPI
567		if (worldRank == 0) {
568		#endif // is_mpi
569	<	delete eorStream;
570	<
569	>	writeClosing(*eorStream);
570	>	delete eorStream;
571		#ifdef IS_MPI
572		}
573		#endif // is_mpi
#	Line 761 | Line 600 | namespace oopse {
600		#ifdef IS_MPI
601		if (worldRank == 0) {
602		#endif // is_mpi
603	<	delete eorStream;
604	<
603	>	writeClosing(*eorStream);
604	>	delete eorStream;
605		#ifdef IS_MPI
606		}
607		#endif // is_mpi
608
609		}
610
611	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
611	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
612
613		std::ostream* newOStream;
614		#ifdef HAVE_LIBZ
615		if (needCompression_) {
616	<	newOStream = new ogzstream(filename.c_str());
616	>	newOStream = new ogzstream(filename.c_str());
617		} else {
618	<	newOStream = new std::ofstream(filename.c_str());
618	>	newOStream = new std::ofstream(filename.c_str());
619		}
620		#else
621		newOStream = new std::ofstream(filename.c_str());
622		#endif
623	+	//write out MetaData first
624	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
625	+	(*newOStream) << "  <MetaData>" << std::endl;
626	+	(*newOStream) << info_->getRawMetaData();
627	+	(*newOStream) << "  </MetaData>" << std::endl;
628		return newOStream;
629	<	}
629	>	}
630
631	<	}//end namespace oopse
631	>	void DumpWriter::writeClosing(std::ostream& os) {
632	>
633	>	os << "</OpenMD>\n";
634	>	os.flush();
635	>	}
636	>
637	>	}//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 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

#	Line 0 | Line 1
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